From 7d5e0453801f568afe2f9329fd3b938ed2ee2bf4 Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 10:11:55 +0200 Subject: [PATCH 01/11] Add initial metadata.yaml for QMzyme project --- mdakits/QMzyme/metadata.yaml | 127 +++++++++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 mdakits/QMzyme/metadata.yaml diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml new file mode 100644 index 00000000..23399174 --- /dev/null +++ b/mdakits/QMzyme/metadata.yaml @@ -0,0 +1,127 @@ +# 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: QMzyme + +## List(str): a link to the authors file (preferred) or a list of authors +authors: + - https://github.com/Klem-Research-Group/QMzyme#code-contributorsdevelopers + +## 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: + - Klem-Research-Group + - hklem + - MirumKim + +## str: a free form description of the mdakit +description: + QM-based enzyme model generation and validation. + +## List(str): a list of keywords which describe the mdakit +keywords: + - theozyme + - compuzyme + - cluster + - active-site + - biocatalysis + - enzyme-mechanisms + - quantum-mechanics + - QM-input + +## str: the license the mdakit falls under +## See https://spdx.org/licenses/ for valid license specifiers +license: MIT License + +## 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/Klem-Research-Group/QMzyme/ + +## str: the link to the project's documentation +documentation_home: https://qmzyme.readthedocs.io/ + +## str: the type of documentation available [UserGuide, API, README] +documentation_type: UserGuide + API + +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/Klem-Research-Group/QMzyme@main + +## str: the package name used to import the mdakit +import_name: QMzyme + +## 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 +## 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 QMzyme + +## 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: + - git clone latest + - python -m pip install ".[test]" + - pytest -v ./tests + +## str: the organisation name the MDAKit falls under +project_org: Klem-Research-Group + +#------------------------------------------------------------ +# 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 QMzyme + +## 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: + - TBD + +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +community_home: https://qmzyme.readthedocs.io/ + +## str: a link to the MDAKit's changelog +changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md From 51ec87bacc073f8af83af65eb198655a8a7fa4ac Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 10:18:26 +0200 Subject: [PATCH 02/11] Update Python version requirements in metadata.yaml --- mdakits/QMzyme/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index 23399174..ee721128 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -67,7 +67,7 @@ src_install: import_name: QMzyme ## str: a specification for the range of Python versions supported by this MDAKit -python_requires: ">=3.10" +python_requires: ">=3.11, <=3.13.7" ## str: a specification for the range of MDAnalysis versions supported by this MDAKit mdanalysis_requires: ">=2.0.0" From 3523bef238ef5760d6320518528352defd78efee Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 10:47:10 +0200 Subject: [PATCH 03/11] Add conda commands for QMzyme installation --- mdakits/QMzyme/metadata.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index ee721128..65fc007c 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -61,6 +61,8 @@ documentation_type: UserGuide + API ## List(str): a list of commands to use when installing the mdakit from its ## source code. src_install: + - conda create -n qmzyme -y python=3.11 + - conda activate qmzyme - pip install git+https://github.com/Klem-Research-Group/QMzyme@main ## str: the package name used to import the mdakit From cce7a2f41668bb3713171fd51c57a213937ad48a Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 10:57:08 +0200 Subject: [PATCH 04/11] Modify run_tests commands in metadata.yaml Updated test run commands in metadata.yaml to include cloning the repository and changing directory before running tests. --- mdakits/QMzyme/metadata.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index 65fc007c..12e88ebf 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -86,16 +86,16 @@ mdanalysis_requires: ">=2.0.0" ## - pytest -v ./tests ## Feel free to ask for advice on your pull request! run_tests: - - pytest --pyargs QMzyme + - git clone https://github.com/Klem-Research-Group/QMzyme + - cd QMzyme + - pytest -v ## 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: - - git clone latest - python -m pip install ".[test]" - - pytest -v ./tests ## str: the organisation name the MDAKit falls under project_org: Klem-Research-Group From 3e857b5f4fcc7b46b43760e6dbf45c945095667b Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:02:59 +0200 Subject: [PATCH 05/11] Update metadata.yaml --- mdakits/QMzyme/metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index 12e88ebf..bb568a7e 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -86,8 +86,6 @@ mdanalysis_requires: ">=2.0.0" ## - pytest -v ./tests ## Feel free to ask for advice on your pull request! run_tests: - - git clone https://github.com/Klem-Research-Group/QMzyme - - cd QMzyme - pytest -v ## List(str): a list of commands to use to install the necessary dependencies required @@ -95,6 +93,8 @@ run_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: + - git clone https://github.com/Klem-Research-Group/QMzyme + - cd QMzyme - python -m pip install ".[test]" ## str: the organisation name the MDAKit falls under From 8efaf9916508e5cc9e757b8186f2e38a1c1c6422 Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:13:28 +0200 Subject: [PATCH 06/11] Change install to src during tests --- mdakits/QMzyme/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index bb568a7e..ae4c19bb 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -114,7 +114,7 @@ install: ## str: the development status of the MDAKit ## See https://pypi.org/classifiers/ for development status classifiers. -development_status: Production/Stable +development_status: develop ## List(str) a list of publications to cite when using the MDAKit ## Links to scientific publications or stable URLs (typically of the form From 1db6963d3bae8a4bc39645445d7d3e9e3272bb1d Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:19:04 +0200 Subject: [PATCH 07/11] Change development status from 'develop' to 'Beta' --- mdakits/QMzyme/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index ae4c19bb..2c9fe62e 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -114,7 +114,7 @@ install: ## str: the development status of the MDAKit ## See https://pypi.org/classifiers/ for development status classifiers. -development_status: develop +development_status: Beta ## List(str) a list of publications to cite when using the MDAKit ## Links to scientific publications or stable URLs (typically of the form From f374fb5d2cb6b64d27deba1b9ee5c35f896ac6d7 Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:30:11 +0200 Subject: [PATCH 08/11] Update installation command for QMzyme to use python3.11 --- mdakits/QMzyme/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index 2c9fe62e..ad955b11 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -110,7 +110,7 @@ project_org: Klem-Research-Group ## for a conda package installation). ## Here we use a simple PyPi installation: install: - - pip install QMzyme + - python3.11 -m pip install QMzyme ## str: the development status of the MDAKit ## See https://pypi.org/classifiers/ for development status classifiers. From f8f05c1fb6c37dac0e1dd8202e239443b40865dc Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Fri, 5 Jun 2026 11:42:53 +0200 Subject: [PATCH 09/11] Update Python version requirements and clean up metadata --- mdakits/QMzyme/metadata.yaml | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index ad955b11..a0eb985c 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -69,7 +69,7 @@ src_install: import_name: QMzyme ## str: a specification for the range of Python versions supported by this MDAKit -python_requires: ">=3.11, <=3.13.7" +python_requires: ">=3.11" ## str: a specification for the range of MDAnalysis versions supported by this MDAKit mdanalysis_requires: ">=2.0.0" @@ -103,18 +103,6 @@ project_org: Klem-Research-Group #------------------------------------------------------------ # 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: - - python3.11 -m pip install QMzyme - -## str: the development status of the MDAKit -## See https://pypi.org/classifiers/ for development status classifiers. -development_status: Beta ## List(str) a list of publications to cite when using the MDAKit ## Links to scientific publications or stable URLs (typically of the form @@ -125,5 +113,3 @@ publications: ## str: a link to the MDAKit's community (mailing list, github discussions, etc...) community_home: https://qmzyme.readthedocs.io/ -## str: a link to the MDAKit's changelog -changelog: https://github.com/MYNAME/MYPROJECT/blob/main/CHANGELOG.md From ec30ef3aeaf2cb0a0038d4e844481a5ede1d5064 Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Tue, 23 Jun 2026 19:22:14 -0400 Subject: [PATCH 10/11] Apply suggestions from code review Co-authored-by: Oliver Beckstein --- mdakits/QMzyme/metadata.yaml | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index a0eb985c..db21ccec 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -1,16 +1,6 @@ -# 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. -# +# QMzyme MDAKit +# ------------- +# #------------------------------------------------------------ # Required entries #------------------------------------------------------------ @@ -61,8 +51,6 @@ documentation_type: UserGuide + API ## List(str): a list of commands to use when installing the mdakit from its ## source code. src_install: - - conda create -n qmzyme -y python=3.11 - - conda activate qmzyme - pip install git+https://github.com/Klem-Research-Group/QMzyme@main ## str: the package name used to import the mdakit From ca45e95b0ea783c3d47bbe63513f610350093bfd Mon Sep 17 00:00:00 2001 From: Heidi Klem <45046493+hklem@users.noreply.github.com> Date: Tue, 23 Jun 2026 19:32:00 -0400 Subject: [PATCH 11/11] Comment out optional entries --- mdakits/QMzyme/metadata.yaml | 200 +++++++++++++++++------------------ 1 file changed, 100 insertions(+), 100 deletions(-) diff --git a/mdakits/QMzyme/metadata.yaml b/mdakits/QMzyme/metadata.yaml index db21ccec..35d2fced 100644 --- a/mdakits/QMzyme/metadata.yaml +++ b/mdakits/QMzyme/metadata.yaml @@ -1,103 +1,103 @@ # QMzyme MDAKit # ------------- # -#------------------------------------------------------------ -# Required entries -#------------------------------------------------------------ -## str: name of the project (the respository name) -project_name: QMzyme - -## List(str): a link to the authors file (preferred) or a list of authors -authors: - - https://github.com/Klem-Research-Group/QMzyme#code-contributorsdevelopers - -## 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: - - Klem-Research-Group - - hklem - - MirumKim - -## str: a free form description of the mdakit -description: - QM-based enzyme model generation and validation. - -## List(str): a list of keywords which describe the mdakit -keywords: - - theozyme - - compuzyme - - cluster - - active-site - - biocatalysis - - enzyme-mechanisms - - quantum-mechanics - - QM-input - -## str: the license the mdakit falls under -## See https://spdx.org/licenses/ for valid license specifiers -license: MIT License - -## 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/Klem-Research-Group/QMzyme/ - -## str: the link to the project's documentation -documentation_home: https://qmzyme.readthedocs.io/ - -## str: the type of documentation available [UserGuide, API, README] -documentation_type: UserGuide + API - -## List(str): a list of commands to use when installing the mdakit from its -## source code. -src_install: - - pip install git+https://github.com/Klem-Research-Group/QMzyme@main - -## str: the package name used to import the mdakit -import_name: QMzyme - -## str: a specification for the range of Python versions supported by this MDAKit -python_requires: ">=3.11" - -## 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 -v - -## 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: - - git clone https://github.com/Klem-Research-Group/QMzyme - - cd QMzyme - - python -m pip install ".[test]" - -## str: the organisation name the MDAKit falls under -project_org: Klem-Research-Group - -#------------------------------------------------------------ -# Optional entries -#------------------------------------------------------------ - -## 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: - - TBD - -## str: a link to the MDAKit's community (mailing list, github discussions, etc...) -community_home: https://qmzyme.readthedocs.io/ - +#------------------------------------------------------------ +# Required entries +#------------------------------------------------------------ +## str: name of the project (the respository name) +project_name: QMzyme + +## List(str): a link to the authors file (preferred) or a list of authors +authors: + - https://github.com/Klem-Research-Group/QMzyme#code-contributorsdevelopers + +## 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: + - Klem-Research-Group + - hklem + - MirumKim + +## str: a free form description of the mdakit +description: + QM-based enzyme model generation and validation. + +## List(str): a list of keywords which describe the mdakit +keywords: + - theozyme + - compuzyme + - cluster + - active-site + - biocatalysis + - enzyme-mechanisms + - quantum-mechanics + - QM-input + +## str: the license the mdakit falls under +## See https://spdx.org/licenses/ for valid license specifiers +license: MIT License + +## 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/Klem-Research-Group/QMzyme/ + +## str: the link to the project's documentation +documentation_home: https://qmzyme.readthedocs.io/ + +## str: the type of documentation available [UserGuide, API, README] +documentation_type: UserGuide + API + +## List(str): a list of commands to use when installing the mdakit from its +## source code. +src_install: + - pip install git+https://github.com/Klem-Research-Group/QMzyme@main + +## str: the package name used to import the mdakit +import_name: QMzyme + +## str: a specification for the range of Python versions supported by this MDAKit +python_requires: ">=3.11" + +## 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 -v + +## 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: + - git clone https://github.com/Klem-Research-Group/QMzyme + - cd QMzyme + - python -m pip install ".[test]" + +## str: the organisation name the MDAKit falls under +project_org: Klem-Research-Group + +#------------------------------------------------------------ +# Optional entries +#------------------------------------------------------------ + +## 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: +# - TBD + +## str: a link to the MDAKit's community (mailing list, github discussions, etc...) +#community_home: https://qmzyme.readthedocs.io/ +