# ======================================================
# Python: bytecode / caches / compiled artifacts
# ======================================================
__pycache__/
*.py[cod]
*$py.class
*.so

# ======================================================
# Python: packaging / build artifacts
# ======================================================
.Python
*.egg-info/
*.egg
dist/
conda/dist/
conda-bld/
*.whl
*.manifest
*.spec
_version.py

# ======================================================
# Python: virtual environments
# ======================================================
.venv/
.venv-test-docker/

# ======================================================
# Python: type checkers
# ======================================================
.mypy_cache/
dmypy.json
dmypy.log
.pyre/
.pytype/

# ======================================================
# Python: testing / coverage
# ======================================================
.cache/
.pytest_cache/
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
old_tests/
test_output/

# ======================================================
# Python / ML frameworks
# ======================================================
*.pt
*.pth

# ======================================================
# Notebooks / interactive environments
# ======================================================
.ipynb_checkpoints/
profile_default/
ipython_config.py

# ======================================================
# Documentation / site builds
# ======================================================
# Sphinx
docs/_build/
docs/build/_build/
pgsui/docs/_build/
**/doctrees/
*.doctree
doctrees/
*_build/
.buildinfo

# mkdocs
/site

# Other doc/html outputs
html/
*.html

# ======================================================
# Web / Node / Electron
# ======================================================
**/node_modules/
pgsui/electron/app/dist/
pgsui_electron_logs/
.codex/

# ======================================================
# IDEs / editors
# ======================================================
.idea/
.spyderproject
.spyproject
.ropeproject

# ======================================================
# OS / misc
# ======================================================
.DS_Store
*.log
*.zip

# ======================================================
# Framework-specific leftovers (kept from template)
# ======================================================
# Django
local_settings.py
db.sqlite3

# Flask
instance/
.webassets-cache

# Scrapy
.scrapy

# PyBuilder
target/

# ======================================================
# Project-specific outputs
# ======================================================
pgsui_output/
snpio_output/
pgsui_*_output/
autoencoder_*_output/
snpio_simulated_unlinked_output/
sim_unlinked_output/
sim_results/
sim_results/*
summarize/
simulation/
simulation/*
sim_results/
*14K.vcf_output/

# Training / data folders
./training_data/
.training_data.nosync/
training_data_2
training_data_2*

# Other tool outputs / one-offs
monomorphic_sites_mqc.txt
vcf_attributes.h5
dnasp_summary_plots.cleaned.csv

# ======================================================
# Project-specific files to ignore (one-off inputs/trees)
# ======================================================
DEPRECATED*.py
BOX.vcf
BOX2.vcf
BOX_concat_goodOnly_N214.nex
BOX_phylogen_dataset_output/
box_scf.cf.tree
partitioned_all.contree
partitioned_all.iqtree
coala_sims.R
sim_treeparams.py
simulate_rad.py
simulate_wgs.py
summarize_results.zsh
run_sumstats.zsh
run_52.zsh
training_data/
validation_inputs/
validation_inputs_phylip/
validation_inputs_phylip_max150k/
validation_inputs.tar
iqtree_results/
iqtree_results_GTR/
subset_distributions.png
subset_dimensions.csv
subset_filenames.txt
subset_metadata_summary.csv
subset_metadata.csv
subset_phylip.tar.gz
subset_files.zsh
subset_phylip/
snpio_results23*_output/
results23_test_output/
pgsui_validation/
iqtree_results_unique/
iqtree_results_GTR/
dataset_stats_output/
pgsui_validation.nosync/
iqtree_results_GTR.nosync/
iqtree_results_unique.nosync/
summarize.nosync/
subset_phylip.nosync/
pgsui_osf_reviewer_package/
simulation.nosync/
validation_inputs_phylip_max150k.nosync/
gui_test_output/
*.dmg
tmp_test_output/
test_all_output/
test_nlpca_output/
*.slurm
pgsui_subset_phylip_results*/
*_mqc.txt
snpio_*_output/
iqtree_results_GTR_merged.nosync/
results189*_output/
summarize_tuned_params.py
new_ubp_output/
.github/
covid/
skills/
pgsui_subset_phylip_results_refactor2.tar.gz
covid_test_output/
tmpfile.phy
summarize2.nosync/
gti*_output/
*__seed42.nremover.vcf.gz*
gti_*.vcf*
gti_*.txt
mr-Mice*.vcf.gz*
naive-*.vcf.gz*
som-26*.vcf.gz*
variants-gti*.txt
probe.nremover*.vcf.gz*
*_probe_som*
tmp_probe_output/
gtImputation/
gtimputation-results/
scripts/*
test.phy.vcf
iqtree_runs/
imputed.nremover.vcf.gz