release v0.3.0

.bandit.yml

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+### profile may optionally select or skip tests
+
+# (optional) list included tests here:
+tests: []
+
+# (optional) list skipped tests here:
+skips: ['B101', 'B403', 'B404', 'B603', 'B607', 'B301', 'B303', 'B311', 'B310', 'B506']

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a bug report to help us improve
+title: 'Bug Summary'
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. ...
+2. ...
+3. ...
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**System [please complete the following information]:**
+ - OS: e.g. [Ubuntu 20.04]
+ - Language Version: [e.g. Python 3.9]
+ - Virtual environment: [e.g. Conda]
+
+**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 a new feature
+title: 'Feature Request Summary'
+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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/general_question.md

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+---
+name: General question
+about: Ask a question about anything related to this project
+title: 'Question'
+labels: ''
+assignees: ''
+
+---
+
+**Question**
+
+Please ask your question here. It can be about the usage of this project, the internals, the implementation or whatever interests you.
+Please use the BUG template for bugs, and the FEATURE REQUEST template for feature requests.

.github/dependabot.yml

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+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "04:00"
+  open-pull-requests-limit: 99
+  target-branch: development
+  labels:
+  - dependabot
+  commit-message:
+    prefix: "[DEPENDABOT]"
+
+- package-ecosystem: github-actions
+  directory: "/"
+  schedule:
+    interval: daily
+    time: "04:00"
+  open-pull-requests-limit: 99
+  target-branch: development
+  labels:
+  - dependabot
+  commit-message:
+    prefix: "[DEPENDABOT]"

.github/pull_request_template.md

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+Many thanks for contributing to sfaira!
+
+**PR Checklist**
+Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+
+ - [ ] This comment contains a description of changes (with reason)
+ - [ ] Referenced issue is linked
+ - [ ] If you've fixed a bug or added code that should be tested, add tests!
+ - [ ] Documentation in `docs` is updated
+ - [ ] `docs/release-notes.rst` is updated
+
+**Description of changes**
+Please state what you've changed and how it might affect the user.
+
+**Technical details**
+Please state any technical details such as limitations, reasons for additional dependencies, benchmarks etc. here.
+
+**Additional context**
+Add any other context or screenshots here.

.github/workflows/build_package.yml

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+name: Build sfaira Package
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python: [3.7, 3.8]
+    env:
+      PYTHONIOENCODING: utf-8
+
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2.1.4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Upgrade and install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Build sfaira
+        run: pip install .
+
+      - name: Import sfaira
+        run: python -c "import sfaira"
+
+      # Verify that the package does adhere to PyPI's standards
+      - name: Install required twine packaging dependencies
+        run: pip install setuptools wheel twine
+
+      - name: Build twine package
+        run: python setup.py sdist bdist_wheel
+
+      - name: Check twine package
+        run: twine check dist/*

.github/workflows/create_templates.yml

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+name: Create sfaira data-loader templates
+
+on: [push, pull_request]
+
+jobs:
+  create-templates:
+    runs-on: ${{ matrix.os }}
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python: [3.7, 3.8]
+    env:
+      PYTHONIOENCODING: utf-8
+
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2.1.4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Upgrade and install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Build sfaira
+        run: pip install .
+
+      - name: Create single_dataset template
+        run: |
+          cd ..
+          echo -e "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" | sfaira create-dataloader
+          rm -rf d10_1000_j_journal_2021_01_001/

.github/workflows/pr_to_master_from_patch_release_only.yml

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+name: PR to master branch from patch/release branch only
+
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      # PRs to the repository master branch are only ok if coming from any patch or release branch
+      - name: Check PRs
+        run: |
+          { [[ $GITHUB_HEAD_REF = *"release"* ]]; } || [[ $GITHUB_HEAD_REF == *"patch"* ]]
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            The `master` branch should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from any ${{github.event.pull_request.head.repo.full_name}} `release` or `patch` branch.
+
+            You do not need to close this PR, you can change the target branch to `development` by clicking the _"Edit"_ button at the top of this page.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false

.github/workflows/publish_docs.yml

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+name: Build Documentation
+
+on:
+  push:
+    paths:
+      - "docs/**"
+  pull_request:
+    paths:
+      - "docs/**"
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2.1.4
+        with:
+          python-version: 3.8
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install doc dependencies
+        run: pip install -r docs/requirements.txt
+
+      - name: Build docs
+        run: |
+            cd docs
+            make html
+
+      - name: Deploy
+        if: ${{ github.ref == 'refs/heads/master' && github.event_name == 'push' }}
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html

.github/workflows/publish_package.yml

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+name: Publish sfaira to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+    steps:
+    - uses: actions/checkout@v2
+      name: Check out source-code repository
+
+    - name: Set up Python
+      uses: actions/setup-python@v2.1.4
+      with:
+        python-version: '3.9'
+
+    - name: Install pip, setuptools, wheel, twine
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/run_bandit.yml

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+name: Run bandit
+
+on:
+  push:
+    paths:
+      - "**/*.py"
+  pull_request:
+    paths:
+      - "**/*.py"
+
+jobs:
+  run-bandit:
+
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2.1.4
+        with:
+          python-version: 3.9
+
+      - name: Install bandit
+        run: pip install bandit
+
+      - name: Run bandit
+        run: bandit -r sfaira -c .bandit.yml

.github/workflows/run_flake8_linting.yml

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+name: Run flake8 linting
+
+on:
+  push:
+    paths:
+      - "**/*.py"
+  pull_request:
+    paths:
+      - "**/*.py"
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2.1.4
+        with:
+          python-version: 3.9
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Lint with flake8
+        run: |
+            pip install flake8
+            flake8 .