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.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Code with explanation
+2. How to run code
+3. The error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment (please complete the following information):**
+ - OS: [e.g. Linux]
+ -  Package versions implicated in the error (torch, mdlearn versions, etc)
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: 'enhancement'
+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.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/other.md

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+---
+name: Other issue template
+about: Any issue that does not fit the other templates
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Description**

.github/ISSUE_TEMPLATE/question-issue-template.md

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+---
+name: Question issue template
+about: Ask a question about how to use mdlearn
+title: ''
+labels: question
+assignees: ''
+
+---
+
+**Describe the question**

.github/dependabot.yml

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+# Set update schedule for GitHub Actions
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/code.yml

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+name: Unit Tests & Code Coverage
+
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch: # allow manual triggering
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  lint:
+    name: Code style
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Upgrade pip & test with pre-commit
+        run: |
+          set -vxeuo pipefail
+          python -m pip install --upgrade pip
+          python -m pip install pre-commit
+          pre-commit run --all-files
+
+  test-matrix:
+    name: Python ${{ matrix.python-version }} # - Redis ${{ matrix.redis-version }}
+    runs-on: ubuntu-latest
+    needs: lint
+    strategy:
+      matrix:
+        python-version:
+          - "3.11"
+          - "3.12"
+          # - "3.13"  waiting for upstream packages
+        # redis-version:
+        #   # - "6"
+        #   - "7"
+      max-parallel: 5
+    env:
+      DISPLAY: ":99.0"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install OS libraries to test Linux PyQt apps
+        run: |
+          sudo apt update -y
+          sudo apt install -y \
+            libxcb-icccm4 \
+            libxcb-image0 \
+            libxcb-keysyms1 \
+            libxcb-randr0 \
+            libxcb-render-util0 \
+            libxcb-xinerama0 \
+            libxcb-xfixes0 \
+            libxkbcommon-x11-0 \
+            screen \
+            x11-utils \
+            xvfb
+
+      # FIXME: conflicts if redis is running on host (local runners)
+      # - name: Start Redis
+      #   uses: supercharge/redis-github-action@1.7.0
+      #   with:
+      #     redis-version: ${{ matrix.redis-version }}
+      #     redis-remove-container: true # false by default
+
+      - name: Create environment Python ${{ matrix.python-version }} # - Redis ${{ matrix.redis-version }}
+        # needed for Unpack step
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-environment: true
+          cache-environment-key: env-key-${{ matrix.python-version }}
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+            channel-priority: flexible
+          # environment-file: environment.yml
+          environment-name: anaconda-test-env-py-${{ matrix.python-version }} # -${{ matrix.redis-version }}
+          create-args: >-
+            coveralls
+            pytest
+            pytest-cov
+            pytest-qt
+            pytest-xvfb
+            python=${{ matrix.python-version }}
+            setuptools-scm
+            pyqt>5.15
+            pyepics
+
+      - name: Install this package with pip
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          pip install -e .
+
+      - name: Run tests with pytest & coverage
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          coverage run --concurrency=thread --parallel-mode -m pytest -vvv --exitfirst .
+          coverage combine
+          coverage report --precision 3
+
+      - name: Upload coverage data to coveralls.io
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          micromamba list coveralls
+          which coveralls
+          coveralls debug
+          if [ "${GITHUB_TOKEN}" != "" ]; then
+            # only upload from GitHub runner
+            coveralls --service=github
+          else
+            echo "No credentials for upload to coveralls."
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_FLAG_NAME: ${{ matrix.python-version }} # -${{ matrix.redis-version }}
+          COVERALLS_PARALLEL: true
+
+  # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
+  coveralls:
+    name: Report unit test coverage to coveralls
+    needs: test-matrix
+    runs-on: ubuntu-latest
+    container: python:3-slim
+
+    steps:
+      - name: Gather coverage and report to Coveralls
+        run: |
+          set -vxeuo pipefail
+          echo "Finally!"
+          pip3 install --upgrade coveralls
+          # debug mode: output prepared json and reported files list to stdout
+          # https://coveralls-python.readthedocs.io/en/latest/troubleshooting.html
+          coveralls debug
+          if [ "${GITHUB_TOKEN}" != "" ]; then
+            # only upload from GitHub runner
+            coveralls --service=github --finish
+          else
+            echo "No credentials for upload to coveralls."
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docs.yml

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+name: Publish Sphinx docs to GitHub Pages
+# see: https://github.com/marketplace/actions/sphinx-to-github-pages
+
+on:
+  # Build the docs on pushes to main branch, PRs to main branch, and new tags.
+  # Publish only on demand.
+  push:
+    branches:
+      - main
+    tags:
+      - '*'  # all tags
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:   # allow manual triggering
+    inputs:
+      deploy:
+        description: 'Deploy documentation'
+        type: boolean
+        required: true
+        default: false
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+
+  pages:
+    name: Publish documentation
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Deploy Information
+      if: ${{ github.event.inputs.deploy }}
+      run: |
+        echo "The docs will be published from this workflow run."
+
+    - name: Install pandoc
+      run: |
+        set -vxeuo pipefail
+        sudo apt-get update
+        sudo apt-get -y install pandoc
+
+    - name: Set time zone
+      run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
+
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # required for push to dest repo
+
+    - uses: actions/setup-python@v5
+      with:
+          python-version: "3.11"
+
+    - name: Install our package
+      run: pip install -e .[doc]
+
+    - name: Sphinx
+      id: deployment
+      run: make -C docs html
+
+    - name: Publish (push gh-pages branch) only on demand
+      uses: peaceiris/actions-gh-pages@v4
+      if: ${{ github.event.inputs.deploy }}
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html
+        force_orphan: true