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‎.github/workflows/build.yml‎

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run: |
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chmod +x build.sh
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./build.sh
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- name: Check fASP and tsconj installation
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run: |
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python -c "import fASP; print(fASP.version)"
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python -c "import tsconj; print(tsconj.version)"
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- name: Sample Run 1
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run: |

‎README.md‎

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## Run ApproxASP
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First cd to scripts: `cd scripts`
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run on `t1_244.fix.lp` as follows:
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### Running first task
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`Input`:
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- `Boolean network`: a Boolean network (.bnet file)
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For counting minimal trap spaces:
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```
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python3 run_minimal_trap_space.py -t 1 -bn t1_244.bnet
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```
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it should print the count in line: `C-MTS-1:`
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For counting fixed points:
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```
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python3 run_fixed_point.py -t 1 -bn t1_244.bnet
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```
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it should print the count in line: `C-FIX-1:`
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### Running second task
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`Input`:
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- `Boolean network`: a Boolean network (.bnet file)
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- `phenotype`: a phenotype, we specify it in a file. You can see example in file `phen_244.txt`
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For counting minimal trap spaces:
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```
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python run_counting_bn.py -i t1_244.fix.lp
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python3 run_minimal_trap_space.py -t 2 -bn t1_244.bnet -phen phen_244.txt
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```
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it should print the count in line: `C-MTS-2:`
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run on `t1_244.mts.lp` as follows:
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For counting fixed points:
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```
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python run_counting_bn.py -i t1_244.mts.lp
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python3 run_fixed_point.py -t 2 -bn t1_244.bnet -phen phen_244.txt
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```
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it should print the count in line: `C-FIX-2:`
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### Running third task
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`Input`:
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- `Boolean network`: a Boolean network (.bnet file)
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- `phenotype`: a phenotype, we specify it in a file. You can see example in file `phen_244.txt`
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- `perturbation`: a perturbation, we specify it in a file. You can see example in file `pert_244.txt`
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For counting minimal trap spaces:
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```
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python3 run_minimal_trap_space.py -t 3 -bn t1_244.bnet -phen phen_244.txt -pert pert_244.txt
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```
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it should print the count in line: `C-MTS-3:`
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For counting fixed points:
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```
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python3 run_fixed_point.py -t 3 -bn t1_244.bnet -phen phen_244.txt -pert pert_244.txt
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```
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it should print the count in line: `C-FIX-3:`
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## Preprocessing BNs
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We used [tsconj](https://github.com/daemontus/tsconj) and [fASP](https://github.com/giang-trinh/fASP) to process BNs to ASP program, for minimal trap space and fixed points, respectively.
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- [tsconj](https://github.com/daemontus/tsconj), related paper: [AAAI2024](https://ojs.aaai.org/index.php/AAAI/article/view/28943)
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- [fASP](https://github.com/giang-trinh/fASP), related paper: [CP2023](https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2023.35)
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## Benchmark:
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The benchmark of our CP2025 experiments is available at [https://zenodo.org/records/19609732](https://zenodo.org/records/19609732).

‎build.sh‎

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cmake -DCLINGO_BUILD_SHARED=ON ..
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make -j12
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cp approxasp "$ROOT_DIR/script"
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cp "$ROOT_DIR/indsupport/compute_independent_support.py" "$ROOT_DIR/script/"
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echo "Done. Copied binaries to:"
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echo " $ROOT_DIR/script/approxasp"
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echo " $ROOT_DIR/script/approxasp"
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echo "Installing fASP..."
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cd "$ROOT_DIR/fASP"
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pip install .
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echo "Installing tsconj..."
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cd "$ROOT_DIR/tsconj"
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pip install .

‎fASP/.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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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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cover/
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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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.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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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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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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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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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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.env
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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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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/

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