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Tweaks to doctest syntax/style in Tutorial #3759

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merged 10 commits into from Nov 9, 2021
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@peterjc peterjc commented Oct 7, 2021

  • I hereby agree to dual licence this and any previous contributions under both
    the Biopython License Agreement AND the BSD 3-Clause License.

  • I have read the CONTRIBUTING.rst file, have run pre-commit locally,
    and understand that AppVeyor and TravisCI will be used to confirm the Biopython unit
    tests and style checks pass with these changes.

  • I have added my name to the alphabetical contributors listings in the files
    NEWS.rst and CONTRIB.rst as part of this pull request, am listed
    already, or do not wish to be listed. (This acknowledgement is optional.)

This is intended allow the use of blacken-docs v1.11.0 which included adamchainz/blacken-docs#112 from me to support \begin{minted}{pycon} specifically for the Biopython documentation.

These commits either address syntax issues blocking automated use of blacken-docs as seen in #3758 (and adamchainz/blacken-docs#121), or tweak the examples to work better after black formatting.

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codecov bot commented Oct 7, 2021

Codecov Report

Merging #3759 (17b18f1) into master (1e4acd3) will decrease coverage by 1.69%.
The diff coverage is n/a.

❗ Current head 17b18f1 differs from pull request most recent head 7f3dfc3. Consider uploading reports for the commit 7f3dfc3 to get more accurate results
Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3759      +/-   ##
==========================================
- Coverage   83.82%   82.13%   -1.70%     
==========================================
  Files         317      298      -19     
  Lines       52985    49961    -3024     
==========================================
- Hits        44415    41035    -3380     
- Misses       8570     8926     +356     
Impacted Files Coverage Δ
Bio/Phylo/CDAOIO.py 4.46% <0.00%> (-80.36%) ⬇️
Bio/phenotype/pm_fitting.py 12.28% <0.00%> (-75.44%) ⬇️
Bio/PDB/mmtf/__init__.py 28.57% <0.00%> (-61.91%) ⬇️
Bio/Graphics/__init__.py 25.00% <0.00%> (-58.34%) ⬇️
Bio/Phylo/CDAO.py 42.85% <0.00%> (-57.15%) ⬇️
Bio/Phylo/_utils.py 25.00% <0.00%> (-52.41%) ⬇️
Bio/codonalign/codonseq.py 44.16% <0.00%> (-44.31%) ⬇️
Bio/Phylo/_cdao_owl.py 89.47% <0.00%> (-10.53%) ⬇️
Bio/KEGG/KGML/KGML_pathway.py 73.58% <0.00%> (-6.67%) ⬇️
Bio/motifs/jaspar/db.py 3.04% <0.00%> (-5.33%) ⬇️
... and 33 more

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@peterjc peterjc merged commit 21d1150 into biopython:master Nov 9, 2021
@peterjc peterjc deleted the bdocs branch November 9, 2021 11:55
Lucioric2000 pushed a commit to Lucioric2000/biopython that referenced this pull request Nov 14, 2021
* Avoid invalid syntax in examples
* Using more f-strings for consiseness
* Fix missing ... in doctest syntax
* Tweak doctest examples for black style
* Fix strange LaTeX indentation, and test example

This is intended allow the use of blacken-docs v1.11.0 which includes support
for \begin{minted}{pycon}, added specifically for the Biopython documentation.
JoaoRodrigues pushed a commit to cbalbin-bio/biopython that referenced this pull request Aug 7, 2022
* Avoid invalid syntax in examples
* Using more f-strings for consiseness
* Fix missing ... in doctest syntax
* Tweak doctest examples for black style
* Fix strange LaTeX indentation, and test example

This is intended allow the use of blacken-docs v1.11.0 which includes support
for \begin{minted}{pycon}, added specifically for the Biopython documentation.
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