Merge pull request #1489 from cmu-delphi/release/delphi-epidata-4.1.24

Release Delphi Epidata 4.1.24
cmu-delphi · Jul 9, 2024 · aa3dedb · aa3dedb
2 parents 11acb91 + 832422f
commit aa3dedb
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.23
+current_version = 4.1.24
 commit = False
 tag = False
 
@@ -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]
diff --git a/.github/workflows/create-release.yml b/.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 }}

diff --git a/.github/workflows/release-helper.yml b/.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:

diff --git a/dev/local/setup.cfg b/dev/local/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.23
+version = 4.1.24
 
 [options]
 packages =

diff --git a/docs/api/client_libraries.md b/docs/api/client_libraries.md
@@ -6,83 +6,81 @@ nav_order: 1
 
 # Epidata API Client Libraries
 
+To access Delphi Epidata programmatically, we recommend our client libraries:
+
+- R: [epidatr](https://cmu-delphi.github.io/epidatr/),
+- Python: [delphi-epidata](https://pypi.org/project/delphi-epidata/) (soon to be replaced with [epidatpy](https://github.com/cmu-delphi/epidatpy)),
+- Javascript: [delphi-epidata](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js).
+
 For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md).
 
-A full-featured Epidata client for R is available at
-[epidatr](https://github.com/cmu-delphi/epidatr) and
-[also on CRAN](https://cran.r-project.org/web/packages/epidatr/index.html).
-
-We are currently working on a new full-featured Epidata client for Python. It is not ready
-for release yet, but you can track our development progress and help us test it out at
-[epidatpy](https://github.com/cmu-delphi/epidatpy).
-
-In the meantime, minimalist Epidata clients remain available for
-[Python](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.py),
-[JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js),
-and
-[R (legacy)](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.R).
-The following samples show how to import the library and fetch Delphi's COVID-19
-Surveillance Streams from Facebook Survey CLI for county 06001, and days
+The following samples show how to import the library and fetch Delphi's
+COVID-19 Surveillance Streams from Facebook Survey CLI for county 06001 and days
 `20200401` and `20200405-20200414` (11 days total).
 
 ### R
 
-````R
-# [Optional] configure your API key, if desired
-# Interactive. See https://cmu-delphi.github.io/epidatr/articles/epidatr.html#api-keys for details.
+Install [`epidatr` from CRAN](https://cran.r-project.org/package=epidatr)
+with `install.packages("epidatr")`.
+
+```R
+# Configure API key interactively, if needed. See
+# https://cmu-delphi.github.io/epidatr/articles/epidatr.html#api-keys for details.
 #save_api_key()
-# Import
 library(epidatr)
-# Fetch data
 res <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
                      time_values = c(20200401, 20200405:20200414))
 cat(res)
-````
+```
 
 ### Python
 
-Optionally install the [package from PyPI](https://pypi.org/project/delphi-epidata/) using pip(env):
-````bash
-pip install delphi-epidata
-````
+Install [`delphi-epidata` from PyPI](https://pypi.org/project/delphi-epidata/) with
+`pip install delphi-epidata`.
 
-Otherwise, place
-[`delphi_epidata.py`](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.py)
-in the same directory as your Python script.
-
-````python
-# Import
+```python
 from delphi_epidata import Epidata
-# [Optional] configure your API key, if desired
+# Configure API key, if needed.
 #Epidata.auth = ('epidata', <your API key>)
-# Fetch data
 res = Epidata.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, Epidata.range(20200405, 20200414)], '06001')
 print(res['result'], res['message'], len(res['epidata']))
-````
+```
 
 ### JavaScript (in a web browser)
 
-The minimalist JavaScript client does not currently support API keys. If you need API key support in JavaScript, contact delphi-support+privacy@andrew.cmu.edu.
+The minimalist JavaScript client does not currently support API keys.
+If you need API key support in JavaScript, contact delphi-support+privacy@andrew.cmu.edu.
 
-````html
-<!-- Imports -->
+```html
 <script src="delphi_epidata.js"></script>
-<!-- Fetch data -->
 <script>
-  EpidataAsync.covidcast('fb-survey', 'smoothed_cli', 'day', 'county', [20200401, EpidataAsync.range(20200405, 20200414)], '06001').then((res) => {
-    console.log(res.result, res.message, res.epidata != null ? res.epidata.length : 0);
+  EpidataAsync.covidcast(
+    "fb-survey",
+    "smoothed_cli",
+    "day",
+    "county",
+    [20200401, EpidataAsync.range(20200405, 20200414)],
+    "06001"
+  ).then((res) => {
+    console.log(
+      res.result,
+      res.message,
+      res.epidata != null ? res.epidata.length : 0
+    );
   });
 </script>
-````
+```
 
 ### R (legacy)
 
+The old Delphi Epidata R client is available
+[here](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R),
+but its use is discouraged.
+
 ```R
-# [Optional] configure your API key, if desired
+# Configure API key, if needed.
 #option('epidata.auth', <your API key>)
-# Import
 source('delphi_epidata.R')
-# Fetch data
 res <- Epidata$covidcast('fb-survey', 'smoothed_cli', 'day', 'county', list(20200401, Epidata$range(20200405, 20200414)), '06001')
 cat(paste(res$result, res$message, length(res$epidata), "\n"))
 ```
diff --git a/...signals/indicator-combination-inactive.md → ...i/covidcast-signals/indicator-combination b/...signals/indicator-combination-inactive.md → ...i/covidcast-signals/indicator-combination