opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
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Repair the documentation #1298

Closed cdiener closed 2 years ago

cdiener commented 2 years ago

This modernizes some part of the doc building and fixes the RTD builds by switching to the new .readthedocs.yaml which is required to pin a higher Python version (due to sympy needing Python >= 3.8). Also removes one TOC level for the API and adds type hints.

One of the main issues was that the RTD webhook was deleted from the repo. I regenerated it, so the builds should trigger again also for the dev version.

codecov-commenter commented 2 years ago

Codecov Report

Base: 84.56% // Head: 83.81% // Decreases project coverage by -0.74% :warning:

Coverage data is based on head (6c4e854) compared to base (c989e1b). Patch has no changes to coverable lines.

:exclamation: Current head 6c4e854 differs from pull request most recent head 4bd0d1b. Consider uploading reports for the commit 4bd0d1b to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #1298 +/- ## ========================================== - Coverage 84.56% 83.81% -0.75% ========================================== Files 66 66 Lines 5499 5499 Branches 1257 1257 ========================================== - Hits 4650 4609 -41 - Misses 533 573 +40 - Partials 316 317 +1 ``` | [Impacted Files](https://codecov.io/gh/opencobra/cobrapy/pull/1298?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra) | Coverage Δ | | |---|---|---| | [src/cobra/util/process\_pool.py](https://codecov.io/gh/opencobra/cobrapy/pull/1298/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra#diff-c3JjL2NvYnJhL3V0aWwvcHJvY2Vzc19wb29sLnB5) | `39.53% <0.00%> (-27.91%)` | :arrow_down: | | [src/cobra/sampling/optgp.py](https://codecov.io/gh/opencobra/cobrapy/pull/1298/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra#diff-c3JjL2NvYnJhL3NhbXBsaW5nL29wdGdwLnB5) | `75.38% <0.00%> (-16.93%)` | :arrow_down: | | [src/cobra/sampling/core.py](https://codecov.io/gh/opencobra/cobrapy/pull/1298/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra#diff-c3JjL2NvYnJhL3NhbXBsaW5nL2NvcmUucHk=) | `78.78% <0.00%> (-15.16%)` | :arrow_down: | | [src/cobra/flux\_analysis/deletion.py](https://codecov.io/gh/opencobra/cobrapy/pull/1298/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra#diff-c3JjL2NvYnJhL2ZsdXhfYW5hbHlzaXMvZGVsZXRpb24ucHk=) | `82.45% <0.00%> (-7.02%)` | :arrow_down: | | [src/cobra/flux\_analysis/variability.py](https://codecov.io/gh/opencobra/cobrapy/pull/1298/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra#diff-c3JjL2NvYnJhL2ZsdXhfYW5hbHlzaXMvdmFyaWFiaWxpdHkucHk=) | `85.41% <0.00%> (-5.21%)` | :arrow_down: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra)

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cdiener commented 2 years ago

Preview: https://cobrapy-cdiener.readthedocs.io/en/latest/index.html