Recent Releases of emmontopy

What's Changed

Added possibility of specifying iri in new_entity by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/844
Update Metadata so that all metadata-items can be accessed by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/845
Emmocheck now does not check prefLabel for any of entities specific prefixes by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/852
move from sintef/ci-cd safety to safety own setup by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/854
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/849
Made metadata repr easier to read. by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/847
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/856
Handle timeout errors in redirectioncheck by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/864
Added --namespace option to ontoconvert by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/867
Deprecate support for python 3.8 by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/868
Recursive creation of squashed ontologies by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/869

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.8.0...v0.8.1

Changelog

v0.8.1 (2025-08-20)

Full Changelog

Fixed bugs:

check only emmo terms #851

Closed issues:

Add possibility of specifying IRI in new_class etc. #843
How to access metadata such as abstract and creators? #841

Merged pull requests:

Recursive creation of squashed ontologies #869 (@jesper-friis)
Deprecate support for python 3.8 #868 (@francescalb)
Added --namespace option to ontoconvert #867 (@jesper-friis)
Handle timeout errors in redirectioncheck #864 (@jesper-friis)
move from sintef/ci-cd safety to safety own setup #854 (@francescalb)
Emmocheck now does not check prefLabel for any of entities specific prefixes #852 (@francescalb)
Made metadata repr easier to read. #847 (@jesper-friis)
Update Metadata so that all metadata-items can be accessed #845 (@francescalb)
Added possibility of specifying iri in new_entity #844 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb 6 months ago

emmontopy - v0.8.0

Update to use the newly released EMMO 1.0.0 as default ontology.

Support for Python3.13

Note thar due to changes in redirection rules on EMMO, the PyPI elease for version 0.7.3 did not succeed. This is therefore the first release on PyPI including the changes between 0.7.2 and 0.7.3.

What's Changed

Update to emmo 1.0.0 as it is now released by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/839
Updated to include python3.13 by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/831

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.3...v0.8.0

Changelog

v0.8.0 (2025-03-18)

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Closed issues:

Is the variable OWLREADY2_FORMATS incomplete? #219

Merged pull requests:

Update to emmo 1.0.0 as it is now released #839 (@francescalb)
Updated to include python3.13 #831 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb 12 months ago

What's Changed

Handle owlready2:python_names in genated triples in excelparser by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/795
Corrected test when loading rdfs. It used type for is_a. by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/796
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/799
Added figures to generated documentation by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/767
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/803
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/808
Added utils.getdatatypeclass() by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/804
Updated sync_reasoner() such that it works for FaCT++ by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/810
Added testunitdimension_rc1() by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/798
Added find() method by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/807
Minor fix for fact++ by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/817
Importing rdfs schemas by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/814
Updated emmocheck to ahead to latest formulation of units by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/809
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/822
Ignore automatic dependency updates Python3.8 by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/830
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/832
[Auto-generated] Update dependencies by @TEAM4-0 in https://github.com/emmo-repo/EMMOntoPy/pull/836

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.2...v0.7.3

- Python
Published by francescalb 12 months ago

What's Changed

Updated list of IRIs to ignore when checking prefLabel by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/731
Add --copy-annotation option to ontoconvert by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/732
Added additional recognised prefixes by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/734
Copy EMMO annotations by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/733
Load doamin-battery instead of battinfo which is just an extra wrapping by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/745
Added possibility for = in extra annotations defined in excelparser by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/752
Make it possible to run HermiT on EMMO by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/740
Added minor fixes for ontoconvert by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/739
Fixed failing test_save in master by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/756
Rewriting ontodoc based on domain-battery by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/742
Added test for descriptions by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/766
Added releasepat secret to cicdupdatedmaster workflow by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/777
Updated to owlready2==0.44 by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/780
Flb/trusted publisher on pypi by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/791
Corrected publishing info by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/792

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.1...v0.7.2

Changelog

v0.7.2 (2024-10-25)

Full Changelog

Closed issues:

excelparser, allow for = in strings for other annotations. #751
Add options to ontoconvert for adding annotations expected by FOOPS #728
Remove or rename "old" version tags #547
Handle old EMMO Python package version tags #272

Merged pull requests:

Corrected publishing info #792 (@francescalb)
Flb/trusted publisher on pypi #791 (@francescalb)
Updated to owlready2==0.44 #780 (@francescalb)
Added release_pat secret to ci_cd_updated_master workflow #777 (@francescalb)
Added test for descriptions #766 (@jesper-friis)
Fixed failing test_save in master #756 (@jesper-friis)
Added possibility for = in extra annotations defined in excelparser #752 (@francescalb)
Load doamin-battery instead of battinfo which is just an extra wrapping #745 (@francescalb)
Rewriting ontodoc based on domain-battery #742 (@jesper-friis)
Make it possible to run HermiT on EMMO #740 (@jesper-friis)
Added minor fixes for ontoconvert #739 (@jesper-friis)
Added additional recognised prefixes #734 (@jesper-friis)
Copy EMMO annotations #733 (@jesper-friis)
Add --copy-annotation option to ontoconvert #732 (@jesper-friis)
Updated list of IRIs to ignore when checking prefLabel #731 (@jesper-friis)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb over 1 year ago

What's Changed

Updated ontoconvert help by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/715
Added yield from by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/720
Correct saving squashed ontology by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/719

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.7.0...v0.7.1

Changelog

v0.7.1 (2024-02-29)

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v0.7.0.1 (2024-02-29)

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Closed issues:

Implement ontoconvert --base-iri argument #716

Merged pull requests:

Added yield from #720 (@jesper-friis)
Correct saving squashed ontology #719 (@jesper-friis)
Updated ontoconvert help #715 (@jesper-friis)

v0.7.0 (2024-01-26)

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Merged pull requests:

Ontology copy #711 (@francescalb)
Update save recursive and layout #710 (@francescalb)

v0.6.3 (2024-01-25)

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Merged pull requests:

Fix infinite recursion in directory layout #708 (@jesper-friis)
Ensure that saving with squash removes all but current ontology #707 (@jesper-friis)
Turned on directory layout tests for emmo and made them pytest #706 (@francescalb)

v0.6.2 (2024-01-23)

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Merged pull requests:

Allow controling ontology IRI when saving #700 (@jesper-friis)

v0.6.1 (2024-01-18)

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Closed issues:

No tests for ontology.save #684
Allow using HermiT from ontoconvert #664
PrefLabel used by new_entity, and get_by_label even if it is not in the ontology #642
ontology(imported=True) returns all classes in world #640
excel2onto example doesn't come into the github pages documentation #626
owlready2 > 0.41 fails #624
get_by_label and get_by_label all force add label_annotations #621
hasPhysicalDimension convention has changed in EMMO-1.0.0-beta3 #347

Merged pull requests:

Avoid infinite recursion in set_common_prefix() #701 (@jesper-friis)
Updated the getattr patch #699 (@jesper-friis)
WIP: Fix issues with changed IRIs effecting test_excelparser #697 (@jesper-friis)
Added directory_layout() function #696 (@jesper-friis)
Added redirection checking tool #695 (@jesper-friis)
Add test save #686 (@francescalb)
Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5 #678 (@jesper-friis)
Skip checking dimensional units for domain ontologies that doesn't load this class. #677 (@jesper-friis)
HermiT is default reasoner. #671 (@francescalb)
Ci/dependabot updates #662 (@francescalb)
Updated emmocheck to new EMMO quantities and units #658 (@jesper-friis)
Update README.md #657 (@jesper-friis)
Corrected bug so that asking for entities in imported does not return all in world #655 (@francescalb)
Corrected get_by_label to use only labels in the ontology #643 (@francescalb)
Update to comply with owlready2>0.41 #639 (@francescalb)
Ontodoc example in documentation #630 (@francescalb)

v0.6.0 (2023-06-19)

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Closed issues:

pyparsing has been updated #629

Merged pull requests:

Check prefLabels in imported ontologies only if asked for. #628 (@francescalb)

v0.5.4 (2023-06-15)

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v0.5.3.2 (2023-06-15)

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Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3 (2023-06-12)

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v0.5.3.1 (2023-06-12)

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Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

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Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

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Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

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Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

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Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

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v0.1.2 (2021-10-27)

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v0.1.1 (2021-10-27)

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v0.1.0 (2021-10-27)

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Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb almost 2 years ago

What's Changed

Update save recursive and layout by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/710
Ontology.copy() was added by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/711

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.6.3...v0.7.0

Changelog

v0.7.0 (2024-01-26)

Full Changelog

Merged pull requests:

Ontology copy #711 (@francescalb)
Update save recursive and layout #710 (@francescalb)

v0.6.3 (2024-01-25)

Full Changelog

Merged pull requests:

Fix infinite recursion in directory layout #708 (@jesper-friis)
Ensure that saving with squash removes all but current ontology #707 (@jesper-friis)
Turned on directory layout tests for emmo and made them pytest #706 (@francescalb)

v0.6.2 (2024-01-23)

Full Changelog

Merged pull requests:

Allow controling ontology IRI when saving #700 (@jesper-friis)

v0.6.1 (2024-01-18)

Full Changelog

Closed issues:

No tests for ontology.save #684
Allow using HermiT from ontoconvert #664
PrefLabel used by new_entity, and get_by_label even if it is not in the ontology #642
ontology(imported=True) returns all classes in world #640
excel2onto example doesn't come into the github pages documentation #626
owlready2 > 0.41 fails #624
get_by_label and get_by_label all force add label_annotations #621
hasPhysicalDimension convention has changed in EMMO-1.0.0-beta3 #347

Merged pull requests:

Avoid infinite recursion in set_common_prefix() #701 (@jesper-friis)
Updated the getattr patch #699 (@jesper-friis)
WIP: Fix issues with changed IRIs effecting test_excelparser #697 (@jesper-friis)
Added directory_layout() function #696 (@jesper-friis)
Added redirection checking tool #695 (@jesper-friis)
Add test save #686 (@francescalb)
Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5 #678 (@jesper-friis)
Skip checking dimensional units for domain ontologies that doesn't load this class. #677 (@jesper-friis)
HermiT is default reasoner. #671 (@francescalb)
Ci/dependabot updates #662 (@francescalb)
Updated emmocheck to new EMMO quantities and units #658 (@jesper-friis)
Update README.md #657 (@jesper-friis)
Corrected bug so that asking for entities in imported does not return all in world #655 (@francescalb)
Corrected get_by_label to use only labels in the ontology #643 (@francescalb)
Update to comply with owlready2>0.41 #639 (@francescalb)
Ontodoc example in documentation #630 (@francescalb)

v0.6.0 (2023-06-19)

Full Changelog

Closed issues:

pyparsing has been updated #629

Merged pull requests:

Check prefLabels in imported ontologies only if asked for. #628 (@francescalb)

v0.5.4 (2023-06-15)

Full Changelog

v0.5.3.2 (2023-06-15)

Full Changelog

Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3 (2023-06-12)

Full Changelog

v0.5.3.1 (2023-06-12)

Full Changelog

Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb about 2 years ago

What's Changed

Turned on directory layout tests for emmo and made them pytest by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/706
Ensure that saving with squash removes all but current ontology by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/707
Fix infinite recursion in directory layout by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/708

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.6.2...v0.6.3

Changelog

v0.6.3 (2024-01-25)

Full Changelog

Merged pull requests:

Fix infinite recursion in directory layout #708 (@jesper-friis)
Ensure that saving with squash removes all but current ontology #707 (@jesper-friis)
Turned on directory layout tests for emmo and made them pytest #706 (@francescalb)

v0.6.2 (2024-01-23)

Full Changelog

Merged pull requests:

Allow controling ontology IRI when saving #700 (@jesper-friis)

v0.6.1 (2024-01-18)

Full Changelog

Closed issues:

No tests for ontology.save #684
Allow using HermiT from ontoconvert #664
PrefLabel used by new_entity, and get_by_label even if it is not in the ontology #642
ontology(imported=True) returns all classes in world #640
excel2onto example doesn't come into the github pages documentation #626
owlready2 > 0.41 fails #624
get_by_label and get_by_label all force add label_annotations #621
hasPhysicalDimension convention has changed in EMMO-1.0.0-beta3 #347

Merged pull requests:

Avoid infinite recursion in set_common_prefix() #701 (@jesper-friis)
Updated the getattr patch #699 (@jesper-friis)
WIP: Fix issues with changed IRIs effecting test_excelparser #697 (@jesper-friis)
Added directory_layout() function #696 (@jesper-friis)
Added redirection checking tool #695 (@jesper-friis)
Add test save #686 (@francescalb)
Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5 #678 (@jesper-friis)
Skip checking dimensional units for domain ontologies that doesn't load this class. #677 (@jesper-friis)
HermiT is default reasoner. #671 (@francescalb)
Ci/dependabot updates #662 (@francescalb)
Updated emmocheck to new EMMO quantities and units #658 (@jesper-friis)
Update README.md #657 (@jesper-friis)
Corrected bug so that asking for entities in imported does not return all in world #655 (@francescalb)
Corrected get_by_label to use only labels in the ontology #643 (@francescalb)
Update to comply with owlready2>0.41 #639 (@francescalb)
Ontodoc example in documentation #630 (@francescalb)

v0.6.0 (2023-06-19)

Full Changelog

Closed issues:

pyparsing has been updated #629

Merged pull requests:

Check prefLabels in imported ontologies only if asked for. #628 (@francescalb)

v0.5.4 (2023-06-15)

Full Changelog

v0.5.3.2 (2023-06-15)

Full Changelog

Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3 (2023-06-12)

Full Changelog

v0.5.3.1 (2023-06-12)

Full Changelog

Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb about 2 years ago

What's Changed

Allow controling ontology IRI when saving by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/700

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.6.1...v0.6.2

Changelog

v0.6.2 (2024-01-23)

Full Changelog

Merged pull requests:

Allow controling ontology IRI when saving #700 (@jesper-friis)

v0.6.1 (2024-01-18)

Full Changelog

Closed issues:

No tests for ontology.save #684
Allow using HermiT from ontoconvert #664
PrefLabel used by new_entity, and get_by_label even if it is not in the ontology #642
ontology(imported=True) returns all classes in world #640
excel2onto example doesn't come into the github pages documentation #626
owlready2 > 0.41 fails #624
get_by_label and get_by_label all force add label_annotations #621
hasPhysicalDimension convention has changed in EMMO-1.0.0-beta3 #347

Merged pull requests:

Avoid infinite recursion in set_common_prefix() #701 (@jesper-friis)
Updated the getattr patch #699 (@jesper-friis)
WIP: Fix issues with changed IRIs effecting test_excelparser #697 (@jesper-friis)
Added directory_layout() function #696 (@jesper-friis)
Added redirection checking tool #695 (@jesper-friis)
Add test save #686 (@francescalb)
Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5 #678 (@jesper-friis)
Skip checking dimensional units for domain ontologies that doesn't load this class. #677 (@jesper-friis)
HermiT is default reasoner. #671 (@francescalb)
Ci/dependabot updates #662 (@francescalb)
Updated emmocheck to new EMMO quantities and units #658 (@jesper-friis)
Update README.md #657 (@jesper-friis)
Corrected bug so that asking for entities in imported does not return all in world #655 (@francescalb)
Corrected get_by_label to use only labels in the ontology #643 (@francescalb)
Update to comply with owlready2>0.41 #639 (@francescalb)
Ontodoc example in documentation #630 (@francescalb)

v0.6.0 (2023-06-19)

Full Changelog

Closed issues:

pyparsing has been updated #629

Merged pull requests:

Check prefLabels in imported ontologies only if asked for. #628 (@francescalb)

v0.5.4 (2023-06-15)

Full Changelog

v0.5.3.2 (2023-06-15)

Full Changelog

Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3 (2023-06-12)

Full Changelog

v0.5.3.1 (2023-06-12)

Full Changelog

Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb about 2 years ago

What's Changed

Ontodoc example in documentation by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/630
Corrected getbylabel to use only labels in the ontology by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/643
Corrected bug so that asking for entities in imported does not return all in world by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/655
Updated emmocheck to new EMMO quantities and units by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/658
Update to comply with owlready2>0.41 by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/639
HermiT is default reasoner. by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/671
Skip checking dimensional units for domain ontologies that doesn't load this class. by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/677
Add test save by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/686
Added redirection checking tool by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/695
WIP: Fix issues with changed IRIs effecting test_excelparser by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/697
Added directory_layout() function by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/696
Update testunitdimension in emmocheck to EMMO 1.0.0-beta5 by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/678
Avoid infinite recursion in setcommonprefix() by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/701
Updated the getattr patch by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/699

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.6.0...v0.6.1

Changelog

v0.6.1 (2024-01-18)

Full Changelog

Closed issues:

No tests for ontology.save #684
Allow using HermiT from ontoconvert #664
PrefLabel used by new_entity, and get_by_label even if it is not in the ontology #642
ontology(imported=True) returns all classes in world #640
excel2onto example doesn't come into the github pages documentation #626
owlready2 > 0.41 fails #624
get_by_label and get_by_label all force add label_annotations #621
hasPhysicalDimension convention has changed in EMMO-1.0.0-beta3 #347

Merged pull requests:

Avoid infinite recursion in set_common_prefix() #701 (@jesper-friis)
Updated the getattr patch #699 (@jesper-friis)
WIP: Fix issues with changed IRIs effecting test_excelparser #697 (@jesper-friis)
Added directory_layout() function #696 (@jesper-friis)
Added redirection checking tool #695 (@jesper-friis)
Add test save #686 (@francescalb)
Update test_unit_dimension in emmocheck to EMMO 1.0.0-beta5 #678 (@jesper-friis)
Skip checking dimensional units for domain ontologies that doesn't load this class. #677 (@jesper-friis)
HermiT is default reasoner. #671 (@francescalb)
Ci/dependabot updates #662 (@francescalb)
Updated emmocheck to new EMMO quantities and units #658 (@jesper-friis)
Update README.md #657 (@jesper-friis)
Corrected bug so that asking for entities in imported does not return all in world #655 (@francescalb)
Corrected get_by_label to use only labels in the ontology #643 (@francescalb)
Update to comply with owlready2>0.41 #639 (@francescalb)
Ontodoc example in documentation #630 (@francescalb)

v0.6.0 (2023-06-19)

Full Changelog

Closed issues:

pyparsing has been updated #629

Merged pull requests:

Check prefLabels in imported ontologies only if asked for. #628 (@francescalb)

v0.5.4 (2023-06-15)

Full Changelog

v0.5.3.2 (2023-06-15)

Full Changelog

Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3 (2023-06-12)

Full Changelog

v0.5.3.1 (2023-06-12)

Full Changelog

Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb about 2 years ago

What's Changed

prefLabel now only tested on current ontlogy unless check-imported is True.

Changelog

v0.6.0 (2023-06-19)

Full Changelog

Closed issues:

pyparsing has been updated #629

Merged pull requests:

Check prefLabels in imported ontologies only if asked for. #628 (@francescalb)

v0.5.4 (2023-06-15)

Full Changelog

v0.5.3.2 (2023-06-15)

Full Changelog

Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3.1 (2023-06-12)

Full Changelog

v0.5.3 (2023-06-12)

Full Changelog

Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb over 2 years ago

emmontopy - v0.5.4

Just updating version number this is equivalent to v.0.5.3 with a fix on CD-workflows

Changelog

v0.5.4 (2023-06-15)

Full Changelog

v0.5.3.2 (2023-06-15)

Full Changelog

Merged pull requests:

remove warnings_as_errors in cd workflow introduced in 0.5.3 #625 (@francescalb)

v0.5.3 (2023-06-12)

Full Changelog

v0.5.3.1 (2023-06-12)

Full Changelog

Closed issues:

Extend new_entity to include properties #609
Add support for Python 3.11 #599
excelparser - enable object properties creation #587
If there are altLabels that match, get_by_label_all returns only the prefLabels. #511
excel2onto: implement other annotations #462

Merged pull requests:

default_annotations no longer forced in get_by_label #623 (@francescalb)
Updated documentation and excel sheet in example. #622 (@francescalb)
Flb/excel2onto properties #620 (@francescalb)
Fixed failing tests in test_patch.py #618 (@jesper-friis)
Add test for Python 3.11 and support it officially #615 (@jesper-friis)
Added doctest #614 (@jesper-friis)
Item access to classes #613 (@jesper-friis)
Change ontology.new_entity to also allow adding properties #610 (@francescalb)
Added DOI badge #606 (@jesper-friis)

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb over 2 years ago

emmontopy - v0.5.3.2

Fix in cd workflows

- Python
Published by francescalb over 2 years ago

emmontopy - v0.5.3.1

Rerelease v0.5.3 to fix pypi package

- Python
Published by francescalb over 2 years ago

emmontopy - v0.5.3

Added DOI badge by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/606
Change ontology.new_entity to also allow adding properties by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/610
Add test for Python 3.11 and support it officially by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/615
Item access to classes by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/613
Excel2Onto: properties can now be added with ranges and domains by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/620
Excel2Onto: Other annotations can also be added.
Defaultannotations no longer forced in getby_label by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/623

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.5.2...v0.5.3

- Python
Published by francescalb over 2 years ago

What's Changed

Fix internal links in generated documentation generated with ontodoc by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/548
Corrected bug on getting default relation style. by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/561
Changed argument leafs to leaves, with deprecation warning in ontograph by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/564
ontograph: colour updates, examples, bugfix by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/569
Added two additional exceptions to emmocheck by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/577
Added link to excelparser from tools for documentation of excel sheet. by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/594
Add links to the original FaCT++ repo, GitHub profiles, etc. by @blokhin in https://github.com/emmo-repo/EMMOntoPy/pull/600
Added test update to PR template. by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/598
Changed is_defined into a ThingClass property and improved its documentation. by @jesper-friis in https://github.com/emmo-repo/EMMOntoPy/pull/597
getancestors and getdescendants have the same arguments. by @francescalb in https://github.com/emmo-repo/EMMOntoPy/pull/572

Full Changelog: https://github.com/emmo-repo/EMMOntoPy/compare/v0.5.1...v0.5.2

Changelog

v0.5.2 (2023-05-24)

Full Changelog

Fixed bugs:

Auto-merge dependabot PRs workflow invalid #566

Closed issues:

Point to excelparser api from the tools-page #593
BUG: pytest - missing remote file /0.5.0/electrochemicalquantities / ontology #589
Owlready 0.41 support ? #588
Allow space in labels #583
is_defined needs a better description #563
utils line 112 in get_iri_name link = "{lowerlabel}" vs "{label}" #562
ontograph - update colour deafults #559
ontograph - argument leafs should be leaves #558
ontograph - write out more examples on how to use it #557
ontograph --parents not working #556
test_graph2 is failing #555
Add client side redirection in generated html documentation #552
Typos in PR template #523
ontograph, read format from name #497
Harmonize get_descendants and get_ancestors #406
Review default colours and style in ontopy/graph.py #345

Merged pull requests:

Add links to the original FaCT++ repo, GitHub profiles, etc. #600 (@blokhin)
Added test update to PR template. #598 (@jesper-friis)
Changed is_defined into a ThingClass property and improved its documentation. #597 (@jesper-friis)
Added link to excelparser from tools for documentation of excel sheet. #594 (@francescalb)
Bump SINTEF/ci-cd from 2.3.0 to 2.3.1 #584 (@dependabot[bot])
Updated get_by_label() so that it now accepts label, name and full iri #582 (@jesper-friis)
Added two additional exceptions to emmocheck #577 (@jesper-friis)
Bump SINTEF/ci-cd from 2.2.1 to 2.3.0 #575 (@dependabot[bot])
get_ancestors and get_descendants have the same arguments. #572 (@francescalb)
Bump SINTEF/ci-cd from 2.2.0 to 2.2.1 #571 (@dependabot[bot])
ontograph: colour updates, examples, bugfix #569 (@francescalb)
Bump SINTEF/ci-cd from 2.1.0 to 2.2.0 #567 (@dependabot[bot])
Changed argument leafs to leaves, with deprecation warning in ontograph #564 (@francescalb)
Corrected bug on getting default relation style. #561 (@francescalb)
Fix internal links in generated documentation generated with ontodoc #548 (@jesper-friis)

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (@CasperWA)
Revert version to v0.5.0 #544 (@CasperWA)
Fix ontodoc for bigmap #543 (@jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (@CasperWA)
Flb/fix to pylint2.15.4 #535 (@francescalb)
Bypass punning in ontodoc. #532 (@francescalb)
Added possibility to update ontology. #527 (@francescalb)
Only generate new uuid if not already a valid one #526 (@francescalb)
Removed LegacyVersion from ontopy.utils #515 (@francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (@francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (@jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (@francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (@francescalb)
Added correct material.png figure in tool-instructions #498 (@francescalb)
Updated logo #494 (@jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (@CasperWA)
write catalog now writes relative paths per default #483 (@francescalb)
Setting prefix explicitly in excelparser #470 (@francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (@CasperWA)
Allow for adding prefix in manchester notation. #469 (@francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (@jesper-friis)
Added documentation of excel2onto #456 (@jesper-friis)
factpluspluswrapper README file #453 (@jesper-friis)
Improved get_unabbreviated_triples() #449 (@jesper-friis)
Fix loading in windows, url paths #446 (@francescalb)
Fixed reading web destinations defined in catalog #445 (@francescalb)
SUPPORT EMMO-beta4.0 #441 (@francescalb)
Support for userdefined prefixes #439 (@francescalb)
Flb/issue421 #438 (@francescalb)
Update demo #437 (@jesper-friis)
Silence false negative from pylint on github #436 (@jesper-friis)
Better error messages #435 (@jesper-friis)
Updated logo. #418 (@jesper-friis)
cytoscapegraph fails with missing edge labels #414 (@francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (@jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (@CasperWA)
Flb/get descendants #405 (@francescalb)
Corrected expected number of returned arguments #404 (@jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (@jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (@francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (@francescalb)
Workaround for failing test #385 (@CasperWA)
fix #313 remove handle #315 (@sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (@CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (@CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (@jesper-friis)
Warning relation excelparser #366 (@sygout)
Close temporary file before reading it #364 (@jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (@CasperWA)
Use TEAM 4.0[bot] #353 (@CasperWA)
Changed arguments in _has_obj_triples_spo #351 (@francescalb)
Fix serialised ontology iri #341 (@jesper-friis)
Corrected parsing cardinality restrictions #340 (@jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (@jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (@francescalb)
Added sconverting Posix to str in get_ontology #327 (@francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (@francescalb)
Added checking that label is string in get_by_label #312 (@francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (@francescalb)
Fix ontoconvert rdflib import #307 (@CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (@francescalb)
Removed .readthedocs.yml #298 (@jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (@jesper-friis)
Added functionality for more than one parent in new_entity #295 (@francescalb)
Added test for label name length in ontology.new_entity #291 (@francescalb)
add logo to Readme and doc #289 (@m-abdollahi)
Improved representation of blank nodes #283 (@jesper-friis)
Update method name to avoid overwriting inherited #281 (@CasperWA)
Fixed link to OpenModel logo #279 (@francescalb)
Skip FOAF test #277 (@CasperWA)
Added Standard methods to Ontology #246 (@francescalb)
Implement pre-commit & various tools #245 (@CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (@CasperWA)
Update README with PyPI and deprecation msgs #270 (@CasperWA)
Added option: EMMObased = False in ontology.load() #262 (@francescalb)
Added new test "test_physical_quantity_dimension" #258 (@jesper-friis)
Add packaging to list of requirements #256 (@CasperWA)
Fix MkDocs build warnings and CI job #254 (@CasperWA)
Update dependencies #252 (@CasperWA)
Add OpenModel contributing project #247 (@francescalb)
Automate documentation releases #242 (@CasperWA)
Import from collections.abc when possible #240 (@CasperWA)
Ensure all produced files from tests are in a temp dir #239 (@CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (@francescalb)
Use width in img HTML #235 (@CasperWA)
Added function to load the emmo (the ontology) directly #226 (@francescalb)
Created pull request template #225 (@francescalb)
Setup new documentation framework #222 (@CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (@CasperWA)
Unskip test as #210 has been resolved #218 (@CasperWA)
Remove sub-fact++ modules importability #217 (@CasperWA)
Update requirements #216 (@CasperWA)
Avoid using Owlready2 v0.34 #211 (@CasperWA)
Update package names #208 (@CasperWA)
Added function new_entitiy to ontology #207 (@francescalb)
ttl standard for emmo #204 (@francescalb)
Added choice for specifying namespace in get_by_label #202 (@francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (@francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb almost 3 years ago

Fixes for `ontodoc`

Fixes issues with the ontodoc tool for building more correct documentation pages of ontologies.

Changelog

v0.5.1 (2023-02-07)

Full Changelog

Fixed bugs:

Use custom token for GitHub changelog generator #545
Avoid using Azure mirror for APT packages #541

Merged pull requests:

Use SINTEF/ci-cd v2.1.0 in CI/CD workflows #546 (CasperWA)
Revert version to v0.5.0 #544 (CasperWA)
Fix ontodoc for bigmap #543 (jesper-friis)

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (CasperWA)
Flb/fix to pylint2.15.4 #535 (francescalb)
Bypass punning in ontodoc. #532 (francescalb)
Added possibility to update ontology. #527 (francescalb)
Only generate new uuid if not already a valid one #526 (francescalb)
Removed LegacyVersion from ontopy.utils #515 (francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (francescalb)
Added correct material.png figure in tool-instructions #498 (francescalb)
Updated logo #494 (jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (CasperWA)
write catalog now writes relative paths per default #483 (francescalb)
Setting prefix explicitly in excelparser #470 (francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (CasperWA)
Allow for adding prefix in manchester notation. #469 (francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (jesper-friis)
Added documentation of excel2onto #456 (jesper-friis)
factpluspluswrapper README file #453 (jesper-friis)
Improved get_unabbreviated_triples() #449 (jesper-friis)
Fix loading in windows, url paths #446 (francescalb)
Fixed reading web destinations defined in catalog #445 (francescalb)
SUPPORT EMMO-beta4.0 #441 (francescalb)
Support for userdefined prefixes #439 (francescalb)
Flb/issue421 #438 (francescalb)
Update demo #437 (jesper-friis)
Silence false negative from pylint on github #436 (jesper-friis)
Better error messages #435 (jesper-friis)
Updated logo. #418 (jesper-friis)
cytoscapegraph fails with missing edge labels #414 (francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (CasperWA)
Flb/get descendants #405 (francescalb)
Corrected expected number of returned arguments #404 (jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (francescalb)
Workaround for failing test #385 (CasperWA)
fix #313 remove handle #315 (sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (jesper-friis)
Warning relation excelparser #366 (sygout)
Close temporary file before reading it #364 (jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (CasperWA)
Use TEAM 4.0[bot] #353 (CasperWA)
Changed arguments in _has_obj_triples_spo #351 (francescalb)
Fix serialised ontology iri #341 (jesper-friis)
Corrected parsing cardinality restrictions #340 (jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (francescalb)
Added sconverting Posix to str in get_ontology #327 (francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (francescalb)
Added checking that label is string in get_by_label #312 (francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (francescalb)
Fix ontoconvert rdflib import #307 (CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (francescalb)
Removed .readthedocs.yml #298 (jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (jesper-friis)
Added functionality for more than one parent in new_entity #295 (francescalb)
Added test for label name length in ontology.new_entity #291 (francescalb)
add logo to Readme and doc #289 (m-abdollahi)
Improved representation of blank nodes #283 (jesper-friis)
Update method name to avoid overwriting inherited #281 (CasperWA)
Fixed link to OpenModel logo #279 (francescalb)
Skip FOAF test #277 (CasperWA)
Added Standard methods to Ontology #246 (francescalb)
Implement pre-commit & various tools #245 (CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (CasperWA)
Update README with PyPI and deprecation msgs #270 (CasperWA)
Added option: EMMObased = False in ontology.load() #262 (francescalb)
Added new test "test_physical_quantity_dimension" #258 (jesper-friis)
Add packaging to list of requirements #256 (CasperWA)
Fix MkDocs build warnings and CI job #254 (CasperWA)
Update dependencies #252 (CasperWA)
Add OpenModel contributing project #247 (francescalb)
Automate documentation releases #242 (CasperWA)
Import from collections.abc when possible #240 (CasperWA)
Ensure all produced files from tests are in a temp dir #239 (CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (francescalb)
Use width in img HTML #235 (CasperWA)
Added function to load the emmo (the ontology) directly #226 (francescalb)
Created pull request template #225 (francescalb)
Setup new documentation framework #222 (CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (CasperWA)
Unskip test as #210 has been resolved #218 (CasperWA)
Remove sub-fact++ modules importability #217 (CasperWA)
Update requirements #216 (CasperWA)
Avoid using Owlready2 v0.34 #211 (CasperWA)
Update package names #208 (CasperWA)
Added function new_entitiy to ontology #207 (francescalb)
ttl standard for emmo #204 (francescalb)
Added choice for specifying namespace in get_by_label #202 (francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA about 3 years ago

Several fixes and updates

Several fixes and updates have been implemented in this update. See below for an overview.

Changelog

v0.5.0 (2023-02-06)

Full Changelog

Fixed bugs:

LegacyVersion does not exist in packaging.version #540
ontodoc: Expect is_instance_of property to be iterable #506
Reinstate images/material.png #495

Closed issues:

Newest pylint (2.15.4) has intriduced some new rules. #534
sync_attributes according to emmo convention regenerates a new iri even if it already has a valid one #525
Remove dependency on LegacyVersion of packaging #514
pytests are importing packaging 22.0 even though it is not allowed in requirements #513
ontodoc: adding annotations that are not strings fail #510
get_by_label_all only works after sync_attributes #502
excel2onto: support updating ontology #501
excel2onto: allow to use prefLabel already in imported ontologies #500
Drop Python 3.6 support - extend Python >3.7 support #486
Update pypi-release github action #482
Make workflows dispatchable #481
excel2onto: Read catalog file for imported ontology #474
Give option to write_catalog for writing relative paths #473
excel2onto: add choice of prefix for imported ontologies #467

Merged pull requests:

Fix fixtures for Python3.7 #536 (CasperWA)
Flb/fix to pylint2.15.4 #535 (francescalb)
Bypass punning in ontodoc. #532 (francescalb)
Added possibility to update ontology. #527 (francescalb)
Only generate new uuid if not already a valid one #526 (francescalb)
Removed LegacyVersion from ontopy.utils #515 (francescalb)
Added fix for adding annotations that are not strings in ontodoc #512 (francescalb)
Do not trigger an emmocheck failure for ontologies with a foaf:logo annotation #509 (jesper-friis)
New concepts allowed even if name alrady exists in imported ontologies #504 (francescalb)
Corrected so that get_by_label_all also returns all concepts #503 (francescalb)
Added correct material.png figure in tool-instructions #498 (francescalb)
Updated logo #494 (jesper-friis)
Makeover for CI/CD workflows, pre-commit & MkDocs #485 (CasperWA)
write catalog now writes relative paths per default #483 (francescalb)
Setting prefix explicitly in excelparser #470 (francescalb)

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

Update from 'EMMO-python' -> 'EMMOntoPy' #477 (CasperWA)
Allow for adding prefix in manchester notation. #469 (francescalb)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (jesper-friis)
Added documentation of excel2onto #456 (jesper-friis)
factpluspluswrapper README file #453 (jesper-friis)
Improved get_unabbreviated_triples() #449 (jesper-friis)
Fix loading in windows, url paths #446 (francescalb)
Fixed reading web destinations defined in catalog #445 (francescalb)
SUPPORT EMMO-beta4.0 #441 (francescalb)
Support for userdefined prefixes #439 (francescalb)
Flb/issue421 #438 (francescalb)
Update demo #437 (jesper-friis)
Silence false negative from pylint on github #436 (jesper-friis)
Better error messages #435 (jesper-friis)
Updated logo. #418 (jesper-friis)
cytoscapegraph fails with missing edge labels #414 (francescalb)

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (jesper-friis)

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (CasperWA)
Flb/get descendants #405 (francescalb)
Corrected expected number of returned arguments #404 (jesper-friis)
Add functionality for setting name part of IRI to prefLabel #399 (jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (francescalb)
Download EMMO from raw.github deirectly as redirection is broken #392 (francescalb)
Workaround for failing test #385 (CasperWA)
fix #313 remove handle #315 (sygout)

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278
Disable FOAF test as xmlns.com is down #276

Closed issues:

Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
ReadTheDocs #288
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269
Consider MarkDown header styling #231

Merged pull requests:

Use ID! type instead of String! #375 (CasperWA)
Avoided infinite recursion when loading catalog files that recursively #370 (jesper-friis)
Warning relation excelparser #366 (sygout)
Close temporary file before reading it #364 (jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (CasperWA)
Use TEAM 4.0[bot] #353 (CasperWA)
Changed arguments in _has_obj_triples_spo #351 (francescalb)
Fix serialised ontology iri #341 (jesper-friis)
Corrected parsing cardinality restrictions #340 (jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (jesper-friis)
Flb/update excel parser accroding to thermodynamics example #336 (francescalb)
Added sconverting Posix to str in get_ontology #327 (francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (francescalb)
Added checking that label is string in get_by_label #312 (francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (francescalb)
Fix ontoconvert rdflib import #307 (CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (francescalb)
Removed .readthedocs.yml #298 (jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (jesper-friis)
Added functionality for more than one parent in new_entity #295 (francescalb)
Added test for label name length in ontology.new_entity #291 (francescalb)
add logo to Readme and doc #289 (m-abdollahi)
Improved representation of blank nodes #283 (jesper-friis)
Update method name to avoid overwriting inherited #281 (CasperWA)
Fixed link to OpenModel logo #279 (francescalb)
Skip FOAF test #277 (CasperWA)
Added Standard methods to Ontology #246 (francescalb)
Implement pre-commit & various tools #245 (CasperWA)

v0.1.3 (2021-10-27)

Full Changelog

v0.1.2 (2021-10-27)

Full Changelog

v0.1.1 (2021-10-27)

Full Changelog

v0.1.0 (2021-10-27)

Full Changelog

Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (CasperWA)
Update README with PyPI and deprecation msgs #270 (CasperWA)
Added option: EMMObased = False in ontology.load() #262 (francescalb)
Added new test "test_physical_quantity_dimension" #258 (jesper-friis)
Add packaging to list of requirements #256 (CasperWA)
Fix MkDocs build warnings and CI job #254 (CasperWA)
Update dependencies #252 (CasperWA)
Add OpenModel contributing project #247 (francescalb)
Automate documentation releases #242 (CasperWA)
Import from collections.abc when possible #240 (CasperWA)
Ensure all produced files from tests are in a temp dir #239 (CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (francescalb)
Use width in img HTML #235 (CasperWA)
Added function to load the emmo (the ontology) directly #226 (francescalb)
Created pull request template #225 (francescalb)
Setup new documentation framework #222 (CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (CasperWA)
Unskip test as #210 has been resolved #218 (CasperWA)
Remove sub-fact++ modules importability #217 (CasperWA)
Update requirements #216 (CasperWA)
Avoid using Owlready2 v0.34 #211 (CasperWA)
Update package names #208 (CasperWA)
Added function new_entitiy to ontology #207 (francescalb)
ttl standard for emmo #204 (francescalb)
Added choice for specifying namespace in get_by_label #202 (francescalb)

v1.0.1b (2021-07-01)

Full Changelog

Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA about 3 years ago

Examples and docs update

Several examples have been updated, including documentation. Fixes for the excel parser and general graph handling has been implemented, and more are incoming.

The repository name on GitHub has changed (from "EMMO-python" to "EMMOntoPy") to better represent the updated repository and Python API and package name installable from PyPI.

Changelog

v0.4.0 (2022-10-04)

Full Changelog

Fixed bugs:

Update repo files with new repo name #479
Pre-commit hook bandit failing #478
Fix publish/release workflow #476
excel2onto: not all relations are included in the generated ontology #457
Unexpected behaviour of get_unabbreviated_triples() #454
Edge without label crash the graph creation #397

Closed issues:

excel2onto: restrictions does not allow for using "emmo:hasProcessOutput some xx" #464
EMMO is updated to beta4, and now documentation fails #440
some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph #429
Excelparser does not write catalog file correctly #421
Add support for prefix #416
Pre.commit failed with ontology.py #415
visualization of EMMO based ontology #412
Avoid infinite recursion when loading catalog file #369
Excelparser: Automatize emmo-based? #335
What are the applications of EMMO for materials informatics? #325
Provide 'support' for same entities with different namespaces #128
Remove deprecated emmo/ontograph.py that uses pydot #103

Merged pull requests:

[Auto-generated] Update dependencies #480 (TEAM4-0)
Update from 'EMMO-python' -> 'EMMOntoPy' #477 (CasperWA)
[Auto-generated] Update dependencies #471 (TEAM4-0)
Allow for adding prefix in manchester notation. #469 (francescalb)
[Auto-generated] Update dependencies #466 (TEAM4-0)
[Auto-generated] Update dependencies #461 (TEAM4-0)
Fixed issue with exel2onto: not all relations are included in the generated ontology #458 (jesper-friis)
Added documentation of excel2onto #456 (jesper-friis)
factpluspluswrapper README file #453 (jesper-friis)
[Auto-generated] Update dependencies #452 (TEAM4-0)
Improved get_unabbreviated_triples() #449 (jesper-friis)
Fix loading in windows, url paths #446 (francescalb)
Fixed reading web destinations defined in catalog #445 (francescalb)
[Auto-generated] Update dependencies #443 (TEAM4-0)
SUPPORT EMMO-beta4.0 #441 (francescalb)
Support for userdefined prefixes #439 (francescalb)
Flb/issue421 #438 (francescalb)
Update demo #437 (jesper-friis)
Silence false negative from pylint on github #436 (jesper-friis)
Better error messages #435 (jesper-friis)
[Auto-generated] Update dependencies #434 (TEAM4-0)
[Auto-generated] Update dependencies #432 (TEAM4-0)
[Auto-generated] Update dependencies #430 (TEAM4-0)
[Auto-generated] Update dependencies #425 (TEAM4-0)
[Auto-generated] Update dependencies #420 (TEAM4-0)
Updated logo. #418 (jesper-friis)
cytoscapegraph fails with missing edge labels #414 (francescalb)
[Auto-generated] Update dependencies #413 (TEAM4-0)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA over 3 years ago

emmontopy - v0.3.1

Fixed bug in ontoconvert that prevented reasoning

Changelog

v0.3.1 (2022-05-08)

Full Changelog

Merged pull requests:

Fixed typo in ontoconvert #409 (jesper-friis)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by jesper-friis almost 4 years ago

Excelparser improvements and IRI from prefLabel generation

Addressed issues that have come up with external usage of ExcelParser

Ontology.save functionalities reorganised (#399) Error handling in excelparser improved by returning errors (#396) Generation of IRIs from prefLabel (#399) Added get_descendants (#405)

Changelog

v0.3.0 (2022-05-05)

Full Changelog

Fixed bugs:

Documentation is currently not building #407
Pytest is currently failing #384
permission denied when working with temporary file #313

Closed issues:

Make get_descendants(levels=1) #403
Add functionality for setting name part of IRI to prefLabel #398
Generate excelsheet from ontology. #394
Return a list of the concepts that are disregarded during when converting from excel with -force argument #393
Demo - Broken ontology URLs #390
Excelparser: how to handle entities that already exist in one of the imported ontologies? #334

Merged pull requests:

Updated docs python handler #408 (CasperWA)
Flb/get descendants #405 (francescalb)
Corrected expected number of returned arguments #404 (jesper-friis)
[Auto-generated] Update dependencies #402 (TEAM4-0)
[Auto-generated] Update dependencies #400 (TEAM4-0)
Add functionality for setting name part of IRI to prefLabel #399 (jesper-friis)
create_from_excel/pandas return as list of concepts that are worngly defined in the excelfile #396 (francescalb)
[Auto-generated] Update dependencies #395 (TEAM4-0)
Download EMMO from raw.github deirectly as redirection is broken #392 (francescalb)
[Auto-generated] Update dependencies #389 (TEAM4-0)
Workaround for failing test #385 (CasperWA)
[Auto-generated] Update dependencies #380 (TEAM4-0)
fix #313 remove handle #315 (sygout)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by francescalb almost 4 years ago

Updated CI/CD workflows and much more

To see a full list of the changes, please go here and see the changelog below.

Changelog

v0.2.0 (2022-03-02)

Full Changelog

Implemented enhancements:

spaces before or after word in prefLabel makes excelparser fail #332
Make EMMOntopy PyPi #268
Use pre-commit #243
Standard dunder/magic methods for Ontology #228
Update code styling and linting #223
Fix checking PR body & improve error message in CD #318 (CasperWA)
New workflows for dependabot automation #285 (CasperWA)

Fixed bugs:

GH GraphQL type issue for auto-merge workflow #374
Missing warning for excel parser relations and problem with "nan" #365
Ignore NumPy safety warning #360
Seting metadata in excelparser fails if there are no imported ontologies. #331
Edge-case fails CD workflow for dependabot #319
Ontodoc failing due to wrong rdflib import #306
Overwriting get_triples() method #280
OpenModel logo not loading in README #278

Closed issues:

Add NumPy as an explicit dependency #359
Use TEAM 4.0[bot] for GH Actions jobs #352
_get_triples_spo take argumens s, and p, not subject and predicate #350
Add --force to excelparser #333
Cannot load ontology in Windows. #328
make get_ontology accept 'PosixPath' #326
Make EMMOntoPy baseexception and basewarning #321
get_by_label crash if not str #311
make excel parser that creates and ontology from a filled excel file #302
Check out how to get version of ontology #299
Let ontology.new_entity acccept one or more parents directly #294
Make ManchesterSyntaxParser that returns Owlready2 #293
onto.new_entity should throw Error if label name consists of more than one word #290
Add logo to README #287
Write EMMO-python is deprecated and link to EMMOtopy on PyPi #269

Merged pull requests:

[Auto-generated] Update dependencies #378 (TEAM4-0)
Use ID! type instead of String! #375 (CasperWA)
[Auto-generated] Update dependencies #371 (TEAM4-0)
Avoided infinite recursion when loading catalog files that recursively #370 (jesper-friis)
[Auto-generated] Update dependencies #367 (TEAM4-0)
Warning relation excelparser #366 (sygout)
Close temporary file before reading it #364 (jesper-friis)
Ignore safety ID 44715 + add numpy dependency #361 (CasperWA)
[Auto-generated] Update dependencies #358 (TEAM4-0)
[Auto-generated] Update dependencies #357 (TEAM4-0)
Use TEAM 4.0[bot] #353 (CasperWA)
Changed arguments in _has_obj_triples_spo #351 (francescalb)
[Auto-generated] Update dependencies #349 (francescalb)
Fix serialised ontology iri #341 (jesper-friis)
Corrected parsing cardinality restrictions #340 (jesper-friis)
When visualising restrictions, annotate the edges with the restriction type by default #339 (jesper-friis)
[Auto-generated] Update dependencies #338 (francescalb)
Flb/update excel parser accroding to thermodynamics example #336 (francescalb)
[Auto-generated] Update dependencies #330 (francescalb)
Added sconverting Posix to str in get_ontology #327 (francescalb)
[Auto-generated] Update dependencies #324 (francescalb)
Added package specific base exception and base warning for EMMOntoPy #322 (francescalb)
Added checking that label is string in get_by_label #312 (francescalb)
Make excelparser that converts a filled excel sheet to an ontology #309 (francescalb)
[Auto-generated] Update dependencies #308 (francescalb)
Fix ontoconvert rdflib import #307 (CasperWA)
Check first versionIRI then versionInfo in ontology.get_version() #301 (francescalb)
[Auto-generated] Update dependencies #300 (francescalb)
Removed .readthedocs.yml #298 (jesper-friis)
Added support for evaluating Manchester expression to owlready2 #296 (jesper-friis)
Added functionality for more than one parent in new_entity #295 (francescalb)
[Auto-generated] Update dependencies #292 (francescalb)
Added test for label name length in ontology.new_entity #291 (francescalb)
add logo to Readme and doc #289 (m-abdollahi)
Improved representation of blank nodes #283 (jesper-friis)
Update method name to avoid overwriting inherited #281 (CasperWA)
Fixed link to OpenModel logo #279 (francescalb)
Skip FOAF test #277 (CasperWA)
Added Standard methods to Ontology #246 (francescalb)
Implement pre-commit & various tools #245 (CasperWA)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA almost 4 years ago

New publish workflow

This is a test release to ensure the new publish CD workflow functions as intended.

Changelog

v0.1.3 (2021-10-27)

Full Changelog

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA over 4 years ago

New publish workflow

This is a test release to ensure the new publish CD workflow functions as intended.

Changelog

v0.1.2 (2021-10-27)

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* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA over 4 years ago

New publish workflow

This is a test release to ensure the new publish CD workflow functions as intended.

- Python
Published by CasperWA over 4 years ago

EMMOntoPy

This is the first release for the revamped EMMO Python package: EMMOntoPy.

Changelog

v0.1.0 (2021-10-27)

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Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (CasperWA)
Update README with PyPI and deprecation msgs #270 (CasperWA)
Added option: EMMObased = False in ontology.load() #262 (francescalb)
Update pyyaml requirement from <6,>=5.4.1 to >=5.4.1,<7 #260 (dependabot[bot])
Update owlready2 requirement from !=0.32,!=0.34,<0.35,>=0.28 to >=0.28,!=0.32,!=0.34,<0.36 #259 (dependabot[bot])
Added new test "test_physical_quantity_dimension" #258 (jesper-friis)
Add packaging to list of requirements #256 (CasperWA)
Fix MkDocs build warnings and CI job #254 (CasperWA)
Update mkdocstrings requirement from ~=0.16.1 to ~=0.16.2 #253 (dependabot[bot])
Update dependencies #252 (CasperWA)
Add OpenModel contributing project #247 (francescalb)
Automate documentation releases #242 (CasperWA)
Import from collections.abc when possible #240 (CasperWA)
Ensure all produced files from tests are in a temp dir #239 (CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (francescalb)
Use width in img HTML #235 (CasperWA)
Update graphviz requirement from <0.17,>=0.16 to >=0.16,<0.18 #229 (dependabot[bot])
Added function to load the emmo (the ontology) directly #226 (francescalb)
Created pull request template #225 (francescalb)
Setup new documentation framework #222 (CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (CasperWA)
Unskip test as #210 has been resolved #218 (CasperWA)
Remove sub-fact++ modules importability #217 (CasperWA)
Update requirements #216 (CasperWA)
Avoid using Owlready2 v0.34 #211 (CasperWA)
Update package names #208 (CasperWA)
Added function new_entitiy to ontology #207 (francescalb)
ttl standard for emmo #204 (francescalb)
Added choice for specifying namespace in get_by_label #202 (francescalb)

v1.0.1b (2021-07-01)

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Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (francescalb)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA over 4 years ago

emmontopy - 1.0.1b

Updated serach for iris when importing ontologies to search in already exisinting iri_mappings if (re) load of catalog-file of the current ontology is not required.

- Python
Published by francescalb over 4 years ago

emmontopy - 1.0.1

Update so that iris are taken from already read catalog if (re)load not required

- Python
Published by francescalb over 4 years ago

emmontopy - 1.0.0

Improved support for save to turtle and other formats supported by rdflib.

Improved management of ontology metadata.

annotatewithontology function added for retaining ontology information otherwise lost with reasoning.

- Python
Published by francescalb almost 5 years ago

emmontopy - 1.0.0-alpha-30

Further improvements in loading ontologies. Also added a method for Wu-Palmer measure of semantic similarity.

- Python
Published by jesper-friis almost 5 years ago

emmontopy - 1.0.0-alpha-29

Updated to correctly load owlfiles

- Python
Published by francescalb almost 5 years ago

emmontopy - 1.0.0-alpha-28

Added option to read catalog for ontologies loaded directly from a web url

- Python
Published by francescalb almost 5 years ago

emmontopy - 1.0.0-alpha-27

Improved documentation of domain ontologies and made generated documentation prettier.

- Python
Published by jesper-friis almost 5 years ago

emmontopy - 1.0.0-alpha-26

Made it possible to restrict the generated documentation with ontodoc to a given set of namespaces.

- Python
Published by jesper-friis about 5 years ago

emmontopy - 1.0.0-alpha-25

Updated exceptions in emmocheck to account for new entities soon to be included in emmo1.0.0-beta

- Python
Published by francescalb about 5 years ago

emmontopy - 1.0.0-alpha-24

added reasoning with FaCT++
improved loading turtle ontologies
added option to ontodoc for documenting imported ontologies
several additional bug fixesadded reasoning with FaCT++
improved loading turtle ontologies
added option to ontodoc for documenting imported ontologies
several additional bug fixes

- Python
Published by jesper-friis about 5 years ago

emmontopy - 1.0.0-alpha-22

Made it possible to load online turtle ontologies.
Fixed version of Owlready2 to 0.25 since v0.26 results in an exception.

- Python
Published by jesper-friis about 5 years ago

EMMO-python has been updated so that it can be used with EMMO-1.0.0-beta, and emmocheck has been updated accordinglt. A tool, ontoconvert, has been added to convert between ontology formats, and loading a .ttl-ontology is now directly feasible as welll as converting to owl and loading owl as previously. Support for labels (prefLabels...) is also improved.

- Python
Published by francescalb about 5 years ago

emmontopy - 1.0.0-alpha-20b

Updated support for ignoring namespaces and imported ontologies in emmocheck. Also added error messages upon calling emmocheck with wrong arguments.