From d6fdb98a13809a67e972ba87ca5989619cb3e521 Mon Sep 17 00:00:00 2001
From: Sander Roet <sanderroet@hotmail.com>
Date: Fri, 14 Jun 2024 16:47:09 +0200
Subject: [PATCH] add tutorial test yml

---
 .github/workflows/tutorial-tests.yml | 61 ++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 .github/workflows/tutorial-tests.yml

diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml
new file mode 100644
index 00000000..ac8be80f
--- /dev/null
+++ b/.github/workflows/tutorial-tests.yml
@@ -0,0 +1,61 @@
+name: Test Tutorial
+# following example: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+on:
+  workflow_run:
+    workflows: ["Unit tests"]
+    types:
+      - completed
+
+jobs:
+  test-tutorial:
+    if: >
+      github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.conclusion == 'success'
+    runs-on: [self-hosted, linux, x64, gpu]
+    container:
+      image: continuumio/miniconda3
+      options: --runtime=nvidia --gpus all
+    permissions:
+      # Read the action that triggered this one
+      actions: read
+      # Allow to write check runs
+      checks: write
+      # Read and update commit statuses
+      statuses: write
+    steps:
+      - name: Pull code
+        uses: actions/checkout@v4
+        with:
+          repository: github.event.workflow_run.head_repository
+          ref: github.event.workflow_run.head_sha
+      - name: Pull wiki
+        uses: actions/checkout@v4
+        with:
+          # Only check the wiki of the calling repo
+          repository: ${{github.repository}}.wiki 
+          path: wiki
+      - name: Install dependencies, code, and list everything
+        run: |
+          conda install -y -c conda-forge python=3 cupy cuda-version=11.8
+          python -m pip install coverage mdextractor #mdextractor is new and might need to be replaced later
+          python -m pip install .[dev]
+          conda list
+      - name: Grab files needed for tests
+        run: |
+          mkdir wiki/dataset
+          mkdir wiki/templates
+          cd wiki/templates
+          cp ../data/6qzp_60S wiki/templates/
+          curl https://files.wwpdb.org/pub/emdb/structures/EMD-2938/map/emd_2938.map.gz -o emd_2938.map.gz
+          gunzip emd_2938.map.gz
+          mv emd_2938.map emd_2938.mrc
+          cd ../dataset
+          curl -L -O -J -H "X-Dataverse-key:${{ secrets.DATAVERSE_API_TOKEN }}" https://dataverse.nl/api/access/datafiles/384731,384724,384706,384718
+          unzip dataverse_files.zip
+          mv tutorial/* .
+          cd ../
+      - name: Run Tutorial test
+        run: |
+          # Hardcode the conversion line
+          for x in dataset/*.mrc; do python -c "import mrcfile; mrc = mrcfile.mmap('$x', 'r+'); mrc.voxel_size = 13.79"; done
+          python tests/test_tutorial.py