Merging prerelease into pytests_sam

.github/workflows/mopper-conda.yaml

@@ -14,6 +14,7 @@ on:
 jobs:
   build-linux:
     runs-on: ubuntu-latest
+    timeout-minutes: 60
     strategy:
       max-parallel: 5
 
@@ -22,27 +23,28 @@ jobs:
     - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.10
+        python-version: '3.10'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda env update --file conda/environment.yml --name base 
+        conda env update --file env.yaml --name base 
     - name: Lint with flake8
       run: |
-        conda install flake8
+        conda install flake8 --solver classic
         # 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: install package
+      run: |
+        source activate base
+        pip install ./
     - name: Test with pytest
       run: |
-        conda install pytest coverage codecov
+        conda install pytest coverage codecov --solver classic
         conda run python -m pytest
         conda run coverage run --source src -m py.test
     - name: Upload to codecov 

conda/meta.yaml

@@ -1,15 +1,14 @@
-{% set version = "1.0.0" %}
 package:
     name: mopper 
-    version: {{ version }}
+    version: 1.0.0
 
 #source:
 #    path: ./
 
 source:
   #url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR/archive/refs/tags/{{version}}.tar.gz
   git_url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR.git
-  git_rev: {{ version }} 
+  git_rev: "{{ version }}" 
   git_depth: 1 # (Defaults to -1/not shallow)
 
 build:

docs/gettingstarted.rst

@@ -56,7 +56,7 @@ Step2: Set up the working environment
    *mop -c <conf_exp.yaml> setup*
 
 .. code-block:: console 
-https://climate-cms.org/posts/2023-05-31-vscode-are.html
+
    $ mop -c exp_conf.yaml setup
    Simulation to process: cy286
    Setting environment and creating working directory

env.yaml

@@ -0,0 +1,10 @@
+name: mopenv
+channels:
+  - conda-forge
+dependencies:
+  - click
+  - cmor
+  - xarray
+  - numpy
+  - pyyaml
+  - dask

src/mopdb/mopdb_utils.py

@@ -663,7 +663,7 @@ def read_map(fname, alias):
                     notes = row[16]
                 else:
                     notes = row[15]
-                if alias is '':
+                if alias == '':
                     alias = fname.replace(".csv","")
                 var_list.append(row[:11] + [notes, alias])
     return var_list

src/mopper/calculations.py

@@ -39,7 +39,7 @@
 import dask
 import logging
 
-from importlib_resources import files as import_files
+from importlib.resources import files as import_files
 from mopper.setup_utils import read_yaml
 
 # Global Variables
@@ -950,7 +950,7 @@ def tos_3hr(var, landfrac):
     vout : Xarray dataset
     """    
 
-    v = tos_degC(var)
+    v = K_degC(var)
 
     vout = xr.zeros_like(var)
     t = len(var.time)
@@ -1346,6 +1346,7 @@ def get_basin_mask(ctx, lat, lon):
     basin_mask: DataArray
         basin_mask(lat,lon)
     """
+    var_log = logging.getLogger(ctx.obj['var_log'])
     coords = ['t', 't']
     if 'xu' in lon:
         coords[0] = 'u'
@@ -1443,6 +1444,6 @@ def calc_depositions(ctx, var, weight=None):
         varlist.append(v0)
     if weight is None:
         weight = 0.05844
-    deps = sum_vars(varlist) * mole_weight
+    deps = sum_vars(varlist) * weight
     return deps
 

src/mopper/mop_utils.py

@@ -40,7 +40,7 @@
 
 from mopper.calculations import *
 from mopper.setup_utils import read_yaml
-from importlib_resources import files as import_files
+from importlib.resources import files as import_files
 
 
 def config_log(debug, path, stream_level=logging.WARNING):

src/mopper/setup_utils.py

@@ -40,10 +40,11 @@
 from collections import OrderedDict
 from datetime import datetime#, timedelta
 from dateutil.relativedelta import relativedelta
-from importlib_resources import files as import_files
+from importlib.resources import files as import_files
 from json.decoder import JSONDecodeError
 
 from mopdb.mopdb_utils import query
+from mopper.cmip_utils import fix_years
 
 
 def write_var_map(outpath, table, matches):
@@ -166,7 +167,7 @@ def find_custom_tables(ctx):
     mop_log = logging.getLogger('mop_log')
     tables = []
     path = ctx.obj['tables_path']
-    tables = ctx.obj['tables_path'].rglob("*_*.json")
+    table_files = ctx.obj['tables_path'].rglob("*_*.json")
     for f in table_files:
         f = str(f).replace(".json", "")
         tables.append(f)
@@ -626,9 +627,8 @@ def define_files(ctx, cursor, opts, mp):
     if mp['years'] != 'all' and ctx.obj['dreq_years']:
         exp_start, exp_end = fix_years(mp['years'], exp_start[:4], exp_end[:4]) 
         if exp_start is None:
-            mop_log.info("Years requested for variable are outside specified") 
-            mop_log.info((f"period: {table_id}, {var},",  
-                   f"{match['tstart']}, {match['tend']}"))
+            mop_log.info(f"""Years requested for variable are outside
+                specified period: {mp['years']}""")
             return
     tstep_dict = {'10min': ['minutes=10', 'minutes=5'],
               '30min': ['minutes=30', 'minutes=15'],