First commit

.github/codecov.yml

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+codecov:
+  notify:
+    require_ci_to_pass: yes
+
+coverage:
+  precision: 2
+  round: down
+  range: 70..100
+
+  status:
+    project:
+      default:
+        target: 90%
+        threshold: 1%
+    patch: no
+    changes: no
+
+comment: off

.github/dependabot.yml

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+---
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ devel ]
+  pull_request:
+    branches: [ devel ]
+
+jobs:
+
+  Test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        include:
+          - os: ubuntu-latest
+            python-version: "3.12"
+          # - os: windows-latest
+          #   python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.12"
+
+    runs-on: ${{ matrix.os }}
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run tests on ${{ matrix.os }}
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+          # stop the build if there are Python syntax errors or undefined names
+          ruff check . --select=E9,F63,F7,F82
+          pytest

.github/workflows/documentation.yml

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+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+            python-version: 3.12
+
+      - name: Install dependencies
+        run: |
+            python -m pip install --upgrade pip
+            pip install -e .[dev,docs]
+            # stop the build if there are Python syntax errors or undefined names
+            ruff check . --select=E9,F63,F7,F82
+            pytest      
+
+      - name: Sphinx build
+        run: |
+            sphinx-build docs/source/ docs/build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/
+          force_orphan: true

.github/workflows/publish.yml

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+name: Publish Python Package to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  Publish:
+    # prevents this action from running on forks
+    if: github.repository == 'js2264/momics'
+
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build
+        run: python -m build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

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+*.swp
+*.swo
+*~
+
+*.py[cod]
+__pycache__
+
+# test and coverage artifacts
+.cache
+.pytest_cache
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+
+# setup and build artifacts
+docs/_*
+*.egg-info/
+dist/
+build/
+MANIFEST
+
+# dev and virtual environment
+.venv/
+venv/
+.idea/
+
+# OS-generated files
+.DS_Store
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+tmp/
+_scratch/

.readthedocs.yml

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+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev
+        - docs

CHANGES.md

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+# Release notes #
+
+## [v0.1.0](https://github.com/js2264/momics/releases/tag/v0.1)
+
+Date: 2024-07-29
+
+* Working initial prototype
+

CITATION.cff

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+cff-version: 1.2.0
+type: software
+title: momics
+message: >-
+  Please cite this software using the metadata from "preferred-citation".
+abstract: >-
+  momics is a cloud-native, TileDB-based format for multi-omics data. 
+  Follow momics development on GitHub.
+license: "BSD-3-Clause"
+# doi: "10.5281/zenodo.597976"
+url: "https://js2264.github.io/momics"
+repository-code: "https://github.com/js2264/momics"
+keywords:
+  - multi-omics
+  - genomics
+  - epigenomics
+  - Tile-DB
+  - bioinformatics
+  - matrix
+  - sparse
+  - format
+authors:
+  - given-names: Jacques
+    family-names: Serizay
+    orcid: "https://orcid.org/0000-0002-4295-0624"
+preferred-citation:
+  type: software
+  title: "momics: a cloud-native, TileDB-based format for multi-omics data"
+  authors:
+  - given-names: Jacques
+    family-names: Serizay
+    orcid: "https://orcid.org/0000-0002-4295-0624"