From c3eeb8bc4b6f627a82724eb332fe7ab236ada615 Mon Sep 17 00:00:00 2001 From: lexin-chen Date: Sat, 8 Jun 2024 15:40:59 -0400 Subject: [PATCH 1/8] create MDAKit file --- mdakits/mdance/metadata.yaml | 107 +++++++++++++++++++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 mdakits/mdance/metadata.yaml diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml new file mode 100644 index 00000000..63ada9e7 --- /dev/null +++ b/mdakits/mdance/metadata.yaml @@ -0,0 +1,107 @@ +#------------------------------------------------------------ +# Required entries +#------------------------------------------------------------ +## str: name of the project (the respository name) +project_name: MDANCE + +## List(str): a link to the authors file (preferred) or a list of authors +authors: + - Lexin Chen https://github.com/GH_HOST_ACCOUNT/MYPROJECT/blob/main/AUTHORS + +## List(str): a list of maintainers +## Please note these _must_ be GitHub handles +## The maintainers will be tagged in issues if their MDAKit is failing. +maintainers: + - lexin-chen + +## str: a free form description of the mdakit +description: + flexible n-ary clustering package for Molecular Dynamics and other datasets. + +## List(str): a list of keywords which describe the mdakit +keywords: + - clustering + - molecular-dynamics + - post-processing + - protein-refinement + +## str: the license the mdakit falls under +## See https://spdx.org/licenses/ for valid license specifiers +license: MIT + +## str: the link to the project's code +## Please note that this is not limited to GitHub! Can be Gitlab, etc.. +project_home: https://github.com/mqcomplab/MDANCE + +## str: the link to the project's documentation +documentation_home: https://github.com/mqcomplab/MDANCE + +## 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 mamba where possible (e.g. +## mamba -c conda-forge install MYPROJECT +## for a conda package installation). +## Here we use a simple PyPi installation: +install: + - 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/mqcomplab/MDANCE@main + +## str: the package name used to import the mdakit +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 +## 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 "development code" checks 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 MYPACKAGE + +## List(str): a list of commands to use to install the necessary dependencies required +## 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: mqcomplab + +## str: the development status of the MDAKit +## See https://pypi.org/classifiers/ for development status classifiers. +development_status: Production/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: + - URL1 + - URL2 + +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +community_home: URL + +## str: a link to the MDAKit's changelog +changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md From b18ac39813605e722e2b57b4428eaffa1491e55f Mon Sep 17 00:00:00 2001 From: lexin-chen Date: Wed, 10 Jul 2024 21:37:55 -0400 Subject: [PATCH 2/8] update MDANCE entry --- mdakits/mdance/metadata.yaml | 31 ++++++++++++++++--------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index 63ada9e7..38c4a2ba 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -6,7 +6,7 @@ project_name: MDANCE ## List(str): a link to the authors file (preferred) or a list of authors authors: - - Lexin Chen https://github.com/GH_HOST_ACCOUNT/MYPROJECT/blob/main/AUTHORS + - https://github.com/mqcomplab/MDANCE/blob/main/AUTHORS.md ## List(str): a list of maintainers ## Please note these _must_ be GitHub handles @@ -16,13 +16,14 @@ maintainers: ## str: a free form description of the mdakit description: - flexible n-ary clustering package for Molecular Dynamics and other datasets. + flexible n-ary clustering package for Molecular Dynamics trajectories. ## List(str): a list of keywords which describe the mdakit keywords: - clustering + - machine-learning + - algorithms - molecular-dynamics - - post-processing - protein-refinement ## str: the license the mdakit falls under @@ -34,10 +35,10 @@ license: MIT project_home: https://github.com/mqcomplab/MDANCE ## str: the link to the project's documentation -documentation_home: https://github.com/mqcomplab/MDANCE +documentation_home: https://mdance.readthedocs.io/en/latest/ ## str: the type of documentation available [UserGuide, API, README] -documentation_type: README +documentation_type: UserGuide + API #------------------------------------------------------------ # Optional entries @@ -49,7 +50,7 @@ documentation_type: README ## for a conda package installation). ## Here we use a simple PyPi installation: install: - - pip install MYPROJECT + - pip install mdance ## List(str): a list of commands to use when installing the mdakit from its ## source code. @@ -57,7 +58,7 @@ src_install: - pip install git+https://github.com/mqcomplab/MDANCE@main ## str: the package name used to import the mdakit -import_name: MYPACKAGE +import_name: mdance ## str: a specification for the range of Python versions supported by this MDAKit python_requires: ">=3.9" @@ -76,15 +77,15 @@ mdanalysis_requires: ">=2.0.0" ## - git clone latest ## - pytest -v ./tests ## Feel free to ask for advice on your pull request! -run_tests: - - pytest --pyargs MYPACKAGE +#run_tests: +# - pytest --pyargs MYPACKAGE ## List(str): a list of commands to use to install the necessary dependencies required ## 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 +#test_dependencies: +# - mamba install pytest MDAnalysisTests ## str: the organisation name the MDAKit falls under project_org: mqcomplab @@ -97,11 +98,11 @@ development_status: Production/Stable ## Links to scientific publications or stable URLs (typically of the form ## https://doi.org/ or to a preprint server) publications: - - URL1 - - URL2 + - https://doi.org/10.1021/acs.jctc.4c00308 + - https://doi.org/10.1021/acs.jctc.4c00362 # If user used PRIME ## str: a link to the MDAKit's community (mailing list, github discussions, etc...) -community_home: URL +community_home: https://github.com/mqcomplab/MDANCE/issues ## str: a link to the MDAKit's changelog -changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md +#changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md From 8daae6325679e2a4fc13db413fd3d129b22e5064 Mon Sep 17 00:00:00 2001 From: lexin-chen Date: Wed, 10 Jul 2024 21:38:54 -0400 Subject: [PATCH 3/8] update MDANCE entry --- mdakits/mdance/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index 38c4a2ba..f87a7e44 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -35,7 +35,7 @@ license: MIT project_home: https://github.com/mqcomplab/MDANCE ## str: the link to the project's documentation -documentation_home: https://mdance.readthedocs.io/en/latest/ +documentation_home: https://mdance.readthedocs.io ## str: the type of documentation available [UserGuide, API, README] documentation_type: UserGuide + API From f2c8e116d75cd8ed7d91a60aa445525543d56fb4 Mon Sep 17 00:00:00 2001 From: lexin-chen Date: Tue, 30 Jul 2024 22:58:11 -0400 Subject: [PATCH 4/8] Update with tests args --- mdakits/mdance/metadata.yaml | 216 +++++++++++++++++------------------ 1 file changed, 108 insertions(+), 108 deletions(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index f87a7e44..cc883cfd 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -1,108 +1,108 @@ -#------------------------------------------------------------ -# Required entries -#------------------------------------------------------------ -## str: name of the project (the respository name) -project_name: MDANCE - -## List(str): a link to the authors file (preferred) or a list of authors -authors: - - https://github.com/mqcomplab/MDANCE/blob/main/AUTHORS.md - -## List(str): a list of maintainers -## Please note these _must_ be GitHub handles -## The maintainers will be tagged in issues if their MDAKit is failing. -maintainers: - - lexin-chen - -## str: a free form description of the mdakit -description: - flexible n-ary clustering package for Molecular Dynamics trajectories. - -## List(str): a list of keywords which describe the mdakit -keywords: - - clustering - - machine-learning - - algorithms - - molecular-dynamics - - protein-refinement - -## str: the license the mdakit falls under -## See https://spdx.org/licenses/ for valid license specifiers -license: MIT - -## str: the link to the project's code -## Please note that this is not limited to GitHub! Can be Gitlab, etc.. -project_home: https://github.com/mqcomplab/MDANCE - -## str: the link to the project's documentation -documentation_home: https://mdance.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 mamba where possible (e.g. -## mamba -c conda-forge install MYPROJECT -## for a conda package installation). -## Here we use a simple PyPi installation: -install: - - pip install mdance - -## List(str): a list of commands to use when installing the mdakit from its -## source code. -src_install: - - pip install git+https://github.com/mqcomplab/MDANCE@main - -## str: the package name used to import the mdakit -import_name: mdance - -## 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 -## 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 "development code" checks 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 MYPACKAGE - -## List(str): a list of commands to use to install the necessary dependencies required -## 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: mqcomplab - -## str: the development status of the MDAKit -## See https://pypi.org/classifiers/ for development status classifiers. -development_status: Production/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://doi.org/10.1021/acs.jctc.4c00308 - - https://doi.org/10.1021/acs.jctc.4c00362 # If user used PRIME - -## str: a link to the MDAKit's community (mailing list, github discussions, etc...) -community_home: https://github.com/mqcomplab/MDANCE/issues - -## str: a link to the MDAKit's changelog -#changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md +#------------------------------------------------------------ +# Required entries +#------------------------------------------------------------ +## str: name of the project (the respository name) +project_name: MDANCE + +## List(str): a link to the authors file (preferred) or a list of authors +authors: + - https://github.com/mqcomplab/MDANCE/blob/main/AUTHORS.md + +## List(str): a list of maintainers +## Please note these _must_ be GitHub handles +## The maintainers will be tagged in issues if their MDAKit is failing. +maintainers: + - lexin-chen + +## str: a free form description of the mdakit +description: + flexible n-ary clustering package for Molecular Dynamics trajectories. + +## List(str): a list of keywords which describe the mdakit +keywords: + - clustering + - machine-learning + - algorithms + - molecular-dynamics + - protein-refinement + +## str: the license the mdakit falls under +## See https://spdx.org/licenses/ for valid license specifiers +license: MIT + +## str: the link to the project's code +## Please note that this is not limited to GitHub! Can be Gitlab, etc.. +project_home: https://github.com/mqcomplab/MDANCE + +## str: the link to the project's documentation +documentation_home: https://mdance.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 mamba where possible (e.g. +## mamba -c conda-forge install MYPROJECT +## for a conda package installation). +## Here we use a simple PyPi installation: +install: + - pip install mdance + +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/mqcomplab/MDANCE@main + +## str: the package name used to import the mdakit +import_name: mdance + +## 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 +## 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 "development code" checks 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 ./tests + +## List(str): a list of commands to use to install the necessary dependencies required +## 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: mqcomplab + +## str: the development status of the MDAKit +## See https://pypi.org/classifiers/ for development status classifiers. +development_status: Production/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://doi.org/10.1021/acs.jctc.4c00308 + - https://doi.org/10.1021/acs.jctc.4c00362 # If user used PRIME + +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +community_home: https://github.com/mqcomplab/MDANCE/discussions + +## str: a link to the MDAKit's changelog +#changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md From b111f389cd505612e0c290e6604847b92d2e45b2 Mon Sep 17 00:00:00 2001 From: Lexin Chen <110304515+lexin-chen@users.noreply.github.com> Date: Wed, 31 Jul 2024 20:36:54 -0400 Subject: [PATCH 5/8] Update mdakits/mdance/metadata.yaml Co-authored-by: Oliver Beckstein --- mdakits/mdance/metadata.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index cc883cfd..1c8711d6 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -77,7 +77,8 @@ mdanalysis_requires: ">=2.0.0" ## - git clone latest ## - pytest -v ./tests ## Feel free to ask for advice on your pull request! -#run_tests: +run_tests: + - git clone latest - pytest ./tests ## List(str): a list of commands to use to install the necessary dependencies required From 6aebab053854ef90120d6bdc94c639ba2c906c5e Mon Sep 17 00:00:00 2001 From: Lexin Chen <110304515+lexin-chen@users.noreply.github.com> Date: Wed, 31 Jul 2024 20:37:03 -0400 Subject: [PATCH 6/8] Update mdakits/mdance/metadata.yaml Co-authored-by: Oliver Beckstein --- mdakits/mdance/metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index 1c8711d6..3cb01d28 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -85,8 +85,8 @@ run_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 +test_dependencies: + - pip install pytest ## str: the organisation name the MDAKit falls under project_org: mqcomplab From 90ffdd2a1a47eaa67b261a1dbc5fc1a2285485a5 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 1 Aug 2024 12:47:25 -0700 Subject: [PATCH 7/8] use pytest --pyargs mdance for tests Because tests are included in the package, we can try to run them with pytest and without cloning the source. --- mdakits/mdance/metadata.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index 3cb01d28..65261bd1 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -78,8 +78,7 @@ mdanalysis_requires: ">=2.0.0" ## - pytest -v ./tests ## Feel free to ask for advice on your pull request! run_tests: - - git clone latest - - pytest ./tests + - pytest --pyargs mdance ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests. From 135be72a78ab7ca6b9c56d5dd4c73869b6ed8cf9 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 1 Aug 2024 13:00:37 -0700 Subject: [PATCH 8/8] Revert "use pytest --pyargs mdance for tests " This reverts commit 90ffdd2a1a47eaa67b261a1dbc5fc1a2285485a5. pytest --pyargs mdance does not work because ./tests is not included in the package. We need to check out the source. --- mdakits/mdance/metadata.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mdakits/mdance/metadata.yaml b/mdakits/mdance/metadata.yaml index 65261bd1..3cb01d28 100644 --- a/mdakits/mdance/metadata.yaml +++ b/mdakits/mdance/metadata.yaml @@ -78,7 +78,8 @@ mdanalysis_requires: ">=2.0.0" ## - pytest -v ./tests ## Feel free to ask for advice on your pull request! run_tests: - - pytest --pyargs mdance + - git clone latest + - pytest ./tests ## List(str): a list of commands to use to install the necessary dependencies required ## to run the MDAKit's tests.