Add MD-SAPT to MDAKits #47
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| # Required entries | ||
| ## str: name of the project (the respository name) | ||
| project_name: MD-SAPT | ||
| ## List(str): a list of authors (or a link to the authors file) | ||
| authors: | ||
| - Alia Lescoulie | ||
| - Astrid Yu | ||
| - Ashley Ringer McDonald | ||
| ## List(str): a list of maintainers | ||
| maintainers: | ||
| - Alia Lescoulie | ||
| - Ashley Ringer McDonald | ||
| ## str: a free form description of the mdakit | ||
| description: | ||
| SAPT calculations on MD data using Psi4 | ||
| ## List(str): a list of keywords which describe the mdakit | ||
| keywords: | ||
| - SAPT | ||
| - protein | ||
| - quantum | ||
| ## str: the license the mdakit falls under | ||
| license: GPL-3.0-or-later | ||
| ## str: the link to the project's code | ||
| project_home: https://github.com/calpolyccg/MDSAPT | ||
| ## str: the link to the project's documentation | ||
| documentation_home: https://mdsapt.readthedocs.io | ||
| ## str: the type of documentation available [UserGuide, API, README] | ||
| documentation_type: UserGuide + API | ||
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| # 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 psi4/label/dev -c conda-forge mdsapt | ||
| ## List(str): a list of commands to use when installing the mdakit from its | ||
| ## source code. | ||
| src_install: | ||
| # required dependencies from environment.yaml | ||
| - mamba install -c psi4 -c conda-forge -c defaults "psi4>=1.6.1,<1.7" click numpy openmm pandas pdbfixer pytest pydantic pytest-cov pyyaml rdkit | ||
| - pip install git+https://github.com/calpolyccg/MDSAPT@master | ||
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There was a problem hiding this comment. Note that the „develop“ CI installs your source (ie your master branch) and tests against the MDAnalysis develop branch! That’s the configuration to check for the segfault. |
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| ## str: the package name used to import the mdakit | ||
| import_name: mdsapt | ||
| ## str: a specification for the range of Python versions supported by this MDAKit | ||
| python_requires: ">=3.8" | ||
| ## 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 | ||
| - pytest -v ./mdsapt/tests | ||
| ## List(str): a list of commands to use to install the necessary dependencies required | ||
| ## to run the MDAKit's tests | ||
| test_dependencies: | ||
| project_org: calpolyccg | ||
| ## str: the development status of the MDAKit | ||
| development_status: Mature | ||
| ## List(str) a list of publications to cite when using the MDAKit | ||
| publications: | ||
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| community_home: | ||
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There was a problem hiding this comment. Maybe enable GitHub discussions on https://github.com/calpolyccg/MDSAPT ?? There was a problem hiding this comment. Can you add an link to discussions? |
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| ## str: a link to the MDAKit's changelog | ||
| changelog: https://github.com/calpolyccg/MDSAPT/releases | ||
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Question for @IAlibay : Is it correct to do the installation of dependencies before the source pip install if I don't want dependencies to be pip-installed? I'd love to be able to say
mamba install -f environment.ymlbut to my knowledge that doesn't work (only works withmamba create). Because I have to list dependencies explicitly, I also have to explicitly add pinning (like forpsi4). That looks a bit awkward and prone to breakage. Is there a better way?There was a problem hiding this comment.
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🤔 yes that is indeed a bit of a problem.
What would the desired workflow be here? Fetch the yaml file from the remote directory and create the environment using that? Or should we try to read the yaml file and install from there?
This is definitely something to be considered as part of the refactor.
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At the end of the day the package developers should be responsible for keeping the meta data in sync with the package installation. I’d rather keep our side simple and suggest that ultimately packages follow standard procedures. In the meantime explicit pinning should be fine as a temporary measure — if this gets the kit installed correctly.