[sbesson]

Fixes #93

• caps pandas to 2.x - the support of Pandas 3.x will need to be evaluated separately
• removes the unused Jinja2 and PyYAML dependencies - probably a legacy from the old population code in omero-py
• bumps the minimum version of Python to 3.10. Pandas 2.x mandates Python 3.8+ but 3.8 and 3.9 are already EOL

[muhanadz]

Looks good to me.

Tested in a fresh venv. Without PR:

((venv) ) ➜  omero-metadata git:(master) ✗ pip install /Users/muhanad/Glencoe/omero-metadata/dist/omero_metadata-0.13.1.dev0-py3-none-any.whl
...
...
Installing collected packages: appdirs, urllib3, six, PyYAML, portalocker, Pillow, numpy, MarkupSafe, idna, future, charset_normalizer, certifi, requests, python-dateutil, jinja2, pandas, omero-py, omero-metadata
Successfully installed MarkupSafe-3.0.3 Pillow-12.3.0 PyYAML-6.0.3 appdirs-1.4.4 certifi-2026.7.22 charset_normalizer-3.4.9 future-1.0.0 idna-3.18 jinja2-3.1.6 numpy-2.5.1 omero-metadata-0.13.1.dev0 omero-py-5.23.0 pandas-3.0.5 portalocker-4.1.0 python-dateutil-2.9.0.post0 requests-2.34.2 six-1.17.0 urllib3-2.7.0


((venv) ) ➜  omero-metadata git:(master) ✗ pip list |grep pandas    
pandas             3.0.5

With PR:

((venv) ) ➜  omero-metadata git:(pandas2) ✗ pip install /Users/muhanad/Glencoe/omero-metadata/dist/omero_metadata-0.13.1.dev0-py3-none-any.whl
...
...
...
Installing collected packages: pytz, appdirs, urllib3, tzdata, six, PyYAML, portalocker, Pillow, numpy, idna, future, charset_normalizer, certifi, requests, python-dateutil, pandas, omero-py, omero-metadata
Successfully installed Pillow-12.3.0 PyYAML-6.0.3 appdirs-1.4.4 certifi-2026.7.22 charset_normalizer-3.4.9 future-1.0.0 idna-3.18 numpy-2.5.1 omero-metadata-0.13.1.dev0 omero-py-5.23.0 pandas-2.3.3 portalocker-4.1.0 python-dateutil-2.9.0.post0 pytz-2026.3.post1 requests-2.34.2 six-1.17.0 tzdata-2026.3 urllib3-2.7.0

((venv) ) ➜  omero-metadata git:(pandas2) ✗ pip list |grep pandas
pandas             2.3.3

[sbesson]

Thanks @muhanadz, I would be inclined to schedule a release of omero-metadata with this fix so that the issues with Pandas 3.x do no start creeping up into production. This should probably be released as 0.14.0 to communicate the changes in minimal Python version.

Is there anything else in https://github.com/ome/omero-metadata/pulls that should be considered for review and inclusion alongside this fix?

[sbesson]

On second thoughts, the weekly OMERO integration workflow has been reactivated and is now consistently failing due to the incompatibility of the current state of the library with Pandas 3.x which is installed by default in a fresh environment - see https://github.com/ome/omero-metadata/actions/runs/31289021208.

Merging this in order to prepare a release that restores compatibility. I have also manually created a series of GitHub releases for each tag since 0.1.0 consistently with other OME repositories. I will open a follow-up PR to delete the manually maintained changelog and extend the release workflow to create the GitHub release automatically before tagging 0.14.0