check that build action can use TMPDIR

Fixes #52

tests/test_container_template.py

@@ -11,31 +11,47 @@
 import os
 import socket
 import subprocess
+import tempfile
 
 
 # port used by tests
 sock = socket.socket()
 sock.bind(('', 0))
 port = sock.getsockname()[1]
 
-# Check that (1) singularity exist, and (2) if not, check for docker.
+# Check that (1) singularity or apptainer executables exist, 
+# and (2) if not, check for docker.
 # If neither are found, tests will fall back to plain python.
+# This may be useful for testing on a local machine, but should 
+# be revised for the particular usecase.
 try:
     pth = os.path.join('containers', 'container_template.sif')
-    out = subprocess.run('singularity')
+    try:
+        out = subprocess.run('singularity', check=False)
+    except FileNotFoundError:
+        try:
+            out = subprocess.run('apptainer', check=False)
+        except FileNotFoundError as exc:
+            raise FileNotFoundError from exc
     cwd = os.getcwd()
     PREFIX = f'singularity run {pth} python'
     PREFIX_MOUNT = f'singularity run --home={cwd}:/home/ {pth} python'
+    PREFIX_CUSTOM_MOUNT = f'singularity run --home={cwd}:/home/ ' + '{custom_mount}' + f'{pth} python'
 except FileNotFoundError:
     try:
-        out = subprocess.run('docker')
+        out = subprocess.run('docker', check=False)
         pwd = os.getcwd()
         PREFIX = (f'docker run -p {port}:{port} ' +
                   '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 python')
+        PREFIX_CUSTOM_MOUNT = (
+            f'docker run -p {port}:{port} ' +
+            f'--mount type=bind,source={pwd},target={pwd} ' +
+            '{custom_mount} ' +
+            'ghcr.io/precimed/container_template python')
     except FileNotFoundError:
         # neither singularity nor docker found, fall back to plain python
         PREFIX = 'python'
@@ -62,6 +78,17 @@ def test_container_template_python_script():
     assert out.returncode == 0
 
 
+def test_container_template_python_script_from_tempdir():
+    '''test that the tempdir is working'''
+    with tempfile.TemporaryDirectory() as d:
+        os.system(f'cp {pwd}/tests/extras/hello.py {d}/')
+        custom_mount = f'--mount type=bind,source={d},target=/temp/'
+        call = f'{PREFIX_CUSTOM_MOUNT.format(custom_mount=custom_mount)} ' + \
+            '/temp/hello.py'
+        out = subprocess.run(call.split(' '), check=False)
+        assert out.returncode == 0
+
+
 def test_container_template_python_packages():
     '''test that the Python packages are installed'''
     packages = [
@@ -78,3 +105,4 @@ def test_container_template_python_packages():
     call = f"{PREFIX} -c '{importstr}'"
     out = subprocess.run(call, shell=True)
     assert out.returncode == 0
+