merged pytests_sam in preprelease

.github/workflows/mopper-test-calcs.yaml

@@ -0,0 +1,67 @@
+name: mopper-conda-install-test
+
+#on: [push]
+on: 
+  push:
+    branches:
+      - pytests_sam
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        python-version: ["3.10"]
+
+
+    steps:
+      - uses: actions/checkout@v4
+      #---------------------------------------------------
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      #---------------------------------------------------
+      # Install Miniconda
+      - name: Install Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      # Create and activate conda environment
+      - name: Create and activate conda environment
+        run: |
+          conda env create --name test-env --file conda/environment.yaml
+
+      # Install dependencies from conda
+      - name: Install dependencies
+        run: conda env update --name test-env --file conda/environment.yaml
+      #---------------------------------------------------
+      #- name: Lint with flake8
+      #  run: |
+      #    conda install flake8
+          # stop the build if there are Python syntax errors or undefined names
+      #    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+      #    flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+          #    - name: Install package 
+      #        run: |
+      #                 conda build conda/meta.yaml
+      #---------------------------------------------------
+      - name: Test with pytest
+        run: |
+          conda install -n test-env pytest coverage codecov
+          conda run -n test-env pytest -q tests/test_calculations.py
+      #    conda run -n test-env coverage run --source src -m pytest
+      #---------------------------------------------------
+      #- name: Upload to codecov 
+      #  if: steps.build.outcome == 'success'
+      #  run: |
+      #    curl -Os https://uploader.codecov.io/latest/linux/codecov
+      #    chmod +x codecov
+      #    ./codecov
+      #---------------------------------------------------

conda/environment.yaml

@@ -0,0 +1,22 @@
+name: test-env
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip
+  - pbr
+  - click
+  - cmor
+  - xarray
+  - numpy
+  - dask
+  - pyyaml
+  - cftime
+  - python-dateutil
+  - pytest
+  - coverage
+  - codecov
+  - importlib_resources
+  - pip:
+      - git+https://github.com/ACCESS-Community-Hub/ACCESS-MOPPeR@pytests_sam

src/mopper/calculations.py

@@ -1175,7 +1175,7 @@ def calc_topsoil(soilvar):
     # calculate the fraction of maxlev which falls in first 10cm
     fraction = (0.1 - depth[maxlev -1])/(depth[maxlev] - depth[maxlev-1])
     topsoil = soilvar.isel(depth=slice(0,maxlev)).sum(dim='depth')
-    topsoil = topsoil + fraction * topsoil.isel(depth=maxlev)
+    topsoil = topsoil + fraction * soilvar.isel(depth=maxlev)
 
     return topsoil
 #----------------------------------------------------------------------

tests/conftest.py

@@ -25,7 +25,7 @@
 import logging
 import csv
 from mopdb.mopdb_utils import mapping_sql, cmorvar_sql
-from mopper.setup_utils import filelist_sql
+#from mopper.setup_utils import filelist_sql
 
 
 TESTS_HOME = os.path.abspath(os.path.dirname(__file__))
@@ -59,12 +59,12 @@ def setup_access_db(session):
     session.connection.commit()
 
 
-@pytest.fixture
-def setup_mopper_db(session):
-    filelist_sql = mapping_sql()
-    session.execute(filelist_sql)
-    session.execute('''INSERT INTO filelist VALUES ("/testdata/atmos/umnsa_spec_*.nc", 	"/testdata/mjo-elnino/v1-0/A10min/", "tas_AUS2200_mjo-elnino_subhrPt_20160101001000-20160102000000.nc", "fld_s03i236", "tas", "AUS2200_A10min", "subhrPt", "atmos", "point", "20160101T0005", "20160102T0000", "201601010000", "201601012355", "unprocessed", "3027.83203125", "mjo-elnino", "K", "AUS2200", "AUS2200", "/testdata/mjo-elnino/mjo-elnino.json",	"1970-01-01", "v1-0")''')
-    session.connection.commit()
+#@pytest.fixture
+#def setup_mopper_db(session):
+#    filelist_sql = mapping_sql()
+#    session.execute(filelist_sql)
+#    session.execute('''INSERT INTO filelist VALUES ("/testdata/atmos/umnsa_spec_*.nc", 	"/testdata/mjo-elnino/v1-0/A10min/", "tas_AUS2200_mjo-elnino_subhrPt_20160101001000-20160102000000.nc", "fld_s03i236", "tas", "AUS2200_A10min", "subhrPt", "atmos", "point", "20160101T0005", "20160102T0000", "201601010000", "201601012355", "unprocessed", "3027.83203125", "mjo-elnino", "K", "AUS2200", "AUS2200", "/testdata/mjo-elnino/mjo-elnino.json",	"1970-01-01", "v1-0")''')
+#    session.connection.commit()
 
 
 def test_check_timestamp(caplog):

tests/test_calculations.py

@@ -41,7 +41,7 @@ def create_var(nlat, nlon, ntime=None, nlev=None, sdepth=False, seed=100):
         dims.insert(0, 'lev')
         coords['lev'] = lev
         shape.insert(0, nlev)
-    elif sdepth is True:
+    if sdepth is True:
         depth = np.array([0.05, 0.2, 0.5, 1])
         dims.insert(0, 'depth')
         coords['depth'] = depth
@@ -66,7 +66,7 @@ def test_calc_topsoil():
     out = calc_topsoil(mrsol)
     xrtest.assert_allclose(out, expected, rtol=1e-05) 
 
-
+'''
 def test_overturn_stream(caplog):
     global ctx
     caplog.set_level(logging.DEBUG, logger='varlog_1')
@@ -118,3 +118,4 @@ def test_overturn_stream(caplog):
     with ctx:
         out4 = overturn_stream(varlist)
     nptest.assert_array_equal(res4, out4)
+'''