Merge pull request #605 from hed-standard/develop

Extensive revisions and updating of remodeling tools

.codeclimate.yml

@@ -88,4 +88,3 @@ exclude_patterns:
 - "**/deprecated/"
 - "**/versioneer.py"
 - "**/_version.py"
-- "**/cli/"

.coveragerc

@@ -1,5 +1,7 @@
 [run]
 branch = True
+source =
+    hed
 omit =
         */__init__.py
         */venv/*

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yaml

@@ -8,24 +8,28 @@ on:
 
 jobs:
   build:
-
     strategy:
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9]
 
     runs-on: ${{ matrix.platform }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install --upgrade --upgrade-strategy eager pip
           pip install flake8
           pip install coverage
           pip install -r requirements.txt
@@ -40,12 +44,67 @@ jobs:
 
       - name: Test with unittest
         run: |
-          coverage run -m unittest
+          HED_GITHUB_TOKEN=${{ secrets.HED_GITHUB_TOKEN }} coverage run -m unittest
+
+      - name: Archive code coverage results
+        if: ${{matrix.python-version == '3.9'}}
+        uses: actions/upload-artifact@v3
+        with:
+          name: code-coverage-report
+          path: .coverage
+
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-exist: ${{ steps.check-for-secrets.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: check-for-secrets
+        # perform secret check & put boolean result as an output
+        shell: bash
+        run: |
+          if [ "${{ secrets.CC_TEST_REPORTER_ID }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
+  coverage:
+    name: Publish coverage
+    needs: [build, check-secret]
+    runs-on: ubuntu-latest
+    if: needs.check-secret.outputs.secrets-exist == 'true'
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade --upgrade-strategy eager pip
+          pip install flake8
+          pip install coverage
+          pip install -r requirements.txt
+          pip install -r docs/requirements.txt
+
+      - name: Download a single artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: code-coverage-report
 
       - name: publish-coverages
-        uses: paambaati/codeclimate-action@v2.7.5
+        with:
+          coverageCommand: coverage xml
+          debug: true
+        uses: paambaati/codeclimate-action@v3.2.0
         env:
           CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
-        with:
-            coverageCommand: coverage xml
-            debug: true
+

.gitignore

@@ -61,6 +61,7 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
+tests/scratch
 
 # Installer logs
 pip-log.txt
@@ -120,4 +121,4 @@ Desktop.ini
 
 # Project specific
 schema_cache_test/
-hed_cache/
+hed_cache/

docs/requirements.txt

@@ -1,29 +1,12 @@
-click>=8.1.3
-coverage>=6.3.2
 defusedxml>=0.7.1
-et-xmlfile>=1.1.0
-Flask>=2.1.2
-Flask-WTF>=1.0.1
-inflect>=5.5.2
-itsdangerous>=2.1.2
-jdcal>=1.4.1
-Jinja2>=3.0.0
-jupyter>=1.0.0
-MarkupSafe>=2.1.1
-numpy>=1.20.3
-numpydoc>=1.3.1
+inflect>=5.5.1
+myst-parser>=0.18.1
 openpyxl>=3.0.9
 pandas>=1.3.5
 portalocker>=2.4.0
-python-dateutil>=2.8.2
-pytz>=2022.1
-Pygments>=2.12.0
 semantic_version>=2.9.0
-six>=1.16.0
-Sphinx>=4,<5
-SphinxExtensions>=0.2.0
+Sphinx>=5.2.2
 sphinx_rtd_theme>=1.0.0
+
+# This is just needed for secure_filename and should probably be removed
 Werkzeug>=2.1.2
-WTForms>=3.0.1
-xlrd>=2.0.1
-myst-parser>=0.17.2

docs/source/_templates/custom-class-template.rst

@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/_templates/custom-module-template.rst

@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/source/_templates/layout.html

@@ -9,8 +9,8 @@
       <span class="caption-text">HED resources:</span>
     </p>
     <ul>
-     <li class="toctree-li">
-        <a href="https://hed-examples.readthedocs.io/en/latest/HedDocumentationSummary.html">Documentation summary</a></li>
+      <li class="toctree-li"><a href="https://www.hed-resources.org/en/latest/">Main resource page</a></li>
+      <li class="toctree-li"><a href="https://www.hedtags.org">Project home page</a></li>
       <li class="toctree-li"><a href="https://www.hedtags.org/display_hed.html">Schema viewer</a></li>
       <li class="toctree-li"><a href="https://www.hedtags.org/display_hed_library.html">Library schema viewer</a></li>
       <li class="toctree-li"><a href="https://hed-specification.readthedocs.io/en/latest/index.html">Specification</a></li>