Merge a115d65 into 08a1b1a

.github/workflows/run-tests.yml

@@ -24,7 +24,7 @@ jobs:
           - workflow-multi
           - graphics-mpl
         container:
-          - ghcr.io/oggm/untested_base:20211114
+          - ghcr.io/oggm/untested_base:20220320
           - ghcr.io/oggm/untested_base:py3.7
           - ghcr.io/oggm/untested_base:py3.9
         include:

docs/api.rst

@@ -288,9 +288,9 @@ Users usually don't have to care about *where* the data is located.
 
     fdem = gdir.get_filepath('dem')
     fdem
-    import xarray as xr
+    import rioxarray as rioxr
     @savefig plot_gdir_dem.png width=80%
-    xr.open_rasterio(fdem).plot(cmap='terrain');
+    rioxr.open_rasterio(fdem).plot(cmap='terrain');
 
 This persistence on disk allows for example to continue a workflow that has
 been previously interrupted. Initialising a GlacierDirectory from a non-empty

docs/cloud.rst

@@ -18,6 +18,8 @@ link below to get you started!
 .. image:: https://img.shields.io/badge/Launch-OGGM%20tutorials-579ACA.svg?style=popout&logo=data:image/png;base64,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
   :target: https://mybinder.org/v2/gh/OGGM/binder/stable?urlpath=git-pull?repo=https://github.com/OGGM/tutorials%26amp%3Bbranch=master%26amp%3Burlpath=lab/tree/tutorials/notebooks/welcome.ipynb%3Fautodecode
 
+<br>
+
 If you are new to the Jupyter Notebooks or to JupyterLab, you will probably
 find this `introduction to interactive notebooks`_ quite useful.
 

docs/installing-oggm.rst

@@ -64,6 +64,7 @@ GIS tools:
     - shapely
     - pyproj
     - rasterio
+    - rioxarray
     - geopandas
 
 Testing:
@@ -113,7 +114,7 @@ window, type::
     conda create --name oggm_env python=3.X
 
 
-where ``3.X`` is the Python version shipped with conda (currently 3.8).
+where ``3.X`` is the Python version shipped with conda (currently 3.9).
 You can of course use any other name for your environment.
 
 Don't forget to activate it before going on::
@@ -124,15 +125,20 @@ Don't forget to activate it before going on::
 .. _environment: https://conda.io/projects/conda/en/latest/user-guide/concepts/environments.html
 
 
-Feeling adventurous? Try mamba (optional)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In a hurry? Try mamba (optional)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The conda package manager has recently been criticized for being slow (it *is*
-quite slow to be honest). A new, faster tool is now available to replace conda: `mamba <https://mamba.readthedocs.io>`_.
-Mamba is a drop-in replacement for all conda commands.
-If you feel like it, install mamba in your conda environment (``conda install -c conda-forge mamba``)
+The conda package manager has been criticized for being slow (it *is*
+quite slow to be honest). A new, faster tool is now available
+to replace conda: `mamba <https://mamba.readthedocs.io>`_. Mamba is a drop-in
+replacement for all conda commands. If you feel like it, install mamba in your conda
+environment (``conda install -c conda-forge mamba``)
 and replace all occurrences of ``conda`` with ``mamba`` in the instructions below.
 
+*Note March 2022: soon, conda will use mamba per default. See
+`this post <https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community>`_
+for more info.*
+
 
 Install dependencies
 ~~~~~~~~~~~~~~~~~~~~
@@ -272,6 +278,11 @@ If everything worked fine, you should see something like::
 You can safely ignore deprecation warnings and other messages (if any),
 as long as the tests end without errors.
 
+.. important::
+
+   The tests (without the ``--run-slow`` option) should run in 5 to 10 minutes.
+   If this takes too long, this may be an indiv
+
 This runs a minimal suite of tests. If you want to run the entire test suite
 (including graphics and slow running tests), type::
 
@@ -303,7 +314,7 @@ environment from the following ``environment.yml`` file used to work::
     channels:
       - conda-forge
     dependencies:
-      - python=3.8
+      - python=3.9
       - jupyter
       - jupyterlab
       - numpy
@@ -324,6 +335,7 @@ environment from the following ``environment.yml`` file used to work::
       - cartopy
       - geopandas
       - rasterio
+      - rioxarray
       - seaborn
       - pytables
       - salem

docs/requirements.txt

@@ -13,6 +13,7 @@ scikit-image
 configobj
 joblib
 xarray
+rioxarray
 progressbar2
 pytest
 tables

docs/whats-new.rst

@@ -83,7 +83,7 @@ Enhancements
   glacier geometry at the start of the simulation is iteratively changed with
   a short constant climate run with a varying temperature bias
   (:pull:`1342`, :pull:`1361`).
-  By `Patrick Schmitt <https://github.com/pat-schmitt/>`_
+  By `Patrick Schmitt <https://github.com/pat-schmitt>`_
 - Added new options to `write_centerlines_to_shape` which allow to output
   smoother and more correct centerlines (:pull:`1357`).
   By `Fabien Maussion <https://github.com/fmaussion>`_

oggm/__init__.py

@@ -21,6 +21,10 @@
 except ImportError:
     pass
 
+# TODO: remove this when geopandas will behave a bit better
+import warnings
+warnings.filterwarnings(action='ignore', category=FutureWarning, module=r'.*geopandas')
+
 # API
 # Some decorators used by many
 from oggm.utils import entity_task, global_task

oggm/core/centerlines.py

@@ -19,7 +19,7 @@
 import copy
 from itertools import groupby
 from collections import Counter
-from distutils.version import LooseVersion
+from packaging.version import Version
 
 # External libs
 import numpy as np
@@ -28,9 +28,8 @@
 import scipy.signal
 import shapely.geometry as shpg
 from scipy.interpolate import RegularGridInterpolator
-from scipy.ndimage.filters import gaussian_filter1d
-from scipy.ndimage.morphology import distance_transform_edt
-from scipy.ndimage.measurements import label, find_objects
+from scipy.ndimage import (gaussian_filter1d, distance_transform_edt,
+                           label, find_objects)
 
 # Optional libs
 try:
@@ -1326,7 +1325,10 @@ def _point_width(normals, point, centerline, poly, poly_no_nunataks):
     # Make sure we are always returning a MultiLineString for later
     line = line.intersection(poly)
     if line.type == 'LineString':
-        line = shpg.MultiLineString([line])
+        try:
+            line = shpg.MultiLineString([line])
+        except shapely.errors.EmptyPartError:
+            return np.NaN, shpg.MultiLineString()
     elif line.type == 'MultiLineString':
         pass  # nothing to be done
     elif line.type == 'GeometryCollection':
@@ -1605,7 +1607,7 @@ def catchment_intersections(gdir):
                                   to_crs=gdir.grid.proj, inplace=True)
     except TypeError:
         # from_crs not available yet
-        if LooseVersion(gpd.__version__) >= LooseVersion('0.7.0'):
+        if Version(gpd.__version__) >= Version('0.7.0'):
             raise ImportError('You have installed geopandas v0.7 or higher. '
                               'Please also update salem for compatibility.')
         gdfc.crs = gdir.grid

oggm/core/flowline.py

@@ -4721,12 +4721,12 @@ def clean_merged_flowlines(gdir, buffer=None):
             oix = 9999
             if _overlap.length > 0 and fl1 != fl2 and fl2.flows_to != fl1:
                 if isinstance(_overlap, shpg.MultiLineString):
-                    if _overlap[0].coords[0] == fl1.line.coords[0]:
+                    if _overlap.geoms[0].coords[0] == fl1.line.coords[0]:
                         # if the head of overlap is same as the first line,
                         # best guess is, that the heads are close topgether!
-                        _ov1 = _overlap[1].coords[1]
+                        _ov1 = _overlap.geoms[1].coords[1]
                     else:
-                        _ov1 = _overlap[0].coords[1]
+                        _ov1 = _overlap.geoms[0].coords[1]
                 else:
                     _ov1 = _overlap.coords[1]
                 for _i, _p in enumerate(fl1.line.coords):
@@ -4762,7 +4762,7 @@ def clean_merged_flowlines(gdir, buffer=None):
             # if the tributary flowline is longer than the main line,
             # _line will contain multiple LineStrings: only keep the first
             if isinstance(_linediff, shpg.MultiLineString):
-                _linediff = _linediff[0]
+                _linediff = _linediff.geoms[0]
 
             if len(_linediff.coords) < 10:
                 bufferuse -= 1

oggm/core/gis.py

@@ -6,7 +6,7 @@
 import os
 import logging
 import warnings
-from distutils.version import LooseVersion
+from packaging.version import Version
 from functools import partial
 
 # External libs
@@ -16,9 +16,7 @@
 import xarray as xr
 import shapely.geometry as shpg
 import scipy.signal
-from scipy.ndimage.measurements import label
-from scipy.ndimage import binary_erosion
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import label, distance_transform_edt, binary_erosion
 from scipy.interpolate import griddata
 from scipy import optimize as optimization
 
@@ -358,7 +356,7 @@ def _get_nodata(rio_ds):
     if len(dem_list) == 1:
         dem_dss = [rasterio.open(dem_list[0])]  # if one tile, just open it
         dem_data = rasterio.band(dem_dss[0], 1)
-        if LooseVersion(rasterio.__version__) >= LooseVersion('1.0'):
+        if Version(rasterio.__version__) >= Version('1.0'):
             src_transform = dem_dss[0].transform
         else:
             src_transform = dem_dss[0].affine

oggm/shop/gcm_climate.py

@@ -1,7 +1,7 @@
 """Climate data pre-processing"""
 # Built ins
 import logging
-from distutils.version import LooseVersion
+from packaging.version import Version
 import warnings
 
 # External libs
@@ -209,7 +209,7 @@ def process_cesm_data(gdir, filesuffix='', fpath_temp=None, fpath_precc=None,
         fpath_precl = cfg.PATHS['cesm_precl_file']
 
     # read the files
-    if LooseVersion(xr.__version__) < LooseVersion('0.11'):
+    if Version(xr.__version__) < Version('0.11'):
         raise ImportError('This task needs xarray v0.11 or newer to run.')
 
     tempds = xr.open_dataset(fpath_temp)

oggm/tests/__init__.py

@@ -1,5 +1,5 @@
 import os
-from distutils.version import LooseVersion
+from packaging.version import Version
 
 import pytest
 import matplotlib.ft2font
@@ -12,7 +12,7 @@
 
 # Matplotlib version changes plots, too
 HAS_MPL_FOR_TESTS = False
-if LooseVersion(matplotlib.__version__) >= LooseVersion('2'):
+if Version(matplotlib.__version__) >= Version('2'):
     HAS_MPL_FOR_TESTS = True
     BASELINE_DIR = os.path.join(cfg.CACHE_DIR,
                                 'oggm-sample-data-%s' % SAMPLE_DATA_COMMIT,

oggm/tests/test_prepro.py

@@ -1,7 +1,7 @@
 import unittest
 import os
 import shutil
-from distutils.version import LooseVersion
+from packaging.version import Version
 import pytest
 import warnings
 
@@ -301,8 +301,8 @@ def test_glacier_masks(self):
         with pytest.raises(RuntimeError):
             gis.glacier_masks(gdir)
 
-    @pytest.mark.skipif((LooseVersion(rasterio.__version__) <
-                         LooseVersion('1.0')),
+    @pytest.mark.skipif((Version(rasterio.__version__) <
+                         Version('1.0')),
                         reason='requires rasterio >= 1.0')
     def test_simple_glacier_masks(self):
 
@@ -357,8 +357,8 @@ def test_simple_glacier_masks(self):
         assert dft.sum()[0] == 1000
         assert utils.rmsd(dft['ref'], dft['oggm']) < 5
 
-    @pytest.mark.skipif((LooseVersion(rasterio.__version__) <
-                         LooseVersion('1.0')),
+    @pytest.mark.skipif((Version(rasterio.__version__) <
+                         Version('1.0')),
                         reason='requires rasterio >= 1.0')
     def test_glacier_masks_other_glacier(self):
 
@@ -390,8 +390,8 @@ def test_glacier_masks_other_glacier(self):
         np.testing.assert_allclose(dfh['Zmax'], entity.Zmax, atol=20)
         np.testing.assert_allclose(dfh['Zmin'], entity.Zmin, atol=20)
 
-    @pytest.mark.skipif((LooseVersion(rasterio.__version__) <
-                         LooseVersion('1.0')),
+    @pytest.mark.skipif((Version(rasterio.__version__) <
+                         Version('1.0')),
                         reason='requires rasterio >= 1.0')
     def test_rasterio_glacier_masks(self):
 
@@ -3086,7 +3086,7 @@ def test_find_calving_full_fl(self):
         df = inversion.find_inversion_calving(gdir)
 
         assert df['calving_flux'] > 2
-        assert df['calving_rate_myr'] > 500
+        assert df['calving_rate_myr'] > 450
         assert df['calving_mu_star'] == 0
 
         # Test that new MB equal flux

oggm/tests/test_shop.py

@@ -7,6 +7,7 @@
 
 import oggm
 import xarray as xr
+import rioxarray as rioxr
 import numpy as np
 import pandas as pd
 from oggm import utils
@@ -66,9 +67,9 @@ def test_repro_to_glacier(self, class_case_dir, monkeypatch):
         gis.rasterio_to_gdir(gdir, region_files['ALA']['vy'], 'its_live_vy',
                              resampling='bilinear')
 
-        with xr.open_rasterio(gdir.get_filepath('its_live_vx')) as da:
+        with rioxr.open_rasterio(gdir.get_filepath('its_live_vx')) as da:
             _vx = da.where(mask).data.squeeze()
-        with xr.open_rasterio(gdir.get_filepath('its_live_vy')) as da:
+        with rioxr.open_rasterio(gdir.get_filepath('its_live_vy')) as da:
             _vy = da.where(mask).data.squeeze()
 
         _vel = np.sqrt(_vx**2 + _vy**2)
@@ -552,7 +553,7 @@ def test_add_consensus(self, class_case_dir, monkeypatch):
         with xr.open_dataset(gdir.get_filepath('gridded_data')) as ds:
             mine = ds.consensus_ice_thickness
 
-        with xr.open_rasterio(gdir.get_filepath('consensus')) as ds:
+        with rioxr.open_rasterio(gdir.get_filepath('consensus')) as ds:
             ref = ds.isel(band=0)
 
         # Check area

oggm/tests/test_utils.py

@@ -1653,10 +1653,9 @@ def prepare_verify_test(self, valid_size=True, valid_crc32=True,
         file_sha256 = file_sha256.digest()
 
         data = utils.get_dl_verify_data('cluster.klima.uni-bremen.de')
-        s = pd.Series({'size': file_size, 'sha256': file_sha256},
-                      name='test.txt')
-        data = data.append(s)
-        cfg.DATA['dl_verify_data_test.com'] = data
+        s = pd.DataFrame({'size': file_size, 'sha256': file_sha256},
+                         index=['test.txt'])
+        cfg.DATA['dl_verify_data_test.com'] = pd.concat([data, s])
 
         return 'https://test.com/test.txt'
 

oggm/utils/_funcs.py

@@ -8,12 +8,12 @@
 import logging
 import warnings
 import shutil
-from distutils.version import LooseVersion
+from packaging.version import Version
 
 # External libs
 import pandas as pd
 import numpy as np
-from scipy.ndimage import filters
+from scipy.ndimage import convolve1d
 try:
     from scipy.signal.windows import gaussian
 except AttributeError:
@@ -268,7 +268,7 @@ def smooth1d(array, window_size=None, kernel='gaussian'):
         else:
             raise NotImplementedError('Kernel: ' + kernel)
     kernel = kernel / np.asarray(kernel).sum()
-    return filters.convolve1d(array, kernel, mode='mirror')
+    return convolve1d(array, kernel, mode='mirror')
 
 
 def line_interpol(line, dx):
@@ -375,7 +375,7 @@ def clip_scalar(value, vmin, vmax):
     return vmin if value < vmin else vmax if value > vmax else value
 
 
-if LooseVersion(np.__version__) < LooseVersion('1.17'):
+if Version(np.__version__) < Version('1.17'):
     clip_array = np.clip
 else:
     # TODO: reassess this when https://github.com/numpy/numpy/issues/14281
@@ -509,7 +509,7 @@ def polygon_intersections(gdf):
                                        '{}.'.format(line.type))
                 line = gpd.GeoDataFrame([[i, j, line]],
                                         columns=out_cols)
-                out = out.append(line)
+                out = pd.concat([out, line])
 
     return out