Merge pull request #321 from metno/release_0_10_1

Release branch for version 0.10.1

VERSION.md

@@ -1 +1 @@
-0.10.0
+0.10.1

docs/install.rst

@@ -1,23 +1,20 @@
 Installation
 ============
 
-You have several options to install pyaerocom, the first one is the easiest, but may not refer to the most recent (non-released) version of pyaerocom. So please check first, which version you are interested in.
+You can install pyaerocom via conda, pip or from source.
 
 Via conda
 ^^^^^^^^^
 
-**NOTE:** This will install the latest release of pyaerocom.
-
-- It hence, may not include the most recent developments.
-- Requirements are installed automatically.
-
-If you use *conda* as a package manager, the easiest way to install pyaerocom (and all requirements, see previous section) is to use the build provided in the *nordicesmhub* conda channel::
+The easiest way to install pyaerocom and all requirements using conda. You can install pyaerocom into a pre-existing conda environment via::
 
 	conda install -c conda-forge pyaerocom
 
-This will install the latest release of pyaerocom including all requirements. Alternatively, you may install from source as described in the following.
+Or into a new conda environment (recommended) named *pya* via::
+
+	conda create -c conda-forge --name pya pyaerocom
 
-**NOTE**: installation support via conda as described above is quite recent, so please let us know if you run into problems with the installation (best way to do this is by raising an issue `here <https://github.com/metno/pyaerocom/issues>`__).
+This will install the latest release of pyaerocom including all requirements. Alternatively, you may install via  pip or from source as described in the following.
 
 Via PyPi
 ^^^^^^^^
@@ -42,7 +39,7 @@ Alternatively, if you plan to apply local changes to the pyaerocom source code,
 
 	python setup.py develop
 
-You may also download and extract (or clone) the `GitHub repo <https://github.com/metno/pyaerocom>`__ to install the very latest (not yet released) version of pyaerocom.
+You may also download and extract (or clone) the `GitHub repo <https://github.com/metno/pyaerocom>`__ to install the very latest (not yet released) version of pyaerocom. Note, if you install in develop mode, make sure you do not have pyaerocom installed already in the site packages directory, check e.g. `conda list pyaerocom`.
 
 
 Requirements

pyaerocom/colocation.py

@@ -821,9 +821,23 @@ def colocate_gridded_ungridded(gridded_data, ungridded_data, ts_type=None,
             min_num_obs=min_num_obs,
             use_climatology_ref=use_climatology_ref)
 
-        # assign the unified timeseries data to the colocated data array
-        coldata[0, :, i] = _df['ref'].values
-        coldata[1, :, i] = _df['data'].values
+
+        # this try/except block was introduced on 23/2/2021 as temporary fix from
+        # v0.10.0 -> v0.10.1 as a result of multi-weekly obsdata (EBAS) that
+        # can end up resulting in incorrect number of timestamps after resampling
+        # (the error was discovered using EBASMC, concpm10, 2019 and colocation
+        # frequency monthly)
+        try:
+            # assign the unified timeseries data to the colocated data array
+            coldata[0, :, i] = _df['ref'].values
+            coldata[1, :, i] = _df['data'].values
+        except ValueError as e:
+            const.print_log.warning(
+                f'Failed to colocate time for station {obs_stat.station_name}. '
+                f'This station will be skipped (error: {e})'
+                )
+
+
 
         lons.append(obs_stat.longitude)
         lats.append(obs_stat.latitude)

pyaerocom/colocation_auto.py

@@ -661,7 +661,8 @@ def _eval_obs_filters(self):
                                  'Colocator class, which is not a '
                                  'dictionary: {}'.format(obs_filters))
         for key, val in obs_filters.items():
-            if key in self: # can be handled
+            # keep ts_type filter in remaining (added on 17.2.21, 0.100 -> 0.10.1)
+            if key in self and not key == 'ts_type': # can be handled
                 if isinstance(self[key], dict) and isinstance(val, dict):
                     self[key].update(val)
                 else:

pyaerocom/io/iris_io.py

@@ -100,20 +100,6 @@ def load_cubes_custom(files, var_name=None, file_convention=None,
             - list, list of filenames that were successfully loaded
     """
     from pyaerocom import const
-# =============================================================================
-#     if len(files) >= 1000:
-#         try:
-#             cubes =  _load_cubes_custom_multiproc(files, var_name,
-#                                                   file_convention,
-#                                                   perform_fmt_checks,
-#                                                   **kwargs)
-#             # if this worked, all input files were successfully loaded and the
-#             # function terminates, else, the retrieval is done file by file.
-#             # ... Maybe!
-#             return (cubes, files)
-#         except Exception:
-#             pass
-# =============================================================================
     cubes = []
     loaded_files = []
     print_where = False

pyaerocom/test/test_geodesy.py

@@ -31,6 +31,7 @@ def test_is_within_radius_km():
     assert geodesy.is_within_radius_km(0, 15, 0, 16, 1000, 111.2)
 
 @geonum_unavail
+@pytest.mark.skip(reason='https://github.com/tkrajina/srtm.py/issues/51')
 def test_srtm_altitude():
     npt.assert_almost_equal(geodesy.get_topo_altitude(TEST_LAT, TEST_LON), 207)
 

pyaerocom/time_config.py

@@ -11,9 +11,6 @@
 
 # The following import was removed and the information about available unit
 # strings was copied from the netCDF4 module directly here
-# from netCDF4 import (microsec_units, millisec_units, sec_units, min_units,
-#                     hr_units, day_units)
-# from netCDF4._netCDF4 import _dateparse
 microsec_units = ['microseconds', 'microsecond', 'microsec', 'microsecs']
 millisec_units = ['milliseconds', 'millisecond', 'millisec', 'millisecs']
 sec_units = ['second', 'seconds', 'sec', 'secs', 's']

pyaerocom_env.yml

@@ -1,21 +1,18 @@
-# This only installs the requirment of pyaerocom, not pyaerocom itself.
-# Activate the envoirnment and run python setup.py.
-
+# This only installs the requirments of pyaerocom, not pyaerocom itself.
+# Activate the environment and run "python setup.py install".
 channels:
   - conda-forge
 dependencies:
-  - iris >= 2.1.0
-  - xarray >= 0.10.8
+  - iris >= 2.1.0, <3.0.0
+  - xarray >= 0.16.0
   - cartopy >= 0.16.0
   - matplotlib >= 3.0.1
   - scipy >= 1.1.0
-  - pandas >= 0.23.0
+  - pandas >= 0.23.0, <=1.2.2
   - seaborn >= 0.8.0
-  - netcdf4
   - geonum
   - numpy
   - simplejson
   - requests
   - reverse-geocode
   - tqdm
-