#Ignore the build directory (and its sub-directories):
build

#Ignore the distribution directory
dist

#Ignore backup files from some Unix editors,
\#*\#
*~
*.swp
*.bak

#Ignore patches and any original files created by patch command
*.diff
*.patch
*.orig
*.rej

#Ignore these hidden files from Mac OS X
.DS_Store

#Ignore hidden files from Dolphin window manager
.directory

#Ignore all compiled python files (e.g. from running the unit tests):
*.pyc
*.pyo
*.py-e
*.pyd

#Ignore all Jython class files (present if using Jython)
*.class

#Ignore any compiled C code
*.so

#Ignore the .tox directory from running tox locally
.tox/

#Ignore the MANIFEST file created automatically from MANIFEST.in
MANIFEST

#Ignore potential directory created during install:
biopython.egg-info

#The graphics unit tests produce output files for human inspection
#(at the time of writing, only PDF and PNG files are created)
Tests/Graphics/*.pdf
Tests/Graphics/*.eps
Tests/Graphics/*.svg
Tests/Graphics/*.png

# This file is downloaded when testing the Bio.SeqIO.GckIO module.
Tests/Gck/DGVC_GCK.zip

#Ignore the local BioSQL test settings:
Tests/biosql.ini

#TODO - The unit tests shouldn't leave temp files after running:
Tests/BioSQL/temp_sqlite.db
Tests/BioSQL/temp_sqlite.db-journal
Tests/Cluster/cyano_result*
# Created by Tests/test_BWA_tool.py:
Tests/out.bam

#TODO - The Tutorial doctests should leave example files after
#running Tests/test_Tutorial.py
Doc/examples/other_trees.nwk
Doc/examples/tree1.nwk

#Ignore LaTeX temp files, and compiled output
Doc/*.aux
Doc/*.gz
Doc/*.log
Doc/*.out
Doc/*.toc
Doc/*.haux
Doc/*.htoc
Doc/*/*.aux
Doc/*/*.log
Doc/*/*.out
Doc/*/*.toc
Doc/*/*.haux
Doc/*/*.htoc
Doc/*/*/*.aux
Doc/*/*/*.log
Doc/*/*/*.out
Doc/*/*/*.toc
Doc/*/*/*.haux
Doc/*/*/*.htoc
Doc/_minted-Tutorial/
Doc/Tutorial.txt
Doc/Tutorial.pdf
Doc/Tutorial.html
Doc/Tutorial.pyg
Doc/biopdb_faq.pdf
Doc/version.sh
Doc/install/Installation.txt
Doc/install/Installation.pdf
Doc/install/Installation.html
Doc/cookbook/motif/motif.pdf
Doc/cookbook/motif/motif.html

#Ignore the hevea.sty file if present (used for HTML docs)
Doc/hevea.sty
Doc/*/hevea.sty
Doc/*/*/hevea.sty

#Ignore artifacts of building the docs
_build
Doc/api/*.rst

#Ignore IntelliJ IDEA directory and project files
.idea
*.iml

#Ignore unittest cache directory
.cache/

#Ignore vscode directory
.vscode

#Ignore mypy cache directory
.mypy_cache

#Ignore virtual environments
.env
.venv
env/
venv/
ENV/

# Testing
**/.coverage
