Fix create_test_conda_env: isolate version, add submodules, fix tests

- Move __version__ to _version.py to avoid importing cmor during pip build
- Update pyproject.toml to read version from fremorizer._version
- Add submodules: recursive to checkout step in workflow
- Add nccmp to environment.yaml (needed by tests)
- Fix test_find_statics_file_success to use tmp_path (avoid test pollution)
- Fix test_setup_fre_cmor_run_subtool to create output directory

Agent-Logs-Url: https://github.com/ilaflott/fremorizer/sessions/9d29eafc-3795-4808-ba85-95ab00fa460f

Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>

Author: Copilot

.github/workflows/create_test_conda_env.yml

@@ -20,6 +20,8 @@ jobs:
     steps:
       - name: Checkout Files
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Setup Conda
         uses: conda-incubator/setup-miniconda@v3

environment.yaml

@@ -13,3 +13,4 @@ dependencies:
   - conda-forge::pytest
   - conda-forge::pytest-cov
   - conda-forge::pylint
+  - conda-forge::nccmp

fremorizer/__init__.py

@@ -3,9 +3,8 @@
 """
 
 import logging
-import os
-version = os.getenv("GIT_DESCRIBE_TAG", "2026.01.alpha1")
-__version__ = version
+
+from ._version import __version__, version
 
 fre_logger = logging.getLogger(__name__)
 

fremorizer/_version.py

@@ -0,0 +1,7 @@
+"""
+version info for fremorizer, isolated to avoid importing heavy dependencies at build time
+"""
+
+import os
+version = os.getenv("GIT_DESCRIBE_TAG", "2026.01.alpha1")
+__version__ = version

fremorizer/tests/test_cmor_helpers.py

@@ -21,26 +21,25 @@ def test_iso_to_bronx_chunk():
                        match='problem with converting to bronx chunk from the cmor chunk. check cmor_yamler.py'):
         iso_to_bronx_chunk('foo')
 
-def test_find_statics_file_success():
+def test_find_statics_file_success(tmp_path):
     ''' what happens when no statics file is found given a bronx directory structure '''
-    target_file = 'fremorizer/tests/test_files/ascii_files/mock_archive/' + \
-                  'USER/CMIP7/ESM4/DEV/ESM4.5v01_om5b04_piC/' + \
-                  'gfdl.ncrc5-intel23-prod-openmp/pp/ocean_monthly/ts/monthly/5yr/ocean_monthly.000101-000102.sos.nc'
-    if not Path(target_file).exists():
-        Path(target_file).touch()
-    assert Path(target_file).exists()
-
-    expected_answer_statics_file = 'fremorizer/tests/test_files/ascii_files/mock_archive/' + \
-                                   'USER/CMIP7/ESM4/DEV/ESM4.5v01_om5b04_piC/' + \
-                                   'gfdl.ncrc5-intel23-prod-openmp/pp/ocean_monthly/ocean_monthly.static.nc'
-    if not Path(expected_answer_statics_file).exists():
-        Path(expected_answer_statics_file).touch()
-    assert Path(expected_answer_statics_file).exists
-
-    statics_file = find_statics_file( bronx_file_path = target_file
-                                      )
+    mock_root = tmp_path / 'mock_archive'
+    bronx_subpath = ('USER/CMIP7/ESM4/DEV/ESM4.5v01_om5b04_piC/'
+                     'gfdl.ncrc5-intel23-prod-openmp/pp/ocean_monthly')
+
+    target_file = mock_root / bronx_subpath / 'ts/monthly/5yr/ocean_monthly.000101-000102.sos.nc'
+    target_file.parent.mkdir(parents=True, exist_ok=True)
+    target_file.touch()
+    assert target_file.exists()
+
+    expected_answer_statics_file = mock_root / bronx_subpath / 'ocean_monthly.static.nc'
+    expected_answer_statics_file.parent.mkdir(parents=True, exist_ok=True)
+    expected_answer_statics_file.touch()
+    assert expected_answer_statics_file.exists()
+
+    statics_file = find_statics_file( bronx_file_path = str(target_file) )
     assert Path(statics_file).exists()
-    assert statics_file == expected_answer_statics_file
+    assert statics_file == str(expected_answer_statics_file)
 
 
 def test_find_statics_file_nothing_found():

fremorizer/tests/test_cmor_run_subtool.py

@@ -68,6 +68,7 @@ def test_setup_fre_cmor_run_subtool(capfd):
     ncgen_input = f"{ROOTDIR}/reduced_ascii_files/{FILENAME}.cdl"
     ncgen_output = f"{ROOTDIR}/ocean_sos_var_file/{FILENAME}.nc"
 
+    Path(ncgen_output).parent.mkdir(parents=True, exist_ok=True)
     if Path(ncgen_output).exists():
         Path(ncgen_output).unlink()
     assert Path(ncgen_input).exists()

pyproject.toml

@@ -41,7 +41,7 @@ dynamic = [
 
 
 [tool.setuptools.dynamic]
-version = {attr = "fremorizer.__version__"}
+version = {attr = "fremorizer._version.__version__"}
 
 
 [project.scripts]