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… establish system without transport
Instead of having standalone rhs functions for each system, the rhs is defined as a method in the respective system class. The `_rhs` function then only needs to call the method of the system object.
Otherwise, it does not render correctly when the font is not installed.
…ing in MC sampling in transport_with_pymc.ipynb
Add logo to the repository
Delete Pixi-related configuration and lock files (pixi.toml and generated pixi.lock). Cleans up repository by removing unused/generated dependency metadata and config for Pixi.
Merge `develop` into `36-add-badges`
Update CI workflow to generate and persist a coverage badge. Adds write permission for repository contents, installs genbadge, outputs an XML coverage report (reports/coverage/coverage.xml), generates badges/coverage-badge.svg, and commits/pushes the badge back to the repo on push events (uses a bot user and commits with "[skip ci]"). This keeps the coverage badge up-to-date from the workflow run.
Insert project logo image at the top of README and update the main heading to a shorter form.
Remove Pixi files
Add badges to README and update workflow
…efactoring-and-adding-new-test-suite Update documentation
Fetch full repo history for the coverage workflow (fetch-depth: 0) so subsequent git operations have needed refs. Replace the staged-diff check with a --cached check that exits when there are no changes, then commit changes and run a git pull --rebase origin develop before pushing
CI: adjust coverage workflow checkout & push
Replace the custom badge generation and auto-commit with a codecov/codecov-action. Removed the permissions block, checkout fetch-depth override, genbadge installation, and the steps that generated/committed badges; workflow now uploads reports/coverage/coverage.xml to Codecov to simplify coverage reporting.
Update README badge to use Codecov (linking to the reactix repo on the develop branch) instead of the previous coverage image.
TODO: Make sure that units and parameter values are consistent throughout the notebook.
Parameter values are now roughly oriented at the ones in Schijven et el. (1999) Schijven, J. F., Hoogenboezem, W., Hassanizadeh, M., & Peters, J. H. (1999). Modeling removal of bacteriophages MS2 and PRD1 by dune recharge at Castricum, Netherlands. Water Resources Research, 35(4), 1101–1111. https://doi.org/10.1029/1998WR900108
Integrate Codecov for coverage reporting and update badges
Delete `.gitattributes`
Polish example notebooks
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Closes:
[TODO: List which issues]
Restructuring and Improvements:
SystemtoTransportSystemthroughout the docs, updated all references, and clarified parameter and method documentation to distinguish betweenTransportSystem(for spatially resolved models) and the newMixedSystem. This is also reflected in the documentation; docstrings and Quarto docs updated.CI/CD and Coverage Reporting:
Other Minor Changes:
README.md..gitattributesrule forpixi.lockto avoid merge issues and unnecessary highlighting.