Merge pull request #227 from ESMValGroup/fix_nightly_build

Fix nightly tests

Author: mattiarighi

.circleci/config.yml

@@ -51,7 +51,7 @@ jobs:
             conda update -y conda > /logs/conda.txt 2>&1
             conda env update >> /logs/conda.txt 2>&1
             set +x; conda activate esmvaltool; set -x
-            conda install -yS r-base r-yaml julia ncl -c conda-forge
+            conda install -yS r-base r-yaml ncl -c conda-forge
             pip install . > /logs/install.txt 2>&1
             # Log versions
             dpkg -l > /logs/versions.txt
@@ -120,6 +120,7 @@ jobs:
             conda update -y conda > /logs/conda.txt 2>&1
             conda env update >> /logs/conda.txt 2>&1
             set +x; conda activate esmvaltool; set -x
+            conda install -yS r-base r-yaml ncl -c conda-forge
             pip install -e .[develop] > /logs/install.txt 2>&1
             # Log versions
             dpkg -l > /logs/versions.txt

conda_build_config.yaml

@@ -5,7 +5,7 @@ channels:
 
 dependencies:
   - esmpy
-  - iris>=2.2
+  - iris>=2.2.1
   - graphviz
   - gcc_linux-64
   - libunwind  # Needed for Python3.7+

environment.yml

@@ -107,7 +107,7 @@ def derive(cubes,
                     "'%s' not found", fx_var, short_name)
 
     # Derive variable
-    DerivedVariable = ALL_DERIVED_VARIABLES[short_name]  # noqa: N806
+    DerivedVariable = ALL_DERIVED_VARIABLES[short_name.lower()]  # noqa: N806
     cube = DerivedVariable().calculate(cubes)
 
     # Set standard attributes

esmvalcore/preprocessor/_derive/__init__.py

@@ -22,23 +22,23 @@ build:
   # Increment the build number when building a new conda package of the same
   # esmvalcore version, reset to 0 when building a new version.
   number: 0
+  noarch: python
   script: |
       python setup.py install --single-version-externally-managed --record=/tmp/record.txt
 
 requirements:
   build:
     - git
-    - python {{ python }}
+    - python>=3.6
     # Normally installed via pip:
     - pytest-runner
     - setuptools_scm
   run:
     # esmvaltool
-    - python
+    - python>=3.6
     - libunwind  # specifically for Python3.7+
     - graphviz
-    - iris>=2.2
-    - matplotlib<3,>=2  # required by iris
+    - iris>=2.2.1
     - python-stratify
     # Normally installed via pip:
     - cf-units
@@ -52,7 +52,7 @@ requirements:
     - psutil
     - pydot
     - pyyaml
-    - yamale  # in esmvalgroup and birdhouse channel
+    - yamale  # in esmvalgroup channel
 
 test:
   # TODO: add unit tests? This seems to require installing the tests
@@ -68,5 +68,5 @@ about:
   home: https://www.esmvaltool.org
   license: Apache License, Version 2.0
   license_file: LICENSE
-  summary: "ESMValCore: core functionalities for the ESMValTool, a community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP."
-  description: "ESMValCore: core functionalities for the ESMValTool, a community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP."
+  summary: "ESMValCore: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts."
+  description: "ESMValCore: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts."

esmvalcore/preprocessor/_derive/cSoil_grid.py renamed to esmvalcore/preprocessor/_derive/csoil_grid.py

@@ -1,7 +1,9 @@
+import iris
 from iris.cube import Cube, CubeList
 
 from esmvalcore.preprocessor import derive
 from esmvalcore.preprocessor._derive import get_required
+from esmvalcore.preprocessor._derive.csoil_grid import DerivedVariable
 
 
 def test_get_required():
@@ -67,3 +69,32 @@ def test_derive_noop():
 
     print(cube)
     assert cube is alb
+
+
+def test_derive_mixed_case_with_fx(tmp_path, monkeypatch):
+
+    short_name = 'cSoil_grid'
+    long_name = 'Carbon Mass in Soil Pool relative to grid cell area'
+    units = 'kg m-2'
+
+    csoil_cube = Cube([])
+    fx_cube = Cube([])
+    fx_cube.var_name = 'sftlf'
+    fx_file = str(tmp_path / 'sftlf_file.nc')
+    iris.save(fx_cube, target=fx_file)
+
+    def mock_calculate(self, cubes):
+        assert len(cubes) == 2
+        assert cubes[0] == csoil_cube
+        assert cubes[1].var_name == fx_cube.var_name
+        return Cube([])
+
+    monkeypatch.setattr(DerivedVariable, 'calculate', mock_calculate)
+
+    derive(
+        [csoil_cube],
+        short_name,
+        long_name,
+        units,
+        fx_files={'sftlf': fx_file},
+    )

esmvalcore/preprocessor/_derive/cVeg_grid.py renamed to esmvalcore/preprocessor/_derive/cveg_grid.py

@@ -1,15 +1,15 @@
 """Test derivation of `cSoil_grid`."""
 import mock
 
-import esmvalcore.preprocessor._derive.cSoil_grid as cSoil_grid
+from esmvalcore.preprocessor._derive import csoil_grid
 
 CUBES = 'mocked cubes'
 STD_NAME = 'soil_carbon_content'
 
 
-@mock.patch.object(cSoil_grid, 'grid_area_correction', autospec=True)
-def test_cSoil_grid_calculation(mock_grid_area_correction):
+@mock.patch.object(csoil_grid, 'grid_area_correction', autospec=True)
+def test_csoil_grid_calculation(mock_grid_area_correction):
     """Test calculation of `cSoil_grid."""
-    derived_var = cSoil_grid.DerivedVariable()
+    derived_var = csoil_grid.DerivedVariable()
     derived_var.calculate(CUBES)
     mock_grid_area_correction.assert_called_once_with(CUBES, STD_NAME)

meta.yaml

@@ -1,15 +1,15 @@
 """Test derivation of `cVeg_grid`."""
 import mock
 
-import esmvalcore.preprocessor._derive.cVeg_grid as cVeg_grid
+from esmvalcore.preprocessor._derive import cveg_grid
 
 CUBES = 'mocked cubes'
 STD_NAME = 'vegetation_carbon_content'
 
 
-@mock.patch.object(cVeg_grid, 'grid_area_correction', autospec=True)
-def test_cVeg_grid_calculation(mock_grid_area_correction):
+@mock.patch.object(cveg_grid, 'grid_area_correction', autospec=True)
+def test_cveg_grid_calculation(mock_grid_area_correction):
     """Test calculation of `cVeg_grid."""
-    derived_var = cVeg_grid.DerivedVariable()
+    derived_var = cveg_grid.DerivedVariable()
     derived_var.calculate(CUBES)
     mock_grid_area_correction.assert_called_once_with(CUBES, STD_NAME)