Merge branch 'main' into hextof_workflow_steps

.github/workflows/linting.yml

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+name: linting
+
+# Triggers the workflow on push for all branches
+on: [push]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      # Check out repo and set up Python
+      - uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      # Use cached python and dependencies, install poetry
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      # Linting steps, excute all linters even if one fails
+      - name: pycodestyle
+        run:
+          poetry run pycodestyle --ignore=E203,E501,W503 sed tests
+      - name: pylint
+        if: ${{ always() }}
+        run:
+          poetry run pylint --good-names=i,j,k,ex,x,y,t,k,v,ax,df,ec,mc,dc,ct --disable=fixme,too-many-branches,too-many-locals,too-many-statements,too-many-arguments,too-many-lines,too-many-public-methods,too-many-instance-attributes,too-few-public-methods sed tests
+      - name: mypy
+        if: ${{ always() }}
+        run:
+          poetry run mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional sed tests

.github/workflows/testing_coverage.yml

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+name: pytest and coverage report
+
+# Triggers the workflow on push and PR for all branches
+on: [push, pull_request]
+
+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
+
+      # Use cached python and dependencies, install poetry
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      # Run pytest with coverage report, saving to xml
+      - name: Run tests on python 3.8
+        run: |
+          poetry run pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/
+      
+      # Take report and upload to coveralls
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          file: ./cobertura.xml

.github/workflows/testing_multiversion.yml

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+name: pytest multiversion
+
+on:
+  push:
+    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
+
+      # Use cached python and dependencies, install poetry
+      - name: Run tests on python ${{matrix.python-version}}
+        run: |
+          poetry run pytest--full-trace --show-capture=no -sv -n auto tests/

.github/workflows/update_dependencies.yml

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+name: Update depencies in poetry lockfile
+
+on:
+  schedule:
+    - cron:  '0 1 * * 1'
+  workflow_dispatch:
+  push:
+    paths:
+      - pyproject.toml
+
+jobs:
+  update_dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      # Check out repo and set up Python
+      - uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - uses: tibdex/github-app-token@v1
+        id: generate-token
+        with:
+          app_id: ${{ secrets.APP_ID }}
+          private_key: ${{ secrets.APP_PRIVATE_KEY }}
+
+      # Use cached python and dependencies, install poetry
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      # update poetry lockfile
+      - name: "Update poetry lock file"
+        id: update
+        run: |
+          poetry self update
+          exec 5>&1
+          UPDATE_OUTPUT=$(poetry update|tee >(cat - >&5))
+          echo "UPDATE_OUTPUT<<EOF" >> $GITHUB_OUTPUT
+          echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      - name: Export requirements.txt
+        run: |
+          poetry export --without-hashes --format=requirements.txt -o docs/requirements.txt -E docs -E notebook
+
+      - name: Obtain git status
+        id: status
+        run: |
+          exec 5>&1
+          STATUS=$(git status|tee >(cat - >&5))
+          echo "STATUS<<EOF" >> $GITHUB_OUTPUT
+          echo "$STATUS" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      # create pull request if necessary
+      - name: "Create Pull Request"
+        uses: peter-evans/create-pull-request@v5
+        if: ${{ contains(steps.status.outputs.STATUS, 'poetry.lock') || contains(steps.status.outputs.STATUS, 'requirements.txt')}}
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          commit-message: Update dependencies
+          title: "Update dependencies"
+          body: |
+            Dependency updates using Poetry:
+            ${{ steps.update.outputs.UPDATE_OUTPUT }}