first commit

.ci/self_hosted_conda_creation.sh

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+#!/bin/sh
+
+# Check that the env folder exists or create it
+if [ -d ~/envs ]
+then
+    echo "Found existing envs folder"
+else
+    echo "Did not find envs folder, creating"
+    mkdir ~/envs
+fi
+
+# Check if conda environment exists. if it does, remove it.
+if [ -d "~/envs/fedomics_python_$1" ]
+then
+    echo "Found existing fedomics conda environment, removing"
+    conda env remove --prefix "~/envs/fedomics_python_$1" -y
+fi
+conda init bash
+. ~/.bashrc
+#
+echo "Creating environment"
+yes | conda create --prefix "~/envs/fedomics_python_$1" python="$1"
+echo "Created env fedomics_python_$1"
+eval "$(conda shell.bash hook)"
+conda activate "~/envs/fedomics_python_$1"

.ci/self_hosted_conda_removal.sh

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+#!/bin/sh
+
+# Check if conda environment exists. if it does, remove it.
+if [ -d "~/envs/fedomics_python_$1" ]
+then
+    echo "Found existing fedomics conda environment, removing"
+    conda env remove --prefix "~/envs/fedomics_python_$1" -y
+fi

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG] "
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Provide snippets of code and steps on how to reproduce the behavior.
+Please also specify the version you are using.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 0.02]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+<!--
+Thanks for contributing a pull request! Please ensure you have taken a look at
+the contribution guidelines: https://pydeseq2.readthedocs.io/en/latest/usage/contributing.html
+Make sure that you have added unit tests if applicable.
+-->
+
+#### Reference Issue or PRs
+<!--
+If this PR is related to an existing issue or PR please reference it, eg:
+Fixes #1234.
+You can use github keywords as described:
+https://github.com/blog/1506-closing-issues-via-pull-requests
+-->
+
+
+#### What does your PR implement? Be specific.

.github/workflows/pr_push_validation.yml

@@ -0,0 +1,66 @@
+name: Python dev
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.10", "3.11", "3.12"]
+    name: Testing Python ${{ matrix.python }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install Poetry
+        run: |
+          python --version
+          pip install poetry==1.8.2
+
+      - name: Install dependencies
+        run: |
+          python --version
+          poetry install --with testing
+
+      - name: Download data
+        run: |
+          mkdir -p /opt/conda
+          wget https://repo.anaconda.com/miniconda/Miniconda3-py39_24.5.0-0-Linux-x86_64.sh -O /opt/conda/miniconda.sh
+          bash /opt/conda/miniconda.sh -b -p /opt/miniconda
+          poetry run fedpydeseq2-download-data --only_luad --raw_data_output_path /home/runner/work/fedpydeseq2-datasets/fedpydeseq2-datasets/data/raw --conda_activate_path /opt/miniconda/bin/activate
+
+      - name: Testing
+        run: |
+          poetry run pytest -v tests
+
+  linting:
+    runs-on: ubuntu-latest
+    name: Test Linting
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install Poetry
+        run: pip install poetry==1.8.2
+
+      - name: Install dependencies
+        run: |
+          which python
+          python --version
+          poetry install --with linting
+
+      - name: Pre-commit checks
+        run: |
+          poetry run pre-commit run --all-files --show-diff-on-failure

.gitignore

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+# 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/#use-with-ide
+.pdm.toml
+
+# 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/
+
+# VSCode
+.vscode/
+
+# DS_Store
+.DS_Store
+
+# Data
+data/centers_data/*
+data/pooled_data/*
+data/processed/*
+data/raw/tcga/*
+
+
+fedpydeseq2_datasets/download_data/.snakemake/*
+fedpydeseq2_datasets/download_data/workflow/.snakemake
+fedpydeseq2_datasets/download_data/logs/
+fedpydeseq2_datasets/download_data/results/
+
+!data/raw/tcga/centers.csv
+
+*logs/
+
+data/*

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+default_language_version:
+    python: python3.11
+repos:
+  - repo: https://github.com/sirosen/check-jsonschema
+    rev: 0.27.0
+    hooks:
+      - id: check-github-actions
+      - id: check-github-workflows
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+        name: Trim trailing whitespace
+      - id: end-of-file-fixer
+        name: Fix end of files
+        exclude: \.ipynb$
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+        additional_dependencies: ["click==8.0.4"]
+        args: # arguments to configure black
+          - --line-length=88
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.5
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.0
+    hooks:
+      - id: mypy
+        exclude: ^(tests/|docs/source/conf.py|datasets/)