Initial commit

.github/workflows/lint.py

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+import os
+import shutil
+import nbformat
+from nbformat.v4 import new_notebook
+
+def clean_notebook(file_path):
+    with open(file_path, 'r', encoding='utf-8') as f:
+        notebook = nbformat.read(f, as_version=4)
+
+    # Clean cells
+    for cell in notebook.cells:
+        if 'outputs' in cell:
+            cell['outputs'] = []
+        if 'execution_count' in cell:
+            cell['execution_count'] = None
+        if 'metadata' in cell:
+            cell['metadata'] = {}
+
+    # Clean notebook metadata
+    if 'metadata' in notebook:
+        notebook['metadata'] = {}
+
+    with open(file_path, 'w', encoding='utf-8') as f:
+        nbformat.write(notebook, f)
+
+def delete_checkpoints_dirs(root_dir):
+    # Walk through the directory tree
+    for dirpath, dirnames, filenames in os.walk(root_dir):
+        for dirname in dirnames:
+            # Check if the directory name is 'checkpoints'
+            if dirname == '.ipynb_checkpoints':
+                # Construct the full path to the directory
+                dir_to_delete = os.path.join(dirpath, dirname)
+                # Delete the directory
+                shutil.rmtree(dir_to_delete)
+                print(f'Deleted {dir_to_delete}')
+                print('Consider adding .ipynb_checkpoints to your .gitignore file!')
+
+
+if __name__ == "__main__":
+    # Change this to the directory containing your notebooks
+    notebook_dir = '../../'
+
+    for root, dirs, files in os.walk(notebook_dir):
+        for file in files:
+            if file.endswith('.ipynb'):
+                file_path = os.path.join(root, file)
+                clean_notebook(file_path)
+                print(f'Cleaned {file_path}')
+
+    # Delete all 'checkpoints' directories
+    delete_checkpoints_dirs(notebook_dir)
+

.github/workflows/notebook-lint.yaml

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+name: 'Lint Notebook'
+on:
+  push:
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  lint:
+    name: 'Linting'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+
+      - name: Install requirements.txt
+        run: |
+          python3 -m pip install --upgrade pip
+          pip3 install nbformat
+
+      - name: Notebook Linting
+        working-directory: .github/workflows
+        run: |
+          python3 lint.py
+
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          author_name: github-action
+          author_email: [email protected]
+          message: 'Github Action: Refresh stats'

.github/workflows/requirements.txt

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+nbformat==5.10.4

.gitignore

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+# Jupyter Notebook cache
+**.ipynb_checkpoints/
+
+# 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/
+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
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# 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
+
+# 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/

LICENSE

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+MIT License
+
+Copyright (c) 2024 National Institute of General Medical Sciences
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# [Module-Name]
+---------------------------------
+
+## **Contents**
+
++ [Overview](#overview)
++ [Background](#background)
++ [Before Starting](#before-starting)
++ [Getting Started](#getting-started)
++ [Software Requirements](#software-requirements)
++ [Architecture Design](#architecture-design)
++ [Data](#data)
++ [Funding](#funding)
++ [License for Data](#license-for-data)
+
+## **Overview**
+
+
+## **Background**
+
+
+## **Before Starting**
+
+
+## **Getting Started**
+
+
+## **Software Requirements**
+
+
+## **Architecture Design**
+
+
+## **Data**
+
+
+## **Funding**
+
+
+## **License for Data**
+