Get tutorial-tests.yml working (#226)

* reset working directory install step tutorial-tests.yml

* temporarily only run on test branch

* also install curl

* and unzip

* Update tutorial-tests.yml

* no * expansion on github workflow shell, it seems

* actually structure the data correctly

* see if file actually runs

* elaborate more on the codeblocks

* more debug prints

* test behavior some more

* try to strip out extra code-block typing

* sanitize input to subprocess

* stop test if something fails

* don't change .map to .mrc

* fix template filename in Tutorial.md

* switch to unbuffered python output for my sanity

* reduce tqdm clutter

* Install complete suite instead of just dev

* deal with stdout rerouting

* stdout needs to be an open file

* allow for non-existent output file

* undo all debug stuff

* try to compile cupy instead

* GCC is also needed now

* revert back to state:  9c89c20

.github/workflows/tutorial-tests.yml

@@ -4,6 +4,11 @@ on:
   push:
     branches:
       - main
+    tags:
+      - "[0-9]+.[0-9]+.[0-9]+"
+  schedule:
+    # Weekly on saturday 23:59
+    - cron: "59 23 * * 6"
 
 
 jobs:
@@ -19,10 +24,11 @@ jobs:
       - name: Pull code
         uses: actions/checkout@v4
       - name: Install dependencies, code, and list everything
+        working-directory: ./
         run: |
-          conda install -y -c conda-forge python=3 cupy cuda-version=11.8
+          conda install -y -c conda-forge python=3 cupy cuda-version=11.8 curl unzip
           python -m pip install coverage mdextractor #mdextractor is new and might need to be replaced later
-          python -m pip install .[dev]
+          python -m pip install .[all]
           conda list
       - name: Grab files needed for tests
         run: |
@@ -34,12 +40,15 @@ jobs:
           cp ../data/6qzp_60S.mrc .
           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:${{ secrets.DATAVERSE_API_TOKEN }}" https://dataverse.nl/api/access/datafiles/384731,384724,384706,384718
           unzip dataverse_files.zip
+          # this inflates into a 'tutorial' folder, moving everything out
+          mv tutorial/* .
+      - name: Set TQDM_MININTERVAL
+        run: echo "TQDM_MININTERVAL=10" >> "$GITHUB_ENV"
       - 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
+          python -u tests/test_tutorial.py

docs/tutorials/Tutorial.md

@@ -25,7 +25,7 @@ tm_tutorial/
 ¦  +- ...
 +- templates/
 ¦  +- 6qzp_60S.mrc
-¦  +- emd_2938.mrc
+¦  +- emd_2938.map
 +- results_80S/
 +- results_60S/
 ```

docs/tutorials/tests/test_tutorial.py

@@ -2,9 +2,33 @@
 import subprocess
 from mdextractor import extract_md_blocks
 
+
+def sanitize_block(block):
+    block = block.split()
+    out = [i for i in block if i and i != "\\"]
+    return out
+
+
+print("Doing tutorial tests")
 lines = "".join(open("Tutorial.md").readlines())
 blocks = extract_md_blocks(lines)
+n_blocks = len(blocks)
+print(f"Found {n_blocks} code blocks")
+if n_blocks == 0:
+    raise ValueError("Did not find any code blocks")
 for block in blocks:
+    # strip out extra typing
+    block = block.strip("bash")
     if block.split()[0].endswith(".py"):
         print(f"Running: {block}")
-        subprocess.run(block)
+
+        block = sanitize_block(block)
+        outfile = None
+        # Deal with stdout redirect
+        if block[-2] == ">":
+            outfile = open(block[-1], "a+")
+            block = block[:-2]
+        # Check=True makes sure this code returns early
+        subprocess.run(block, check=True, stdout=outfile)
+        if outfile is not None:
+            outfile.close()