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Open Source Science

https://github.com/biolink/ontobio

python library for working with ontologies and ontology associations

https://github.com/biolink/ontobio

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    7 of 21 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.8%) to scientific vocabulary

Keywords

bioinformatics gene-ontology graph obo obofoundry ontology ontology-tools python rdf semantic-web sparql

Keywords from Contributors

knowledge-graphs monarchinitiative owl ncats-translator linkml biolink-model standards data-modeling annotation biolink
Last synced: 5 months ago · JSON representation

Repository

python library for working with ontologies and ontology associations

Basic Info
Statistics
  • Stars: 128
  • Watchers: 20
  • Forks: 33
  • Open Issues: 135
  • Releases: 5
Topics
bioinformatics gene-ontology graph obo obofoundry ontology ontology-tools python rdf semantic-web sparql
Created almost 9 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License

README-developers.md

  • Note: pandoc must be installed before this works. You can install with brew or apt-get or yum.

This section is only relevant for project maintainers. In order to release you must have a pypi account and be a "maintainer" on the ontobio project

To create a new release, do the following:

Release Instructions -- Makefile

  1. Ensure you're on master and up to date. Ensure also that twine is installed (pip install twine) > I always do this in my virtual environment activated
  2. Obeying Semantic Versioning (https://semver.org/) bump the version number in ontobio/ontobio/__init__.py at the __version__ variable. > At this point you should have one modified file, saved: ontobio/ontobio/__init__.py. You can check with git diff and/or git status.
  3. Run the make relase target $ make USER=sauron release where the USER should be set to your pypi.org username.

This will perform all the steps outlined in the below manual release section.

  1. pypi will ask for your password. (You may also setup credentials with pypi, but that's now how the author who is writing this documentation has it setup.)

Failure

If at any point this fails (wrong password, master is not updated, etc) you will have to just perform the steps manually as outlined in the below section.

Likely you will not be able to just rerun the release as the git portion of the release is not idempotent. Just note where you had an error and continue the steps corrected manually. I usually use the the Makefile as a direct reference if a command fails.

Release instructions -- Manual

  1. First check whether the __version__ in ontobio/__init__.py matches with the latest tag or PyPI release. If the version is the same then you need to bump the version to make a new release. Follow semantic versioning guidelines to decide whether the bump in version is major or minor.

  2. If you did bump the version then run the following commands:

sh TAG=v`python setup.py --version` git add ontobio/__init__.py git commit --message="Upgrade to $TAG" git push git tag --annotate $TAG --message="Upgrade to $TAG" git push --tags

  1. Releasing on PyPI

To ensure this is successful, make sure you have relevant permissions to Ontobio package on PyPI

Run the following commands (note, you will need a pypi token to do this work, see: https://pypi.org/help/#apitoken and make a ~/.pypirc file to store your token):

sh make cleandist python setup.py sdist bdist_wheel twine upload --repository-url https://upload.pypi.org/legacy/ --username __token__ dist/*

to use a poetry development environment

  1. create the pyproject.toml file and generate the .venv directory bash make poetry this command deletes any existing pyproject.toml and poetry.lock files as well as the .venv virtual environment if it finds one. It then creates a new pyproject.toml file out of the requirements.txt file, creates a .venv directory, and finally installs the dependencies into it. This also creates a poetry.lock file. At the moment, the poetry.lock and pyproject.toml files are both in .gitignore so that the source of truth for the built environment is still requirements.txt.

  2. to recreate the poetry virtual environment, just run the same make poetry command again, or if you want to avoid reinstalling all the dependencies, just rm -rf .venv which will remove the local virtual environment and then run poetry install to install via the poetry.lock file created in step 1 above.

helpful poetry commands: bash poetry install # install dependencies from poetry.lock poetry run <command> # run a command in the poetry virtual environment poetry env list # list all virtual environments and tags the one currently in use for the project poetry show --why --tree [pypi_package_name] # show the dependency tree for pypi_package_name poetry show [pypi_package_name] # show the version of pypi_package_name that is install in the current venv.

If we use a pyproject.toml file then we can use poetry to manage the dependencies and the virtual environment. But for now, managing the dependencies in the requirements.txt file means that we don't want to add/update/remove dependencies from pyproject.toml directly, nor do we want it to ever be the source of truth for the dependencies.

```bash poetry add # add a package to the pyproject.toml file and install it in the virtual environment poetry remove # remove a package from the pyproject.toml file and uninstall it from the virtual environment poetry update # update all packages in the pyproject.toml file and the poetry.lock file poetry update # update the specified package in the pyproject.toml file and the poetry.lock file poetry lock --no-update # update the poetry.lock file without updating the pyproject.toml file -- used when editing the

pyproject.toml file directly.

```

Owner

  • Name: biolink
  • Login: biolink
  • Kind: organization

GitHub Events

Total
  • Create event: 8
  • Release event: 1
  • Issues event: 3
  • Watch event: 10
  • Issue comment event: 8
  • Push event: 15
  • Pull request event: 10
  • Pull request review event: 5
  • Fork event: 3
Last Year
  • Create event: 8
  • Release event: 1
  • Issues event: 3
  • Watch event: 10
  • Issue comment event: 8
  • Push event: 15
  • Pull request event: 10
  • Pull request review event: 5
  • Fork event: 3

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 1,454
  • Total Committers: 21
  • Avg Commits per committer: 69.238
  • Development Distribution Score (DDS): 0.746
Past Year
  • Commits: 140
  • Committers: 4
  • Avg Commits per committer: 35.0
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
Eric Douglass e****s@l****v 370
Chris Mungall c****m@b****g 320
Sierra Taylor Moxon s****r@g****m 219
dustine32 d****2@g****m 149
Eric Douglass e****s@g****m 109
kshefchek k****k@g****m 104
Anushya Muruganujan m****u@u****u 74
Deepak Unni d****3@g****m 62
lhannest l****t@g****m 12
kltm g****m@g****t 9
Richard Bruskiewich r****h@d****m 6
Laurent-Philippe Albou 2****u 4
Faisal Alquaddoomi f****i@c****u 3
Anne Thessen a****n@g****m 3
Damien Goutte-Gattat d****t@i****g 2
selewis s****s@l****v 2
vanaukenk v****n@c****u 2
Jim Balhoff j****m@b****g 1
Mark Diekhans m****d@s****u 1
dependabot[bot] 4****] 1
Valerio Arnaboldi v****a@c****u 1
Committer Domains (Top 20 + Academic)
caltech.edu: 2 lbl.gov: 2 soe.ucsc.edu: 1 balhoff.org: 1 incenp.org: 1 cuanschutz.edu: 1 delphinai.com: 1 genkisugi.net: 1 usc.edu: 1 berkeleybop.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 45
  • Total pull requests: 124
  • Average time to close issues: 3 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 19
  • Total pull request authors: 13
  • Average comments per issue: 1.51
  • Average comments per pull request: 1.37
  • Merged pull requests: 115
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 2
  • Pull requests: 13
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 7 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 3.5
  • Average comments per pull request: 0.15
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • dustine32 (18)
  • sierra-moxon (3)
  • kltm (3)
  • dosumis (3)
  • balhoff (2)
  • realmarcin (2)
  • dougli1sqrd (2)
  • valearna (1)
  • remerjohnson (1)
  • falquaddoomi (1)
  • kshefchek (1)
  • AITCM (1)
  • kcortes133 (1)
  • mugitty (1)
  • cthoyt (1)
Pull Request Authors
  • mugitty (51)
  • sierra-moxon (43)
  • dustine32 (32)
  • kshefchek (8)
  • dougli1sqrd (5)
  • dependabot[bot] (4)
  • deepakunni3 (2)
  • vanaukenk (2)
  • kltm (2)
  • falquaddoomi (2)
  • gouttegd (1)
  • sransara (1)
  • balhoff (1)
Top Labels
Issue Labels
bug (3) enhancement (1)
Pull Request Labels
dependencies (4) enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,715 last-month
  • Total docker downloads: 147
  • Total dependent packages: 1
  • Total dependent repositories: 21
  • Total versions: 208
  • Total maintainers: 6
pypi.org: ontobio

Library for working with OBO Library Ontologies and associations

  • Versions: 208
  • Dependent Packages: 1
  • Dependent Repositories: 21
  • Downloads: 2,715 Last month
  • Docker Downloads: 147
Rankings
Dependent repos count: 3.2%
Downloads: 5.1%
Average: 5.9%
Stargazers count: 6.7%
Forks count: 7.1%
Dependent packages count: 7.3%
Maintainers (6)
cmungall smoxon deepakunni3 dustine32 kltm mugitty
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • PyShEx >=0.7.11
  • SPARQLWrapper >=1.8.0
  • bidict >=0.20.0
  • chardet *
  • click *
  • dacite >=1.6.0
  • dataclasses *
  • diskcache >=4.0.0
  • jsobject >=0.0
  • jsonpath_rw >=0.0
  • jsonpickle >=0.0
  • marshmallow >=3.0.0b11,<4.0
  • matplotlib >=2.0.0
  • networkx >=2.3
  • pandas >=0.0
  • pip >=9.0.1
  • plotly >=2.0.7
  • prefixcommons >=0.1.9
  • pydotplus >=0.0
  • pyparsing ==2.4.7
  • pysolr *
  • pysolr >=3.6.0
  • pytest >=0.0
  • pytest_logging >=0.0
  • python-dateutil *
  • pyyaml *
  • requests >=0.0
  • scipy >=1.2.0
  • twine *
  • wheel >0.25.0
  • yamldown >=0.1.7
setup.py pypi
  • for *