Merge remote-tracking branch 'origin/main' into pre-commit-ci-update-…

…config

.github/workflows/build.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         numpy-version: ['numpy<2.0', 'numpy>=2.0']
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     # Skip CI if 'skip ci' is contained in latest commit message
     if: "!contains(github.event.head_commit.message, 'skip ci')"
@@ -33,15 +33,17 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install "${{ matrix.numpy-version }}"
-        pip install -e .
+        pip install -e .[dev]
         pip install ray
+        python -c 'import setuptools;print(f"Using setuptools version: {setuptools.__version__}")'
 
     - name: Test with pytest
       run: |
-        python setup.py test
+        pytest
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         file: ./coverage.xml
         flags: unittests
+        token: ${{ secrets.CODECOV_TOKEN }}

docs/conf.py

@@ -70,7 +70,7 @@
 
 # prolog taken nearly verbatim from https://github.com/spatialaudio/nbsphinx/blob/98005a9d6b331b7d6d14221539154df69f7ae51a/doc/conf.py#L38
 nbsphinx_prolog = r"""
-{% set docname = 'docs/' + env.doc2path(env.docname, base=None) %}
+{% set docname = 'docs/' + env.doc2path(env.docname, base=None) | string() %}
 
 .. raw:: html
 

reciprocalspaceship/VERSION

@@ -1 +1 @@
-1.0.2
+1.0.3

reciprocalspaceship/__init__.py

@@ -1,8 +1,15 @@
 # Version number for reciprocalspaceship
 def getVersionNumber():
-    import pkg_resources
+    version = None
+    try:
+        from setuptools.version import metadata
+
+        version = metadata.version("reciprocalspaceship")
+    except ImportError:
+        from setuptools.version import pkg_resources
+
+        version = pkg_resources.require("reciprocalspaceship")[0].version
 
-    version = pkg_resources.require("reciprocalspaceship")[0].version
     return version
 
 

reciprocalspaceship/dataset.py

@@ -1177,7 +1177,7 @@ def unstack_anomalous(self, columns=None, suffixes=("(+)", "(-)")):
 
         return result
 
-    def is_isomorphous(self, other, cell_threshold=0.05):
+    def is_isomorphous(self, other, cell_threshold=0.5):
         """
         Determine whether DataSet is isomorphous to another DataSet. This
         method confirms isomorphism by ensuring the spacegroups are equivalent,
@@ -1214,7 +1214,8 @@ def is_isomorphous(self, other, cell_threshold=0.05):
         for param in params:
             param1 = self.cell.__getattribute__(param)
             param2 = other.cell.__getattribute__(param)
-            if (np.abs((param1 - param2)) / 100.0) > cell_threshold:
+            diff = 200.0 * np.abs(param1 - param2) / (param1 + param2)
+            if diff > cell_threshold:
                 return False
 
         return True

reciprocalspaceship/io/crystfel.py

@@ -487,9 +487,7 @@ def read_crystfel(
         The type of byte-encoding (optional, 'utf-8').
     columns : list (optional)
         Optionally specify the columns of the output by a list of strings.
-        The default list is:
-            [ "H", "K", "L", "I", "SigI", "BATCH", "s1x", "s1y", "s1z", "ewald_offset",
-            "angular_ewald_offset", "XDET", "YDET" ]
+        The default list is: [ "H", "K", "L", "I", "SigI", "BATCH", "s1x", "s1y", "s1z", "ewald_offset", "angular_ewald_offset", "XDET", "YDET" ]
         See `rs.io.crystfel.StreamLoader().available_column_names` for a list of available
         column names and *Notes* for a description of the returned columns
     parallel : bool (optional)

tests/test_dataset.py

@@ -603,6 +603,48 @@ def test_is_isomorphous(data_unmerged, data_fmodel, sg1, sg2, cell1, cell2):
             assert not result
 
 
+@pytest.mark.parametrize("threshold", [5.0, 1.0, 0.5, 0.1])
+def test_is_isomorphous_threshold(threshold):
+    """
+    Test that DataSet.is_isorphous(self, other, cell_threshold) method's
+    cell_threshold operates on percent difference.
+    """
+    epsilon = 1e-12
+    cell = np.array([34.0, 45.0, 98.0, 90.0, 90.0, 90.0])
+    spacegroup = 19
+
+    ds = rs.DataSet(cell=cell, spacegroup=spacegroup)
+    cell_resize_factor = (200.0 + threshold) / (200.0 - threshold)
+
+    # Make a cell that should be exactly threshold percent bigger
+    other_cell = cell_resize_factor * cell
+    too_big_cell = other_cell + epsilon
+    big_cell = other_cell - epsilon
+
+    # Make a cell that should be exactly threshold percent smaller
+    other_cell = cell / cell_resize_factor
+    too_small_cell = other_cell - epsilon
+    small_cell = other_cell + epsilon
+
+    # Construct data sets
+    too_big = rs.DataSet(cell=too_big_cell, spacegroup=spacegroup)
+    big = rs.DataSet(cell=big_cell, spacegroup=spacegroup)
+    too_small = rs.DataSet(cell=too_small_cell, spacegroup=spacegroup)
+    small = rs.DataSet(cell=small_cell, spacegroup=spacegroup)
+
+    # Cell is barely too big to be isomorphous
+    assert not ds.is_isomorphous(too_big, threshold)
+
+    # Cell is barely too small to be isomorphous
+    assert not ds.is_isomorphous(too_small, threshold)
+
+    # Cell is almost too big to be isomorphous
+    assert ds.is_isomorphous(big, threshold)
+
+    # Cell is almost too small to be isomorphous
+    assert ds.is_isomorphous(small, threshold)
+
+
 def test_to_gemmi_withNans(data_merged):
     """
     GH144: Test whether DataSet.to_gemmi() works with NaN-containing data.