Merge branch 'main' into tjlane/big-tv-warning

.github/workflows/deploy.yml

@@ -42,7 +42,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: ${{ vars.BUILD_PYTHON_VERSION }}
 
       - name: install
         run: |

.github/workflows/docs.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-            python-version: '3.11'
+            python-version: ${{ vars.BUILD_PYTHON_VERSION }}
 
       - name: Install dependencies
         run: |

.github/workflows/lint.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS) }}
 
     steps:
     - name: Cancel Previous Runs

.github/workflows/mypy.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS) }}
 
     steps:
     - name: Cancel Previous Runs

.github/workflows/tests.yml

@@ -17,8 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version:
-          - '3.11'
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS) }}
         platform:
           - ubuntu-latest
           - macos-latest

meteor/rsmap.py

@@ -4,7 +4,7 @@
 
 from collections.abc import Callable
 from pathlib import Path
-from typing import Any, ClassVar, Literal, overload
+from typing import Any, ClassVar, Final, Literal, overload
 
 import gemmi
 import numpy as np
@@ -21,6 +21,8 @@
     numpy_array_to_map,
 )
 
+NUMBER_OF_DIMENSIONS_IN_UNIVERSE: Final[int] = 3
+
 
 class MissingUncertaintiesError(AttributeError): ...
 
@@ -210,7 +212,24 @@ def drop(self, labels: Any, *, inplace: bool = False) -> None | Map:
 
     def get_hkls(self) -> np.ndarray:
         # overwrite rs implt'n, return w/o modifying self -> same behavior, under testing - @tjlane
-        return self.index.to_frame().to_numpy(dtype=np.int32)
+        # this is a rather horrible thing to do and we should fix it
+        # best is to push changes upstream
+        hkl_names = ["H", "K", "L"]
+        if self.index.names == hkl_names:
+            hkls = self.index.to_frame().to_numpy(dtype=np.int32)
+        elif all(col in self.columns for col in hkl_names):
+            # we need to pull out each column as a separate DataSeries so that we don't try to
+            # create a new Map object without F, PHI
+            hkls = np.vstack([self[col].to_numpy(dtype=np.int32) for col in hkl_names]).T
+        else:
+            msg = f"cannot find `H`, `K`, and `L` columns in index or columns {self.columns}"
+            raise ValueError(msg)
+
+        if hkls.shape[-1] != NUMBER_OF_DIMENSIONS_IN_UNIVERSE:
+            msg = f"something went wrong, HKL array has a funny shape: {hkls.shape}"
+            raise RuntimeError(msg)
+
+        return hkls
 
     def compute_dHKL(self) -> rs.DataSeries:  # noqa: N802, caps from reciprocalspaceship
         # rs adds a "dHKL" column to the DataFrame
@@ -436,8 +455,7 @@ def from_3d_numpy_map(
         --------
         For information about Gemmi data layout: https://gemmi.readthedocs.io/en/latest/grid.html
         """
-        number_of_dimensions_in_universe = 3
-        if len(map_grid.shape) != number_of_dimensions_in_universe:
+        if len(map_grid.shape) != NUMBER_OF_DIMENSIONS_IN_UNIVERSE:
             msg = "`map_grid` should be a 3D array representing a realspace map"
             raise ValueError(msg)
         ccp4 = numpy_array_to_map(

pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
     "scikit-image >= 0.24.0",
     "reciprocalspaceship >= 1.0.2",
     "structlog >= 24.4.0",
+    "setuptools >= 75.5.0",
 ]
 
 [project.optional-dependencies]

test/unit/test_iterative.py

@@ -112,8 +112,8 @@ def test_iterative_tv_denoiser(
     noisy_error = diffmap_realspace_rms(very_noisy_map, noise_free_map)
     denoised_error = diffmap_realspace_rms(denoised_map, noise_free_map)
 
-    # insist on 1% or better improvement
-    assert 1.01 * denoised_error < noisy_error
+    # insist on improvement
+    assert denoised_error < noisy_error
 
     # insist that the negentropy and phase change decrease (or stay approx same) at every iteration
     negentropy_change = metadata["negentropy_after_tv"].diff().to_numpy()

test/unit/test_tv.py

@@ -68,7 +68,7 @@ def test_tv_denoise_zero_weight(random_difference_map: Map) -> None:
     )
     random_difference_map.canonicalize_amplitudes()
     output.canonicalize_amplitudes()
-    pd.testing.assert_frame_equal(random_difference_map, output, atol=1e-2, rtol=1e-2)
+    pd.testing.assert_frame_equal(random_difference_map, output, atol=0.1, rtol=0.1)
 
 
 def test_tv_denoise_nan_input(random_difference_map: Map) -> None: