Build (lint) is failing (ligand_neighbourhood_alignment)

[alanbchristie]

The ligand_neighbourhood_alignment repository CI build is failing (has been failing for some time). Before considering this code to be ready for production I think the CI build needs to be successful, even if this means pulling broken stuff out of it.

Broken builds should not be considered production ready.

[mwinokan]

@tdudgeon is this still failing?

[tdudgeon]

Yes. @alanbchristie set this up so he will need to investigate.

[alanbchristie]

There are a number of initial local development problems as it is difficult to develop on modern hardware. xchem align does not work for Python 3.12 (there is no distutils in Python 3.12) and rdkit fails to install on Apple M1 (ARM) hosts. The requires-python in the pyproject.toml probably needs to exclude Python 3.12 unless the developers think that 3.12 should be supported?

Also numpy was updated on 16th June (to version 2) and pandas appears to be ratehr sloppy in its requirements because it happily pulls in the latest numpy with the result that basic test fail, with the following error: -

ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

(see https://stackoverflow.com/questions/78634235/)

We also need to try and fix build errors earlier because they have been failing now for more than 10 months?

[alanbchristie]

I’ve fixed the CI build and the only risk is the explicit requirement of the last v1 release of the numpy package (1.26.4). There was no explicit version in the project’s pyproject.toml but without it pandas pulls in v2.0.0, which breaks the code.

I have also removed the use of mypy. This has been broken for a long time and now issues more than 50 errors. If mypy remains a project requirement I suggest a specific issue is raised to adjust the code so that it passes the mypy tests (which may be a significant level of effort).

Changes (fixes) have been merged to the xchemn-align master branch.

Future breaks in the CI build must be treated with higher priority.

[mwinokan]

@alanbchristie has fixed the build (by disabling two tests) but those two tests will need fixing to be included in the CI build

[tdudgeon]

@ConorFWild is needed to get the tests working

[alanbchristie]

The failed tests are documented in the following xchem-align issues: -

• test-data/config_2 fails with KeyError xchem/xchem-align#27
• test-data/config_3 fails with reference errors xchem/xchem-align#28

[mwinokan]

Now that XCA is stable it will be very useful to fix the automated testing to correctly flag errors from new dev

[alanbchristie]

After fixing what appeared to be the initial lint failure (related to the docs.yml workflow), and committed on branch issue_1301, what followed was a very large number of lint errors relating to the code. Sadly far too of these errors require code changes and I am not in a position to make any source code changes in this repository.

Someone who understands the code and its CI needs to fix this or we now need to switch the CI off altogether, and tackle the CI as a separate section of effort after the release. Be aware, as the CI has been broken for a very (very) long time this could take many days of effort to resolve.

Then, when done, fix CI issues when they arise.

Additionally, is pre-commit up to date on this repository and is it being used?