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Merged
cbielow merged 11 commits into from
Dec 12, 2024
Merged

doc enhancements #449

cbielow merged 11 commits into from
Dec 12, 2024

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@cbielow
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@cbielow cbielow commented Dec 3, 2024

  • lots of fixes affecting rendering
  • fixes for correctness (referencing the correct lines etc)
  • more elaborate explanation of terms in texts (protein accession etc)
  • sort glossary for easier maintenance
  • update dev build instructions for pyOpenMS
  • glossary fixes: improved descriptions
  • improve QuantData tutorial

jpfeuffer
jpfeuffer reviewed Dec 3, 2024
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docs/source/user_guide/oligonucleotides_rna.rst Outdated
library (you can install BioPython with ``pip install biopython``):

.. code-block:: pseudocode
.. code-block:: python
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@jpfeuffer jpfeuffer Dec 3, 2024

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You probably have to be careful. All python code-blocks will be tested. Not sure if this code is functional.
Just saying, you might need to fix it in CI.

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@cbielow cbielow Dec 4, 2024

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I reverted to pseudocode, just to avoid installing biopython, which is rather large

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yep. fine with me

cbielow
cbielow commented Dec 4, 2024
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cbielow commented Dec 4, 2024

building the snippets fails in areas I have not touched.
e.g. https://github.com/OpenMS/pyopenms-docs/actions/runs/12162622521/job/33920001766?pr=449#step:8:84
This probably means that pyopenms-docs has not been build for quite some time.
It seems pyopenms has changed and now breaks the snippets?

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jpfeuffer commented Dec 4, 2024

Yes, or they were never touched since CI was introduced.
I think we always just had incremental CI.
No one ever tested everything.

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cbielow commented Dec 12, 2024

tests pass.
will merge

@cbielow cbielow merged commit 57c4d18 into OpenMS:master Dec 12, 2024
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@cbielow @jpfeuffer