reciprocalspaceship 1.0.0__tar.gz → 1.0.2__tar.gz

{reciprocalspaceship-1.0.0/reciprocalspaceship.egg-info → reciprocalspaceship-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reciprocalspaceship
-Version: 1.0.0
+Version: 1.0.2
 Summary: Tools for exploring reciprocal space
 Home-page: https://rs-station.github.io/reciprocalspaceship/
 Author: Kevin M. Dalton, Jack B. Greisman
@@ -9,7 +9,6 @@ License: MIT
 Project-URL: Bug Tracker, https://github.com/rs-station/reciprocalspaceship/issues
 Project-URL: Documentation, https://rs-station.github.io/reciprocalspaceship/
 Project-URL: Source Code, https://github.com/rs-station/reciprocalspaceship
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -18,7 +17,7 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Programming Language :: Python
-Requires-Python: >3.7
+Requires-Python: >=3.9
 Provides-Extra: dev
 Provides-Extra: examples
 License-File: LICENSE
@@ -42,5 +41,3 @@ Features of this library include:
     use space groups, unit cell parameters, and crystallographic symmetry
     operations.
   - Support for reading and writing MTZ reflection files.
-
-

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/README.md

@@ -1,10 +1,10 @@
-# 1 /:rocket: = reciprocalspaceship
+# 1 / 🚀 = reciprocalspaceship
 ![Build](https://github.com/rs-station/reciprocalspaceship/workflows/Build/badge.svg)
 [![Documentation](https://github.com/rs-station/reciprocalspaceship/workflows/Documentation/badge.svg)](https://rs-station.github.io/reciprocalspaceship)
 [![PyPI](https://img.shields.io/pypi/v/reciprocalspaceship?color=blue)](https://pypi.org/project/reciprocalspaceship/)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/reciprocalspaceship/badges/version.svg)](https://anaconda.org/conda-forge/reciprocalspaceship)
 [![codecov](https://codecov.io/gh/rs-station/reciprocalspaceship/branch/main/graph/badge.svg)](https://codecov.io/gh/rs-station/reciprocalspaceship)
-[![apm](https://img.shields.io/apm/l/vim-mode.svg)](https://github.com/rs-station/reciprocalspaceship/blob/main/LICENSE)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/rs-station/reciprocalspaceship/blob/main/LICENSE)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/rs-station/reciprocalspaceship/main?filepath=docs%2Fexamples)
 [![DOI](https://img.shields.io/badge/DOI-10.1107%2FS160057672100755X-blue)](https://doi.org/10.1107/S160057672100755X)
 

reciprocalspaceship-1.0.2/reciprocalspaceship/VERSION

@@ -0,0 +1 @@
+1.0.2

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/reciprocalspaceship/__init__.py

@@ -37,6 +37,7 @@ from reciprocalspaceship.dtypes import StructureFactorAmplitudeDtype  # F
 from reciprocalspaceship.dtypes import WeightDtype  # W
 from reciprocalspaceship.dtypes import summarize_mtz_dtypes
 from reciprocalspaceship.io import (
+    read_cif,
     read_crystfel,
     read_csv,
     read_mtz,

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/reciprocalspaceship/algorithms/scale_merged_intensities.py

@@ -185,6 +185,7 @@ def scale_merged_intensities(
     mean_intensity_method="isotropic",
     bins=100,
     bw=2.0,
+    minimum_sigma=-np.inf,
 ):
     """
     Scales merged intensities using Bayesian statistics in order to
@@ -240,6 +241,9 @@ def scale_merged_intensities(
         parameter controls the distance that each reflection impacts in
         reciprocal space. Only affects output if mean_intensity_method is
         \"anisotropic\".
+    minimum_sigma : float
+        Minimum value imposed on Sigma (default: -np.inf, that is: no minimum).
+
 
     Returns
     -------
@@ -281,14 +285,11 @@ def scale_merged_intensities(
     I, Sig = ds[intensity_key].to_numpy(), ds[sigma_key].to_numpy()
     if mean_intensity_method == "isotropic":
         dHKL = ds["dHKL"].to_numpy(dtype=np.float64)
-        Sigma = (
-            mean_intensity_by_resolution(I / multiplicity, dHKL, bins) * multiplicity
-        )
+        Sigma = mean_intensity_by_resolution(I / multiplicity, dHKL, bins)
     elif mean_intensity_method == "anisotropic":
-        Sigma = (
-            mean_intensity_by_miller_index(I / multiplicity, ds.get_hkls(), bw)
-            * multiplicity
-        )
+        Sigma = mean_intensity_by_miller_index(I / multiplicity, ds.get_hkls(), bw)
+    Sigma = np.clip(Sigma, a_min=minimum_sigma, a_max=np.inf)
+    Sigma = Sigma * multiplicity
 
     # Initialize outputs
     ds[outputI] = 0.0

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/reciprocalspaceship/commandline/mtzdump.py

@@ -81,7 +81,6 @@ def summarize(mtz, precision):
 
 
 def main():
-
     # Parse commandline arguments
     parser = parse_arguments()
     args = parser.parse_args()

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/reciprocalspaceship/dataset.py

@@ -12,7 +12,8 @@ from reciprocalspaceship.decorators import (
     range_indexed,
     spacegroupify,
 )
-from reciprocalspaceship.dtypes.base import MTZDtype, MTZInt32Dtype
+from reciprocalspaceship.dtypes.base import MTZDtype
+from reciprocalspaceship.dtypes.integer import MTZInt32Dtype
 from reciprocalspaceship.utils import (
     apply_to_hkl,
     assign_with_binedges,
@@ -1233,6 +1234,11 @@ class DataSet(pd.DataFrame):
         # Compute new HKLs and phase shifts
         hkls = dataset.get_hkls()
         compressed_hkls, inverse = np.unique(hkls, axis=0, return_inverse=True)
+
+        # The behavior of np.unique changed with v2.0. This block maintains v1 compatibility
+        if inverse.shape[-1] == 1:
+            inverse = inverse.squeeze(-1)
+
         asu_hkls, isym, phi_coeff, phi_shift = hkl_to_asu(
             compressed_hkls, dataset.spacegroup, return_phase_shifts=True
         )

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/reciprocalspaceship/decorators.py

@@ -100,7 +100,7 @@ def spacegroupify(func=None, *sg_args):
             for arg in sg_args:
                 if arg in bargs.arguments:
                     bargs.arguments[arg] = _convert_spacegroup(bargs.arguments[arg])
-            return f(**bargs.arguments)
+            return f(*bargs.args, **bargs.kwargs)
 
         return wrapped
 
@@ -155,7 +155,7 @@ def cellify(func=None, *cell_args):
             for arg in cell_args:
                 if arg in bargs.arguments:
                     bargs.arguments[arg] = _convert_unitcell(bargs.arguments[arg])
-            return f(**bargs.arguments)
+            return f(*bargs.args, **bargs.kwargs)
 
         return wrapped
 

{reciprocalspaceship-1.0.0 → reciprocalspaceship-1.0.2}/reciprocalspaceship/dtypes/__init__.py

@@ -1,22 +1,24 @@
-from reciprocalspaceship.dtypes.anomalousdifference import AnomalousDifferenceDtype
-from reciprocalspaceship.dtypes.batch import BatchDtype
-from reciprocalspaceship.dtypes.hklindex import HKLIndexDtype
-from reciprocalspaceship.dtypes.intensity import FriedelIntensityDtype, IntensityDtype
-from reciprocalspaceship.dtypes.m_isym import M_IsymDtype
-from reciprocalspaceship.dtypes.mtzint import MTZIntDtype
-from reciprocalspaceship.dtypes.mtzreal import MTZRealDtype
-from reciprocalspaceship.dtypes.phase import HendricksonLattmanDtype, PhaseDtype
-from reciprocalspaceship.dtypes.stddev import (
+from reciprocalspaceship.dtypes.floating import (
+    AnomalousDifferenceDtype,
+    FriedelIntensityDtype,
+    FriedelStructureFactorAmplitudeDtype,
+    HendricksonLattmanDtype,
+    IntensityDtype,
+    MTZRealDtype,
+    NormalizedStructureFactorAmplitudeDtype,
+    PhaseDtype,
     StandardDeviationDtype,
     StandardDeviationFriedelIDtype,
     StandardDeviationFriedelSFDtype,
-)
-from reciprocalspaceship.dtypes.structurefactor import (
-    FriedelStructureFactorAmplitudeDtype,
-    NormalizedStructureFactorAmplitudeDtype,
     StructureFactorAmplitudeDtype,
+    WeightDtype,
+)
+from reciprocalspaceship.dtypes.integer import (
+    BatchDtype,
+    HKLIndexDtype,
+    M_IsymDtype,
+    MTZIntDtype,
 )
-from reciprocalspaceship.dtypes.weight import WeightDtype
 
 # ExtensionDtypes are appended to the end of the Dtype registry.
 # Since we want to overwrite a few of the one-letter strings, we need

reciprocalspaceship-1.0.2/reciprocalspaceship/dtypes/base.py

@@ -0,0 +1,37 @@
+from reciprocalspaceship.dtypes.internals import NumericArray, NumericDtype
+
+
+class MTZDtype(NumericDtype):
+    """Base ExtensionDtype for implementing persistent MTZ data types"""
+
+    def __repr__(self) -> str:
+        return f"{self.name}"
+
+    @property
+    def _is_numeric(self) -> bool:
+        return True
+
+    @classmethod
+    def construct_array_type(cls):
+        """
+        Return the array type associated with this dtype.
+
+        Returns
+        -------
+        type
+        """
+        return NotImplementedError
+
+    @classmethod
+    def construct_from_string(cls, string):
+        if not isinstance(string, str):
+            raise TypeError(
+                f"'construct_from_string' expects a string, got {type(string)}"
+            )
+        elif string != cls.name and string != cls.mtztype:
+            raise TypeError(f"Cannot construct a '{cls.__name__}' from '{string}'")
+        return cls()
+
+    def is_friedel_dtype(self):
+        """Returns whether MTZ dtype represents a Friedel dtype"""
+        raise NotImplementedError