MDAKit registration: DomHMM

[m-a-r-i-u-s]

Dear MDAKit Maintainer/Developers,

I would like to register our recent project DomHMM as a MDAKit.
DomHMM is a package mainly based on the MDAnalysis library to identify lateral heterogeneities (e.g., liquid-ordered domains) in Molecular Dynamics simulations of lipid bilayers. Our tool is easy to use and should cover a wide range of standard simulation setups (i.e., symmetric and asymmetric membranes, membranes including small proteins). However, this is our first open-source project, and if there is something missing or can be improved, we are open for any suggestions. Note, that we have a documentation describing our package: https://domhmm.readthedocs.io/en/latest/?badge=latest, but more details on the method can be found here: https://doi.org/10.1016/bs.mie.2024.03.006.

The package can be found here: https://github.com/BioMemPhys-FAU/domhmm

With regards,
Marius

[orbeckst]

Hello to Erlangen! My undergrad institution :-)

Thank you for your contribution. We'll have a look and work with you. Please be patient with us and ask if anything is unclear.

[orbeckst]

This looks already really good: you have tests, docs, maintainers, and the develop CI runs successfully.

I would be really good if there were instructions for how to install the latest release. At the moment, the CI tests for latest do not install anything and then happily pass.

But it is really useful for users to know how to install the latest released version (currently your v1.0.0) so although we do require it we very much encourage you to provide this information. We'd be happy to help you upgrade your package. For initial suggestions for two different ways see below:

pypi

Users prefer to be able to just pip install your package, so I very much encourage you to put the released version of the package on PyPi — the Python Packaging Guide's Uploading the distribution archives is a concise description of what needs to be done.

Once you've done that,

• update the install: section of the meta.yml file with the appropriate pip install domhmm (or similar) command
• update your docs with the installation instructions

source package

Alternatively, you can have users install from the released archives from https://github.com/BioMemPhys-FAU/domhmm/releases/tag/v1.0.0 or by cloning the repo and switching to the latest release tag.

• include appropriate docs for users
• update the install: section with the commands I mention in the review comment (namely, the git clone latest where the latest is some of our magic that means for us to find the latest tag on your repo and install it).

[orbeckst]

All you need to do in order for the kit to be registered is to comment out the install: step (as you originally had).

Once you have a PyPi package, you can then update the metadata in a PR.

[orbeckst]

@m-a-r-i-u-s , your kit is registered, congratulations! 🎉

Once you have a PyPi package, please open a PR to add the install step — you can just quickly edit the metadata file on GitHub.

[orbeckst]

ALso thank you for considering my comment on dependency pinning.

[m-a-r-i-u-s]

@orbeckst Yeah! :)
Thank you very much for your input and this amazing project!