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register QMzyme#381

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hklem wants to merge 9 commits into
MDAnalysis:mainfrom
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Open

register QMzyme#381
hklem wants to merge 9 commits into
MDAnalysis:mainfrom
hklem:main

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@hklem

@hklem hklem commented Jun 5, 2026

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QMzyme is a Python toolkit to facilitate (quantum mechanical) QM-based enzyme model generation and validation.

@hklem hklem marked this pull request as draft June 5, 2026 08:16
@hklem hklem marked this pull request as ready for review June 5, 2026 09:46
@hklem

hklem commented Jun 5, 2026

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@MDAnalysis/mdakits-reviewers, ready for review

@orbeckst orbeckst added the new create a new MDAKit label Jun 23, 2026
@orbeckst orbeckst self-assigned this Jun 23, 2026

@orbeckst orbeckst left a comment

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Thank you for submitting your MDAKit. Apologies for the long delay with the review.

Your meta data file already looks pretty good. Can you try changing the src_install section to just be the pip-install so that all packages are installed in the same testing environment? Otherwise I have only minor suggestions.

Please don't hesitate to ping me with @orbeckst for a re-review.

Comment on lines +1 to +13
# 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.
#

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I'd remove the comment and replace it with something meaningful to you, e.g.

Suggested change
# 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
# -------------
#

Comment on lines +64 to +65
- conda create -n qmzyme -y python=3.11
- conda activate qmzyme

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Try just pip-installing and let the MDAKit testing environment set up the conda-forge environment

Suggested change
- conda create -n qmzyme -y python=3.11
- conda activate qmzyme

This is important so that the correct MDAnalysis versions are installed.

It's also better to not prescribe the installed Python version (especially since your package handles Python ≥3.11)

## - pytest -v ./tests
## Feel free to ask for advice on your pull request!
run_tests:
- pytest -v

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I was wondering why you didn't need the git clone latest until I noticed that you're git cloneing your repo for installing the test deps.

Comment on lines +110 to +111
publications:
- TBD

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Comment out and update the metadata with a new PR once you have a publication.

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2 participants