Merge pull request #491 from metno/main-dev

Version 0.12.1

MANIFEST.in

@@ -3,3 +3,4 @@ include README.rst
 include VERSION.md
 include pyaerocom_env.yml
 include pytest.ini
+recursive-include tests/ *

VERSION.md

@@ -1 +1 @@
-0.12.0
+0.12.1

pyaerocom/ungriddeddata.py

@@ -1468,7 +1468,7 @@ def check_unit(self, var_name, unit=None):
                 raise MetaDataError(
                     f'Invalid unit {u} detected (expected {unit})')
 
-    def set_flags_nan(self, inplace=False, verbose=False):
+    def set_flags_nan(self, inplace=False):
         """Set all flagged datapoints to NaN
 
         Parameters

tests/aeroval/test_aeroval_HIGHLEV.py

@@ -1,5 +1,6 @@
 import pytest
 import os, glob
+from ..conftest import geojson_unavail
 from pyaerocom.aeroval import ExperimentProcessor
 from pyaerocom.aeroval.setupclasses import EvalSetup
 from .cfg_test_exp1 import CFG as cfgexp1
@@ -40,6 +41,7 @@
     'ts/diurnal': 0 # number of .json files in subdir
 }
 
+@geojson_unavail
 @pytest.mark.parametrize('cfgdict,chk_files',[
     (cfgexp1,CHK_CFG1),
     (cfgexp2,CHK_CFG2),

tests/aeroval/test_experiment_output.py

@@ -5,7 +5,7 @@
 from pyaerocom._lowlevel_helpers import read_json,write_json
 from pyaerocom.aeroval import experiment_output as mod, ExperimentProcessor
 from pyaerocom.aeroval.setupclasses import EvalSetup
-from ..conftest import does_not_raise_exception
+from ..conftest import does_not_raise_exception, geojson_unavail
 from .cfg_test_exp1 import CFG as cfgexp1
 BASEDIR_DEFAULT = os.path.join(const.OUTPUTDIR, 'aeroval/data')
 from ._outbase import AEROVAL_OUT as BASEOUT
@@ -203,13 +203,15 @@ def test_ExperimentOutput_delete_experiment_data_CFG1():
     proc.exp_output.delete_experiment_data()
     assert not os.path.exists(chk)
 
+@geojson_unavail
 def test_Experiment_Output_clean_json_files_CFG1():
     cfg = EvalSetup(**cfgexp1)
     proc = ExperimentProcessor(cfg)
     proc.run()
     modified = proc.exp_output.clean_json_files()
     assert len(modified) == 0
 
+@geojson_unavail
 def test_Experiment_Output_clean_json_files_CFG1_INVALIDMOD():
     cfg = EvalSetup(**cfgexp1)
     cfg.model_cfg['mod1'] = cfg.model_cfg['TM5-AP3-CTRL']
@@ -219,6 +221,7 @@ def test_Experiment_Output_clean_json_files_CFG1_INVALIDMOD():
     modified = proc.exp_output.clean_json_files()
     assert len(modified) == 15
 
+@geojson_unavail
 def test_Experiment_Output_clean_json_files_CFG1_INVALIDOBS():
     cfg = EvalSetup(**cfgexp1)
     cfg.obs_cfg['obs1'] = cfg.obs_cfg['AERONET-Sun']

tests/aeroval/test_experiment_processor.py

@@ -9,7 +9,8 @@
 from .cfg_test_exp3 import CFG as cfgexp3
 from .cfg_test_exp4 import CFG as cfgexp4
 from .cfg_test_exp5 import CFG as cfgexp5
-from ..conftest import does_not_raise_exception
+from ..conftest import does_not_raise_exception, geojson_unavail
+
 
 @pytest.mark.parametrize('cfgdict,raises', [
     (cfgexp1,does_not_raise_exception())
@@ -21,6 +22,7 @@ def test_ExperimentProcessor___init__(cfgdict,raises):
         assert isinstance(proc.cfg, EvalSetup)
         assert isinstance(proc.exp_output, ExperimentOutput)
 
+@geojson_unavail
 @pytest.mark.parametrize('cfgdict,runkwargs,raises', [
     (cfgexp5,{},does_not_raise_exception()),
     (cfgexp1,{},does_not_raise_exception()),

tests/conftest.py

@@ -106,6 +106,15 @@
 data_unavail = pytest.mark.skipif(not TESTDATA_AVAIL,
                     reason='Skipping tests that require testdata-minimal.')
 
+try:
+    import geojsoncontour
+    geojson_avail = True
+except ModuleNotFoundError:
+    geojson_avail = False
+
+geojson_unavail = pytest.mark.skipif(not geojson_avail,
+                   reason='Skipping tests that require access geojsoncontour')
+
 broken_test = pytest.mark.skip(reason='Method raises Exception')
 
 from pyaerocom import change_verbosity

tests/test_geodesy.py

@@ -1,10 +1,3 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Mon Feb  4 10:36:15 2019
-
-@author: jonasg
-"""
 import numpy.testing as npt
 import pytest