package version clash with updated `environment.yml` file

[annaritz]

I have updated the conda environment with the new environment.yml file requirements (which have been updated with dependencies bumps).

When I run snakemake I get the following error:

ImportError in file "/Users/aritz/Documents/github/projects/spras/Snakefile", line 6:
cannot import name '_is_pandas_dataframe' from 'matplotlib.cbook' (/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/cbook/__init__.py)
  File "/Users/aritz/Documents/github/projects/spras/Snakefile", line 6, in <module>
  File "/Users/aritz/Documents/github/projects/spras/spras/evaluation.py", line 7, in <module>
  File "/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/pyplot.py", line 70, in <module>
  File "/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/figure.py", line 40, in <module>
  File "/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/projections/__init__.py", line 55, in <module>
  File "/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/axes/__init__.py", line 1, in <module>
  File "/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 27, in <module>
  File "/opt/miniconda3/envs/spras/lib/python3.11/site-packages/matplotlib/table.py", line 36, in <module>

I think this import error is when pandas is imported in dataset.py (line 5 of the Snakefile). It seems like the updated version of matplotlib has dropped the _is_pandas_dataframe function in matplotlib 3.9. The environment.yml` matplotlib verison is currently 3.10.3, previously it was 3.6, see this commit.

[tristan-f-r]

That's strange - import matplotlib.pyplot as plt is line 7 for spras/evaluation.py and shouldn't fail on the latest matplotlib. Does import matplotlib.pyplot work locally?

(My immediate guess is that the conda environment is outdated and needs a bump with conda env update, since this error isn't happening in CI)

[agitter]

Was this with an update to an existing spras conda environment? I wasn't able to successfully update my existing environment after all the packages were bumped so I had to remove it and create a fresh environment from file.

[tristan-f-r]

@agitter Was that because of go from #324?

[agitter]

No, this was on a Linux server. There were conflicts when I tried an update.

[agitter]

conda-forge has the specified version of matplotlib for all OSes:

I suspect something is causing conda update to not update an existing version. Was matplotlib pip installed in the environment? If so, try a pip uninstall to get rid of it, then conda update the environment from the yaml file again. I don't think conda can manage packages versions that were pip installed.

Or remove the whole environment if you don't want to track down all pip installed packages like this.

[agitter]

I did a fresh install of the conda environment on Windows. There are probably some version inconsistencies in our conda yml file and pyproject.toml leading to the pip installation of spras uninstalling and reinstalling things still:

Installing collected packages: pip, adjusttext, snakemake, spras
  Attempting uninstall: pip
    Found existing installation: pip 22.1.2
    Uninstalling pip-22.1.2:
      Successfully uninstalled pip-22.1.2
  Attempting uninstall: adjusttext
    Found existing installation: adjustText 1.3.0
    Uninstalling adjustText-1.3.0:
      Successfully uninstalled adjustText-1.3.0
  Attempting uninstall: snakemake
    Found existing installation: snakemake 0.0.0
    Uninstalling snakemake-0.0.0:
      Successfully uninstalled snakemake-0.0.0
Successfully installed adjusttext-0.7.3 pip-25.2 snakemake-9.6.2 spras-0.5.0

The snakemake 0.0.0 confuses me.