math-bibliography

Shared BibTeX bibliography database for research papers by Dueñez and Iovino.

Contents

File / Directory	Purpose
references.bib	Unified database — 808 entries, UTF-8, normalized
.bibtex-tidy-args	Canonical bibtex-tidy flags (used by hooks and sort script)
.pre-commit-config.yaml	Pre-commit hook configuration
hooks/validate-bib.sh	Validation hook (biber)
hooks/sort-bib.sh	Manual re-sort script (run after bulk additions)
migrate.py	Migration script for existing TeX files

Using this database in a new paper repository

Add this repository as a git submodule:

git submodule add https://github.com/eduenez/math-bibliography.git bib

Then in your TeX file:

\bibliography{bib/references}   % from the repo root
\bibliography{../bib/references} % from a subdirectory

When cloning a repo that already contains this submodule:

git clone --recurse-submodules <repo-url>
# or, after a plain clone:
git submodule update --init

Citation keys

The database merges two legacy files (biblioteca.bib and iovino.bib). Keys from each file are preserved as-is:

• biblioteca.bib style: AuthorAbbrevYYYY — e.g. BenYaacov2013, AdlerFoNavM2000
• iovino.bib style: Author-Author:YYYY — e.g. Aerts-Pulmannova:2006, Argyros-Haydon:2011

New entries should follow the Author-Author:YYYY convention (full last names, hyphen-separated, colon before year).

To list all current keys:

python3 migrate.py --print-keys

Formatting and validation (pre-commit hooks)

Install the hooks once after cloning:

pre-commit install

Every git commit then runs two checks automatically:

1. bibtex-tidy — reformats entries in place (lowercase field names, curly-brace values, numeric year/volume, removes obsolete fields). If the file changes, the commit is rejected; git add the reformatted file and recommit.

2. biber --validate-datamodel — checks for missing required fields and malformed syntax. Fails on ERROR-level messages.

Re-sorting after bulk additions

--sort is excluded from the commit hook because bibtex-tidy's sort mode uses stdin/stdout (not in-place), which is fragile in the pre-commit environment. Re-sort manually when needed:

hooks/sort-bib.sh           # sorts references.bib
hooks/sort-bib.sh other.bib # sorts a different file
git add references.bib
git commit

Running the format check without committing

pre-commit run bibtex-tidy-format --all-files
pre-commit run biber-validate --all-files

Migrating existing TeX files

The legacy workflow uses two separate files:

% old — paths as seen from a DImanuscripts subdirectory:
\bibliography{../iovino,../biblioteca}

% old — from an external repo that references DImanuscripts:
\bibliography{../DImanuscripts/iovino,../DImanuscripts/biblioteca}

migrate.py updates these declarations to point to references.bib and can also rename \cite{} keys if the citation key convention is ever unified.

Dry run (default — no files are written)

# Single file:
python3 migrate.py path/to/paper.tex

# Entire directory tree:
python3 migrate.py ~/repos/SomePaper/

# Multiple files:
python3 migrate.py file1.tex file2.tex

The script prints a unified diff of every file that would change and exits with code 1 if any changes are pending (useful in CI).

Applying changes

python3 migrate.py --apply paper.tex
python3 migrate.py --apply ~/repos/SomePaper/

The script computes the correct relative path to references.bib for each TeX file individually, so it works regardless of where the TeX file lives under ~/repos/.

Renaming citation keys (future use)

No keys were renamed during the initial merge. If you later decide to unify the key naming convention, build a JSON rename map and apply it together with the bibliography path update:

# 1. Print all current keys to a file for reference:
python3 migrate.py --print-keys > all-keys.txt

# 2. Create a JSON map of renames (only entries that actually change):
cat > rekey.json <<'EOF'
{
  "BenYaacov2013":  "BenYaacov:2013",
  "AdlerFoNavM2000": "Adler-etal:2000"
}
EOF

# 3. Dry run to review:
python3 migrate.py --map rekey.json paper.tex

# 4. Apply:
python3 migrate.py --apply --map rekey.json paper.tex

\cite{}, \citet{}, \citep{}, and all other cite-command variants are updated. Multiple keys in a single \cite{key1,key2} are each handled independently.

Legacy patterns recognised by migrate.py

The script handles all known variants of the old bibliography declarations, both active and commented out:

Old declaration	Replacement
\bibliography{../iovino,../biblioteca}	\bibliography{<rel-path>/references}
\bibliography{../biblioteca,../iovino}	\bibliography{<rel-path>/references}
\bibliography{../iovino}	\bibliography{<rel-path>/references}
\bibliography{../biblioteca}	\bibliography{<rel-path>/references}
\bibliography{../DImanuscripts/iovino,...}	\bibliography{<rel-path>/references}
\bibliography{bibdatabase,../iovino}	\bibliography{bibdatabase,<rel-path>/references}
\bibliography{bibdatabase,iovino}	\bibliography{bibdatabase,<rel-path>/references}

The bibdatabase, prefix (used in the ergodic sub-project) is preserved alongside the new path.