MRG: Merge pull request #112 from octue/move-children-schema-to-strands

Move children schema to strands

.github/workflows/python-ci.yml

@@ -11,30 +11,25 @@ on:
 jobs:
   check-semantic-version:
     if: "!contains(github.event.head_commit.message, 'skipci')"
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - uses: octue/[email protected]
-        with:
-          path: setup.py
-          breaking_change_indicated_by: minor
+    uses: octue/workflows/.github/workflows/check-semantic-version.yml@main
+    with:
+      path: setup.py
+      breaking_change_indicated_by: minor
 
   run-tests:
     if: "!contains(github.event.head_commit.message, 'skipci')"
     runs-on: ubuntu-latest
     env:
-      USING_COVERAGE: '3.8'
+      USING_COVERAGE: '3.9'
     strategy:
       matrix:
-        python: [3.8]
+        python: ['3.8', '3.9']
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
@@ -45,10 +40,11 @@ jobs:
         run: tox
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           files: coverage.xml
           fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   publish:
     if: "!contains(github.event.head_commit.message, 'skipci')"
@@ -62,9 +58,9 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.9"
 
       - name: Make package
         run: |

.github/workflows/release.yml

@@ -12,16 +12,16 @@ jobs:
     if: "github.event.pull_request.merged == true"
     runs-on: ubuntu-latest
     env:
-      USING_COVERAGE: '3.8'
+      USING_COVERAGE: '3.9'
     strategy:
       matrix:
-        python: [ 3.8 ]
+        python: ['3.8', '3.9']
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
@@ -32,10 +32,11 @@ jobs:
         run: tox
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           files: coverage.xml
           fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   release:
     needs: run-tests
@@ -68,7 +69,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

.github/workflows/update-pull-request.yml

@@ -1,30 +1,18 @@
 # This workflow updates the pull request description with an auto-generated section containing the categorised commit
-# message headers of the commits since the last pull request merged into main. The auto generated section is enveloped
-# between two comments: "<!--- START AUTOGENERATED NOTES --->" and "<!--- END AUTOGENERATED NOTES --->". Anything
-# outside these in the description is left untouched. Auto-generated updates can be skipped for a commit if
+# message headers of the pull request's commits. The auto generated section is enveloped between two comments:
+# "<!--- START AUTOGENERATED NOTES --->" and "<!--- END AUTOGENERATED NOTES --->". Anything outside these in the
+# description is left untouched. Auto-generated updates can be skipped for a commit if
 # "<!--- SKIP AUTOGENERATED NOTES --->" is added to the pull request description.
 
 name: update-pull-request
 
-# Only trigger for pull requests into main branch.
-on:
-  pull_request:
-    branches:
-      - main
+on: [pull_request]
 
 jobs:
   description:
-    if: "!contains(github.event.pull_request.body, '<!--- SKIP AUTOGENERATED NOTES --->')"
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: octue/[email protected]
-      id: pr-description
-      with:
-        pull_request_url: ${{ github.event.pull_request.url }}
-        api_token: ${{ secrets.GITHUB_TOKEN }}
-    - name: Update pull request body
-      uses: riskledger/update-pr-description@v2
-      with:
-        body: ${{ steps.pr-description.outputs.pull_request_description }}
-        token: ${{ secrets.GITHUB_TOKEN }}
+    uses: octue/workflows/.github/workflows/generate-pull-request-description.yml@main
+    secrets:
+      token: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read
+      pull-requests: write

.pre-commit-config.yaml

@@ -41,17 +41,16 @@ repos:
     - id: pydocstyle
 
   - repo: https://github.com/thclark/pre-commit-sphinx
-    rev: 0.0.1
+    rev: 0.0.3
     hooks:
       - id: build-docs
         language_version: python3
         additional_dependencies:
-          - 'Sphinx>=2,<3'
-          - 'sphinx-rtd-theme==0.5.0'
-          - 'sphinx-tabs==1.2.1'
-          - 'sphinx-charts==0.0.4'
-          - 'scipy~=1.5.2'
-          - 'jsonschema~=3.2.0'
+          - 'Sphinx'
+          - 'sphinx-rtd-theme'
+          - 'sphinx-tabs'
+          - 'sphinx-charts'
+          - 'jsonschema'
 
   - repo: https://github.com/windpioneers/pre-commit-hooks
     rev: 0.0.5

.readthedocs.yaml

@@ -0,0 +1,16 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt

docs/requirements.txt

@@ -1,8 +1,6 @@
-
 # Required by the python script for building documentation
-Sphinx>=2,<3
-sphinx-rtd-theme==0.5.0
-sphinx-tabs==1.2.1
-sphinx-charts==0.0.4
-scipy~=1.5.2
-jsonschema~=3.2.0
+Sphinx
+sphinx-rtd-theme
+sphinx-tabs
+sphinx-charts
+jsonschema

docs/source/_ext/sphinx_accordion/accordion.py

@@ -246,7 +246,7 @@ def setup(app):
             if 'add_script_file' in dir(app):
                 app.add_script_file(path)
             else:
-                app.add_javascript(path)
+                app.add_js_file(path)
 
     app.connect('html-page-context', update_context)
     app.connect('build-finished', copy_assets)

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name="twined",
-    version="0.5.3",
+    version="0.5.4",
     py_modules=[],
     install_requires=["jsonschema ~= 4.4.0", "python-dotenv"],
     url="https://www.github.com/octue/twined",
@@ -33,6 +33,7 @@
         "Topic :: Software Development :: Libraries :: Python Modules",
         "License :: OSI Approved :: MIT License",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Operating System :: OS Independent",
     ],
     python_requires=">=3.6",

tests/test_children.py

@@ -5,24 +5,22 @@
 
 
 class TestChildrenTwine(BaseTestCase):
-    """Tests related to the twine itself - ensuring that valid and invalid
-    `children` entries in a twine file work as expected
-    """
+    """Tests ensuring that valid and invalid `children` entries in a twine file work as expected."""
 
     def test_invalid_children_dict_not_array(self):
-        """Ensures InvalidTwine exceptions are raised when instantiating twines where `children` entry is incorrectly
-        specified as a dict, not an array
+        """Ensure that `InvalidTwine` exceptions are raised when instantiating twines where `children` entry is
+        incorrectly specified as a dict, not an array.
         """
         with self.assertRaises(exceptions.InvalidTwine):
             Twine(source="""{"children": {}}""")
 
     def test_invalid_children_no_key(self):
-        """Ensures InvalidTwine exceptions are raised when instantiating twines where a child
-        is specified without the required `key` field
+        """Ensure that `InvalidTwine` exceptions are raised when instantiating twines where a child is specified without
+        the required `key` field.
         """
         source = """
             {
-                "children": [{"purpose": "The purpose.", "notes": "Here are some notes.", "filters": "tags:gis"}]
+                "children": [{"purpose": "The purpose.", "notes": "Here are some notes."}]
             }
         """
 
@@ -33,7 +31,7 @@ def test_valid_children(self):
         """Ensures that a twine with one child can be instantiated correctly."""
         source = """
             {
-                "children": [{"key": "gis", "purpose": "The purpose.", "notes": "Some notes.", "filters": "tags:gis"}]
+                "children": [{"key": "gis", "purpose": "The purpose.", "notes": "Some notes."}]
             }
         """
         self.assertEqual(len(Twine(source=source).children), 1)
@@ -49,7 +47,7 @@ class TestChildrenValidation(BaseTestCase):
 
     VALID_TWINE_WITH_CHILDREN = """
         {
-            "children": [{"key": "gis", "purpose": "The purpose", "notes": "Some notes.", "filters": "tags:gis"}]
+            "children": [{"key": "gis", "purpose": "The purpose", "notes": "Some notes."}]
         }
     """
 

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = {py38}
+envlist = {py38,py39}
 
 [testenv]
 setenv =