Restructure the package (#7)

* setting up the folder structure

* move scripts to cli and setting up package meta for cli access

* restructure the rest of the files

* Refactor attributions (#8)

* attribution refactoring low level api design

* updates of api of attirbutions and cli

* attribution cli

* wandb login, resources -> hub, and depreated tools.interpret

* update for multiple genes

* cli update to support multiple genes and attribution methods

* testcase fix

* test ci fix

* genome

---------

Co-authored-by: Muhammed Hasan Celik <[email protected]>

* vep added

* vep implemented

* vep logs and api update

* decima vep bug fix

* bug fix

* tangermeme version

* ci

* attr window bug

* fix of typo and depreceated

* mutate function deleted and fix of string literal

* Refactor vep (#9)

* vep added

* vep implemented

* vep logs and api update

* decima vep bug fix

* bug fix

* tangermeme version

* ci

* attr window bug

* fix of typo and depreceated

* mutate function deleted and fix of string literal

---------

Co-authored-by: Muhammed Hasan Celik <[email protected]>

* pr code review

---------

Co-authored-by: Muhammed Hasan Celik <[email protected]>
Co-authored-by: Muhammed Hasan Celik <[email protected]>

Author: 3 people

.github/workflows/run-tests.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     name: Python ${{ matrix.python-version }}
     steps:

.gitignore

@@ -1,54 +1,182 @@
-# Temporary and binary files
-*~
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
+*$py.class
+
+# C extensions
 *.so
-*.cfg
-!.isort.cfg
-!setup.cfg
-*.orig
-*.log
-*.pot
-__pycache__/*
-.cache/*
-.*.swp
-*/.ipynb_checkpoints/*
-.DS_Store
 
-# Project files
-.ropeproject
-.project
-.pydevproject
-.settings
-.idea
-.vscode
-tags
-
-# Package files
-*.egg
-*.eggs/
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
 .installed.cfg
-*.egg-info
+*.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
 
-# Unittest and coverage
-htmlcov/*
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
 .coverage
 .coverage.*
-.tox
-junit*.xml
+.cache
+nosetests.xml
 coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
 .pytest_cache/
+cover/
 
-# Build and docs folder/files
-build/*
-dist/*
-sdist/*
-docs/api/*
-docs/_rst/*
-docs/_build/*
-cover/*
-MANIFEST
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
 
-# Per-project virtualenvs
-.venv*/
-.conda*/
-.python-version
+# Cursor
+#  Cursor is an AI-powered code editor.`.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+wandb/

.pre-commit-config.yaml

@@ -6,6 +6,7 @@ repos:
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
+    args: ["--maxkb=2000"]
   - id: check-ast
   - id: check-json
   - id: check-merge-conflict

docs/requirements.txt

@@ -1,9 +1,9 @@
+furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-myst-nb
-furo
 sphinx-autodoc-typehints

scripts/predict_genes.py

@@ -49,6 +49,8 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
+    click
+    more_itertools
     wandb
     numpy
     torch
@@ -63,6 +65,9 @@ install_requires =
     captum
     anndata
     h5py
+    pyBigWig
+    pyarrow
+    tangermeme<0.5
 
 [options.packages.find]
 where = src
@@ -73,6 +78,8 @@ exclude =
 # Add here additional requirements for extra features, to install with:
 # `pip install decima[PDF]` like:
 # PDF = ReportLab; RXP
+optional =
+    cyvcf2
 
 # Add here test requirements (semicolon/line-separated)
 testing =
@@ -82,8 +89,8 @@ testing =
 
 [options.entry_points]
 # Add here console scripts like:
-# console_scripts =
-#     script_name = decima.module:function
+console_scripts =
+    decima = decima.cli:main
 # For example:
 # console_scripts =
 #     fibonacci = decima.skeleton:run