test

.github/workflows/container_build.yml

@@ -56,8 +56,9 @@ jobs:
             ./dockerfiles/container_template/Dockerfile
       - name: Run unit tests
         run: |
-          docker run --rm ${{ env.TEST_TAG }} 
-          docker run --rm -v $PWD:/home ${{ env.TEST_TAG }} py.test -v tests
+          docker run --rm ${{ env.TEST_TAG }}
+          ls -l
+          docker run --rm -v .:/home ${{ env.TEST_TAG }} py.test -v tests
 
       - name: Build
         uses: docker/build-push-action@v6

tests/test_container_template.py

@@ -24,22 +24,22 @@
     pth = os.path.join('containers', 'container_template.sif')
     out = subprocess.run('singularity')
     cwd = os.getcwd()
-    PREFIX = f'singularity run {pth} '
-    PREFIX_MOUNT = PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} '
+    PREFIX = f'singularity run {pth} python'
+    PREFIX_MOUNT = PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} python'
 except FileNotFoundError:
     try:
         out = subprocess.run('docker')
         pwd = os.getcwd()
         PREFIX = (f'docker run -p {port}:{port} ' +
-                  'ghcr.io/precimed/container_template ')
+                  'ghcr.io/precimed/container_template python')
         PREFIX_MOUNT = (
             f'docker run -p {port}:{port} ' +
             f'--mount type=bind,source={pwd},target={pwd} ' +
-            'ghcr.io/precimed/container_template ')
+            'ghcr.io/precimed/container_template python')
     except FileNotFoundError:
         # neither singularity nor docker found, fall back to plain python
-        PREFIX = ''
-        PREFIX_MOUNT = ''
+        PREFIX = 'python'
+        PREFIX_MOUNT = 'python'
 
 
 def test_assert():
@@ -49,15 +49,15 @@ def test_assert():
 
 def test_container_template_python():
     """test that the Python installation works"""
-    call = f'{PREFIX}python --version'
+    call = f'{PREFIX} --version'
     out = subprocess.run(call.split(' '))
     assert out.returncode == 0
 
 
 def test_container_template_python_script():
     '''test that Python can run a script'''
     pwd = os.getcwd() if PREFIX.rfind('docker') >= 0 else '.'
-    call = f'''{PREFIX_MOUNT}python {pwd}/tests/extras/hello.py'''
+    call = f'''{PREFIX_MOUNT} {pwd}/tests/extras/hello.py'''
     out = subprocess.run(call.split(' '), capture_output=True)
     assert out.returncode == 0
 
@@ -75,6 +75,6 @@ def test_container_template_python_packages():
         'jupyterlab',
     ]
     importstr = 'import ' + ', '.join(packages)
-    call = f"{PREFIX}python -c '{importstr}'"
+    call = f"{PREFIX} -c '{importstr}'"
     out = subprocess.run(call, shell=True)
     assert out.returncode == 0