Documentation PR

.github/workflows/document_tutorials.yml

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+name: autogenerate docs from tutorials
+# Not finished! Only will run on a specific branch for now so can be left
+on:
+  # Triggers the workflow on push but only for the main branch
+  push:
+    branches: [ workflow_trials ]
+    paths: ['**.ipynb']
+
+jobs:
+  docs-from-tutorials:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      #  Check out repo and set up Python
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      #
+      - name: run python script after setting up
+        run: |
+          poetry run pip install nbconvert
+          poetry install
+          mkdir tutorial
+          poetry run python renaming.py
+
+      - name: remove notebooks from docs
+        run: rm *.ipynb
+
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          default_author: github_actions
+          message: 'Updating tutorial rsts for docs'
+          add: 'sed/docs/tutorial/'

.github/workflows/linting.yml

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+# This workflow will install Python dependencies, lint and run tests with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# TODO: switch to the cached version
+name: linting
+
+on: [push]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        linter: [pylint, mypy, flake8]
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          lfs: true
+      - uses: advanced-security/python-lint-code-scanning-action@v1
+        with:
+          linter: ${{ matrix.linter }}

.github/workflows/testing.yml

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+name: testing
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pytest:
+    # Using matrix strategy
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    runs-on: ubuntu-latest
+    steps:
+      #-------------------------------------#
+      #  Check out repo and set up Python   #
+      #-------------------------------------#
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: ${{matrix.python-version}}
+          poetry-version: 1.2.2
+
+      #------------------------#
+      #  Run pytest
+      #------------------------#
+      - name: Run tests on python ${{matrix.python-version}}
+        run: |
+          poetry run pytest --cov=sed -n auto tests/
+      - name: Coveralls Parallel
+        uses: coverallsapp/github-action@v2
+        with:
+          flag-name: run-${{ join(matrix.*, '-') }}
+          parallel: true
+
+  finish:
+    needs: pytest
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+    # Coveralls missing
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        parallel-finished: true
+        carryforward: "run-3.8,run-3.9,run-3.10"

.github/workflows/update_requirements.yml

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+name: update requirements.txt
+
+on:
+  # Triggers the workflow on push but only for the main branch
+  push:
+    branches: [ main ]
+    paths: [pyproject.toml]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      #  Check out repo and set up Python
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      #  Generates and commits a requirements.txt used by readthedocs
+      - name: Export requirements.txt
+        run: poetry export --without-hashes --format=requirements.txt -o docs/requirements.txt -E docs -E notebook
+
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          default_author: github_actions
+          message: 'Updating requirements for docs'
+          add: 'docs/requirements.txt'