MANIFEST.in

# Include documentation files
include README.md
include LICENSE
include CITATION.cff
include CODE_OF_CONDUCT.md
include CONTRIBUTING.md
include SECURITY.md
include SUPPORT.md
include CHANGELOG.md
include requirements.txt
# requirements/requirements-base.txt MUST ship: pyproject.toml declares
# dynamic dependencies and reads them from that file at build time, so an
# sdist without it produces a package with an empty dependency list.
include requirements/*.txt
include .zenodo.json

# Include configuration files
recursive-include qbiocode/apps/qprofiler/configs *.yaml *.py
recursive-include qbiocode/apps/quvine/configs *.yaml *.py
# In-tree module documentation (e.g. the random-graph generator reference).
recursive-include qbiocode *.md
recursive-include tutorial/QProfiler/configs *.yaml
recursive-include tutorial/Quantum_Projection_Learning/configs *.yaml

# Include documentation source files
recursive-include docs/source *.rst *.md *.py
recursive-include docs/source/_static *.png *.jpg *.svg *.gif
recursive-include docs/source/_templates *.rst

# Include tutorial notebooks and the fixtures they read.
#
# Named individually rather than swept in by extension. `tutorial/**/data/` and
# `tutorial/**/*.png` are notebook *output* and gitignored, with four fixtures
# force-added as exceptions -- so `recursive-include tutorial *.csv *.png *.pkl`
# packaged whatever run artifacts happened to be lying around. On a checkout
# where the data-generation notebook had been run once, that was 239 untracked
# CSVs and 111 MB, making the sdist's size a function of the builder's shell
# history rather than of the repository.
recursive-include tutorial *.ipynb
include tutorial/QProfiler/data/pbmc5k_small_cd4_vs_cd8.h5ad
recursive-include tutorial/QProfiler/data/sc_binary *.csv
recursive-include tutorial/QEnsemble/experiments *.csv *.pkl

# Exclude build artifacts and cache
global-exclude *.pyc
global-exclude *.pyo
global-exclude __pycache__
global-exclude .DS_Store
global-exclude *.so
global-exclude .git*

# Exclude test and development files
prune tests
prune .pytest_cache
prune archive