Fixes & minor improvements

[RemDelaporteMathurin]

Description

Summary

This PR contains a few bug fixes (see below) and some minor improvements.

Related Issues

Fixes:

• Store timesteps in problem class #1075
• [BUG] data in Profile1D export is not reset between 2 simulations #1076
• [BUG] Milestones ignored if not adaptive stepsize #1045
• Expose element for immobile species #1004

Motivation and Context

Type of Change

• 🐛 Bug fix (non-breaking change which fixes an issue)
• ✨ New feature (non-breaking change which adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
• 🔨 Code refactoring (no functional changes, no API changes)
• 📝 Documentation update
• ✅ Test update (adding missing tests or correcting existing tests)
• 🔧 Build/CI configuration change

Testing

• All existing tests pass locally (pytest)
• I have added new tests that prove my fix is effective or that my feature works

Code Quality Checklist

• My code follows the code style of this project (Ruff formatted: ruff format .)
• My code passes linting checks (ruff check .)
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas

Documentation

• I have updated the documentation accordingly (if applicable)
• I have added docstrings to new functions/classes following the project conventions

Breaking Changes

Screenshots/Examples

Additional Notes

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.84%. Comparing base (db5d831) to head (96fa9e2).
⚠️ Report is 14 commits behind head on fenicsx.

Additional details and impacted files

@@             Coverage Diff             @@
##           fenicsx    #1091      +/-   ##
===========================================
+ Coverage    94.80%   94.84%   +0.04%     
===========================================
  Files           44       44              
  Lines         3194     3220      +26     
===========================================
+ Hits          3028     3054      +26     
  Misses         166      166              

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[RemDelaporteMathurin]

This change was needed because the Docker runs started to fail ...

[jhdark]

What does this do?

[RemDelaporteMathurin]

This was suggested by the error message in the Docker-based workflows.

see for instance this failed run

WARNING: The directory '/github/home/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
Processing /__w/FESTIM/FESTIM
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'error'
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [16 lines of output]
      /tmp/pip-build-env-jgsrcgze/overlay/lib/python3.12/site-packages/vcs_versioning/_backends/_git.py:360: UserWarning: "/__w/FESTIM/FESTIM" is shallow and may cause errors
        pre_parse(wd)
      running egg_info
      creating src/FESTIM.egg-info
      writing src/FESTIM.egg-info/PKG-INFO
      writing dependency_links to src/FESTIM.egg-info/dependency_links.txt
      writing requirements to src/FESTIM.egg-info/requires.txt
      writing top-level names to src/FESTIM.egg-info/top_level.txt
      writing manifest file 'src/FESTIM.egg-info/SOURCES.txt'
      /tmp/pip-build-env-jgsrcgze/overlay/lib/python3.12/site-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
        return get_active_overrides().subprocess_timeout
      fatal: detected dubious ownership in repository at '/__w/FESTIM/FESTIM'
      To add an exception for this directory, call:
      
          git config --global --add safe.directory /__w/FESTIM/FESTIM
      git introspection failed: fatal: detected dubious ownership in repository at '/__w/FESTIM/FESTIM'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.

Notice:  A new release of pip is available: 25.2 -> 26.0.1
Notice:  To update, run: pip install --upgrade pip
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
Error: Process completed with exit code 1.