Merge pull request #696 from heerden/master

Activate Rt model 1 again, but bypass confidence internal for SA data

.github/workflows/realtime_rt_action.yaml

@@ -0,0 +1,64 @@
+# This workflow was created by @heerden
+# Do not modify this action before discussing
+
+# If you have an analysis notebook or script that can export data, chat to @heerden and @vukosim
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - data/covid19za_provincial_cumulative_timeline_confirmed.csv
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.6'
+
+    - name: Ensure Data Directory Exists
+      run: |
+        mkdir -p data/calc
+        ls
+
+    - name: Setup Python Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pandas numpy matplotlib scipy IPython
+
+    - name: Run Jupyter Notebook and Export csv
+      uses: yaananth/run-notebook@v1
+      env:
+        RUNNER: ${{ toJson(runner) }}
+        SECRETS: ${{ toJson(secrets) }}
+        GITHUB: ${{ toJson(github) }}
+      with:
+        notebook: "notebooks/Realtime R0.ipynb"
+        params: ""
+        isReport: False
+        poll: True
+
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        # Required
+        commit_message: Rt model 1 action run
+        # Optional branch to push to, defaults to the current branch
+        #branch: master
+        # Optional options appended to `git-commit`
+        #commit_options: '--no-verify --signoff'
+        # Optional glob pattern of files which should be added to the commit
+        file_pattern: data/calc/*.csv
+        # Optional local file path to the repository
+        #repository: .
+        # Optional commit user and author settings
+        # Optional tag message
+        # Action will create and push a new tag to the remote repository and the defined branch
+        #tagging_message: 'v1.0.0'
+        # Optional options appended to `git-push`
+        push_options: '--force'
+        commit_author: github-actions <[email protected]>

.github/workflows/rtlive-model-za.yml

@@ -18,6 +18,8 @@ jobs:
 
     - name: Setup Python
       uses: actions/setup-python@v1
+      with:
+        python-version: '3.6'
 
     - name: Setup Python Dependencies
       run: |
@@ -46,5 +48,5 @@ jobs:
         # Action will create and push a new tag to the remote repository and the defined branch
         #tagging_message: 'v1.0.0'
         # Optional options appended to `git-push`
-        #push_options: '--force'
+        push_options: '--force'
         commit_author: github-actions <[email protected]>