adding github actions workflow

.github/workflows/bulidAndDeployWebsite.yml

@@ -0,0 +1,42 @@
+name: build-and-deploy-website
+run-name: build and deploy website
+on:
+  workflow_dispatch:
+  schedule:
+    # daily at 19:30: '30 19 * * *'
+    - cron: '*/5 * * * *'
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.HOW_BAD_IS_MY_BATCH_ACCESS_TOKEN }}
+      - name: installing dependencies
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: howbadismybatch-venv
+          environment-file: environment.yml
+      - name: installing Google Chrome
+        shell: bash -el {0}
+        run: |
+          wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
+          sudo dpkg -i google-chrome-stable_current_amd64.deb
+          sudo apt install google-chrome-stable
+          pip install selenium webdriver-manager
+          pip install pycountry
+      - name: executing HowBadIsMyBatch.ipynb
+        shell: bash -el {0}
+        run: |
+          git config --global user.email "Knoll_Frank@web.de"
+          git config --global user.name "FK"
+          ipython kernel install --user --name=howbadismybatch-venv-kernel
+          cd src
+          jupyter nbconvert --ExecutePreprocessor.kernel_name="howbadismybatch-venv-kernel" --to notebook --allow-errors --execute HowBadIsMyBatch.ipynb
+          jupyter nbconvert --to html HowBadIsMyBatch.nbconvert.ipynb
+      - name: Archiving HowBadIsMyBatch.nbconvert.html
+        uses: actions/upload-artifact@v3
+        with:
+          name: HowBadIsMyBatch.nbconvert.html
+          path: src/HowBadIsMyBatch.nbconvert.html

.gitignore

@@ -15,3 +15,4 @@ src/HowBadIsMyBatch.nbconvert.ipynb
 src/HowBadIsMyBatch.nbconvert.html
 src/__pycache__/
 src/intensivstationen/__pycache__/
+google-chrome-stable_current_amd64*

environment.yml

@@ -1,6 +1,7 @@
 name: howbadismybatch-venv
 channels:
   - defaults
+  # - conda-forge
 dependencies:
   - python=3
   - ipykernel
@@ -13,4 +14,8 @@ dependencies:
   - jupyter
   - tensorflow
   - nb_conda_kernels
+  - pillow
+  # - selenium
+  # - webdriver-manager
+  # - pycountry
 prefix: /home/frankknoll/anaconda3/envs/howbadismybatch-venv

src/HowBadIsMyBatch.ipynb

@@ -63,7 +63,7 @@
    "outputs": [],
    "source": [
     "updateVAERSFiles(\n",
-    "        needsUpdate = needsUpdate,\n",
+    "        needsUpdate = True,\n",
     "        years = years_from_2020_to_present,\n",
     "        workingDirectory = os.getcwd())"
    ]
@@ -107,7 +107,6 @@
    "outputs": [],
    "source": [
     "def publishGitHubPages():\n",
-    "    %cd /home/frankknoll/Dokumente/Corona/projects/HowBadIsMyBatch-pages\n",
     "    ! git add -A\n",
     "    ! git commit -m \"updating data for batch codes\"\n",
     "    ! git push"
@@ -148,7 +147,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.8 (main, Nov 24 2022, 14:13:03) [GCC 11.2.0]"
   },
   "vscode": {
    "interpreter": {