Testing suite should be machine and user agnostic

[lewisblake]

When trying to run the test suit on PPI, I ran into an issue with permissions. e.g.,

PermissionError: [Errno 13] Permission denied: '/lustre/storeA/project/aerocom/aerocom2/pyaerocom_out/testdata-minimal/scripts/create_subset_ebas.py'

After chatting with @jgriesfeller and @avaldebe and a ticket to IT to change ownership of the directories needed for testing to @jgriesfeller, we concluded that testing is not multi-user capable.

/modules/centos7/user-apps/aerocom/anaconda3/envs/pyadev-applied/lib/python3.9/pathlib.py:1120: in _opener
    return self._accessor.open(self, flags, mode)
E   PermissionError: [Errno 13] Permission denied: '/tmp/test_iris_io/invalid.nc'

(pyadev-applied) jang@ppi-clogin-a1:~/.../Python3/pyaerocom$ ll /tmp/test_iris_io/invalid.nc
-rw-rw-r-- 1 danielh danielh 0 Jul  4 12:44 /tmp/test_iris_io/invalid.nc

In order for tests to be run agnostically, they should not depend on /tmp, but rather be specific to the machine and $USER (@jgriesfeller please let me know if I am forgetting anything). The Python module tempfile may be starting point for thinking of a solution.

[avaldebe]

/modules/centos7/user-apps/aerocom/anaconda3/envs/pyadev-applied/lib/python3.9/pathlib.py:1120: in _opener
    return self._accessor.open(self, flags, mode)
E   PermissionError: [Errno 13] Permission denied: '/tmp/test_iris_io/invalid.nc'

(pyadev-applied) jang@ppi-clogin-a1:~/.../Python3/pyaerocom$ ll /tmp/test_iris_io/invalid.nc
-rw-rw-r-- 1 danielh danielh 0 Jul  4 12:44 /tmp/test_iris_io/invalid.nc

The lines that create this file are

pyaerocom/tests/io/test_iris_io.py

Lines 66 to 68 in e9f2666

	FAKE_FILE = Path(tempfile.gettempdir()) / "test_iris_io/invalid.nc"
	FAKE_FILE.parent.mkdir(exist_ok=True, parents=True)
	FAKE_FILE.write_text("")

The quick'n dirty solution would be to create a temporary directory each time with tempfile.mkdtemp() as follows

- FAKE_FILE = Path(tempfile.gettempdir()) / "test_iris_io/invalid.nc"
+ FAKE_FILE = Path(tempfile.mkdtemp()) / "test_iris_io/invalid.nc"

IMO, this file should be created inside a fixture and modify the tests consuming this file to use the fixture.

[avaldebe]

I can find only one other usage of tempfile on the test suite

pyaerocom/tests/test_config.py

Lines 18 to 25 in e9f2666

	TMP_PATH = Path(tempfile.mkdtemp())
	CFG_FILE_WRONG = TMP_PATH / "paths.txt"
	CFG_FILE_WRONG.write_text("")
	LOCAL_DB_DIR = TMP_PATH / "data"
	LOCAL_DB_DIR.mkdir()
	(LOCAL_DB_DIR / "modeldata").mkdir()
	(LOCAL_DB_DIR / "obsdata").mkdir()

Fortunately, tempfile.mkdtemp() is used here. It creates a new temporary directory each time, so there is no interference between users.

However, like on my last comment I would prefer these temporary files to be provided by fixtures.

[avaldebe]

PR #694 dealt with the use of temporary files, and PR #691 updates the testdata-minimal scripts.
Should this issue be closed then #691 gets merged or is there more than needs to be patched up?