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‎.env.example‎

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WANDB_API_KEY=
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GENET_EPEGRNA_DIR=

‎.gitattributes‎

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# =============================================================================
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# .gitattributes — export-ignore rules for git archive (publication)
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#
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# Files and directories listed here will be EXCLUDED from `git archive` output.
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# This keeps the development repository intact while producing a clean archive
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# for the publication repository.
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# =============================================================================
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# ----- PRIDICT2 submodule (broken, no longer needed) -------------------------
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PRIDICT2 export-ignore
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scripts/14.0-PRIDICT2-comparison.py export-ignore
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scripts/plot_comparison.py export-ignore
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# ----- WandB / internal infrastructure scripts ------------------------------
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scripts/download_checkpoint.py export-ignore
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scripts/download_comparison_tables.py export-ignore
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scripts/find_wandb_runs.py export-ignore
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scripts/get_wandb_table.py export-ignore
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scripts/list_artifacts.py export-ignore
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scripts/generate_predictions_skw_batch.py export-ignore
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scripts/normalize_data.py export-ignore
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scripts/save_rq3_splits.py export-ignore
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scripts/compare_models.py export-ignore
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scripts/schedule.sh export-ignore
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# ----- Development / exploratory notebooks -----------------------------------
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notebooks/1.0-ju-genet-example.ipynb export-ignore
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notebooks/2.0-ju-rank-class-imbalance-visualization.ipynb export-ignore
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notebooks/3.0-rank-by-regression-5pes.ipynb export-ignore
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notebooks/3.1-rank-by-regression-4pes.ipynb export-ignore
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notebooks/3.2-rank-by-regression-3pes.ipynb export-ignore
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notebooks/3.3-rank-by-regression-2pes.ipynb export-ignore
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notebooks/3.3.1-rank-by-regression-2pes.ipynb export-ignore
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notebooks/4.0-rank-by-regression-5pes-5pct.ipynb export-ignore
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notebooks/4.2-rank-by-regression-3pes-5pct.ipynb export-ignore
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notebooks/5.0-rank-by-regression-5pes-10pct.ipynb export-ignore
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"notebooks/6.3-rank-by-regression-2pes-20pct copy.ipynb" export-ignore
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notebooks/7.0-genet-orthogonal-test.ipynb export-ignore
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notebooks/10.0-pe6-vs-pe7-ranking-comparison.ipynb export-ignore
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notebooks/10.0.1-stratification-investigation.ipynb export-ignore
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notebooks/10.1-pe6-vs-pe7-fold-change-prediction.ipynb export-ignore
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notebooks/__init__.py export-ignore
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notebooks/.gitkeep export-ignore
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# ----- Development experiment configs (SKW / legacy / duplicates) ------------
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configs/experiment/pe6-small-skw-6-2-DP-dev.yaml export-ignore
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configs/experiment/pe6-small-skw-6-2-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-6-3-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-6-4-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-7-2-DP-from-maxdRNaseH-FT.yaml export-ignore
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configs/experiment/pe6-small-skw-7-2-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-7-3-DP-from-6b-FT.yaml export-ignore
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configs/experiment/pe6-small-skw-7-3-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-7-4-DP-from-6c-FT.yaml export-ignore
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configs/experiment/pe6-small-skw-7-4-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-pair-2-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-pair-3-DP.yaml export-ignore
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configs/experiment/pe6-small-skw-pair-4-DP.yaml export-ignore
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configs/experiment/pe6a.yaml export-ignore
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configs/experiment/pe6b.yaml export-ignore
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configs/experiment/pe6c.yaml export-ignore
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configs/experiment/pe6d.yaml export-ignore
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configs/experiment/pemaxdrnaseh.yaml export-ignore
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configs/experiment/pe6a-DP-baseline.yaml export-ignore
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configs/experiment/pe6b-DP-baseline.yaml export-ignore
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configs/experiment/pe6b-DP-baseline-from-scratch.yaml export-ignore
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configs/experiment/pe6c-DP-baseline.yaml export-ignore
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configs/experiment/pe6c-DP-baseline-from-scratch.yaml export-ignore
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configs/experiment/pe6d-DP-baseline.yaml export-ignore
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configs/experiment/pemax-DP-baseline.yaml export-ignore
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configs/experiment/pemax-DP-baseline-original.yaml export-ignore
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configs/experiment/pemaxdrnaseh-DP-baseline.yaml export-ignore
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configs/experiment/pemaxdrnaseh-DP-baseline-from-scratch.yaml export-ignore
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configs/experiment/example.yaml export-ignore
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# ----- Development data configs (SKW / PE6d / PE6g) -------------------------
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configs/data/pe6-small-skw-6-2.yaml export-ignore
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configs/data/pe6-small-skw-6-3.yaml export-ignore
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configs/data/pe6-small-skw-6-4.yaml export-ignore
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configs/data/pe6-small-skw-7-2.yaml export-ignore
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configs/data/pe6-small-skw-7-3.yaml export-ignore
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configs/data/pe6-small-skw-7-4.yaml export-ignore
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configs/data/pe6d.yaml export-ignore
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configs/data/pe6g.yaml export-ignore
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# ----- HPO sweep configs ----------------------------------------------------
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configs/hparams_search/ export-ignore
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# ----- PE6d / PE6g train configs ---------------------------------------------
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configs/train_6d.yaml export-ignore
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configs/train_6g.yaml export-ignore
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# ----- Debug configs ---------------------------------------------------------
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configs/debug/ export-ignore
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# ----- Unused model configs --------------------------------------------------
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configs/model/pe6_delta.yaml export-ignore
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configs/model/pe6_resnet.yaml export-ignore
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configs/model/pe6_simple.yaml export-ignore
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# ----- CI/CD, GitHub infra, dev tools ----------------------------------------
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.github/ export-ignore
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.pre-commit-config.yaml export-ignore
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.editorconfig export-ignore
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.vscode/ export-ignore
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Makefile export-ignore
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pyproject.toml export-ignore
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# ----- DVC (internal Synology NAS) -------------------------------------------
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.dvc/ export-ignore
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.dvcignore export-ignore
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data/DeepPrime.dvc export-ignore
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data/MNIST.dvc export-ignore
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data/pe6.dvc export-ignore
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src/models/weights.dvc export-ignore
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# ----- Credentials / secrets -------------------------------------------------
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.env export-ignore
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# ----- Miscellaneous dev artifacts -------------------------------------------
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data/.gitignore export-ignore
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data/.gitkeep export-ignore
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src/.gitignore export-ignore
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src/models/.gitignore export-ignore
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src/models/components/utils/.gitkeep export-ignore
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logs/.gitkeep export-ignore
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configs/local/.gitkeep export-ignore
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# ----- Tests (internal, not needed for reproduction) -------------------------
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tests/ export-ignore
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# ----- Development figures (not directly in paper) ---------------------------
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figures/2.0-ju-rank-class-imbalance-visualization/ export-ignore
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figures/14.0-pridict2-comparison/ export-ignore
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# ----- Unused model / data source code ---------------------------------------
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src/models/pe6_delta_module.py export-ignore
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src/data/pe6_delta_datamodule.py export-ignore
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src/data/components/data_model/pe6_delta_dataset.py export-ignore
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src/models/components/pe6_resnet.py export-ignore
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src/models/components/pe6_dense_net.py export-ignore
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src/utils/optuna_patch.py export-ignore

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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### VisualStudioCode
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# .vscode/*
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!.vscode/settings.json
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!.vscode/tasks.json
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!.vscode/launch.json
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!.vscode/extensions.json
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*.code-workspace
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# **/.vscode
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# JetBrains
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.idea/
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# Data & Models
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*.h5
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*.tar
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*.tar.gz
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# Lightning-Hydra-Template
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configs/local/default.yaml
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# /data/
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/logs/
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.env
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# Aim logging
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.aim
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nohup.out
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extensions.list
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.gitconfig
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/notebooks/artifacts
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*.out
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notebooks/pe6to7.parquet
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notebooks/wandb/latest-run
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notebooks/wandb/**
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*.zip
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*.csv
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*.png

‎.project-root‎

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# this file is required for inferring the project root directory
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# do not delete

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