reciprocalspaceship 1.0.1__py3-none-any.whl → 1.0.2__py3-none-any.whl

reciprocalspaceship/utils/__init__.py

@@ -52,4 +52,9 @@ from reciprocalspaceship.utils.symmetry import (
     phase_shift,
     polar_axes,
 )
-from reciprocalspaceship.utils.units import angstroms2ev, ev2angstroms
+from reciprocalspaceship.utils.units import (
+    Angstroms2eV,
+    angstroms2ev,
+    ev2angstroms,
+    eV2Angstroms,
+)

reciprocalspaceship/utils/cell.py

@@ -24,6 +24,11 @@ def compute_dHKL(H, cell):
     # Compress the hkls so we don't do redudant computation
     H = np.array(H, dtype=np.float32)
     hkls, inverse = np.unique(H, 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)
+
     F = np.array(cell.fractionalization_matrix.tolist()).astype(np.float64)
     dhkls = np.reciprocal(np.linalg.norm((hkls @ F), 2, 1)).astype(np.float32)
     return dhkls[inverse]

reciprocalspaceship/utils/stats.py

@@ -41,8 +41,6 @@ def compute_redundancy(
     if dmin is None:
         dmin = dhkl.min()
     hobs = hobs[dhkl >= dmin]
-    decimals = 5.0  # Round after this many decimals
-    dmin = np.floor(dmin * 10**decimals) * 10**-decimals
     hobs, isym = rs.utils.hkl_to_asu(hobs, spacegroup)
     if anomalous:
         fminus = isym % 2 == 0
@@ -107,15 +105,15 @@ def weighted_pearsonr(x, y, w):
     """
     z = np.reciprocal(w.sum(-1))
 
-    mx = z * (w * x).sum(-1)
-    my = z * (w * y).sum(-1)
+    mx = z * np.einsum("...a,...a->...", w, x)
+    my = z * np.einsum("...a,...a->...", w, y)
 
     dx = x - np.expand_dims(mx, axis=-1)
     dy = y - np.expand_dims(my, axis=-1)
 
-    cxy = z * (w * dx * dy).sum(-1)
-    cx = z * (w * dx * dx).sum(-1)
-    cy = z * (w * dy * dy).sum(-1)
+    cxy = z * np.einsum("...a,...a,...a->...", w, dx, dy)
+    cx = z * np.einsum("...a,...a,...a->...", w, dx, dx)
+    cy = z * np.einsum("...a,...a,...a->...", w, dy, dy)
 
     r = cxy / np.sqrt(cx * cy)
     return r

reciprocalspaceship/utils/structurefactors.py

@@ -104,6 +104,11 @@ def is_centric(H, spacegroup):
     """
     group_ops = spacegroup.operations()
     hkl, inverse = np.unique(H, 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)
+
     centric = group_ops.centric_flag_array(hkl)
     return centric[inverse]
 

reciprocalspaceship/utils/units.py

@@ -1,9 +1,19 @@
+import numpy as np
 from scipy.constants import Planck, c, electron_volt
 
+_conversion_factor = Planck * c / 1e-10 / electron_volt
 
-def ev2angstroms(ev):
-    return Planck * c / ev / 1e-10 / electron_volt
 
+def eV2Angstroms(ev):
+    out = np.empty_like(ev)
+    np.divide(_conversion_factor, ev, out=out)
+    return out
 
-def angstroms2ev(angstroms):
-    return Planck * c / angstroms / 1e-10 / electron_volt
+
+def Angstroms2eV(angstroms):
+    return eV2Angstroms(angstroms)
+
+
+# Add legacy aliases
+ev2angstroms = eV2Angstroms
+angstroms2ev = Angstroms2eV

{reciprocalspaceship-1.0.1.dist-info → reciprocalspaceship-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reciprocalspaceship
-Version: 1.0.1
+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
@@ -18,36 +17,37 @@ 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
 License-File: LICENSE
-Requires-Dist: gemmi <=0.6.2,>=0.5.5
-Requires-Dist: pandas <=2.0.3,>=1.4.0
+Requires-Dist: gemmi<=0.6.6,>=0.5.5
+Requires-Dist: pandas<=2.2.2,>=2.2.2
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: ipython
 Provides-Extra: dev
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: pytest-cov ; extra == 'dev'
-Requires-Dist: pytest-xdist ; extra == 'dev'
-Requires-Dist: sphinx ; extra == 'dev'
-Requires-Dist: sphinx-rtd-theme ; extra == 'dev'
-Requires-Dist: nbsphinx ; extra == 'dev'
-Requires-Dist: sphinx-design ; extra == 'dev'
-Requires-Dist: sphinxcontrib-autoprogram ; extra == 'dev'
-Requires-Dist: autodocsumm ; extra == 'dev'
-Requires-Dist: jupyter ; extra == 'dev'
-Requires-Dist: tqdm ; extra == 'dev'
-Requires-Dist: matplotlib ; extra == 'dev'
-Requires-Dist: seaborn ; extra == 'dev'
-Requires-Dist: celluloid ; extra == 'dev'
-Requires-Dist: scikit-image ; extra == 'dev'
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: ray; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: nbsphinx; extra == "dev"
+Requires-Dist: sphinx-design; extra == "dev"
+Requires-Dist: sphinxcontrib-autoprogram; extra == "dev"
+Requires-Dist: autodocsumm; extra == "dev"
+Requires-Dist: jupyter; extra == "dev"
+Requires-Dist: tqdm; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: seaborn; extra == "dev"
+Requires-Dist: celluloid; extra == "dev"
+Requires-Dist: scikit-image; extra == "dev"
 Provides-Extra: examples
-Requires-Dist: jupyter ; extra == 'examples'
-Requires-Dist: tqdm ; extra == 'examples'
-Requires-Dist: matplotlib ; extra == 'examples'
-Requires-Dist: seaborn ; extra == 'examples'
-Requires-Dist: celluloid ; extra == 'examples'
-Requires-Dist: scikit-image ; extra == 'examples'
+Requires-Dist: jupyter; extra == "examples"
+Requires-Dist: tqdm; extra == "examples"
+Requires-Dist: matplotlib; extra == "examples"
+Requires-Dist: seaborn; extra == "examples"
+Requires-Dist: celluloid; extra == "examples"
+Requires-Dist: scikit-image; extra == "examples"
 
 
 ``reciprocalspaceship`` provides a ``pandas``-style interface for
@@ -68,5 +68,3 @@ Features of this library include:
     use space groups, unit cell parameters, and crystallographic symmetry
     operations.
   - Support for reading and writing MTZ reflection files.
-
-

{reciprocalspaceship-1.0.1.dist-info → reciprocalspaceship-1.0.2.dist-info}/RECORD

@@ -1,46 +1,46 @@
-reciprocalspaceship/VERSION,sha256=ROFh5ElcrCz3hYBD6eZBjpV58N3ProJvmjcmIpaM4GY,6
+reciprocalspaceship/VERSION,sha256=n9KGQtOsoZHlx_wjg8_W-rsqrIdD8Cnau4mJrFhOMbw,6
 reciprocalspaceship/__init__.py,sha256=69LJFzMjF05nmlwROByI53LTwM37sgrgYAp5k1n6wCs,1842
 reciprocalspaceship/concat.py,sha256=v2eg8-RBiNLYHkkPDeaozh3HvGCaFbmlC15FaeNJMgY,1695
 reciprocalspaceship/dataseries.py,sha256=ibU1bHMd8zORFxRtDswtvLh_n-miAyBqO0ghLmY29Js,6188
-reciprocalspaceship/dataset.py,sha256=g7sQ9eMD3XM2jQ6LkQcuUtzhp1qVPXpwcYph_uovWOA,56836
-reciprocalspaceship/decorators.py,sha256=pMdbyH6_VAPGz5K4rUVXQ2zsjvN_TbPaPaO930ANmi0,5592
+reciprocalspaceship/dataset.py,sha256=YUcpvaTifmlQeR4qewHkzo-RSz6DOq_xLalFRXa_O94,57008
+reciprocalspaceship/decorators.py,sha256=U2gfm29infWHVGzQnfnpRsjxOihDD6Iah7oHd4uD8jk,5612
 reciprocalspaceship/algorithms/__init__.py,sha256=r5IYCGswTHXpSs9Q7c6PfEz8_P8d1fEei2SyTkp5aYY,258
 reciprocalspaceship/algorithms/intensity.py,sha256=iDHaqqrMAe0v-aTVT5jf54JwkNQLSQ7HhezPw6qZndg,2657
 reciprocalspaceship/algorithms/merge.py,sha256=iwPrDfjtliBwLqEzHbcIfoTkvS_0s2_CszS5IfrEUXI,2154
-reciprocalspaceship/algorithms/scale_merged_intensities.py,sha256=hliqToBoz9CHluC6FtgMARDOQc1RG87H8IIUuHEgBno,11130
+reciprocalspaceship/algorithms/scale_merged_intensities.py,sha256=hNKKISCCDvchail1PZ_0r6sq1Rbgoraqaz1aDCayTYQ,11269
 reciprocalspaceship/commandline/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 reciprocalspaceship/commandline/mtzdump.py,sha256=JBg_W-CWQ6rbOOVmtK7TsErFXhCBR5pmC5RRSCapEZg,2939
 reciprocalspaceship/dtypes/__init__.py,sha256=cO0M2F6pO_0jtqx-MlkbzqxLSmK1Ibmon5p_ksWmcbk,1038
 reciprocalspaceship/dtypes/base.py,sha256=1X56U4jKt_wjVkW930C9gP2Di0RpCMDZsDKNTxYle5I,1052
-reciprocalspaceship/dtypes/floating.py,sha256=EhJsAY3K5WdjfUS5zjoeiM1DRui_cMMhQaxJ2FY9rMQ,19922
+reciprocalspaceship/dtypes/floating.py,sha256=jOQ25GZEE4QromaJA3_oeu0Tkjq1iT4dHCke_7W6TYo,19675
 reciprocalspaceship/dtypes/inference.py,sha256=jLgF8VfKtITGRzQbfeyZzEoJ1fQlbHXB_gXIJ9-AQxk,3029
-reciprocalspaceship/dtypes/integer.py,sha256=qArB8csctxdN5euAP9V7VgvR-LaXYzFNgZ1efCHxEWA,16085
-reciprocalspaceship/dtypes/internals.py,sha256=Zh21mUpao1-0kIhAGYXzpVY36y68Vt3rYjpI3vOl_sw,40507
+reciprocalspaceship/dtypes/integer.py,sha256=fPaLTWfMsJ-wuEPkm9oEJez3NDqzB4XKVHFRFEb585A,15816
+reciprocalspaceship/dtypes/internals.py,sha256=BkkqUDEvTTlebLXjcu7EiQV295-qR7GdMJXqrOKbbU0,47596
 reciprocalspaceship/dtypes/summarize.py,sha256=1w6-N3odFcI3ZEQP5qgrog6ucbGjO71vSgabmjklkbc,1114
 reciprocalspaceship/io/__init__.py,sha256=ZMQ_rGfLmfzijbErnjEFphJuZokPvZyyVRk65DC0gLA,400
 reciprocalspaceship/io/ccp4map.py,sha256=yztiHPTdyR9FiCKRg-eVmL-_MyZTKThPI9uuHuuPF_0,1029
-reciprocalspaceship/io/crystfel.py,sha256=sFuMqlcgkWEa9LBNFZSajbZb66dvSsRdmhyvSqCMEIA,8695
+reciprocalspaceship/io/crystfel.py,sha256=lKpGzM2OLNXBjy6njwahtk1IsI3MH0edaGSmaQ6NbGk,21662
 reciprocalspaceship/io/csv.py,sha256=A2ZnqAnFwFUQskF7_3EsQAPCcrJ5KEgjhZls6MDViv8,1194
 reciprocalspaceship/io/mtz.py,sha256=8XqFVoSJz47vjK-kEzwSu7NxwQnEyyHd0pgt1CaBavM,8074
 reciprocalspaceship/io/pickle.py,sha256=clnSTK8T2O_d7midS_E54WHmXEHrL10d386gWx7ztsM,818
 reciprocalspaceship/io/precognition.py,sha256=DWRE2erXPVpm9-y5DjIWUHfmv9jZcsqoa47ienp1Sao,3641
 reciprocalspaceship/stats/__init__.py,sha256=jdAWbpD_CKAn0W0sO_MKSnTu3bZSoLAXgb1_Y6jDMzk,197
 reciprocalspaceship/stats/completeness.py,sha256=1QM-Ac_V58nTLJoewbOK5CL69qsb0C0sc8L0c59WorQ,6702
-reciprocalspaceship/utils/__init__.py,sha256=IS3C9L1IAFnyzK4wSXGl49AWsOM5Yq1WLx83iZ9K0HU,1665
+reciprocalspaceship/utils/__init__.py,sha256=bKJwbkxXa-TX2etIQgIESKkv9kdag1rHL77JLhI-2B8,1714
 reciprocalspaceship/utils/asu.py,sha256=WwxvIq-_QEF2UvyELuNudVo53daty9wiN-vaOYAUbKI,8680
 reciprocalspaceship/utils/binning.py,sha256=CHf5z8EsHSg34ZgC-yM_8Gd3D2BB8cqTtHAf7vwfgLo,2786
-reciprocalspaceship/utils/cell.py,sha256=GtPjtonimLHGcM9wnREOpdLTu_9JuwNltA2j5DPMiS0,1893
+reciprocalspaceship/utils/cell.py,sha256=aNIaugA3F8CRs9n8Ck0Rjc8YI7qHZcW3lJPE7yvj0dk,2053
 reciprocalspaceship/utils/grid.py,sha256=xB7sw1xrhgzFojrVHbC_uVBT3NMTBsvKsCqaRrVfvTQ,1893
 reciprocalspaceship/utils/math.py,sha256=m6Iq9u0fjiieftzjQPAEHTN2htBIOwLhBCJdrcIN5Ao,1019
 reciprocalspaceship/utils/phases.py,sha256=zyiE99bq-TV_4aI6ZhBi4MLAvKwE3Sx1dFqppJL5rkE,2438
 reciprocalspaceship/utils/rfree.py,sha256=qFgepLOfgdU-cvZIMu8WfzlFExTc4jILff2ro7iu8FQ,3411
-reciprocalspaceship/utils/stats.py,sha256=1ShlFe3PogRq4rfmlL_ks6J2qkB2TCxVHdMgil3d0a0,3689
-reciprocalspaceship/utils/structurefactors.py,sha256=xybipMkn61jr6rNANZW7ZXau04zNRtBOaqdr81ZiD9U,3526
+reciprocalspaceship/utils/stats.py,sha256=p_1R3bTVVAVlDWh-hzcurlT8GOHkJA8ovFuQjD0w5AY,3681
+reciprocalspaceship/utils/structurefactors.py,sha256=ZW6CVPn_04dxay0DDnA0-byUrZnGraQ0kItqN1m5F3k,3686
 reciprocalspaceship/utils/symmetry.py,sha256=xsYmEUo0PTH57-kctJdUq_-k14ci5LUGeG5LwzmjjPU,2963
-reciprocalspaceship/utils/units.py,sha256=e6bLfED1LcDdMyOI7G09ZDBD8HlBYlZbjup5e0GM8ss,217
+reciprocalspaceship/utils/units.py,sha256=ng-2hzZBERYo9bnQDPr-HLr7xPah-JzOthfrpHH816Y,388
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/conftest.py,sha256=bQZClqzu3lonsI01OdP5X38asMd7F76fAGzlWWYPXAI,3930
-tests/test_dataseries.py,sha256=2mzzW_SdTsGnyr5cOhjuLLccnUlE_XaFWuvTS_xcWII,3304
+tests/test_dataseries.py,sha256=go-q5tT8lLq3tlRVnmrwUytK7PlaoKs3CBPjWryGfGg,3309
 tests/test_dataset.py,sha256=dMFW6-pCs1rjIYEqbfstVqFRiYwKfz5rHlncVL9grQg,22231
 tests/test_dataset_anomalous.py,sha256=LQb1inSS_oDbVYEIyyx_GBFAkXGlEQYZ-ZhpwMeyMmQ,6963
 tests/test_dataset_binning.py,sha256=NgD_vy-TUh3vQrUVgysVBSZu75xN66LR6hRu2_qAUTs,3564
@@ -50,9 +50,9 @@ tests/test_dataset_preserve_attributes.py,sha256=gwQQJGsiBZld2KKmLrcMkuc9zesR3FD
 tests/test_dataset_symops.py,sha256=PV86tLu1qDACuk-YqjYQszk8Ctb0-h_NsQRnuCDFnOU,10864
 tests/test_decorators.py,sha256=ExR7mCU0iIqhHo4ho6ywPrZIEaGcsElaI4jtH9o5afE,5331
 tests/test_summarize_mtz_dtypes.py,sha256=JE0ctXMWii1AV-cmKogF6hjb8NCHrgvxNZ0ZRCHh-Ho,696
-reciprocalspaceship-1.0.1.dist-info/LICENSE,sha256=E22aZlYy5qJsJCJ94EkO_Vt3COio5UcLg59dZLPam7I,1093
-reciprocalspaceship-1.0.1.dist-info/METADATA,sha256=xFjMfolINcdDUM-kvmo0YXHTwZcNEy1wjMgmGuBTyZk,3063
-reciprocalspaceship-1.0.1.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-reciprocalspaceship-1.0.1.dist-info/entry_points.txt,sha256=E2msBLAQZuAfS8Bk_fdzZTLFgQR-l5AlwhPiL_ip1Z0,77
-reciprocalspaceship-1.0.1.dist-info/top_level.txt,sha256=tOo679MsLFS7iwiYZDwnKTuTpJLYVFBk6g9xnnB_s-w,26
-reciprocalspaceship-1.0.1.dist-info/RECORD,,
+reciprocalspaceship-1.0.2.dist-info/LICENSE,sha256=E22aZlYy5qJsJCJ94EkO_Vt3COio5UcLg59dZLPam7I,1093
+reciprocalspaceship-1.0.2.dist-info/METADATA,sha256=36KZFStMfUhplc6K1h7vpF-FVJ-TrExqWI3XXdW5oTE,3056
+reciprocalspaceship-1.0.2.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
+reciprocalspaceship-1.0.2.dist-info/entry_points.txt,sha256=Bqjl2J8UrG4UAHHhPbdH5r-xYaOdLCEdyRH6zJ9joDw,76
+reciprocalspaceship-1.0.2.dist-info/top_level.txt,sha256=tOo679MsLFS7iwiYZDwnKTuTpJLYVFBk6g9xnnB_s-w,26
+reciprocalspaceship-1.0.2.dist-info/RECORD,,

{reciprocalspaceship-1.0.1.dist-info → reciprocalspaceship-1.0.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.44.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{reciprocalspaceship-1.0.1.dist-info → reciprocalspaceship-1.0.2.dist-info}/entry_points.txt

@@ -1,3 +1,2 @@
 [console_scripts]
 rs.mtzdump = reciprocalspaceship.commandline.mtzdump:main
-

tests/test_dataseries.py

@@ -39,7 +39,7 @@ def test_constructor_expanddim(data, series_name, frame_name, dtype):
 
     assert isinstance(d, rs.DataSet)
     assert len(d.columns) == 1
-    assert isinstance(d.dtypes[0], type(ds.dtype))
+    assert isinstance(d.dtypes.iloc[0], type(ds.dtype))
 
     # Test hierarchy for column naming
     if frame_name: