force `subprocess.run` to check return code is 0

In general, this should help to capture unintentional errors.

Where the change has created failures, they have been fixed. (Mostly because the git repository that was looked for was missing.)

tests.py

@@ -9,6 +9,35 @@ import pytest
 mod = importlib.import_module("mpsd-software-environment")
 
 
+def create_mock_git_repository(target_directory, create_directory=True):
+    """
+    Create a git repository in the directory `target_directory`.
+
+    Arguments
+    ---------
+    target_directory : pathlib.Path
+      - path at which the root of the repository should be located (i.e. `.git` folder)
+
+    create_directory : bool
+      - create `target_directory` and parent directories if True
+
+    """
+    # create directory first
+    if create_directory:
+        target_directory.mkdir(parents=True)
+
+    # then create git repository:
+    with mod.os_chdir(str(target_directory)):
+        subprocess.run("git init .", shell=True, check=True)
+        subprocess.run("echo 'fake content' > readme.txt", shell=True, check=True)
+        subprocess.run("git add readme.txt", shell=True, check=True)
+        subprocess.run("pwd", shell=True)
+        subprocess.run(
+            'git commit -m "first commit" readme.txt', shell=True, check=True
+        )
+
+
+
 def test_os_chdir(tmp_path):
     # create a temporary directory for testing
     temp_dir = tmp_path / "test_os_chdir"
@@ -43,18 +72,7 @@ def test_prepare_environment(tmp_path):
     # log that information. For this to work, we need to execute the command
     # within a directory tree that has a git repository at the same or high
     # level. Let's create one:
-
-    # create directory first
-    script_dir.mkdir(parents=True)
-    # then create git repository:
-    with mod.os_chdir(str(script_dir)):
-        subprocess.run("git init .", shell=True, check=True)
-        subprocess.run("echo 'fake content' > readme.txt", shell=True, check=True)
-        subprocess.run("git add readme.txt", shell=True, check=True)
-        subprocess.run("pwd", shell=True)
-        subprocess.run(
-            'git commit -m "first commit" readme.txt', shell=True, check=True
-        )
+    create_mock_git_repository(script_dir)
 
     # now call the function we want to test
     result = mod.prepare_environment(