Improve code, documentation and modularize test cases for config

benchcab/benchcab.py

@@ -133,7 +133,6 @@ def fluxsite_submit_job(
     ) -> None:
         """Submits the PBS job script step in the fluxsite test workflow."""
         config = self._get_config(config_path)
-
         self._validate_environment(project=config["project"], modules=config["modules"])
         if self.benchcab_exe_path is None:
             msg = "Path to benchcab executable is undefined."

benchcab/config.py

@@ -3,7 +3,6 @@
 
 """A module containing all *_config() functions."""
 import os
-import sys
 from pathlib import Path
 
 import yaml
@@ -91,10 +90,14 @@ def read_optional_key(config: dict):
             raise ValueError(msg)
         config["project"] = os.environ["PROJECT"]
 
-    # Directory List is obtained from Gadi Resources - https://opus.nci.org.au/display/Help/0.+Welcome+to+Gadi
-    data_dirs = ["/g/data", "/scratch"]
     groups = list(
-        set([group for data_dir in data_dirs for group in os.listdir(data_dir)])
+        set(
+            [
+                group
+                for data_dir in internal.USER_PROJECT_DIRS
+                for group in os.listdir(data_dir)
+            ]
+        )
     )
 
     if config["project"] not in groups:

benchcab/internal.py

@@ -10,7 +10,7 @@
 
 _, NODENAME, _, _, _ = os.uname()
 
-CONFIG_REQUIRED_KEYS = ["realisations", "modules", "experiment"]
+CONFIG_REQUIRED_KEYS = ["realisations", "modules"]
 
 # Parameters for job script:
 QSUB_FNAME = "benchmark_cable_qsub.sh"
@@ -28,6 +28,10 @@
 # Path to the user's current working directory
 CWD = Path.cwd()
 
+# Directory List is obtained from Gadi User Guide in Section - Gadi Resources
+# https://opus.nci.org.au/display/Help/0.+Welcome+to+Gadi
+USER_PROJECT_DIRS = ["/g/data", "/scratch"]
+
 # Path to the user's home directory
 HOME_DIR = Path(os.environ["HOME"])
 

tests/test_config.py

@@ -12,10 +12,21 @@
 import benchcab.internal as bi
 import benchcab.utils as bu
 
-# Temporarily set $PROJECT for testing module
+NO_OPTIONAL_CONFIG_PROJECT = "hh5"
 OPTIONAL_CONFIG_PROJECT = "ks32"
 
 
+# Temporarily set $PROJECT for testing module
+@pytest.fixture(autouse=True, scope="module")
+def _set_project_validation_dirs():
+    with mock.patch("os.listdir") as mocked_listdir:
+        mocked_listdir.return_value = [
+            NO_OPTIONAL_CONFIG_PROJECT,
+            OPTIONAL_CONFIG_PROJECT,
+        ]
+        yield
+
+
 @pytest.fixture(autouse=True)
 def _set_project_env_variable(monkeypatch):
     # Clear existing environment variables first
@@ -24,13 +35,6 @@ def _set_project_env_variable(monkeypatch):
         yield
 
 
-@pytest.fixture(autouse=True)
-def _set_project_validation_dirs():
-    with mock.patch("os.listdir") as mocked_listdir:
-        mocked_listdir.return_value = ["hh5", OPTIONAL_CONFIG_PROJECT]
-        yield
-
-
 @pytest.fixture()
 def config_str(request) -> str:
     """Provide relative YAML path string of data files."""
@@ -50,10 +54,10 @@ def empty_config() -> dict:
 
 
 @pytest.fixture()
-def default_only_config() -> dict:
+def no_optional_config() -> dict:
     """Config with no optional parameters.
 
-    Reads from config-basic.yml
+    Expected value after reading from config-basic.yml
     """
     return {
         "modules": ["intel-compiler/2021.1.1", "netcdf/4.7.4", "openmpi/4.1.0"],
@@ -69,12 +73,12 @@ def default_only_config() -> dict:
 
 
 @pytest.fixture()
-def all_optional_default_config(default_only_config) -> dict:
-    """Config with all optional parameters set as default.
+def all_optional_default_config(no_optional_config) -> dict:
+    """Populate all keys in config with default optional values.
 
-    Reads from config-basic.yml
+    Expected value after reading from config-basic.yml
     """
-    config = default_only_config | {
+    config = no_optional_config | {
         "project": OPTIONAL_CONFIG_PROJECT,
         "fluxsite": {
             "experiment": bi.FLUXSITE_DEFAULT_EXPERIMENT,
@@ -90,13 +94,13 @@ def all_optional_default_config(default_only_config) -> dict:
 
 
 @pytest.fixture()
-def all_optional_custom_config(default_only_config) -> dict:
-    """Config with custom optional parameters.
+def all_optional_custom_config(no_optional_config) -> dict:
+    """Populate all keys in config with custom optional values.
 
-    Reads from config-optional.yml
+    Expected value after reading from config-optional.yml
     """
-    config = default_only_config | {
-        "project": "hh5",
+    config = no_optional_config | {
+        "project": NO_OPTIONAL_CONFIG_PROJECT,
         "fluxsite": {
             "experiment": "AU-Tum",
             "multiprocess": False,
@@ -126,7 +130,7 @@ def all_optional_custom_config(default_only_config) -> dict:
 @pytest.mark.parametrize(
     ("config_str", "output_config", "pytest_error"),
     [
-        ("config-basic.yml", "default_only_config", does_not_raise()),
+        ("config-basic.yml", "no_optional_config", does_not_raise()),
         ("config-optional.yml", "all_optional_custom_config", does_not_raise()),
         ("config-missing.yml", "empty_config", pytest.raises(FileNotFoundError)),
     ],
@@ -155,44 +159,45 @@ def test_validate_config(config_str, pytest_error):
         assert bc.validate_config(config)
 
 
-@pytest.mark.parametrize(
-    ("input_config", "output_config"),
-    [
-        ("default_only_config", "all_optional_default_config"),
-        ("all_optional_default_config", "all_optional_default_config"),
-        ("all_optional_custom_config", "all_optional_custom_config"),
-    ],
-)
-def test_read_optional_key_add_data(input_config, output_config, request):
-    """Test default key-values are added if not provided by config.yaml, and existing keys stay intact."""
-    config = request.getfixturevalue(input_config)
-    bc.read_optional_key(config)
-    assert pformat(config) == pformat(request.getfixturevalue(output_config))
-
+class TestReadOptionalKey:
+    """Tests related to adding optional keys in config."""
 
-def test_no_project_name(default_only_config, monkeypatch):
-    """If project key and $PROJECT are not provided, then raise error."""
-    monkeypatch.delenv("PROJECT")
-    err_msg = re.escape(
-        """Couldn't resolve project: check 'project' in config.yaml
-                and/or $PROJECT set in ~/.config/gadi-login.conf
-                """
+    @pytest.mark.parametrize(
+        ("input_config", "output_config"),
+        [
+            ("no_optional_config", "all_optional_default_config"),
+            ("all_optional_default_config", "all_optional_default_config"),
+            ("all_optional_custom_config", "all_optional_custom_config"),
+        ],
     )
-    with pytest.raises(ValueError, match=err_msg):
-        bc.read_optional_key(default_only_config)
-
+    def test_read_optional_key_add_data(self, input_config, output_config, request):
+        """Test default key-values are added if not provided by config.yaml, and existing keys stay intact."""
+        config = request.getfixturevalue(input_config)
+        bc.read_optional_key(config)
+        assert pformat(config) == pformat(request.getfixturevalue(output_config))
 
-def test_user_not_in_project(default_only_config):
-    """If user is not in viewable NCI projects, raise error."""
-    default_only_config["project"] = "non_existing"
-    err_msg = re.escape(
-        "User is not a member of project [non_existing]: Check if project key is correct"
-    )
-    with pytest.raises(
-        ValueError,
-        match=err_msg,
-    ):
-        bc.read_optional_key(default_only_config)
+    def test_no_project_name(self, no_optional_config, monkeypatch):
+        """If project key and $PROJECT are not provided, then raise error."""
+        monkeypatch.delenv("PROJECT")
+        err_msg = re.escape(
+            """Couldn't resolve project: check 'project' in config.yaml
+                and/or $PROJECT set in ~/.config/gadi-login.conf
+            """
+        )
+        with pytest.raises(ValueError, match=err_msg):
+            bc.read_optional_key(no_optional_config)
+
+    def test_user_not_in_project(self, no_optional_config):
+        """If user is not in viewable NCI projects, raise error."""
+        no_optional_config["project"] = "non_existing"
+        err_msg = re.escape(
+            "User is not a member of project [non_existing]: Check if project key is correct"
+        )
+        with pytest.raises(
+            ValueError,
+            match=err_msg,
+        ):
+            bc.read_optional_key(no_optional_config)
 
 
 @pytest.mark.parametrize(