From d01aa45dcbf49e9f53a83b33a7757a75c6b27e86 Mon Sep 17 00:00:00 2001 From: Stephen Farr Date: Thu, 25 May 2023 22:56:21 +0100 Subject: [PATCH 01/28] add openmm-mdareporter (#43) * add openmm-mdareporter --- mdakits/openmm-mdareporter/metadata.yaml | 52 ++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 mdakits/openmm-mdareporter/metadata.yaml diff --git a/mdakits/openmm-mdareporter/metadata.yaml b/mdakits/openmm-mdareporter/metadata.yaml new file mode 100644 index 00000000..0cb69210 --- /dev/null +++ b/mdakits/openmm-mdareporter/metadata.yaml @@ -0,0 +1,52 @@ +# Required entries +## str: name of the project (the respository name) +project_name: openmm-mdanalysis-reporter +## List(str): a list of authors (or a link to the authors file) +authors: + - https://github.com/sef43/openmm-mdanalysis-reporter/blob/main/AUTHORS.md +## List(str): a list of maintainers +maintainers: + - sef43 +## str: a free form description of the mdakit +description: + MDAnalysis based reporters for OpenMM +## List(str): a list of keywords which describe the mdakit +keywords: + - OpenMM + - Reporters + +## str: the license the mdakit falls under +license: MIT +## str: the link to the project's code +project_home: https://github.com/sef43/openmm-mdanalysis-reporter +## str: the link to the project's documentation +documentation_home: https://github.com/sef43/openmm-mdanalysis-reporter/blob/main/README.md +## str: the type of documentation available [UserGuide, API, README] +documentation_type: README + +# Optional entries +## List(str): a list of commands to use when installing the latest +## release of the code. Note: only one installation method can currently +## be defined. We suggest using conda/mamba where possible. +install: + - mamba install -c jaimergp/label/unsupported-cudatoolkit-shim -c conda-forge --strict-channel-priority openmm + - pip install openmm-mdanalysis-reporter +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - mamba install -c jaimergp/label/unsupported-cudatoolkit-shim -c conda-forge --strict-channel-priority openmm + - git clone https://github.com/sef43/openmm-mdanalysis-reporter.git + - cd openmm-mdanalysis-reporter + - pip install . + +## str: the package name used to import the mdakit +import_name: mdareporter +## str: a specification for the range of Python versions supported by this MDAKit +python_requires: ">=3.9" +## str: a specification for the range of MDAnalysis versions supported by this MDAKit +mdanalysis_requires: ">=2.0.0" +openmm_requires: ">=7.7.0" +run_tests: + - pytest --pyargs mdareporter.tests +test_dependencies: + - mamba install -c jaimergp/label/unsupported-cudatoolkit-shim -c conda-forge --strict-channel-priority openmm pytest From ff5ed6792d86c5dd59f965023cc3387ba76b380f Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 28 May 2023 09:25:52 +0100 Subject: [PATCH 02/28] rename to match project name --- .../metadata.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename mdakits/{openmm-mdareporter => openmm-mdanalysis-reporter}/metadata.yaml (100%) diff --git a/mdakits/openmm-mdareporter/metadata.yaml b/mdakits/openmm-mdanalysis-reporter/metadata.yaml similarity index 100% rename from mdakits/openmm-mdareporter/metadata.yaml rename to mdakits/openmm-mdanalysis-reporter/metadata.yaml From b19039a3e06b177bfecc6b2cac29b96085e124e0 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 28 May 2023 08:32:52 +0000 Subject: [PATCH 03/28] commit changes to status files --- .../openmm-mdanalysis-reporter/status.yaml | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 mdakits/openmm-mdanalysis-reporter/status.yaml diff --git a/mdakits/openmm-mdanalysis-reporter/status.yaml b/mdakits/openmm-mdanalysis-reporter/status.yaml new file mode 100644 index 00000000..f339e168 --- /dev/null +++ b/mdakits/openmm-mdanalysis-reporter/status.yaml @@ -0,0 +1,22 @@ +badges: + analysis: false + converter: false + coverage: false + reader: false + topology: false + transformation: false + writer: false +develop: + install_mdakit: true + install_mdanalysis: true + install_python: true + install_test_deps: true + numfails: 0 + run_tests: true +latest: + install_mdakit: true + install_mdanalysis: true + install_python: true + install_test_deps: true + numfails: 0 + run_tests: true From 924672f5c19688e0c8832f3cb1994c419c369965 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 28 Jul 2023 12:13:54 -0700 Subject: [PATCH 04/28] add registry and repo links to adding docs --- docs/source/add.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/source/add.rst b/docs/source/add.rst index 0755ef7a..997d8690 100644 --- a/docs/source/add.rst +++ b/docs/source/add.rst @@ -2,18 +2,18 @@ Adding an MDAKit to the Registry ******************************** -Do you have an MDAKit? Consider adding it to the Registry! +Do you have an MDAKit? Consider adding it to the `MDAKit registry`_! .. note:: - The MDAKit registry is still in its infancy, we expect that the + The `MDAKit registry`_ is still in its infancy, we expect that the way in which MDAKits are added, and the type of information required, may change over time. Please reach out via the `issue tracker`_ if you have any questions. Adding an MDAKit is a simple process, and follows the following steps: - * Create a fork the MDAKit repository + * Create a fork the MDAKit repository https://github.com/MDAnalysis/mdakits * Make a new branch * Add a new folder under ``mdakits`` with the name of your MDAKit * Add a metadata YAML file with your MDAKit's details (a template can be found under ``mdakits/template``) @@ -92,3 +92,5 @@ The following is an example metadata file for propkatraj:: .. _`issue tracker`: https://github.com/MDAnalysis/MDAKits/issues +.. _`MDAKit registry`: https://mdakits.mdanalysis.org/mdakits.html + From fa9938441f8da0d124c1e4604cf52e280f66c4ed Mon Sep 17 00:00:00 2001 From: Ian Kenney Date: Wed, 9 Aug 2023 16:44:25 -0700 Subject: [PATCH 05/28] Docs now point to SciPy paper over whitepaper (#55) --- docs/source/about.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/about.rst b/docs/source/about.rst index db9938c1..1b61df8d 100644 --- a/docs/source/about.rst +++ b/docs/source/about.rst @@ -58,18 +58,18 @@ useful to a broader community. :alt: MDAKits, an ecosystem of downstream packages, may be more sustainable -Read our whitepaper! -==================== +Read our SciPy proceedings paper! +================================= To learn more about MDAKits and our vision for more sustainable community -developed molecular simulation tools, please see our `whitepaper`_. +developed molecular simulation tools, please see our `SciPy proceedings paper`_. .. _`MDAnalysis library`: https://docs.mdanalysis.org -.. _`whitepaper`: - https://github.com/MDAnalysis/MDAKits/blob/main/paper/whitepaper/MDAKits_whitepaper.pdf +.. _`SciPy proceedings paper`: + https://conference.scipy.org/proceedings/scipy2023/ian_kenney.html .. _`listed here`: mdakits.html From cf798026dedaeaaaa240f55a2bcaa1e4c8c3cba2 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 27 Aug 2023 03:08:13 +0000 Subject: [PATCH 06/28] commit changes to status files --- mdakits/mdacli/status.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/mdacli/status.yaml b/mdakits/mdacli/status.yaml index f339e168..88cddebc 100644 --- a/mdakits/mdacli/status.yaml +++ b/mdakits/mdacli/status.yaml @@ -18,5 +18,5 @@ latest: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 0 - run_tests: true + numfails: 1 + run_tests: false From 0140ae6eac6352e01693600e641c9878e0ba3636 Mon Sep 17 00:00:00 2001 From: Ian Kenney Date: Mon, 28 Aug 2023 09:58:26 -0700 Subject: [PATCH 07/28] Bumped python version to 3.9 (#58) --- mdakits/template/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/template/metadata.yaml b/mdakits/template/metadata.yaml index 603593ca..57a95be5 100644 --- a/mdakits/template/metadata.yaml +++ b/mdakits/template/metadata.yaml @@ -38,7 +38,7 @@ src_install: ## str: the package name used to import the mdakit import_name: propkatraj ## str: a specification for the range of Python versions supported by this MDAKit -python_requires: ">=3.8" +python_requires: ">=3.9" ## str: a specification for the range of MDAnalysis versions supported by this MDAKit mdanalysis_requires: ">=2.0.0" ## List(str): a list of commands to use when attempting to run the MDAKit's tests From a482ba88fcf59a256cb7cba968145fbf16027c3a Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 17:05:28 +0000 Subject: [PATCH 08/28] commit changes to status files --- mdakits/mdacli/status.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/mdacli/status.yaml b/mdakits/mdacli/status.yaml index 88cddebc..f339e168 100644 --- a/mdakits/mdacli/status.yaml +++ b/mdakits/mdacli/status.yaml @@ -18,5 +18,5 @@ latest: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 1 - run_tests: false + numfails: 0 + run_tests: true From 71553ba705b6f07fbb2380293fefce48b3a357f8 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 28 Aug 2023 18:19:44 +0100 Subject: [PATCH 09/28] turn off auto conda for docs deployment --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 4e7cbd11..038de787 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -195,7 +195,7 @@ jobs: uses: conda-incubator/setup-miniconda@v2 with: python-version: 3.9 - auto-update-conda: true + auto-update-conda: false channel-priority: flexible channels: conda-forge add-pip-as-python-dependency: true From 166e7f6b241aefe2f8500082e3a46f5d5e38a422 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 18:39:37 +0100 Subject: [PATCH 10/28] switch docs deployment to setup-micromamba --- .github/workflows/gh-ci-cron.yaml | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 038de787..8bbbcca0 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -191,18 +191,13 @@ jobs: runs-on: ubuntu-22.04 steps: - uses: actions/checkout@v3 - - name: setup_miniconda - uses: conda-incubator/setup-miniconda@v2 + - name: setup_micromamba with: - python-version: 3.9 - auto-update-conda: false - channel-priority: flexible - channels: conda-forge - add-pip-as-python-dependency: true - architecture: x64 - use-mamba: true - miniforge-variant: Mambaforge environment-file: docs/requirements.yaml + environment_name: MDAKitRegistry-docs + create-args: >- + python=3.9 + pip - name: build_docs run: | cd docs && sphinx-build -b html source build From b206c36dd4dfec12c53a665f6e32c18bc8289142 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 18:42:19 +0100 Subject: [PATCH 11/28] don't forget uses --- .github/workflows/gh-ci-cron.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 8bbbcca0..983fa4e7 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -192,6 +192,7 @@ jobs: steps: - uses: actions/checkout@v3 - name: setup_micromamba + uses: mamba-org/setup-micromamba@v1 with: environment-file: docs/requirements.yaml environment_name: MDAKitRegistry-docs From 7730f184c056da38bd6cfe211ac2314950bed337 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 17:49:38 +0000 Subject: [PATCH 12/28] commit changes to status files --- mdakits/prolif/status.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/prolif/status.yaml b/mdakits/prolif/status.yaml index f339e168..6f2b0191 100644 --- a/mdakits/prolif/status.yaml +++ b/mdakits/prolif/status.yaml @@ -11,8 +11,8 @@ develop: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 0 - run_tests: true + numfails: 1 + run_tests: false latest: install_mdakit: true install_mdanalysis: true From 047cea649548e99edf8a4bf8ffa8c09bff8ed4d6 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 18:51:18 +0100 Subject: [PATCH 13/28] dash not underscore --- .github/workflows/gh-ci-cron.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 983fa4e7..aaf8efa9 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -195,7 +195,7 @@ jobs: uses: mamba-org/setup-micromamba@v1 with: environment-file: docs/requirements.yaml - environment_name: MDAKitRegistry-docs + environment-name: MDAKitRegistry-docs create-args: >- python=3.9 pip From 99a50f757d6cb4f8c5263d6efb5888b91efb18a3 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 17:59:22 +0000 Subject: [PATCH 14/28] commit changes to status files --- mdakits/prolif/status.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/prolif/status.yaml b/mdakits/prolif/status.yaml index 6f2b0191..66f069e5 100644 --- a/mdakits/prolif/status.yaml +++ b/mdakits/prolif/status.yaml @@ -11,7 +11,7 @@ develop: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 1 + numfails: 2 run_tests: false latest: install_mdakit: true From d58e5221aff6fc2f0c439df9a52d8b96bb767b79 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 19:02:16 +0100 Subject: [PATCH 15/28] Actually have a channels section (how?) --- docs/requirements.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/requirements.yaml b/docs/requirements.yaml index a8eeff23..a9d5a920 100644 --- a/docs/requirements.yaml +++ b/docs/requirements.yaml @@ -1,5 +1,7 @@ name: MDAKitRegistry-docs channels: + - conda-forge + - defaults dependencies: # Base depends - python From d6645e647c38bad1724083cfbe71574954aeab71 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 18:08:35 +0000 Subject: [PATCH 16/28] commit changes to status files --- mdakits/prolif/status.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/prolif/status.yaml b/mdakits/prolif/status.yaml index 66f069e5..05ccb150 100644 --- a/mdakits/prolif/status.yaml +++ b/mdakits/prolif/status.yaml @@ -11,7 +11,7 @@ develop: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 2 + numfails: 3 run_tests: false latest: install_mdakit: true From 0755828301bf65ea919272c13ef8c7d0dd15632a Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 28 Aug 2023 19:27:06 +0100 Subject: [PATCH 17/28] Try out some PEP508 magic on ProLIF (#60) --- mdakits/prolif/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/prolif/metadata.yaml b/mdakits/prolif/metadata.yaml index b386e398..b955e2f7 100644 --- a/mdakits/prolif/metadata.yaml +++ b/mdakits/prolif/metadata.yaml @@ -20,7 +20,7 @@ install: - conda install -c conda-forge prolif src_install: - pip install rdkit - - pip install git+https://github.com/chemosim-lab/ProLIF@master + - pip install "prolif[dev] @ git+https://github.com/chemosim-lab/ProLIF@master" python_requires: ">=3.8" mdanalysis_requires: ">=2.2.0" run_tests: From ca8746a0699c11fb6e0e949d92af13ef527bc491 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 28 Aug 2023 18:34:32 +0000 Subject: [PATCH 18/28] commit changes to status files --- mdakits/prolif/status.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/prolif/status.yaml b/mdakits/prolif/status.yaml index 05ccb150..f339e168 100644 --- a/mdakits/prolif/status.yaml +++ b/mdakits/prolif/status.yaml @@ -11,8 +11,8 @@ develop: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 3 - run_tests: false + numfails: 0 + run_tests: true latest: install_mdakit: true install_mdanalysis: true From 30fb580dfaaf7f066f9e28e0b3d36587b8aa2898 Mon Sep 17 00:00:00 2001 From: Ian Kenney Date: Wed, 30 Aug 2023 13:11:21 -0700 Subject: [PATCH 19/28] Adding mdaencore (#57) * Added mdaencore metadata * Updated install instructions to use PyPI --- mdakits/mdaencore/metadata.yaml | 63 +++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 mdakits/mdaencore/metadata.yaml diff --git a/mdakits/mdaencore/metadata.yaml b/mdakits/mdaencore/metadata.yaml new file mode 100644 index 00000000..cb6a05ed --- /dev/null +++ b/mdakits/mdaencore/metadata.yaml @@ -0,0 +1,63 @@ +# Required entries +## str: name of the project (the respository name) +project_name: mdaencore +## List(str): a list of authors (or a link to the authors file) +authors: + - https://github.com/MDAnalysis/mdaencore/blob/main/AUTHORS.md +## List(str): a list of maintainers +maintainers: + - ianmkenney + - IAlibay +## str: a free form description of the mdakit +description: + Quantitative ensemble similarity analysis for molecular data +## List(str): a list of keywords which describe the mdakit +keywords: + - ensemble + - similarity + - covariance + - PCA +## str: the license the mdakit falls under +license: GPL-2.0-or-later +## str: the link to the project's code +project_home: https://github.com/MDAnalysis/mdaencore/ +## str: the link to the project's documentation +documentation_home: https://www.mdanalysis.org/mdaencore/ +## str: the type of documentation available [UserGuide, API, README] +documentation_type: README + API + +# Optional entries +## List(str): a list of commands to use when installing the latest +## release of the code. Note: only one installation method can currently +## be defined. We suggest using conda/mamba where possible. +install: + - pip install mdaencore + +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/MDAnalysis/mdaencore.git +## str: the package name used to import the mdakit +import_name: mdaencore +## str: a specification for the range of Python versions supported by this MDAKit +python_requires: ">=3.9" +## str: a specification for the range of MDAnalysis versions supported by this MDAKit +mdanalysis_requires: ">=2.0.0" +## List(str): a list of commands to use when attempting to run the MDAKit's tests +run_tests: + - pytest --pyargs mdaencore.tests +## List(str): a list of commands to use to install the necessary dependencies required +## to run the MDAKit's tests +test_dependencies: + - mamba install pytest MDAnalysisTests +## str: the organisation name the MDAKit falls under +project_org: MDAnalysis +## str: the development status of the MDAKit +development_status: Mature +## List(str) a list of publications to cite when using the MDAKit +publications: + - https://doi.org/10.1371/journal.pcbi.1004415 +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +community_home: +## str: a link to the MDAKit's changelog +changelog: https://github.com/MDAnalysis/mdaencore/blob/main/CHANGELOG.md From 7a25bbdbe8f308dc3f0b86621888ca8456237f3f Mon Sep 17 00:00:00 2001 From: IAlibay Date: Wed, 30 Aug 2023 20:18:26 +0000 Subject: [PATCH 20/28] commit changes to status files --- mdakits/mdaencore/status.yaml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 mdakits/mdaencore/status.yaml diff --git a/mdakits/mdaencore/status.yaml b/mdakits/mdaencore/status.yaml new file mode 100644 index 00000000..f339e168 --- /dev/null +++ b/mdakits/mdaencore/status.yaml @@ -0,0 +1,22 @@ +badges: + analysis: false + converter: false + coverage: false + reader: false + topology: false + transformation: false + writer: false +develop: + install_mdakit: true + install_mdanalysis: true + install_python: true + install_test_deps: true + numfails: 0 + run_tests: true +latest: + install_mdakit: true + install_mdanalysis: true + install_python: true + install_test_deps: true + numfails: 0 + run_tests: true From 056353eedf8c787905c885d9b9df6cb6f854e7e2 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 4 Sep 2023 08:41:59 +0100 Subject: [PATCH 21/28] Try switching themes (#61) * Switch to mdanalysis-sphinx-theme * Fix old doc build errors and warnings --- docs/requirements.yaml | 4 +- docs/scripts/gen_mdakits.py | 2 +- docs/source/_static/custom.css | 225 -------------- docs/source/_static/readable.css | 463 ----------------------------- docs/source/_templates/footer.html | 11 - docs/source/conf.py | 33 +- docs/source/makingakit.rst | 6 +- utils/mdakit.py | 6 +- 8 files changed, 15 insertions(+), 735 deletions(-) delete mode 100644 docs/source/_static/custom.css delete mode 100644 docs/source/_static/readable.css delete mode 100644 docs/source/_templates/footer.html diff --git a/docs/requirements.yaml b/docs/requirements.yaml index a9d5a920..a3604287 100644 --- a/docs/requirements.yaml +++ b/docs/requirements.yaml @@ -7,8 +7,8 @@ dependencies: - python - pip - - sphinx==5.3.0 - - sphinx_rtd_theme + - sphinx + - mdanalysis-sphinx-theme - pyyaml - pydantic diff --git a/docs/scripts/gen_mdakits.py b/docs/scripts/gen_mdakits.py index 5b744672..f1df12df 100644 --- a/docs/scripts/gen_mdakits.py +++ b/docs/scripts/gen_mdakits.py @@ -71,7 +71,7 @@ def generate_mdakit_index(target='.', excludedirs=["template",]): " 2. Provide sufficient details to allow others to use and " "potentially participate in the development of the MDAKits\n" " 3. Provide information about the current state of the MDAKits " - "and how they interact with the latest versions of MDAnalysis\n" + "and how they interact with the latest versions of MDAnalysis\n\n" "Each of the MDAKits in the following table links to a page with " "more details about what the MDAKits do, how they can be " "installed and how to participate in their development.\n") diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css deleted file mode 100644 index de8d2e67..00000000 --- a/docs/source/_static/custom.css +++ /dev/null @@ -1,225 +0,0 @@ -/* override css for readable.css */ - -/* styles/fonts to match http://mdanalysis.org (see public/css) */ -/* MDAnalysis orange: #FF9200 */ -/* MDAnalysis gray: #808080 */ -/* MDAnalysis white: #FFFFFF */ -/* MDAnalysis black: #000000 */ -/* Very light orange: #FFEBD0 */ -/* Code orange: #ca6500 */ -/* RTD dark grey: #343131 */ -/* RTD light grey: #e6e6e6 */ - -/* -- page layout --------------------------------------------------------- */ - -body { - font-family: 'PT Sans', Helvetica, Arial, 'sans-serif'; - font-size: 17px; -} - -div.body { - color: #000000; -} - -div.sphinxsidebar a:hover { - text-decoration: none !important; -} - -div.sphinxsidebar p { - color: #808080; -} - -/* Home MDAnalysis colour */ -.wy-side-nav-search > a { - color: #343131; -} - -/* Side MDAnalysis version colour */ -.wy-side-nav-search > div.version { - color: #808080; -} - -/* Menubar caption colour */ -div.wy-menu-vertical span.caption-text { - color: #FF9200; -} - -/* Mobile layout menubar option */ -nav.wy-nav-top { - background: #343131; -} - -/* Menu search bar outline (default blue) */ -.wy-side-nav-search input[type="text"] { - border-color: #808080; -} - - -/* -- body styles --------------------------------------------------------- */ - -/* Different coloured links for sidebar vs body) */ -div.rst-content a { - color: #FF9200; - text-decoration: none; -} - -div.rst-content a:visited { - color: #FF9200; -} - -a:hover { - color: #FF9200 !important; - text-decoration: underline; -} - - -pre, tt, code { - font-family: Menlo, Monaco, 'Courier New', monospace -} - - -div.body h1 { - font-weight: bolder; -} - -a.headerlink { - color: #808080; - font-size: 0.8em; - padding: 0 4px 0 4px; - text-decoration: none; -} - -a.headerlink:hover { - background-color: #808080; - color: #fff; -} - -/* ------- admonition boxes ------- */ - -div.admonition { - margin: 10px 0px; - padding: 10px 10px; -} - -div.admonition p.admonition-title { - font-size: 100%; - font-weight: bolder; -} - -/* ----- Tables ----- */ - -/* override table width restrictions */ -/* wrap tables instead of scrolling */ -@media screen and (min-width: 767px) { - - .wy-table-responsive table td, .wy-table-responsive table th { - /* !important prevents the common CSS stylesheets from overriding - this as on RTD they are loaded after this stylesheet */ - white-space: normal !important; - } - - .wy-table-responsive { - overflow: visible !important; - max-width: 100% !important; - } - } - -/* ----- Field lists ------ */ - -.section > dl.field-list { - display: flex; - flex-wrap: wrap; - margin: 0; - padding: 0; -} - -dl.field-list > dt::after { - content: ":"; 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-} - -.viewcode-back { - font-family: Arial, sans-serif; -} - -div.viewcode-block:target { - background-color: #fef9e9; - border-top: 1px solid #fbe091; - border-bottom: 1px solid #fbe091; -} - -@media screen and (max-width: 870px) { - - div.document { - width: auto; - margin: 0; - } - - div.documentwrapper { - float: none; - } - - div.bodywrapper { - margin: 0; - } - - div.body { - min-height: 0; - padding: 0 20px 30px 20px; - } - - div.footer { - background-color: #333; - color: #888; - margin: 0; - padding: 10px 20px 20px; - text-align: left; - width: auto; - } - - div.footer a { - color: #bbb; - } - - div.footer a:hover { - color: #fff; - } - - div.sphinxsidebar { - background-color: #333; - color: #fff; - float: none; - margin: 0; - padding: 10px 20px; - width: auto; - } - - div.sphinxsidebar h3, - div.sphinxsidebar h4, - div.sphinxsidebar p, - div.sphinxsidebar h3 a { - color: #fff; - } - - div.sphinxsidebar ul { - color: #999; - } - - div.sphinxsidebar a { - color: #aaa; - } - - div.sphinxsidebar a:hover { - color: #fff; - } - -} diff --git a/docs/source/_templates/footer.html b/docs/source/_templates/footer.html deleted file mode 100644 index 5fd6ad48..00000000 --- a/docs/source/_templates/footer.html +++ /dev/null @@ -1,11 +0,0 @@ -{% extends "!footer.html" %} - -{% block extrafooter %} -{{ super() }} -

Please see - our Privacy Policy - to learn how MDAnalysis collects data.

- -
-{% endblock %} diff --git a/docs/source/conf.py b/docs/source/conf.py index bcdf6eec..7d0df881 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -96,29 +96,14 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_rtd_theme' +html_theme = 'mdanalysis_sphinx_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -color = {'orange': '#FF9200', - 'gray': '#808080', - 'white': '#FFFFFF', - 'black': '#000000', } html_theme_options = { - 'canonical_url': '', - 'logo_only': True, - 'display_version': True, - 'prev_next_buttons_location': 'bottom', - 'style_external_links': False, - 'style_nav_header_background': 'white', # '#e76900', # dark orange - # Toc options - 'collapse_navigation': True, - 'sticky_navigation': True, - 'navigation_depth': 4, - 'includehidden': True, - 'titles_only': False, + 'mda_official': True, } # Add any paths that contain custom static files (such as style sheets) here, @@ -126,12 +111,11 @@ # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_css_files = [ - 'custom.css', - 'https://cdn.datatables.net/1.13.4/css/jquery.dataTables.min.css', + 'https://cdn.datatables.net/1.13.6/css/jquery.dataTables.min.css', ] html_js_files = [ - 'https://cdn.datatables.net/1.13.4/js/jquery.dataTables.min.js', + 'https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js', 'main.js', ] @@ -214,12 +198,7 @@ # -- Extension configuration ------------------------------------------------- -rst_epilog = """ -.. |MDAKit_Registry_version| replace:: {0} -""".format(version) - - intersphinx_mapping = { - 'https://docs.python.org/3/': None, - 'https://docs.mdanalysis.org/stable/': None, + 'python': ('https://docs.python.org/3/', None), + 'mdanalysis': ('https://docs.mdanalysis.org/stable/', None), } diff --git a/docs/source/makingakit.rst b/docs/source/makingakit.rst index 301be466..cea3c303 100644 --- a/docs/source/makingakit.rst +++ b/docs/source/makingakit.rst @@ -358,7 +358,7 @@ After this point, two more requirements are satisfied: Providing documentation *********************** -The cookiecutter includes a `Read the Docs `_ +The cookiecutter includes a `Read the Docs `__ configuration as well a premade documentation environment file that is used by Read the Docs and for building locally. First, we need to install the correct environment for building the documentation. In the ``docs/`` directory, run: @@ -500,7 +500,7 @@ Refeshing the RMSF documentation will now show a properly formatted citation usi Deploying the documentation ~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Log into `Read the Docs `_ and navigate to the +Log into `Read the Docs `__ and navigate to the dashboard. Click the "Import a Project" button and find the repository in the list. Click the "+" and confirm that the name, URL, and default branch are correct. @@ -628,4 +628,4 @@ Apart from actively developing the kit, changes in kit dependencies, or even Pyt For this reason, the kits' continuous integration is rerun weekly to confirm the kits expected behavior. In the event that a kit no longer passes its tests, an issue in MDAnalysis/MDAKits is automatically raised while notifying the maintainers indicated in the `metadata.yaml` file. While the registry developers will be happy to help where possible, ultimately, the maintainers of the MDAKit are responsible for resolving such issues and ensuring that the tests pass. -The issue will automatically close after the next CI run if the tests pass again. \ No newline at end of file +The issue will automatically close after the next CI run if the tests pass again. diff --git a/utils/mdakit.py b/utils/mdakit.py index 7aa1c1dc..30932c25 100644 --- a/utils/mdakit.py +++ b/utils/mdakit.py @@ -386,9 +386,9 @@ def write_mdakit_page(self): urls = [] authors = self.gen_authors(urls) - title = ("************************\n" + title = ("************************************************\n" f"{name}\n" - "************************\n\n") + "************************************************\n\n") description = (f"| **Description:**\n" f"| *{self.metadata.description}*\n") @@ -453,7 +453,7 @@ def write_mdakit_page(self): ) if self.metadata.src_install is not None: installation_instructions += ( - f"The source code of {name} can be " + f"\nThe source code of {name} can be " "installed using the following:\n\n" ".. code-block:: bash\n\n" ) From 4e43cd86b34b22707f42311feefafda733809b1b Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 4 Sep 2023 07:49:16 +0000 Subject: [PATCH 22/28] commit changes to status files --- mdakits/prolif/status.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/prolif/status.yaml b/mdakits/prolif/status.yaml index f339e168..88cddebc 100644 --- a/mdakits/prolif/status.yaml +++ b/mdakits/prolif/status.yaml @@ -18,5 +18,5 @@ latest: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 0 - run_tests: true + numfails: 1 + run_tests: false From cbb8f7f6e97f1f8cd1aa8c3007313c5aecb85b28 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 10 Sep 2023 03:08:02 +0000 Subject: [PATCH 23/28] commit changes to status files --- mdakits/prolif/status.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/prolif/status.yaml b/mdakits/prolif/status.yaml index 88cddebc..cbb456f4 100644 --- a/mdakits/prolif/status.yaml +++ b/mdakits/prolif/status.yaml @@ -18,5 +18,5 @@ latest: install_mdanalysis: true install_python: true install_test_deps: true - numfails: 1 + numfails: 2 run_tests: false From c3942e492c575a61eee7877d982e2c9fd35aecb5 Mon Sep 17 00:00:00 2001 From: Paul Smith Date: Wed, 13 Sep 2023 21:09:23 +0100 Subject: [PATCH 24/28] Register mda-tui as an MDAKit (#66) * Add mda-tui MDAKit * clone the kit repo before installing and running tests * remove '/' from end of project_name --- mdakits/MDAnalysis-tui/metadata.yaml | 52 ++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 mdakits/MDAnalysis-tui/metadata.yaml diff --git a/mdakits/MDAnalysis-tui/metadata.yaml b/mdakits/MDAnalysis-tui/metadata.yaml new file mode 100644 index 00000000..b6a41d8c --- /dev/null +++ b/mdakits/MDAnalysis-tui/metadata.yaml @@ -0,0 +1,52 @@ +# Required entries +## str: name of the project (the respository name) +project_name: mda-tui +## List(str): a list of authors (or a link to the authors file) +authors: + - https://github.com/p-j-smith/mda-tui/blob/main/AUTHORS.md +## List(str): a list of maintainers +maintainers: + - p-j-smith +## str: a free form description of the mdakit +description: + Trajectory transformations in your terminal +## List(str): a list of keywords which describe the mdakit +keywords: + - transformations + - TUI +## str: the license the mdakit falls under +license: GPL-2.0-or-later +## str: the link to the project's code +project_home: https://github.com/p-j-smith/mda-tui +## str: the link to the project's documentation +documentation_home: https://p-j-smith.github.io/mda-tui/ +## str: the type of documentation available [UserGuide, API, README] +documentation_type: README + UserGuide + +# Optional entries +## List(str): a list of commands to use when installing the latest +## release of the code. Note: only one installation method can currently +## be defined. We suggest using conda/mamba where possible. +install: + - pip install mda-tui +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/p-j-smith/mda-tui@main +## str: the package name used to import the mdakit +import_name: mda_tui +## str: a specification for the range of Python versions supported by this MDAKit +python_requires: ">=3.10" +## str: a specification for the range of MDAnalysis versions supported by this MDAKit +mdanalysis_requires: ">=2.0.0" +## List(str): a list of commands to use when attempting to run the MDAKit's tests +run_tests: + - git clone latest + - python -m pip install ".[test]" + - pytest -v ./tests +## str: the development status of the MDAKit +development_status: Alpha +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +community_home: "https://github.com/p-j-smith/mda-tui/discussions" +## str: a link to the MDAKit's changelog +changelog: "https://github.com/p-j-smith/mda-tui/blob/main/CHANGELOG.md" From 193ec75c958551a77df4badc92a76bf1c3b510ae Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 14 Sep 2023 12:53:09 +0100 Subject: [PATCH 25/28] Add prolif test dependencies (#71) * add extra test dependencies for mamba install --- mdakits/prolif/metadata.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdakits/prolif/metadata.yaml b/mdakits/prolif/metadata.yaml index b955e2f7..03cad4e9 100644 --- a/mdakits/prolif/metadata.yaml +++ b/mdakits/prolif/metadata.yaml @@ -17,13 +17,14 @@ documentation_type: UserGuide + API ## Optional entries install: - - conda install -c conda-forge prolif + - mamba install -c conda-forge prolif src_install: - pip install rdkit - pip install "prolif[dev] @ git+https://github.com/chemosim-lab/ProLIF@master" python_requires: ">=3.8" mdanalysis_requires: ">=2.2.0" run_tests: + - mamba install ipython py3Dmol "matplotlib>=3.5" - git clone latest - pytest -v ./tests test_dependencies: From ff6c3503fb26de33f2398ae6e0929c5ad53f950c Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 14 Sep 2023 09:14:35 -0400 Subject: [PATCH 26/28] made template metadata.yaml clearer (#69) * made template metadata.yaml clearer - fix #68 - removed all propkatraj specific entries and replaced with generic entries - added more comments * update metadata.yaml with suggestions --- mdakits/template/metadata.yaml | 77 +++++++++++++++++++++++----------- 1 file changed, 53 insertions(+), 24 deletions(-) diff --git a/mdakits/template/metadata.yaml b/mdakits/template/metadata.yaml index 57a95be5..09386db5 100644 --- a/mdakits/template/metadata.yaml +++ b/mdakits/template/metadata.yaml @@ -1,63 +1,92 @@ +# TEMPLATE MDAKit file +# -------------------- +# +# Please replace ALL entries with appropriate content for YOUR MDAKit. +# Below we use the placeholder GH_HOST_ACCOUNT for the GitHub account where +# the source code repository is held, typically your username or the +# organization that you're part off. +# MYPROJECT is the name of your project (the repository name and here +# we assume that this is also the PyPi/conda package name) whereas +# MYPACKAGE is how you import it in python. +# +# See https://mdakits.mdanalysis.org/add.html for more information. +# # Required entries ## str: name of the project (the respository name) -project_name: propkatraj -## List(str): a list of authors (or a link to the authors file) +project_name: MYPROJECT +## List(str): a link to the authors file (preferred) or a list of authors authors: - - https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS + - https://github.com/GH_HOST_ACCOUNT/MYPROJECT/blob/main/AUTHORS ## List(str): a list of maintainers maintainers: - - ianmkenney - - IAlibay - - orbeckst + - NAME1 + - OPTIONAL_NAME2 + - OPTIONAL_NAME3 ## str: a free form description of the mdakit description: - pKa estimates for proteins using an ensemble approach + (REPLACE WITH A SHORT DESCRIPTION OF WHAT YOUR MDAKit DOES.) ## List(str): a list of keywords which describe the mdakit keywords: - - pKa - - protein + - KEYWORD1 + - KEYWORD2 ## str: the license the mdakit falls under license: GPL-2.0-or-later ## str: the link to the project's code -project_home: https://github.com/Becksteinlab/propkatraj/ +project_home: https://github.com/GH_HOST_ACCOUNT/MYPROJECT/ ## str: the link to the project's documentation -documentation_home: https://becksteinlab.github.io/propkatraj/ +documentation_home: https://MYPROJECT.readthedocs.io ## str: the type of documentation available [UserGuide, API, README] documentation_type: UserGuide + API # Optional entries ## List(str): a list of commands to use when installing the latest ## release of the code. Note: only one installation method can currently -## be defined. We suggest using conda/mamba where possible. +## be defined. We suggest using mamba where possible (e.g. +## mamba -c conda-forge install MYPROJECT +## for a conda package installation) install: - - pip install propkatraj + - pip install MYPROJECT ## List(str): a list of commands to use when installing the mdakit from its ## source code. src_install: - - pip install git+https://github.com/Becksteinlab/propkatraj@main + - pip install git+https://github.com/GH_HOST_ACCOUNT/MYPROJECT@main ## str: the package name used to import the mdakit -import_name: propkatraj +import_name: MYPACKAGE ## str: a specification for the range of Python versions supported by this MDAKit python_requires: ">=3.9" ## str: a specification for the range of MDAnalysis versions supported by this MDAKit mdanalysis_requires: ">=2.0.0" ## List(str): a list of commands to use when attempting to run the MDAKit's tests +## If you package your tests inside your package then you can typically use the +## pytest --pyargs MYPACKAGE.tests +## command as shown below. +## Otherwise you need to include commands to make the tests available. +## For example, if the tests are in the repository at the top level under `./tests`: +## First use `git clone latest` to either clone the top commit for "develop" runs or check out +## the latest tag for "latest release" checks. Then then run pytest: +## - git clone latest +## - pytest -v ./tests +## Feel free to ask for advice on your pull request! run_tests: - - pytest --pyargs propkatraj.tests + - pytest --pyargs MYPACKAGE.tests ## List(str): a list of commands to use to install the necessary dependencies required -## to run the MDAKit's tests +## to run the MDAKit's tests. +## The default below _might_ be sufficient or you might not even need MDAnalysisTests: +## make sure that it is appropriate for how you run tests. test_dependencies: - mamba install pytest MDAnalysisTests ## str: the organisation name the MDAKit falls under -project_org: Becksteinlab +project_org: GH_HOST_ACCOUNT ## str: the development status of the MDAKit -development_status: Mature +## See https://pypi.org/classifiers/ for development status classifiers. +development_status: Productions/Stable ## List(str) a list of publications to cite when using the MDAKit +## Links to scientific publications or stable URLs (typically of the form +## https://doi.org/ or to a preprint server) publications: - - https://zenodo.org/record/7647010 - - https://doi.org/10.1021/ct200133y - - https://doi.org/10.1085/jgp.201411219 + - URL1 + - URL2 ## str: a link to the MDAKit's community (mailing list, github discussions, etc...) -community_home: +community_home: URL ## str: a link to the MDAKit's changelog -changelog: +changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGES From 15591c48a2dfd0622b71e99466c1ac4a6bb99aac Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 15 Sep 2023 18:59:43 +0100 Subject: [PATCH 27/28] Remove unecessary lower() call in json writing --- utils/write-ci-status-json.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utils/write-ci-status-json.py b/utils/write-ci-status-json.py index 0eb27ba9..c64d9d0b 100644 --- a/utils/write-ci-status-json.py +++ b/utils/write-ci-status-json.py @@ -65,7 +65,7 @@ def get_statuses(env_values: List[str]) -> Dict[str, str]: status_dict = get_statuses(env_statuses) - outfile = f"{args.mdakit.lower()}-{args.tag}-statuses.json" + outfile = f"{args.mdakit}-{args.tag}-statuses.json" with open(outfile, 'w') as f: json.dump(status_dict, f) From f46ee7d2d6aaf0753cf2076ae3db66bc16a4b289 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Fri, 15 Sep 2023 19:38:42 +0100 Subject: [PATCH 28/28] switch mda-tui directory to name of project (#73) --- mdakits/mda-tui/metadata.yaml | 52 +++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 mdakits/mda-tui/metadata.yaml diff --git a/mdakits/mda-tui/metadata.yaml b/mdakits/mda-tui/metadata.yaml new file mode 100644 index 00000000..b6a41d8c --- /dev/null +++ b/mdakits/mda-tui/metadata.yaml @@ -0,0 +1,52 @@ +# Required entries +## str: name of the project (the respository name) +project_name: mda-tui +## List(str): a list of authors (or a link to the authors file) +authors: + - https://github.com/p-j-smith/mda-tui/blob/main/AUTHORS.md +## List(str): a list of maintainers +maintainers: + - p-j-smith +## str: a free form description of the mdakit +description: + Trajectory transformations in your terminal +## List(str): a list of keywords which describe the mdakit +keywords: + - transformations + - TUI +## str: the license the mdakit falls under +license: GPL-2.0-or-later +## str: the link to the project's code +project_home: https://github.com/p-j-smith/mda-tui +## str: the link to the project's documentation +documentation_home: https://p-j-smith.github.io/mda-tui/ +## str: the type of documentation available [UserGuide, API, README] +documentation_type: README + UserGuide + +# Optional entries +## List(str): a list of commands to use when installing the latest +## release of the code. Note: only one installation method can currently +## be defined. We suggest using conda/mamba where possible. +install: + - pip install mda-tui +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/p-j-smith/mda-tui@main +## str: the package name used to import the mdakit +import_name: mda_tui +## str: a specification for the range of Python versions supported by this MDAKit +python_requires: ">=3.10" +## str: a specification for the range of MDAnalysis versions supported by this MDAKit +mdanalysis_requires: ">=2.0.0" +## List(str): a list of commands to use when attempting to run the MDAKit's tests +run_tests: + - git clone latest + - python -m pip install ".[test]" + - pytest -v ./tests +## str: the development status of the MDAKit +development_status: Alpha +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +community_home: "https://github.com/p-j-smith/mda-tui/discussions" +## str: a link to the MDAKit's changelog +changelog: "https://github.com/p-j-smith/mda-tui/blob/main/CHANGELOG.md"