.gitignore

# compiled files
*.pyc

# python cache
__pycache__/

#distribution files
/build/
/dist/
/sdists/
*.egg-info

# test reports
tests/reports

# coverage file
.coverage*
htmlcov/
.tox/

# profiling data
prof/

# .rst-formatted README
README.rst

# compiled documentation
docs/source
docs/_build
docs/.doctrees/

# pytest .cache directory
.cache/
.pytest_cache/

# passwords
tests/fixtures/secret/

# IDE configuration
.idea/
.spyderproject
.ropeproject

# temporary files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
.~lock.*
Thumbs.db
~$*.xlsx
~$*.xls
.~*.xlsx

# temporary files for building alphabets
bpforms/alphabet/DNAmod.sqlite
bpforms/alphabet/rna.sqlite
bpforms/alphabet/repairtoire.xlsx
# bpforms/alphabet/rnamods/
bpforms/alphabet/resid/
bpforms/alphabet/protein.sqlite
bpforms/alphabet/protein.report.txt
bpforms/alphabet/pdb/
bpforms/alphabet/onto.obo
bpforms/web/data/
bpforms/web/img/alphabet/
bpforms/web/img/example/
bpforms/web/img/crosslink/

# files generated by examples
examples/*.fasta
examples/*.obo
examples/*.owl
examples/*.pdf
examples/*.pkl
examples/*.png
examples/*.sqlite
examples/*.svg
examples/*.swp
examples/*.tsv
examples/*.xlsx
examples/pro_input_structure/
examples/pro_input_viz/
examples/pro_input_viz.zip

# Paul's temporary work
paulTmpTests

# assets for building Docker image
Dockerfile_assets/