autora-gui 1.1.2__tar.gz

autora_gui-1.1.2/.coveragerc

@@ -0,0 +1,9 @@
+[run]
+omit =
+    **/_*.py
+    setup.py
+    */tests/*
+    _version.py
+[report]
+exclude_lines =
+    @abstractmethod

autora_gui-1.1.2/.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      all-minor-and-patch-dependency-updates:
+        applies-to: version-updates
+        patterns:
+          - "*"
+        update-types:
+          - "minor"
+          - "patch"

autora_gui-1.1.2/.github/workflows/ci.yml

@@ -0,0 +1,172 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  lint:
+    name: lint with ruff with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          pip3 install -r requirements/dev.txt
+        shell: bash
+      - name: Lint
+        run: tox -e check-style
+        shell: bash
+
+  test:
+    name: pytests on Python ${{ matrix.python-version }} and ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.11]
+        os: [ubuntu-latest, macos-latest]
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python-version }}
+    steps:
+    - uses: actions/checkout@v4
+      with:
+          lfs: true
+    - uses: actions/setup-python@v4
+      with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+    - name: Install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip3 install -r requirements/dev.txt
+      shell: bash
+    - name: pip install package
+      run: pip install .
+    - name: Test with tox (pytest)
+      run: tox -e test
+    - name: Archive coverage report
+      uses: actions/upload-artifact@v4.4.3
+      with:
+        name: code-coverage-report-python${{ matrix.python-version }}-${{ matrix.os }}
+        path: coverage.xml
+        retention-days: 14
+        if-no-files-found: error
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        env_vars: OS,PYTHON
+        fail_ci_if_error: false
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        verbose: true
+
+  test-js:
+    name: JS/React tests on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      OS: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+          cache: 'npm'
+          cache-dependency-path: autora_gui/react_app/package-lock.json
+      - name: Install dependencies
+        run: npm ci
+        working-directory: autora_gui/react_app
+      - name: Run Vitest with coverage
+        run: npm run test:coverage
+        working-directory: autora_gui/react_app
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: autora_gui/react_app/coverage/lcov.info
+          flags: javascript
+          env_vars: OS
+          fail_ci_if_error: false
+
+  docs:
+    name: Build docs with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    strategy:
+      matrix:
+        python-version: [ 3.11 ]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install tox
+        run: python -m pip install tox
+        shell: bash
+      - name: Build sphinx docs.
+        # Comment the env: SPHINXOPTS if you want to ignore warnings during doc build
+        env:
+          SPHINXOPTS: '-W'
+        run: tox -e build-docs
+        shell: bash
+
+  build:
+    name: Build and Publish.
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

autora_gui-1.1.2/.github/workflows/deploy-pages.yml

@@ -0,0 +1,151 @@
+name: Standalone Version and Documentation
+
+on:
+  push:
+    branches:
+      - main
+      - create_json
+  workflow_dispatch:  # Allow manual trigger
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Create deployment directory
+        run: mkdir -p deploy
+
+      # Build React version from main branch
+      - name: Checkout React branch
+        uses: actions/checkout@v4
+        with:
+          ref: main
+          path: main-branch
+
+      - name: Build main standalone version
+        run: |
+          cd main-branch/autora_gui/react_app
+          npm install
+          python build_standalone.py
+          mkdir -p ../../../deploy/main
+          cp ../../index.html ../../../deploy/main/index.html
+        continue-on-error: true
+
+      # Build component JSON generation version from create_json branch
+      - name: Checkout create_json branch
+        uses: actions/checkout@v4
+        with:
+          ref: create_json
+          path: create_json-branch
+
+      - name: Build component JSON generation standalone version
+        run: |
+          cd create_json-branch/autora_gui/react_app
+          npm install
+          python build_standalone.py
+          mkdir -p ../../../deploy/create_json
+          cp ../../index.html ../../../deploy/create_json/index.html
+        continue-on-error: true
+
+      # Build Sphinx docs from main branch
+      - name: Checkout main branch for docs
+        uses: actions/checkout@v4
+        with:
+          ref: main
+          path: main-branch
+
+      - name: Build Sphinx docs
+        run: |
+          cd main-branch
+          pip install tox
+          tox -e build-docs
+          mkdir -p ../deploy/docs
+          cp -r docs/_build/html/* ../deploy/docs/
+        continue-on-error: true
+
+      # Build front-end (JavaScript) API docs from the JSDoc comments and nest
+      # them under the Sphinx docs at /docs/frontend/.
+      - name: Build frontend JS docs
+        run: |
+          cd main-branch/autora_gui/react_app
+          npm install
+          npm run docs:api
+          mkdir -p ../../../deploy/docs/frontend
+          cp -r frontend-docs/* ../../../deploy/docs/frontend/
+        continue-on-error: true
+
+      # Create landing page as main index
+      - name: Create landing page
+        run: |
+          cat > deploy/index.html << 'EOF'
+          <!DOCTYPE html>
+          <html lang="en">
+          <head>
+          <meta charset="UTF-8">
+          <meta name="viewport" content="width=device-width, initial-scale=1.0">
+          <title>AutoRA Workflow Editor and Documentation</title>
+          <style>
+          body{font-family:-apple-system,BlinkMacSystemFont,'Segoe UI',Roboto,sans-serif;background:#1a1a2e;color:#e8e8e8;display:flex;justify-content:center;align-items:center;min-height:100vh;margin:0}
+          .container{text-align:center;padding:40px}
+          h1{color:#4a90d9;margin-bottom:40px}
+          .versions{display:flex;gap:30px;justify-content:center;flex-wrap:wrap}
+          .version-card{background:#16213e;border:2px solid #2a2a4a;border-radius:12px;padding:30px 40px;text-decoration:none;color:#e8e8e8;transition:all 0.3s}
+          .version-card:hover{border-color:#4a90d9;transform:translateY(-5px)}
+          .version-card h2{margin:0 0 10px 0;color:#4a90d9}
+          .version-card p{margin:0;color:#808080;font-size:14px}
+          </style>
+          </head>
+          <body>
+          <div class="container">
+          <h1>AutoRA Workflow Editor and Documentation</h1>
+          <div class="versions">
+          <a href="./main/" class="version-card"><h2>Workflow Editor</h2><p>React-based GUI</p></a>
+          <a href="./create_json/" class="version-card"><h2>Workflow Editor with JSON Generation</h2><p>React-based GUI with component JSON generation</p></a>
+          <a href="./docs/" class="version-card"><h2>Documentation</h2><p>API reference and guides</p></a>
+          </div>
+          </div>
+          </body>
+          </html>
+          EOF
+
+      - name: List deployment contents
+        run: |
+          echo "Deployment directory contents:"
+          find deploy -type f
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: deploy
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Standalone Version and Documentation
+        id: deployment
+        uses: actions/deploy-pages@v4

autora_gui-1.1.2/.github/workflows/dist.yml

@@ -0,0 +1,79 @@
+name: DIST
+on:
+  release:
+    types: [ released, prereleased ]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.14"
+    - name: Install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip3 install -r requirements/dev.txt
+      shell: bash
+    - name: Build a binary wheel and a source tarball
+      run: tox -e build-dist
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4.4.3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  # To publish packages to PyPI, first obtain an account and then create a
+  # (pending) publisher using the form at
+  # https://pypi.org/manage/account/publishing/. Fill in the fields as follows:
+  #
+  # * PyPI Project Name: name of pypi package
+  # * Owner: org, e.g. ssec-jhu
+  # * Repository name: name of repo not-including org, e.g. autoRA-gui
+  # * Workflow name: dist.yml
+  # * Environment name: testpypi (for TestPyPI) or pypi (for PyPI)
+  #
+  # This should be done separately for both testpypi and pypi (these need
+  # separate accounts).
+  #
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4.1.7
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+    - build
+    - publish-to-testpypi
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+    - name: Download dists from 
+      uses: actions/download-artifact@v4.1.7
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

autora_gui-1.1.2/.github/workflows/security.yml

@@ -0,0 +1,33 @@
+name: Security
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  security:
+    name: Check security concerns with bandit on Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ 3.11 ]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          pip3 install bandit>=1.7 tox
+        shell: bash
+      - name: Run bandit (via tox)
+        run: tox -e check-security
+        shell: bash

autora_gui-1.1.2/.gitignore

@@ -0,0 +1,185 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/generated
+docs/source/_autosummary/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# VS Code
+.vscode
+
+# File system
+.DS_Store
+
+# Claude files
+.claude
+SKILL.md
+CLAUDE.md
+
+# JS tests
+node_modules
+
+# React files
+.vite
+dist
+coverage
+
+# Generated JSDoc API docs
+frontend-docs

autora_gui-1.1.2/.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+python:
+  install:
+    - requirements: requirements/docs.txt
+    - method: pip
+      path: .
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - htmlzip
+  - pdf
+  - epub
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"

autora_gui-1.1.2/.zenodo.json

@@ -0,0 +1,23 @@
+{
+    "creators": [
+        {
+            "affiliation": "Scientific Software Engineering Center at JHU",
+            "name": "Fatemeh Abbasinejad",
+            "orcid": "0009-0006-3239-7112"
+        },
+        {
+            "affiliation": "Scientific Software Engineering Center at JHU",
+            "name": "Vladimir Kluzner",
+            "orcid": "0009-0000-5844-661X"
+        },
+        {
+            "affiliation": "Scientific Software Engineering Center at JHU",
+            "name": "Gerard Lemson",
+            "orcid": "0000-0001-5041-2458"
+        }
+    ],
+    "description": "GUI for AutoRA project",
+    "license": "bsd-3-clause",
+    "upload_type": "software",
+    "access_right": "open"
+}