Merge branch 'dev' into nsspDocs

Author: nmdefries

.bumpversion.cfg

@@ -9,10 +9,6 @@ tag = False
 
 [bumpversion:file:src/client/delphi_epidata.R]
 
-[bumpversion:file:src/client/delphi_epidata.py]
-
 [bumpversion:file:src/client/packaging/npm/package.json]
 
-[bumpversion:file:src/client/packaging/pypi/setup.py]
-
 [bumpversion:file:dev/local/setup.cfg]

.github/workflows/create-release.yml

@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
     inputs:
       versionName:
-        description: 'Semantic Version Number (i.e., 5.5.0 or patch, minor, major, prepatch, preminor, premajor, prerelease)'
+        description: 'Semantic Version Number (i.e., 5.5.0 or patch, minor, major)'
         required: true
         default: patch
 
@@ -27,11 +27,43 @@ jobs:
           python-version: 3.8
       - name: Change version number
         id: version
+        # See this issue for explanation and testing:
+        # https://github.com/cmu-delphi/delphi-epidata/pull/1473
         run: |
           python -m pip install bump2version
-          echo -n "::set-output name=next_tag::"
-          bump2version --list ${{ github.event.inputs.versionName }} | grep new_version | sed -r s,"^.*=",,
-      - name: Create pull request into prod
+          if [[ ${{ github.event.inputs.versionName }} =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+            # use given version number
+            NEXT_TAG="${{ github.event.inputs.versionName }}"
+          elif [[ ${{ github.event.inputs.versionName }} =~ ^(major|minor|patch)$ ]]; then
+            # calculate new version number based on given tag
+            NEXT_TAG=$(bump2version --dry-run --list ${{ github.event.inputs.versionName }} | grep ^new_version | sed -r s,"^.*=",,)
+          else
+            echo "\nInvalid version name: ${{ github.event.inputs.versionName }}"
+            exit 1
+          fi
+          # apply given or calculated version number
+          bump2version --new-version $NEXT_TAG _ignored_arg_
+          # save version number for later
+          echo "next_tag=$NEXT_TAG" >> $GITHUB_OUTPUT
+      - name: Get Python client file changes
+        id: changed-py
+        uses: dorny/paths-filter@v3
+        with:
+            base: "main"
+            ref: "dev"
+            filters: |
+              python_client_changed:
+                - src/client/delphi_epidata.py
+                - src/client/packaging/pypi/**
+      - name: Bump Python versions if client files changed
+        if: steps.changed-py.outputs.python_client_changed == 'true'
+        # _ignored_arg_ below is required because of tool quirk
+        # https://github.com/c4urself/bump2version/issues/22
+        run: |
+          cd src/client/packaging/pypi
+          # this is using the new literal version number (steps.version.outputs.next_tag) output from the bump2version step above, not the workflow input (github.event.inputs.versionName) which can be relative
+          bump2version --allow-dirty --new-version ${{ steps.version.outputs.next_tag }} _ignored_arg_
+      - name: Create pull request into main
         uses: peter-evans/create-pull-request@v3
         with:
           branch: release/delphi-epidata-${{ steps.version.outputs.next_tag }}

.github/workflows/release-helper.yml

@@ -13,6 +13,29 @@ jobs:
         if: github.repository_owner != 'cmu-delphi'
         run: exit 1
 
+  client_changed:
+    needs: correct_repository
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+      - name: Get Python client file changes
+        id: changed-py
+        uses: dorny/paths-filter@v3
+        with:
+          # when base and ref are the same, changes are detected against the most recent commit before the push.
+          # see https://github.com/dorny/paths-filter#usage for details.
+          base: 'main'
+          ref: 'main'
+          filters: |
+            python_client_changed:
+              - src/client/delphi_epidata.py
+              - src/client/packaging/pypi/**
+    outputs:
+      python_client_changed: ${{ steps.changed-py.outputs.python_client_changed }}
+
   create_release:
     needs: correct_repository
     runs-on: ubuntu-latest
@@ -29,8 +52,8 @@ jobs:
         id: extract_version
         run: |
           python -m pip install bump2version
-          echo -n "::set-output name=version::"
-          bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,
+          VERSION=$(bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,)
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
       - name: Create Release
         id: create_release
         uses: release-drafter/release-drafter@v5
@@ -45,7 +68,8 @@ jobs:
       tag_name: ${{ steps.create_release.outputs.tag_name }}
 
   release_python_client:
-    needs: create_release
+    needs: [client_changed, create_release]
+    if: needs.client_changed.outputs.python_client_changed == 'true'
     runs-on: ubuntu-latest
     steps:
       - name: Check out code
@@ -57,14 +81,14 @@ jobs:
       - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install wheel twine
+          pip install build wheel twine
       - name: Prepare package
         run: |
           cp src/client/*.py src/client/packaging/pypi/delphi_epidata/
       - name: Create release
         working-directory: src/client/packaging/pypi
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build --sdist --wheel
       - uses: actions/upload-artifact@v2
         with:
           name: delphi_epidata_py
@@ -80,8 +104,8 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.DELPHI_PYPI_PROD_TOKEN }}
-          packages_dir: src/client/packaging/pypi/dist/
-          skip_existing: true
+          packages-dir: src/client/packaging/pypi/dist/
+          skip-existing: true
           # repository_url: https://test.pypi.org/legacy/
 
   release_js_client:
@@ -95,7 +119,7 @@ jobs:
         uses: actions/checkout@v2
       - uses: actions/setup-node@v2
         with:
-          node-version: '16.x'
+          node-version: "16.x"
       - name: Cache Node.js modules
         uses: actions/cache@v2
         with:

docs/api/covidcast-signals/indicator-combination-inactive.md renamed to docs/api/covidcast-signals/indicator-combination

@@ -159,5 +159,5 @@ not enough samples can be filled in from the parent state for smoothed signals s
 no data is reported for that area on that day; an API query for all reported geographic areas on
 that day will not include it.
 
-## Flu Tests (inactive)
-These signals were updated until May 19, 2020. Documentation is still available on the [inactive Quidel page](quidel-inactive.md).
+## Flu Tests
+These signals are inactive. They were updated until May 19, 2020. Documentation is still available on the [Quidel influenza page](quidel-flu.md).

docs/api/covidcast-signals/quidel-inactive.md renamed to docs/api/covidcast-signals/quidel-flu.md

@@ -36,7 +36,7 @@ Attribution license](https://creativecommons.org/licenses/by/4.0/):
 
 * [Doctor Visits](covidcast-signals/doctor-visits.md)
 * [Hospital Admissions](covidcast-signals/hospital-admissions.md)
-* [Indicator Combination](covidcast-signals/indicator-combination-inactive.md): signals
+* [Indicator Combination](covidcast-signals/indicator-combination.md): signals
   with names beginning `nmf_*`
 * [Quidel](covidcast-signals/quidel.md)
 * [COVID-19 Trends and Impact Survey](covidcast-signals/fb-survey.md)
@@ -61,7 +61,7 @@ These data streams are essentially mirrors of their respective sources, and are
 published here subject to the original license provided by the source:
 
 * [Google Health Trends](covidcast-signals/ght.md)
-* [Indicator Combination](covidcast-signals/indicator-combination-inactive.md): cases and
+* [Indicator Combination](covidcast-signals/indicator-combination.md): cases and
   deaths signals
 * [JHU Cases and Deaths](covidcast-signals/jhu-csse.md)
 * [SafeGraph Mobility](covidcast-signals/safegraph.md)