.gitignore

# editors / tooling
.vscode
.quarto
.vdoc.py
.mypy_cache
*.otter.py
/os

# our own program output
kimmdy.log
jobscript.sh
tmp/
*.gif
*.log
*.csv
example/**/*[0-9][0-9][0-9]/
pytest_topol.top
\#*\#
*.xtc
*.trr
.nvimlog
render/
cat-center.gro
*.cpt
*.dill
*.pickle
.*.npz
.*.lock
*.tail
example/**/pycallgraph.png

# tutorials and example output files
guide/kimmdy-tutorial


# excludes
!tests/test_files/test_coordinates/pull.trr
!tests/test_files/test_coordinates/relax.trr
!tests/test_files/test_coordinates/relax.xtc
!tests/test_files/test_config/pull.trr
!tests/test_files/test_integration/hexalanine_single_reaction/pull.trr
!example/hexalanine_single_reaction/pull.trr

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
artifacts
htmlcov/
htmlcov*
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Sphinx documentation
docs/_build/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# Environments
.env
.venv
.venv*/
env/
venv/
ENV/
env.bak/
venv.bak/

# tooling
node_modules
package-lock.json


/.quarto/

/.luarc.json