Fix nightly NumPy cron job, add numpy 1.25-dev0 fixes (#3977)

* Fix cron jobs against nightly wheels
* Address incompatibilities with NumPy 1.25 changes in streamlines and streamlines_3d

.coveragerc

@@ -7,7 +7,7 @@ omit =
     */legacy/*
     */due.py
 concurrency = thread, multiprocessing
-parallel = True
+parallel = true
 
 [report]
 exclude_lines =

.github/workflows/gh-ci-cron.yaml

@@ -35,26 +35,32 @@ jobs:
     - name: setup_miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.9
-        auto-update-conda: true
-        channel-priority: flexible
+        python-version: "3.10"
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        channel-priority: strict
         channels: conda-forge, bioconda
-        mamba-version: "*"
         add-pip-as-python-dependency: true
         architecture: x64
 
-    - name: install_dev_versions
-      run: |
-        pip install -i https://pypi.anaconda.org/scipy-wheels-nightly/simple numpy
-        pip install -i https://pypi.anaconda.org/scipy-wheels-nightly/simple scipy
-
-    - name: install_other_deps
+    - name: install_deps
       uses: ./.github/actions/setup-deps
       with:
         mamba: true
-        numpy: ""
-        scipy: ""
+        full-deps: true
 
+      # overwrite installs by picking up nightly wheels
+    - name: nightly_wheels
+      run: |
+        pip install --pre -U -i https://pypi.anaconda.org/scipy-wheels-nightly/simple scipy numpy h5py matplotlib
+
+
+    - name: list_deps
+      run: |
+        mamba list
+        pip list
+
+      # Intentionally going with setup.py builds so we can build with latest
     - name: build_srcs
       uses: ./.github/actions/build-src
       with:
@@ -64,7 +70,7 @@ jobs:
 
     - name: run_tests
       run: |
-        pytest -n $numprocs testsuite/MDAnalysisTests --disable-pytest-warnings --durations=50
+        pytest -n $numprocs testsuite/MDAnalysisTests --durations=50 -W error::FutureWarning
 
 
   # Issue #3442

package/CHANGELOG

@@ -13,13 +13,16 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-12/21/22 IAlibay
+01/04/23 IAlibay
 
  * 2.4.2
 
 Fixes
   * np.histogramdd calls in :class:`DensityAnalysis` now pass the `density`
     argument rather than the NumPy 1.24 removed `normed` (PR #3976)
+  * visualization.streamlines_3D and visualization.streamlines no longer
+    rely on the scalar return of an numpy array elementwise comparison which
+    is no longer supported as of NumPy 1.25 (PR #3977)
 
 
 12/17/22 IAlibay

package/MDAnalysis/visualization/streamlines.py

@@ -176,7 +176,7 @@ def produce_list_centroids_this_frame(list_indices_in_polygon):
         list_centroids_this_frame = []
         for indices in list_indices_in_polygon:
             if not indices[0].size > 0:  # if there are no particles of interest in this particular square
-                list_centroids_this_frame.append('empty')
+                list_centroids_this_frame.append(None)
             else:
                 current_coordinate_array_in_square = relevant_particle_coordinate_array_xy[indices]
                 current_square_indices_centroid = np.average(current_coordinate_array_in_square, axis=0)
@@ -201,7 +201,7 @@ def produce_list_centroids_this_frame(list_indices_in_polygon):
             xy_deltas_to_write = []
             for square_1_centroid, square_2_centroid in zip(list_centroids_this_frame_using_indices_from_last_frame,
                                                             list_previous_frame_centroids):
-                if square_1_centroid == 'empty' or square_2_centroid == 'empty':
+                if square_1_centroid is None or square_2_centroid is None:
                     xy_deltas_to_write.append([0, 0])
                 else:
                     xy_deltas_to_write.append(np.subtract(square_1_centroid, square_2_centroid).tolist())

package/MDAnalysis/visualization/streamlines_3D.py

@@ -61,7 +61,9 @@
 
 import MDAnalysis
 
-def determine_container_limits(topology_file_path, trajectory_file_path, buffer_value):
+
+def determine_container_limits(topology_file_path, trajectory_file_path,
+                               buffer_value):
     """Calculate the extent of the atom coordinates + buffer.
 
     A function for the parent process which should take the input trajectory
@@ -281,15 +283,15 @@ def update_dictionary_point_in_cube_start_frame(array_simulation_particle_coordi
                                                            axis=0)
                 cube['centroid_of_particles_first_frame'] = centroid_particles_in_cube
             else:  # empty cube
-                cube['centroid_of_particles_first_frame'] = 'empty'
+                cube['centroid_of_particles_first_frame'] = None
             cube_counter += 1
 
     def update_dictionary_end_frame(array_simulation_particle_coordinates, dictionary_cube_data_this_core):
         """Update the cube dictionary objects again as appropriate for the second and final frame."""
         cube_counter = 0
         for key, cube in dictionary_cube_data_this_core.items():
             # if there were no particles in the cube in the first frame, then set dx,dy,dz each to 0
-            if cube['centroid_of_particles_first_frame'] == 'empty':
+            if cube['centroid_of_particles_first_frame'] is None:
                 cube['dx'] = 0
                 cube['dy'] = 0
                 cube['dz'] = 0

testsuite/MDAnalysisTests/visualization/test_streamlines.py

@@ -21,6 +21,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 import numpy as np
+from numpy.testing import assert_allclose
 import MDAnalysis
 from MDAnalysis.visualization import (streamlines,
                                       streamlines_3D)
@@ -83,6 +84,29 @@ def test_streamplot_2D(membrane_xtc, univ, tmpdir):
     with open(plot_outpath, 'rb'):
         pass
 
+
+def test_streamplot_2D_zero_return(membrane_xtc, univ, tmpdir):
+    # simple roundtrip test to ensure that
+    # zeroed arrays are returned by the 2D streamplot
+    # code when called with an empty selection
+    u1, v1, avg, std = streamlines.generate_streamlines(topology_file_path=Martini_membrane_gro,
+                                                        trajectory_file_path=membrane_xtc,
+                                                        grid_spacing=20,
+                                                        MDA_selection='name POX',
+                                                        start_frame=1,
+                                                        end_frame=2,
+                                                        xmin=univ.atoms.positions[...,0].min(),
+                                                        xmax=univ.atoms.positions[...,0].max(),
+                                                        ymin=univ.atoms.positions[...,1].min(),
+                                                        ymax=univ.atoms.positions[...,1].max(),
+                                                        maximum_delta_magnitude=2.0,
+                                                        num_cores=1)
+    assert_allclose(u1, np.zeros((5, 5)))
+    assert_allclose(v1, np.zeros((5, 5)))
+    assert avg == approx(0.0)
+    assert std == approx(0.0)
+
+
 def test_streamplot_3D(membrane_xtc, univ, tmpdir):
     # because mayavi is too heavy of a dependency
     # for a roundtrip plotting test, simply