Merge pull request #893 from neutrons/fix_numpy2_errors

Fix numpy2 errors

.github/workflows/ci.yml

@@ -51,6 +51,11 @@ jobs:
           conda activate PyRS
           flake8 . --count
 
+      - name: Print Conda Packages
+        run: |
+          conda activate PyRS
+          conda list
+
       - name: mypy
         run: |
           conda activate PyRS
@@ -71,11 +76,6 @@ jobs:
           python -c "import qtpy"
           python -c "import mantidqt"
 
-      - name: Print Conda Packages
-        run: |
-          conda activate PyRS
-          conda list
-
       - name: Run PyRS tests
         run: |
           conda activate PyRS

environment.yml

@@ -17,6 +17,7 @@ dependencies:
 - libarchive=3.5.2
 - flake8
 - mypy
+- matplotlib
 - numpy
 - pandas
 - types-six

pyrs/dataobjects/sample_logs.py

@@ -423,7 +423,7 @@ def constant_logs(self, atol=0.):
             elif key in self._plottable:  # plottable logs contain numbers
                 if self._data[key].std() <= atol:
                     result.append(key)
-            elif np.alltrue(self._data[key] == self._data[key][0]):  # all values are equal
+            elif np.all(self._data[key] == self._data[key][0], where=np.bool_(True)):  # all values are equal
                 result.append(key)
         return result
 

pyrs/interface/peak_fitting/plot.py

@@ -1,5 +1,5 @@
 import numpy as np
-from matplotlib.cm import coolwarm
+from matplotlib import colormaps
 from matplotlib.pyplot import Normalize
 from mpl_toolkits.mplot3d import Axes3D   # noqa: F401
 from scipy.interpolate import griddata
@@ -12,6 +12,8 @@
 
 from pyrs.interface.peak_fitting.config import LIST_AXIS_TO_PLOT
 
+coolwarm = colormaps['coolwarm']
+
 
 class Plot:
 

pyrs/interface/texture_fitting/texture_fitting_crtl.py

@@ -1,7 +1,9 @@
 import numpy as np
 from scipy.interpolate import griddata
 import matplotlib.pyplot as plt
-from matplotlib.cm import coolwarm
+from matplotlib import colormaps
+
+coolwarm = colormaps['coolwarm']
 
 
 class TextureFittingCrtl:

tests/integration/test_write_stress_csv.py

@@ -1,8 +1,7 @@
-
 import pytest
-from filecmp import cmp
 from os import remove
-import subprocess
+import pandas as pd
+from pandas.testing import assert_frame_equal
 
 from pyrs.peaks import PeakCollectionLite  # type: ignore
 from pyrs.dataobjects.sample_logs import PointList
@@ -12,6 +11,13 @@
 from pyrs.core.summary_generator_stress import SummaryGeneratorStress
 
 
+def compare_csv(file1, file2):
+    df1 = pd.read_csv(file1, comment="#")
+    df2 = pd.read_csv(file2, comment="#")
+
+    assert_frame_equal(df1, df2, check_exact=False, rtol=1e-5)
+
+
 def strain_instantiator(name, values, errors, x, y, z):
     return StrainField(name,
                        peak_collection=PeakCollectionLite(name, strain=values, strain_error=errors),
@@ -81,7 +87,8 @@ def test_write_summary_csv(test_data_dir: str, project_tags: str, expected_file:
     stress_csv = SummaryGeneratorStress(stress_csv_filename, stress_facade)
     stress_csv.write_summary_csv()
 
-    assert cmp(stress_csv_filename, expected_file)
+    compare_csv(stress_csv_filename, expected_file)
+
     # cleanup
     remove(stress_csv_filename)
 
@@ -104,7 +111,8 @@ def test_write_summary_33calculated_csv(test_data_dir: str, project_tags: str, e
     stress_csv = SummaryGeneratorStress(stress_csv_filename, stress)
     stress_csv.write_summary_csv()
 
-    assert cmp(stress_csv_filename, expected_file)
+    compare_csv(stress_csv_filename, expected_file)
+
     # cleanup
     remove(stress_csv_filename)
 
@@ -127,7 +135,8 @@ def test_write_summary_33inplanestress_csv(test_data_dir: str, project_tags: str
     stress_csv = SummaryGeneratorStress(stress_csv_filename, stress)
     stress_csv.write_summary_csv()
 
-    assert cmp(stress_csv_filename, expected_file)
+    compare_csv(stress_csv_filename, expected_file)
+
     # cleanup
     remove(stress_csv_filename)
 
@@ -167,7 +176,8 @@ def test_write_full_csv(test_data_dir: str, project_tags: str, expected_file: st
     stress_csv = SummaryGeneratorStress(stress_csv_filename, stress_facade)
     stress_csv.write_full_csv()
 
-    assert cmp(stress_csv_filename, expected_file)
+    compare_csv(stress_csv_filename, expected_file)
+
     # cleanup
     remove(stress_csv_filename)
 
@@ -190,11 +200,8 @@ def test_write_full_33calculated_csv(test_data_dir: str, project_tags: str, expe
     stress_csv = SummaryGeneratorStress(stress_csv_filename, stress)
     stress_csv.write_full_csv()
 
-    result = cmp(stress_csv_filename, expected_file)
-    if not result:
-        subprocess.run(["diff", stress_csv_filename, expected_file])
+    compare_csv(stress_csv_filename, expected_file)
 
-    assert result
     # cleanup
     remove(stress_csv_filename)
 
@@ -217,11 +224,8 @@ def test_write_full_33inplanestress_csv(test_data_dir: str, project_tags: str, e
     stress_csv = SummaryGeneratorStress(stress_csv_filename, stress)
     stress_csv.write_full_csv()
 
-    result = cmp(stress_csv_filename, expected_file)
-    if not result:
-        subprocess.run(["diff", stress_csv_filename, expected_file])
+    compare_csv(stress_csv_filename, expected_file)
 
-    assert result
     # cleanup
     remove(stress_csv_filename)
 

tests/unit/pyrs/peaks/test_peak_collection.py

@@ -130,7 +130,8 @@ def check_peak_collection(peak_shape, background, NUM_SUBRUN, target_errors,
         np.testing.assert_equal(obs_eff_peaks['Mixing'], raw_peaks_array['Mixing'])
     else:
         np.testing.assert_equal(obs_eff_peaks['Height'], raw_peaks_array['Height'])
-        np.testing.assert_equal(obs_eff_peaks['FWHM'], 2. * np.sqrt(2. * np.log(2.)) * raw_peaks_array['Sigma'])
+        np.testing.assert_allclose(obs_eff_peaks['FWHM'], 2. * np.sqrt(2. * np.log(2.)) * raw_peaks_array['Sigma'])
+
     np.testing.assert_equal(obs_eff_peaks['A0'], NUM_SUBRUN * [0.])
     np.testing.assert_equal(obs_eff_peaks['A1'], NUM_SUBRUN * [0.])