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move bibliography refs from database.py and difference_family.py to master index#41861

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aksharabhardwaj766-commits wants to merge 7 commits intosagemath:developfrom
aksharabhardwaj766-commits:move-refs-designs-database-diffamily
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move bibliography refs from database.py and difference_family.py to master index#41861
aksharabhardwaj766-commits wants to merge 7 commits intosagemath:developfrom
aksharabhardwaj766-commits:move-refs-designs-database-diffamily

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Part of #28445.
Moves locally defined references from

src/sage/combinat/designs/database.py
src/sage/combinat/designs/difference_family.py

into the centralized bibliography at

src/doc/en/reference/references/index.rst.

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cxzhong commented Mar 26, 2026

@vbraun workflows please

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Pull request overview

This PR centralizes bibliography/citation definitions by removing locally defined REFERENCES blocks from combinatorics design modules and adding the corresponding citation entries to the master references index (src/doc/en/reference/references/index.rst) as part of #28445.

Changes:

  • Removed locally defined reference blocks from difference_family.py and database.py docstrings.
  • Added the moved citation entries (and some related design-theory references) to the centralized references/index.rst.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File Description
src/sage/combinat/designs/difference_family.py Removes embedded citation definitions from module/function docstrings to rely on centralized references.
src/sage/combinat/designs/database.py Removes embedded citation definitions; leaves one docstring with a now-bare URL that likely needs reformatting.
src/doc/en/reference/references/index.rst Adds centralized citation entries for the moved references (but includes at least one formatting error that breaks citation resolution).

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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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@cxzhong Any updates on the workflow approval? Thank you!

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cxzhong commented Apr 18, 2026

[70/192] Generating src/doc/doc-inventory-reference-combinat with a custom command
FAILED: [code=1] src/doc/inventorycombinat 
/usr/share/miniconda/envs/sage-dev/bin/python3.12 /home/runner/work/sage/sage/src/build-docs.py --no-prune-empty-dirs --no-pdf-links reference/combinat inventory -o src/doc --source /home/runner/work/sage/sage/builddir/src/doc
[combinat ] building [inventory]: targets for 399 source files that are out of date
[combinat ] updating environment: [new config] 399 added, 0 changed, 0 removed
[combinat ] /usr/share/miniconda/envs/sage-dev/lib/python3.12/site-packages/sage/combinat/designs/database.py:docstring of sage.combinat.designs.database:69: WARNING: Bullet list ends without a blank line; unexpected unindent. [docutils]
[combinat ] The inventory file is in src/doc/inventory/en/reference/combinat.
Error building the documentation.
Traceback (most recent call last):
  File "/home/runner/work/sage/sage/src/build-docs.py", line 11, in <module>
    main()
  File "/home/runner/work/sage/sage/src/sage_docbuild/__main__.py", line 555, in main
    build()
  File "/home/runner/work/sage/sage/src/sage_docbuild/builders.py", line 670, in _wrapper
    getattr(DocBuilder, build_type)(self, *args, **kwds)
  File "/home/runner/work/sage/sage/src/sage_docbuild/builders.py", line 143, in f
    runsphinx()
  File "/home/runner/work/sage/sage/src/sage_docbuild/sphinxbuild.py", line 324, in runsphinx
    sys.stderr.raise_errors()
  File "/home/runner/work/sage/sage/src/sage_docbuild/sphinxbuild.py", line 255, in raise_errors
    raise OSError(self._error)
OSError: /usr/share/miniconda/envs/sage-dev/lib/python3.12/site-packages/sage/combinat/designs/database.py:docstring of sage.combinat.designs.database:69: WARNING: Bullet list ends without a blank line; unexpected unindent. [docutils]

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cxzhong commented Apr 18, 2026

please fix this

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