Update repository links for aiida-amber and aiida-gromacs

[jkalayan]

aiida-gromacs and aiida-amber repositories have been moved from PSDI-UK to CCPBioSim github organisation. PyPI and documentation links also updated for aiida-amber

[github-actions]

PR Preview Action v1.6.2
🚀 View preview at https://aiidateam.github.io/aiida-registry/pr-preview/pr-361/
Built to branch gh-pages at 2025-10-31 12:50 UTC. Preview will be ready when the GitHub Pages deployment is complete.

[jimboid]

Please note, we fixed the entry point warning that is currently displaying on the registry here CCPBioSim/aiida-gromacs#218

[superstar54]

Hi @jimboid , I think you need to make a new release or aiida-gromacs to fix the entry point warning, as the warning is still shown in the preview. Because, pip_url: aiida-gromacs is provided, the registry inspects the aiida-gromacs from the pypi package, which points to the 2.1.0.

We can also merge this PR directly if you don't want to make a new release, please let me know so we can proceed.

[jimboid]

@superstar54 thanks for coming back. Ah I see, we need to make a release to update the warnings. One issue we do have before we make a release, I wanted to ask about is that we have some issue with docs failing CI since we moved repos. We now get many warnings like this:

/home/runner/work/aiida-amber/aiida-amber/aiida_amber/helpers.py:docstring of aiida_amber.helpers.get_code:7: WARNING: py:class reference target not found: aiida.orm.nodes.data.code.installed.InstalledCode [ref.class]
/home/runner/work/aiida-amber/aiida-amber/aiida_amber/helpers.py:docstring of aiida_amber.helpers.get_computer:9: WARNING: py:class reference target not found: aiida.orm.computers.Computer [ref.class]
/home/runner/work/aiida-amber/aiida-amber/aiida_amber/calculations/antechamber.py:docstring of aiida_amber.calculations.antechamber.AntechamberCalculation:1: WARNING: py:class reference target not found: aiida.engine.processes.calcjobs.calcjob.CalcJob [ref.class]

These did not occur before the repo migration, have you seen this before with migrated repos? It could just be coincidence and that there is a new thing for us to debug, but it happened on both aiida-amber and aiida-gromacs at the same time when we migrated the repos..

[jimboid]

@superstar54 are you able to merge this as you suggested please. We are struggling to make a release whilst the docs CI is failing, we wouldn't want to make a release ourselves until we can resolve this, otherwise the RTD docs will be broken for the new release. I'm suspecting that there is some issue related to the incomplete migration somehow.