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Recent Releases of https://github.com/aiidateam/aiida-optimade

https://github.com/aiidateam/aiida-optimade - v1.2.0

Update Python support

Drop Python 3.8 support, while adding Python 3.11 support. This ensures support for the latest versions of AiiDA, OPTIMADE Python tools and pymatgen.

Thanks to @eimrek for upgrading the repository.

Changelog

v1.2.0 (2023-11-06)

Full Changelog

Closed issues:

  • Drop python 3.8 support #499

Merged pull requests:

  • Update dependencies #505 (@CasperWA)
  • Drop py38 #500 (@eimrek)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA over 2 years ago

https://github.com/aiidateam/aiida-optimade - v1.1.2

Update dependencies prior to dropping Python 3.8 support

This is a patch update to include dependency updates for a v1.1 release, prior to releasing v1.2, which drops Python 3.8 support.

Changelog

v1.1.2 (2023-11-06)

Full Changelog

Merged pull requests:

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA over 2 years ago

https://github.com/aiidateam/aiida-optimade -

  • fixes #381 by #471 # Changelog

v1.1.1 (2023-06-09)

Full Changelog

Fixed bugs:

  • codecov dependency error #451
  • Remove/Update pre-commit hook for yamlfmt #450
  • Update auto-merge workflow #426
  • Dependabot configuration file should only use strings #418
  • Changed optimade extra dependency #416

Closed issues:

  • available_api_versions broken url #381

Merged pull requests:

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by unkcpz about 3 years ago

https://github.com/aiidateam/aiida-optimade - v1.1.0

Use Groups to serve curated data

You can now use an AiiDA Group to serve the data you desire, i.e., a subset of all structure data within a single AiiDA database.

Furthermore, the code base has been updated with more developer-friendly formatting tools (isort and a YAML formatter).

Changelog

v1.1.0 (2022-10-11)

Full Changelog

Implemented enhancements:

  • [MCLOUD] Allow for data curation #237

Merged pull requests:

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by CasperWA almost 4 years ago

https://github.com/aiidateam/aiida-optimade - v1.0.1

What's Changed

  • Update optimade[mongo] requirement from ~=0.18.0 to ~=0.19.2 (#375) by @unkcpz in https://github.com/aiidateam/aiida-optimade/pull/383

Full Changelog: https://github.com/aiidateam/aiida-optimade/compare/v1.0.0...v1.0.1

Changelog

v1.0.1 (2022-09-22)

Full Changelog

Merged pull requests:

  • Update optimade[mongo] requirement from ~=0.18.0 to ~=0.19.2 (#375) #383 (unkcpz)

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by unkcpz almost 4 years ago

https://github.com/aiidateam/aiida-optimade - v1.0.0

AiiDA 2.x support.

What's Changed

  • Update readme with how to release by @unkcpz in https://github.com/aiidateam/aiida-optimade/pull/374
  • Migrate to aiida-core 2.0 by @unkcpz in https://github.com/aiidateam/aiida-optimade/pull/331
  • Update dependencies by @CasperWA in https://github.com/aiidateam/aiida-optimade/pull/378

Full Changelog: https://github.com/aiidateam/aiida-optimade/compare/v0.20.0...v1.0.0

Changelog

v1.0.0 (2022-09-21)

Full Changelog

Merged pull requests:

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by unkcpz almost 4 years ago

https://github.com/aiidateam/aiida-optimade - v0.20.0

IMPORTANT: This is the last version with aiida-core v1 support

What's Changed

  • Update dependencies & use vMAJOR for GH Actions by @CasperWA in https://github.com/aiidateam/aiida-optimade/pull/285
  • Update optimade[mongo] requirement from ~=0.16.3 to ~=0.16.4 by @dependabot in https://github.com/aiidateam/aiida-optimade/pull/286
  • Update CI and CD by @CasperWA in https://github.com/aiidateam/aiida-optimade/pull/289
  • Fix bash variable naming by @CasperWA in https://github.com/aiidateam/aiida-optimade/pull/292
  • Install requests for auto-merge CI by @CasperWA in https://github.com/aiidateam/aiida-optimade/pull/294
  • fix skip: 0 case by @eimrek in https://github.com/aiidateam/aiida-optimade/pull/373
  • Using pytest move route test class to functions, where fixtures can be used to set variables by @unkcpz in https://github.com/aiidateam/aiida-optimade/pull/330

New Contributors

  • @eimrek made their first contribution in https://github.com/aiidateam/aiida-optimade/pull/361
  • @unkcpz made their first contribution in https://github.com/aiidateam/aiida-optimade/pull/330

Full Changelog: https://github.com/aiidateam/aiida-optimade/compare/v0.19.0...v0.20.0

Changelog

v0.20.0 (2022-08-12)

Full Changelog

Fixed bugs:

  • Missing dependencies in CI auto-merge workflow #293
  • Bug in auto-merge CI workflow #291
  • [MaterialsCloud] OpenAPI (and all /extensions/*) not available #169

Closed issues:

  • Add support to python 3.10 #359
  • Update CI/CD to be more automatic #288

Merged pull requests:

* This Changelog was automatically generated by githubchangeloggenerator

- Python
Published by unkcpz almost 4 years ago

https://github.com/aiidateam/aiida-optimade - v0.19.0

Updates: - Moved to the latest optimade, v0.16.3 (#282). This introduced extra validations, leading to a fix of the calculation of the chemical_formula_anonymous field. - Moved to the latest AiiDA version, 1.6.5 (#274).

Developer updates: - Updated dependencies (#270, #274, #277, #282): - pre-commit~=2.15 - uvicorn~=0.15.0 - pylint~=2.10 - Update various GH Actions.

- Python
Published by CasperWA almost 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.18.0

Major updates: - Dropped Python 3.6 support, added Python 3.9 support (#232). - Update the AiiDA filter transformer class and entry collections to be compatible with v0.16.0 of optimade (#252). - Update to AiiDA v1.6 (#232, #236, #252).

Developer updates: - Several minor code optimizations to use more of the upstream optimade code (#252, #262). - Several dependency updates (#226, #232, #235, #236, #247, #248, #252). - Update to full version GH Actions (#243). - Remove use of CODECOV_TOKEN (#234).

- Python
Published by CasperWA almost 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.17.0

Major updates: - Initialize a server with the MongoDB backend with entries from a JSON file (#220). - Use the latest MongoDB v4 (v4.4) for tests and in docker-compose files (#220).

Developer updates: - Dependencies updated: - optimade (v0.13.3), which uses the latest pydantic (v1.8) version. - pymatgen (v2021.3) using semantic versioning to stay in v2021.

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.16.3

Minor updates: - Update to optimade v0.13.2 (#219).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.16.2

Minor updates: - Use optimade v0.13.1, which ups the OPTIMADE API version to v1.0.1 (#218).

Developer updates: - Update tqdm (#218).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.16.1

Fixes: - Fix setting log level via the environment variable AIIDA_OPTIMADE_LOG_LEVEL (#215).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.16.0

Major changes: - Update species.mass field to new value for OPTIMADE API v1.0.1-develop (#213). The value is now a list of floats that should match up with the elemental mass in a.m.u. from the species.chemical_symbols list. In order to be compliant, species.mass is now either a list with one or two (in the case of a vacancy) value(s) or None. - Update to optimade v0.13.0 (#213).

Minor and development changes: - Use while instead of if for removing end-of-line URL slashes (/) (#213). - Properly report exceptions and errors for CLI commands calc and init (#213). - Update README with instructions for testing the MongoDB backend (#213). - Use complete path imports from aiida (AiiDA-Core) instead of wildcard importing from aiida.orm (#213). - Properly test and cover code for initializing structures with partial occupancy (#213). - Update various dependencies (#214).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.15.0

Major changes: - Allow usage of MongoDB instead of AiiDA (and PostgreSQL) (#204). With this change, one can run aiida-optimade init --mongo and initialize an AiiDA server and instead of storing the calculated OPTIMADE fields in each Node's extras, they will be stored as a document in a MongoDB database collection, along with other relevant fields for completeness. This makes it possible to serve very large, preferrably static, AiiDA DBs with much greater response speeds and utilizes the MongoDB backend setup and configuration already implemented in the upstream optimade package.

Development updates: - Use Python 3.8 and clean up Dockerfile (#199, #204). - Update dependencies, ensuring supporting numpy for the supported Python versions (#203) - Update invoke tasks to support new docker-compose and server config files introduced through #204 (#205).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.14.1

Changes: - aiida-optimade calc now only calculates the passed fields (#198). This is true also if a field is requested, which is not calculated for some Nodes.

Fixes: - Ensure the database is not touched for regular requests (#198).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.14.0

Major changes - Only use a single retrieval query for similar requests (#191). When the server is running after an initial query, and the same request is repeated (similar filter, page_limit, page_offset) there will only be a single AiiDA QueryBuilder invocation, where there used to be up to 4 separate invocations.

Development updates - Update dependencies (#187, #190, #192, #195). - Fine-tune CI (#186, #191).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.13.1

Changes: - Update AiiDA config template to the latest version (v4) (#185). - Don't use an AiiDA CalcFunction to convert a CifData to StructureData during the initialization / calculation of OPTIMADE fields for CifData (#185, @giovannipizzi). Instead the functionality is copy-pasted from AiiDA-Core and optimized for speed.

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.13.0

Major changes: - CifData support (#183). AiiDA-OPTIMADE will now serve both StructureData and CifData Nodes from an AiiDA database. For now, the CifData Nodes will be converted to StructureData via pymatgen (new dependency) and the OPTIMADE fields are calculated from there. This will result in loading each Node, making the initialization quite slow for CifData Nodes. This will be optimized in the future.

Other updates: - Update dependencies, now supporting AiiDA v1.5.2 and OPTIMADE Python tools v0.12.5.

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.12.0

Changes: - Update to AiiDA v1.5.0 (#158). - Store all float values as hex strings in the AiiDA Node's extra to ensure accuracy (#162). For a more in-depth explanation of this choice, see the commit message for 4ce308b. Note: This fixes the long-standing issue of elements_ratios not being supported for querying.

OPTIMADE compliance: - Ensure provider-specific fields are excluded if not included in the response_fields query parameter value (#159). - Ensure fields are always shown if explicitly requested via the response_fields query parameter (even if the value is null) (#162).

Developer updates: - Use the latest optimade version for the validator action in the docker CI (#162). - Update tests for aiida-optimade calc and improve printed output (#163).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.11.0

Major updates: - aiida-optimade calc New CLI command calc (#151). This command will allow one to specify particular OPTIMADE fields that one wants to have recalculated for all StructureData Nodes in a database. Compared to the init command, where the -f/--force option will first remove all OPTIMADE fields before recalculating all of them, the calc command will be more picky, only updating the chosen OPTIMADE fields. - New CLI options Add -y/--force-yes and update -q/--silent for the calc and init CLI commands (#153). -y/--force-yes will force a "Yes" when asked to continue in the calc CLI command. -q/--silent will silence any non-critical output to the console. - Progress bar and better output in CLI Utilize tqdm for a progress bar and wrapped click.echo commands from aiida-core to improve the calc and init CLI command outputs (#153). The tqdm progress bar is wrapped around the list of Nodes when an extra is removed or (re)calculated. The improved click.echo-wrapper commands from aiida-core introduce a more colorful output with "Info:", "Success:", "Warning:" or similar prefixes.

Changes: - Update to support aiida-core v1.4.2 (#140, #142). - Update to support optimade v0.12.3 (#147). - Use updated uvicorn v0.12.2 (#141, #143).

Fixes: - Ordering in chemical_formula_anonymous is now correct according to the specification (#147). The amount of each element must be descending, example: A48 B32 C10 D10 E F.

Developer updates: - Use the updated CasperWA/push-protected@v2 in the publish workflow (#145). - Use the latest pre-commit v2.8 (#146). - Run CI workflow for all PRs and otherwise only for pushes to master and CasperWA/push-protected relevant branches (#151). - New CI job build-package utilizes CasperWA/check-sdist-action GitHub Action to ensure the source distribution for the aiida_optimade Python package can be built and installed (#152). - Move imports in invoke tasks script into their relevant functions and branches therein (#154).

- Python
Published by CasperWA over 5 years ago

https://github.com/aiidateam/aiida-optimade - v0.10.3

Changes: - Update central dependencies optimade (v0.12.1) and aiida-core (v1.4.1) (#139). - Add JSON config files to MANIFEST.in, including them in the source distribution (#134). - Fallback to config.json if OPTIMADE_CONFIG_FILE environment variable is not defined or points to a non-existing file (#134).

Developer: - Update CI GitHub Actions workflow (#133, #139) The workflow is more stream-lined and shouldn't fail as often due to bad hooks. - Update use of # pragma: no cover (#134).

- Python
Published by CasperWA almost 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.10.2

Changes: - Add -f/--force option to aiida-optimade init, which will force re-calculation of all OPTIMADE fields for Nodes in the AiiDA database (#130). - Initialize AiiDA database prior to starting the server when using Docker (#132).

- Python
Published by CasperWA almost 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.10.1

Bug fixes: - Set scalars to 0 if absolute value is below 1e-8, units being Å (#121, @csadorf)

Development fixes: - Pin OPTIMADE Validator version to v0.12.0 (#122, @csadorf) - Make local running server available in clients in debug mode (#125) - Publish to PyPI via GitHub releases (#127)

- Python
Published by CasperWA almost 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.10.0

Major updates: - Use the OPTIMADE Validator action to check the implementation, both in CI and in the pytesting (#114) - Add middleware from optimade to (#114): - Ensure a wrongly versioned base URL returns HTTP code 553. - Add support for the api_hint query parameter. - Catch Python Warnings and report them in the response as OPTIMADE Warning objects. Note, for this to work, one has to subclass optimade.server.warnings.OptimadeWarning.

Minor updates: - Support optimade v0.12.0 (#114)

Bug fixes: - Fix OPTIMADE badge in README (#112)

- Python
Published by CasperWA almost 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.9.0

Major changes: - aiida-optimade CLI (#85) New CLI with which one can run the server and initialize an AiiDA database. - Custom Python Warnings (#94) All AiiDA-OPTIMADE warnings can be caught by the custom AiidaOptimadeWarning class. - Logger (#94) Log various events in the code, useful for debugging and testing.

OPTIMADE-specific changes: - Add new nperiodic_dimensions Structure attribute to translator (#93) - Add type attribute to the introspective /info/structures endpoint (#93) - Add /versions-endpoint and use un-versioned URLs (#94)

Minor changes: - Update license and authorship (#85) - Use Python 3.8 in CI (#93) - Use Dependabot v2 (#95) - Update to latest OPTIMADE Python tools and AiiDA versions (0.11.0 and 1.3.1, respectively) (#97, #109) - Rely on OPTIMADE Python tools for certain direct dependencies: FastAPI, the Lark parser, and pydantic (#106)

- Python
Published by CasperWA almost 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.8.0

Changes: - New tests based on optimade-python-tools, but all in the flavor of pytest (#74) - Add "sortable" field to /info/structures endpoint's "properties" (#84) All fields that are not containers (JSON arrays and objects) can be sorted. - Using custom StructureResourceAttributes with AiiDA-specific properties (ctime) (#84) - Add /links endpoint (#86) - Update to the new LinksResource schema (#86) - Update dependencies, now all dependencies have a specific version number, but are still using ~= (#86)

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.6.1

Changes: - Use OPTIMADE Python tools v0.7.0. This introduced minor API and grammar changes (#62) - Update codecov-action to use v1, which always points to the newest v1.x.y (#62) - Update minimum versions for dependencies to the newest for lark-parser and explicitly set a version for uvicorn (#62)

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.6.0

Changes: - Further testing of docker image and all possible base URLs (#55) - Update to optimade-python-tools v0.6.0 (#59) - Add debug mode and run parameter (#59) - Remove /optimade from base URL (#59) - Use CORS, allowing all (*) in cross-origin (#59)

Bug fixes: - Fix CI concerning usage of PostgreSQL (#57)

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.5.0

Highlight: - Close AiiDA SQLA sessions after an endpoint has collected its data from the AiiDA database (#34). This fixes the issue of the QueuePool being filled up, since the connections were never released.

Changes: - Add optimade-python-tools version to Dockerfile (#45) - aiida-core version compatibility badge (#46) - Use versioned base URLs for endpoint prefixes (#51) - Further minimize code-reproduction and reuse code from optimade (#51) - Use RedirectSlashedURLs from optimade (#51) - Move mapper aliases to config.json file (#51) - Subclass ResourceMapper from optimade and incorporate new REQUIRED levels from the spec (#52)

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.4.1

Changes: - Use more tools implemented in optimade-python-tools to not copy too much code over into this repo. - Fold back changes from mcloud branch, specifically concerning Docker. - Implement changes from optimade-python-tools v0.3.2.

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.4.0

Due to rebase and commit for v0.3.0, some commits will be redone. This cannot be undone without losing pointers to the v0.3.0 published commit. One should either merge with --ff-only from command line or make a merge commit and then merge back into develop using a merge commit as well. This update is considered from commit 12d2237.

Updates: - OPTiMaDe spec v0.10.1. - optimade-python-tools v0.3.1 (with grammar for v0.10.1). - Redone HTTP middleware to handle session per request. - Update to pydantic v1. - Add implementation information, i.e., information about which version of aiida-optimade the server is using, to all meta responses. - Use server.cfg. - Fix broken Docker build, and add it to CI (@ltalirz)

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.7.0

Major changes: - Use optimade-python-tools' v0.8 config-system (#70, @CasperWA) This allows to configure the server through environment variables and more, utilizing pydantic's powerful config system. See the relevant PR in optimade-python-tools for more information.

Updates: - Use new OPTIMADE capitalization throughout the code (#67, @CasperWA) - Update to latest AiiDA version (#67, @CasperWA) - Run reentry scan in Dockerfile after installing aiida-core (#67, @CasperWA) - Move to using GH Action services for testing with AiiDA-needed services (PostgreSQL & RabbitMQ) (#67, @CasperWA) - Redirect all non-major version prefix URLs to major-version prefix URLs for the OpenAPI docs endpoints (#72, @CasperWA) - Fix building source distribution, including missing files in MANIFEST.in (#76, @thatch) - Fix misplaced keys in .codecov.yml (#78, @CasperWA)

- Python
Published by CasperWA about 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.3.0

Minimum AiiDA version: 1.0.0 Recommended AiiDA version: 1.0.1

Updates:

  • CI with GitHub Actions
  • Avoid unwilling loading of CONFIG from optimade-python-tools
  • Add codecov coverage and update README with various badges
  • server.cfg config file to tell config.py where to find a configuration file for the server
    • This is needed due to a recent update to optimade-python-tools and a re-configuration of its config.py

- Python
Published by CasperWA over 6 years ago

https://github.com/aiidateam/aiida-optimade - v0.2.0

Minimum AiiDA version: 1.0.0

First public release of aiida-optimade: An OPTiMaDe API implementation for AiiDA.

README:

Optimade API implementation for AiiDA

This is a RESTful API server created with FastAPI that exposes an AiiDA database according to the OPTiMaDe specification.

The server is based on the test server "template" used in the optimade-python-tools package. Indeed, the filter grammar and parser and pydantic models from optimade-python-tools are used directly here.

Lastly, the server utilizes the FastAPI concept of routers, which means each endpoint can be "setup" several times, allowing multiple base URLs and more flexibility.

Prerequisites

Environment where AiiDA is installed.
AiiDA database containing StructureData nodes, since these are the only AiiDA nodes that are currently exposed with this API (under the /structures endpoint).

Note: At the moment, aiida-optimade works most optimally with an AiiDA database using the SQLAlchemy backend.

Installation

shell git clone https://github.com/Materials-Consortia/optimade-python-tools pip install -e optimade-python-tools/ git clone https://github.com/aiidateam/aiida-optimade pip install -e aiida-optimade/

Running the server locally

```shell

specify AiiDA profile (will use default otherwise)

export AIIDA_PROFILE=optimade sh run.sh ```

Navigate to http://127.0.0.1:5000/optimade/info

Running via docker

Adapt profiles/quicksetup.json and profiles/docker-compose.yml appropriately.

shell docker-compose -f profiles/docker-compose.yml up --build

Navigate to http://127.0.0.1:3253/optimade/info

Stop by using

shell docker-compose -f profiles/docker-compose.yml down

Design choices

Q: Why create an individual config.json file instead of just mounting an existing .aiida directory and using that directly?
A: This, currently, wouldn't work because the REPOSITORY_URI needs to point to the right path inside the container, not on the host. Furthermore, storing all configurations in the same file can be fragile.

- Python
Published by CasperWA over 6 years ago