Fix warnings in tests (#1093)

* Replace np.alltrue with np.all
* Remove return statements from test
* Use set_layout_engine instead of set_tight_layout
* Silence precision warnings in comparison test with mock data
* Use importlib instead of pkg_resources
* Silence expected warnings in tests
* Filter cli soma volume warning

neurom/apps/__init__.py

@@ -27,11 +27,21 @@
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 """Helper code for neurom applications."""
+import sys
 import logging
-
+from pathlib import Path
 import yaml
+
 from neurom.exceptions import ConfigError
 
+if sys.version_info >= (3, 9):  # pragma: no cover
+    import importlib.resources as importlib_resources
+else:
+    import importlib_resources  # pragma: no cover
+
+EXAMPLE_CHECK_CONFIG = Path(importlib_resources.files("neurom.apps"), "config", "morph_check.yaml")
+EXAMPLE_STATS_CONFIG = Path(importlib_resources.files("neurom.apps"), "config", "morph_stats.yaml")
+
 L = logging.getLogger(__name__)
 
 

neurom/apps/cli.py

@@ -33,7 +33,7 @@
 import click
 import matplotlib.pyplot as plt
 
-from neurom.apps import morph_stats, morph_check
+from neurom.apps import morph_stats, morph_check, EXAMPLE_CHECK_CONFIG, EXAMPLE_STATS_CONFIG
 from neurom import load_morphology
 from neurom.view import matplotlib_impl, matplotlib_utils
 
@@ -85,7 +85,7 @@ def view(input_file, is_3d, plane, backend, realistic_diameters):
                         'https://neurom.readthedocs.io/en/latest/morph_stats.html')
 @click.argument('datapath', required=False)
 @click.option('-C', '--config', type=click.Path(exists=True, dir_okay=False),
-              default=morph_stats.EXAMPLE_CONFIG, show_default=True,
+              default=EXAMPLE_STATS_CONFIG, show_default=True,
               help='Configuration File')
 @click.option('-o', '--output', type=click.Path(exists=False, dir_okay=False),
               help='Path to output file, if it ends in .json, a json file is created,'
@@ -106,7 +106,7 @@ def stats(datapath, config, output, full_config, as_population, ignored_exceptio
                         'https://neurom.readthedocs.io/en/latest/morph_check.html')
 @click.argument('datapath')
 @click.option('-C', '--config', type=click.Path(exists=True, dir_okay=False),
-              default=morph_check.EXAMPLE_CONFIG, show_default=True,
+              default=EXAMPLE_CHECK_CONFIG, show_default=True,
               help='Configuration File')
 @click.option('-o', '--output', type=click.Path(exists=False, dir_okay=False),
               help='Path to output json summary file', required=True)

neurom/apps/morph_check.py

@@ -29,13 +29,9 @@
 """Check on morphologies."""
 
 import json
-from pathlib import Path
-import pkg_resources
-from neurom.apps import get_config
+from neurom.apps import get_config, EXAMPLE_CHECK_CONFIG
 from neurom.check.runner import CheckRunner
 
-EXAMPLE_CONFIG = Path(pkg_resources.resource_filename('neurom.apps', 'config'), 'morph_check.yaml')
-
 
 def main(datapath, config, output):
     """Main function that checks morphologies.
@@ -45,7 +41,7 @@ def main(datapath, config, output):
         config (str|Path): path to a statistics config file
         output (str|Path): path to output the resulted checks file
     """
-    config = get_config(config, EXAMPLE_CONFIG)
+    config = get_config(config, EXAMPLE_CHECK_CONFIG)
     checker = CheckRunner(config)
     summary = checker.run(datapath)
     with open(output, 'w') as json_output:

neurom/apps/morph_stats.py

@@ -38,14 +38,13 @@
 from collections.abc import Sized
 from copy import deepcopy
 from functools import partial
-from pathlib import Path
-import pkg_resources
+
 import numpy as np
 import pandas as pd
 from morphio import SomaError
 
 import neurom as nm
-from neurom.apps import get_config
+from neurom.apps import get_config, EXAMPLE_STATS_CONFIG
 from neurom.core.morphology import Morphology, Neurite
 from neurom.core.population import Population
 from neurom.exceptions import ConfigError
@@ -56,7 +55,6 @@
 
 L = logging.getLogger(__name__)
 
-EXAMPLE_CONFIG = Path(pkg_resources.resource_filename('neurom.apps', 'config'), 'morph_stats.yaml')
 IGNORABLE_EXCEPTIONS = {'SomaError': SomaError}
 
 
@@ -117,7 +115,7 @@ def extract_dataframe(morphs, config, n_workers=1):
     return pd.DataFrame(columns=pd.MultiIndex.from_tuples(columns), data=rows)
 
 
-extract_dataframe.__doc__ += str(EXAMPLE_CONFIG)
+extract_dataframe.__doc__ += str(EXAMPLE_STATS_CONFIG)
 
 
 def _get_feature_stats(feature_name, morphs, modes, kwargs):
@@ -234,7 +232,7 @@ def extract_stats(morphs, config):
     return dict(stats)
 
 
-extract_stats.__doc__ += str(EXAMPLE_CONFIG)
+extract_stats.__doc__ += str(EXAMPLE_STATS_CONFIG)
 
 
 def _get_header(results):
@@ -366,7 +364,7 @@ def main(datapath, config, output_file, is_full_config, as_population, ignored_e
         as_population (bool): treat ``datapath`` as directory of morphologies population
         ignored_exceptions (list|tuple|None): exceptions to ignore when loading a morphology
     """
-    config = full_config() if is_full_config else get_config(config, EXAMPLE_CONFIG)
+    config = full_config() if is_full_config else get_config(config, EXAMPLE_STATS_CONFIG)
 
     if 'neurite' in config and 'neurite_type' not in config:
         error = ConfigError('"neurite_type" missing from config, but "neurite" set')

neurom/view/matplotlib_utils.py

@@ -220,7 +220,7 @@ def plot_style(fig, ax,  # pylint: disable=too-many-arguments, too-many-locals
         ax.set_aspect(aspect_ratio)
 
     if tight:
-        fig.set_tight_layout(True)
+        fig.set_layout_engine("tight")
 
 
 def plot_title(ax, pretitle='', title='Figure', posttitle='', title_fontsize=14, title_arg=None):

pyproject.toml

@@ -35,6 +35,7 @@ dependencies = [
     'pyyaml>=3.10',
     'scipy>=1.2.0',
     'tqdm>=4.8.4',
+    'importlib_resources>=1.3; python_version < "3.9"',
 ]
 dynamic = ["version"]
 

tests/apps/test_cli.py

@@ -1,6 +1,7 @@
 import json
 from pathlib import Path
 import tempfile
+import pytest
 
 import pandas as pd
 import yaml
@@ -73,6 +74,7 @@ def test_morph_stat():
                                    'all:max_section_branch_orders', 'morphology:mean_soma_radius'}
 
 
+@pytest.mark.filterwarnings('ignore::UserWarning')
 def test_morph_stat_full_config():
     runner = CliRunner()
     filename = DATA / 'h5/v1/Neuron.h5'

tests/apps/test_morph_stats.py

@@ -186,7 +186,9 @@ def test_stats_new_format_set_arg():
 
 
 def test_extract_stats_scalar_feature():
+
     m = nm.load_morphology(DATA_PATH / 'neurolucida' / 'bio_neuron-000.asc')
+
     config = {
         'neurite_type': ['ALL'],
         'neurite': {
@@ -196,7 +198,11 @@ def test_extract_stats_scalar_feature():
             'soma_volume': ['sum'],
         }
     }
-    res = ms.extract_stats(m, config)
+    with warnings.catch_warnings():
+        # silence warning about approximating soma volume with a sphere
+        warnings.simplefilter("ignore", category=UserWarning)
+        res = ms.extract_stats(m, config)
+
     assert res == {'all': {'max_number_of_forking_points': 277},
                    'morphology': {'sum_soma_volume': 1424.4383771584492}}
 

tests/geom/test_geom.py

@@ -52,7 +52,7 @@ def test_bounding_box():
     obj = PointObj()
     obj.points = pts
 
-    assert np.alltrue(geom.bounding_box(obj) == [[-100, -2, -3], [42, 55, 33]])
+    assert np.all(geom.bounding_box(obj) == [[-100, -2, -3], [42, 55, 33]])
 
 
 def test_bounding_box_morphology():
@@ -78,7 +78,7 @@ def test_convex_hull_points():
     # This leverages scipy ConvexHull and we don't want
     # to re-test scipy, so simply check that the points are the same.
     hull = geom.convex_hull(NRN)
-    assert np.alltrue(hull.points == NRN.points[:, :3])
+    assert np.all(hull.points == NRN.points[:, :3])
 
 
 def test_convex_hull_volume():

tests/test_import.py

@@ -27,8 +27,4 @@
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 def test_import_neurom():
-    try:
-        import neurom
-        return True
-    except Exception:
-        return False
+    import neurom

tests/test_stats.py

@@ -31,7 +31,6 @@
 Since the stats module consists of simple wrappers to scipy.stats functions,
 these tests are only sanity checks.
 """
-
 import numpy as np
 from neurom import stats as st
 
@@ -201,11 +200,15 @@ def test_compare_two_wilcoxon():
     assert_almost_equal(results2.dist, 0.0, decimal=5)
     assert_almost_equal(results2.pvalue, 0.0, decimal=5)
 
+
+@pytest.mark.filterwarnings("ignore")  # Ignore precision warnings
 def test_compare_two_ttest():
 
     results1 = st.compare_two(distr1, distr1, test=st.StatTests.ttest)
+
     assert np.isnan(results1.dist)
     assert np.isnan(results1.pvalue)
+
     results2 = st.compare_two(distr1, distr2, test=st.StatTests.ttest)
     assert np.isinf(results2.dist)
     assert_almost_equal(results2.pvalue, 0.0, decimal=5)

tests/test_viewer.py

@@ -27,6 +27,7 @@
 # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 import os
+import warnings
 import tempfile
 from pathlib import Path
 
@@ -35,7 +36,14 @@
 if 'DISPLAY' not in os.environ:  # noqa
     matplotlib.use('Agg')  # noqa
 
-from neurom import NeuriteType, load_morphology, viewer
+from neurom.exceptions import NeuroMDeprecationWarning
+
+with warnings.catch_warnings():
+    # no need to warn about the deprecated module in this test
+    warnings.simplefilter("ignore", category=NeuroMDeprecationWarning)
+    from neurom import viewer
+
+from neurom import NeuriteType, load_morphology
 from neurom.view import matplotlib_utils
 
 import pytest