feat(repo): initiate repository

Establish workflow, after anonymising from previous work.

.github/workflows/cicd.yaml

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+name: CI/CD
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - main
+
+  workflow_dispatch:
+
+jobs:
+  py_check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Cache Nox
+        uses: actions/cache@v2
+        env:
+          CACHE_NUMBER: 1
+        with:
+          path: .nox
+          key:
+            ${{ runner.os }}-nox-${{ env.CACHE_NUMBER }}-${{ hashFiles('noxfile.py') }}
+      - name: Setup Nox
+        uses: excitedleigh/setup-nox@v2.0.0
+      - name: black_isort_flake8_mypy
+        run: nox -s form lint type
+      - name: safety
+        run: nox -s security
+
+  snake_check:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Cache Conda
+        uses: actions/cache@v2
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('workflow/envs/cicd_min.yaml') }}
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: cicd_min
+          channel-priority: strict
+          environment-file: workflow/envs/cicd_min.yaml
+          use-only-tar-bz2: true
+          miniforge-variant: Mambaforge
+          miniforge-version: 4.10.3-6
+          use-mamba: true
+      - name: Snakefmt_lint
+        run: |
+          snakemake --lint
+          snakefmt workflow
+          # - name: Snakemake unit tests
+          # run: pytest .tests/unit
+          # - name: Snakemake integration tests
+          # run: pytest .tests/integration
+
+  R_check:
+    # There is a cacheable install, but it requires a proper R package
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: "4.1.1"
+          use-public-rspm: true
+      - name: Install Dependencies
+        run: install.packages(c("lintr", "styler"))
+        shell: Rscript {0}
+      - name: lintr
+        run: lintr::lint_dir()
+        shell: Rscript {0}
+      - name: styler
+        run: styler::style_dir()
+        shell: Rscript {0}
+
+  release:
+    runs-on: ubuntu-latest
+    if: ${{ github.ref == 'refs/heads/main' }}
+    needs: [py_check, snake_check, R_check]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Python Semantic Release
+        uses: relekang/python-semantic-release@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# Local things
+/results
+/data
+/resources
+/jobs
+/.snakemake
+/.conda
+/.cache
+/.config
+/.nv
+/.DS_store
+report.html

.pre-commit-config.yaml

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+default_stages: [commit]
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.0.1
+  hooks:
+  - id: check-yaml
+  - id: check-toml
+  - id: fix-encoding-pragma
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: check-added-large-files
+    args: ['--maxkb=5000']
+- repo: https://github.com/PyCQA/isort
+  rev: 5.9.3
+  hooks:
+  - id: isort
+- repo: https://github.com/psf/black
+  rev: 21.9b0
+  hooks:
+  - id: black
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.910-1
+  hooks:
+  - id: mypy
+    args: ['--ignore-missing-imports', '--disable-error-code', 'name-defined', '--disable-error-code', 'attr-defined']
+- repo: https://github.com/PyCQA/flake8
+  rev: 4.0.1
+  hooks:
+  - id: flake8
+    entry: pflake8
+    additional_dependencies:
+    - flake8-annotations
+    - flake8-bandit
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-docstrings
+    - flake8-pytest-style
+    - flake8-spellcheck
+    - darglint
+    - pyproject-flake8
+- repo: https://github.com/snakemake/snakefmt
+  rev: 0.4.4
+  hooks:
+    - id: snakefmt
+- repo: local
+  hooks:
+    - id: snakelint
+      name: snakelint
+      language: system
+      files: 'workflow/Snakefile'
+      pass_filenames: false
+      entry: snakemake --lint
+- repo: https://github.com/lorenzwalthert/precommit
+  rev: v0.1.3.9133
+  hooks:
+    - id: style-files
+    - id: parsable-R
+    - id: lintr
+      verbose: true

.snakemake-workflow-catalog.yml

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+usage:
+  mandatory-flags:
+    desc: In order to take advantage of GPU acceleration, Singularity must be made aware of Nvidia
+    flags: "--singularity-args='--nv'"
+  software-stack-deployment:
+    conda: true
+    singularity: true
+    singularity+conda: true
+  report: true