reciprocalspaceship 1.0.3__tar.gz → 1.0.5__tar.gz

{reciprocalspaceship-1.0.3/reciprocalspaceship.egg-info → reciprocalspaceship-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: reciprocalspaceship
-Version: 1.0.3
+Version: 1.0.5
 Summary: Tools for exploring reciprocal space
 Home-page: https://rs-station.github.io/reciprocalspaceship/
 Author: Kevin M. Dalton, Jack B. Greisman
@@ -18,9 +18,51 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Programming Language :: Python
 Requires-Python: >=3.9
+License-File: LICENSE
+Requires-Dist: gemmi<=0.7.1,>=0.7.0
+Requires-Dist: pandas<=2.2.3,>=2.2.2
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: ipython
+Requires-Dist: msgpack
+Requires-Dist: setuptools
 Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: ray; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinxcontrib-autoprogram; extra == "doc"
+Requires-Dist: autodocsumm; extra == "doc"
+Requires-Dist: jupyter; extra == "doc"
+Requires-Dist: tqdm; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: seaborn; extra == "doc"
+Requires-Dist: celluloid; extra == "doc"
+Requires-Dist: scikit-image; extra == "doc"
 Provides-Extra: examples
-License-File: LICENSE
+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"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 
 ``reciprocalspaceship`` provides a ``pandas``-style interface for

reciprocalspaceship-1.0.5/reciprocalspaceship/VERSION

@@ -0,0 +1 @@
+1.0.5

reciprocalspaceship-1.0.5/reciprocalspaceship/commandline/cifdump.py

@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+"""
+Summarize the contents of a CIF file.
+
+Examples
+--------
+In order to summarize contents of file.cif::
+
+    > rs.cifdump file.cif
+
+If you would like to interactively inspect file.cif in an IPython
+shell, use the "--embed" argument::
+
+    > rs.cifdump file.cif --embed
+
+If multiple CIF files are listed, they will be summarized sequentially,
+and can be accessed in an IPython shell as a dictionary called `cifs`::
+
+    > rs.cifdump file1.cif file2.cif file3.cif --embed
+
+Usage Details
+-------------
+"""
+import argparse
+
+import pandas as pd
+
+import reciprocalspaceship as rs
+
+# If matplotlib is available, use pylab to setup IPython environment
+try:
+    from pylab import *
+except:
+    pass
+
+
+def parse_arguments():
+    """Parse commandline arguments"""
+
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.RawTextHelpFormatter, description=__doc__
+    )
+
+    # Required arguments
+    parser.add_argument("cif", nargs="+", help="CIF file(s) to summarize")
+
+    # Optional arguments
+    parser.add_argument(
+        "--embed",
+        action="store_true",
+        help=(
+            "CIF file(s) will be summarized, and an IPython " "shell will be started"
+        ),
+    )
+    parser.add_argument(
+        "-p",
+        "--precision",
+        type=int,
+        default=3,
+        help="Number of significant digits to output for floats",
+    )
+
+    return parser
+
+
+def summarize(cif, precision):
+    """Summarize contents of CIF file"""
+    with pd.option_context("display.precision", precision):
+        print(f"Spacegroup: {cif.spacegroup.short_name()}")
+        print(f"Extended Hermann-Mauguin name: {cif.spacegroup.xhm()}")
+        print(
+            (
+                f"Unit cell dimensions: {cif.cell.a:.3f} {cif.cell.b:.3f} {cif.cell.c:.3f} "
+                f"{cif.cell.alpha:.3f} {cif.cell.beta:.3f} {cif.cell.gamma:.3f}"
+            )
+        )
+        print(f"\ncif.head():\n\n{cif.head()}")
+        print(f"\ncif.describe():\n\n{cif.describe()}")
+        print(f"\ncif.dtypes:\n\n{cif.dtypes}")
+    return
+
+
+def main():
+    # Parse commandline arguments
+    parser = parse_arguments()
+    args = parser.parse_args()
+
+    if len(args.cif) == 1:
+        cif = rs.read_cif(args.cif[0])
+        summarize(cif, args.precision)
+    else:
+        cifs = dict(zip(args.cif, map(rs.read_cif, args.cif)))
+        for key, value in cifs.items():
+            print(f"CIF file: {key}\n")
+            summarize(value, args.precision)
+            print(f"{'-'*50}")
+
+    # Begin IPython shell
+    if args.embed:
+        from IPython import embed
+
+        bold = "\033[1m"
+        end = "\033[0m"
+        if "cifs" in locals():
+            header = f"rs.DataSets stored in {bold}cifs{end} dictionary"
+        else:
+            header = f"rs.DataSet stored as {bold}cif{end}"
+        print()
+        embed(colors="neutral", header=header)
+
+    return
+
+
+if __name__ == "__main__":
+    parser = main()

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship/commandline/mtzdump.py

@@ -74,9 +74,13 @@ def summarize(mtz, precision):
                 f"{mtz.cell.alpha:.3f} {mtz.cell.beta:.3f} {mtz.cell.gamma:.3f}"
             )
         )
-        print(f"\nmtz.head():\n\n{mtz.head()}")
-        print(f"\nmtz.describe():\n\n{mtz.describe()}")
-        print(f"\nmtz.dtypes:\n\n{mtz.dtypes}")
+        if mtz.cell is not None:
+            dHKL = mtz.compute_dHKL().dHKL
+            print(f"Resolution range:  {dHKL.max():.3f} - {dHKL.min():.3f} Å")
+        with pd.option_context("display.max_rows", None):
+            print(f"\nmtz.head():\n\n{mtz.head()}")
+            print(f"\nmtz.describe().T:\n\n{mtz.describe().T}")
+            print(f"\nmtz.dtypes:\n\n{mtz.dtypes}")
     return
 
 

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship/dataset.py

@@ -43,6 +43,23 @@ class DataSet(pd.DataFrame):
     and attributes, please see the `Pandas.DataFrame documentation`_.
 
     .. _Pandas.DataFrame documentation: https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html
+
+    Attributes
+    ----------
+    acentrics : rs.DataSet
+        Access only the acentric reflections in this dataset
+    cell : gemmi.UnitCell
+        The unit cell
+    centrics : rs.DataSet
+        Access only the centric reflections in this dataset
+    hkls : ndarray, shape=(n_reflections, 3)
+        Miller indices in DataSet.
+    merged : bool
+        Whether this is a merged dataset or unmerged
+    spacegroup : gemmi.SpaceGroup
+        The space group
+    reindexing_ops : list
+        Possible reindexing ops consistent with the cell and spacegroup
     """
 
     _metadata = ["_spacegroup", "_cell", "_index_dtypes", "_merged"]
@@ -131,6 +148,38 @@ class DataSet(pd.DataFrame):
     def merged(self, val):
         self._merged = val
 
+    @property
+    @range_indexed
+    def hkls(self):
+        """Miller indices"""
+        hkl = self[["H", "K", "L"]].to_numpy(dtype=np.int32)
+        return hkl
+
+    def get_hkls(self):
+        """Get the Miller indices of the dataset."""
+        return self.hkls
+
+    @hkls.setter
+    @range_indexed
+    def hkls(self, hkls):
+        if isinstance(hkls, DataSet):
+            """Convert to numpy if hkls is a dataset"""
+            hkls = hkls.hkls
+        if isinstance(hkls, np.ndarray):
+            h, k, l = hkls[..., 0], hkls[..., 1], hkls[..., 2]
+        else:
+            """Try coercing to numpy"""
+            try:
+                hkls = np.array(hkls)
+                h, k, l = hkls[..., 0], hkls[..., 1], hkls[..., 2]
+            except:
+                raise ValueError(
+                    "Unable to convert hkls to a suitable type. Please ensure hkls is a numpy array or rs.DataSet"
+                )
+        self["H"] = DataSeries(h, index=self.index, dtype="H")
+        self["K"] = DataSeries(k, index=self.index, dtype="H")
+        self["L"] = DataSeries(l, index=self.index, dtype="H")
+
     @property
     def centrics(self):
         """Access centric reflections in DataSet"""
@@ -1585,24 +1634,6 @@ class DataSet(pd.DataFrame):
         warnings.simplefilter("always")
         warnings.warn(message, DeprecationWarning)
 
-        if dmin is not None:
-            ds = self.loc[self.compute_dHKL().dHKL >= dmin, [key]]
-        else:
-            ds = self.loc[:, [key]]
-
-        if gridsize is None:
-            gridsize = self.get_reciprocal_grid_size(dmin=dmin, sample_rate=sample_rate)
-
-        # Set up P1 unit cell
-        p1 = ds.expand_to_p1()
-        p1 = p1.expand_anomalous()
-
-        # Get data and indices
-        data = p1[key].to_numpy()
-        H = p1.get_hkls()
-
-        # Populate grid
-        grid = np.zeros(gridsize, dtype=data.dtype)
-        grid[H[:, 0], H[:, 1], H[:, 2]] = data
-
-        return grid
+        return self.to_reciprocal_grid(
+            key, sample_rate=sample_rate, dmin=dmin, grid_size=gridsize
+        )

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship/io/precognition.py

@@ -31,7 +31,7 @@ def read_precognition(hklfile, spacegroup=None, cell=None, logfile=None):
         F = pd.read_csv(
             hklfile,
             header=None,
-            delim_whitespace=True,
+            sep="\\s+",
             names=["H", "K", "L", "F(+)", "SigF(+)", "F(-)", "SigF(-)"],
             usecols=usecols,
         )
@@ -49,7 +49,7 @@ def read_precognition(hklfile, spacegroup=None, cell=None, logfile=None):
         F = pd.read_csv(
             hklfile,
             header=None,
-            delim_whitespace=True,
+            sep="\\s+",
             names=[
                 "H",
                 "K",

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship/utils/cell.py

@@ -29,7 +29,7 @@ def compute_dHKL(H, cell):
     if inverse.shape[-1] == 1:
         inverse = inverse.squeeze(-1)
 
-    F = np.array(cell.fractionalization_matrix.tolist()).astype(np.float64)
+    F = np.array(cell.frac.mat, dtype=np.float64)
     dhkls = np.reciprocal(np.linalg.norm((hkls @ F), 2, 1)).astype(np.float32)
     return dhkls[inverse]
 

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship/utils/grid.py

@@ -50,6 +50,7 @@ def get_reciprocal_grid_size(cell, dmin, sample_rate=3.0, spacegroup=None):
 
     # Use gemmi.Mtz to find valid grid (FFT-friendly and obeys symmetry)
     m = gemmi.Mtz()
-    m.spacegroup = spacegroup
+    if spacegroup is not None:
+        m.spacegroup = spacegroup
 
     return m.get_size_for_hkl(min_size=min_size)

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship/utils/structurefactors.py

@@ -131,4 +131,4 @@ def is_absent(H, spacegroup):
     absent : array
         Boolean array of length n. absent[i] == True if H[i] is systematically absent in sg.
     """
-    return spacegroup.operations().systematic_absences(H)
+    return spacegroup.operations().systematic_absences(np.array(H, dtype=np.int32))

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5/reciprocalspaceship.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: reciprocalspaceship
-Version: 1.0.3
+Version: 1.0.5
 Summary: Tools for exploring reciprocal space
 Home-page: https://rs-station.github.io/reciprocalspaceship/
 Author: Kevin M. Dalton, Jack B. Greisman
@@ -18,9 +18,51 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Programming Language :: Python
 Requires-Python: >=3.9
+License-File: LICENSE
+Requires-Dist: gemmi<=0.7.1,>=0.7.0
+Requires-Dist: pandas<=2.2.3,>=2.2.2
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: ipython
+Requires-Dist: msgpack
+Requires-Dist: setuptools
 Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: ray; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinxcontrib-autoprogram; extra == "doc"
+Requires-Dist: autodocsumm; extra == "doc"
+Requires-Dist: jupyter; extra == "doc"
+Requires-Dist: tqdm; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: seaborn; extra == "doc"
+Requires-Dist: celluloid; extra == "doc"
+Requires-Dist: scikit-image; extra == "doc"
 Provides-Extra: examples
-License-File: LICENSE
+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"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 
 ``reciprocalspaceship`` provides a ``pandas``-style interface for

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship.egg-info/SOURCES.txt

@@ -20,6 +20,7 @@ reciprocalspaceship/algorithms/intensity.py
 reciprocalspaceship/algorithms/merge.py
 reciprocalspaceship/algorithms/scale_merged_intensities.py
 reciprocalspaceship/commandline/__init__.py
+reciprocalspaceship/commandline/cifdump.py
 reciprocalspaceship/commandline/mtzdump.py
 reciprocalspaceship/dtypes/__init__.py
 reciprocalspaceship/dtypes/base.py

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship.egg-info/entry_points.txt

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

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/reciprocalspaceship.egg-info/requires.txt

@@ -1,15 +1,18 @@
-gemmi<=0.6.7,>=0.5.5
+gemmi<=0.7.1,>=0.7.0
 pandas<=2.2.3,>=2.2.2
 numpy
 scipy
 ipython
 msgpack
+setuptools
 
 [dev]
 pytest
 pytest-cov
 pytest-xdist
 ray
+
+[doc]
 sphinx
 sphinx_rtd_theme
 nbsphinx

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/setup.py

@@ -74,22 +74,25 @@ setup(
     project_urls=PROJECT_URLS,
     python_requires=">=3.9",
     install_requires=[
-        "gemmi>=0.5.5, <=0.6.7",
+        "gemmi>=0.7.0, <=0.7.1",
         "pandas>=2.2.2, <=2.2.3",
         "numpy",
         "scipy",
         "ipython",
         "msgpack",
+        "setuptools",
     ],
     setup_requires=["pytest-runner"],
     tests_require=tests_require,
     extras_require={
-        "dev": tests_require + docs_require + examples_require,
+        "dev": tests_require,
+        "doc" : docs_require + examples_require,
         "examples": examples_require,
     },
     entry_points={
         "console_scripts": [
             "rs.mtzdump=reciprocalspaceship.commandline.mtzdump:main",
+            "rs.cifdump=reciprocalspaceship.commandline.cifdump:main",
         ]
     },
     classifiers=[

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/tests/test_dataset.py

@@ -711,3 +711,50 @@ def test_select_mtzdtype_ValueError(data_merged, dtype):
     """
     with pytest.raises(ValueError):
         data_merged.select_mtzdtype(dtype)
+
+
+@pytest.mark.parametrize("merged", [True, False])
+@pytest.mark.parametrize("hkl_type", ["ds", "index", "numpy"])
+@pytest.mark.parametrize("range_index", [True, False])
+def test_hkls_property_setter(
+    data_merged, data_unmerged, merged, hkl_type, range_index
+):
+    """
+    Test the setter for the .hkls property of rs datasets
+    """
+    if merged:
+        input_ds = data_merged
+    else:
+        input_ds = data_unmerged
+
+    hkls = input_ds.copy().reset_index()[["H", "K", "L"]]
+
+    ds = input_ds.copy()
+    if range_index:
+        ds = ds.reset_index()
+
+    # Confirm we're starting with equivalent miller indices
+    expected = ds.hkls
+    value = hkls
+
+    # Shuffle the hkls
+    hkls = hkls.sample(frac=1.0)
+
+    # confirm shuffling
+    assert not np.array_equal(hkls, ds.hkls)
+
+    # confirm setter
+    if hkl_type == "ds":
+        ds.hkls = hkls
+    elif hkl_type == "index":
+        ds.hkls = hkls.set_index(["H", "K", "L"])
+    elif hkl_type == "numpy":
+        ds.hkls = hkls.to_numpy()
+    expected = ds.hkls
+    value = hkls.hkls
+    assert np.array_equal(value, expected)
+
+    # Test that all data remained the same
+    for k in input_ds:
+        if k not in ["H", "K", "L"]:
+            assert np.array_equal(ds[k], input_ds[k])

{reciprocalspaceship-1.0.3 → reciprocalspaceship-1.0.5}/tests/test_dataset_grid.py

@@ -22,10 +22,10 @@ def test_to_reciprocal_grid_gemmi(mtz_by_spacegroup, sample_rate, p1, use_sf):
     grid_size = dataset.get_reciprocal_grid_size(sample_rate=sample_rate)
 
     if use_sf:
-        gemmigrid = gemmimtz.get_f_phi_on_grid("FMODEL", "PHIFMODEL", size=grid_size)
-        expected = np.array(gemmigrid, copy=False)
         dataset["sf"] = dataset.to_structurefactor("FMODEL", "PHIFMODEL")
         result = dataset.to_reciprocal_grid("sf", grid_size=grid_size)
+        gemmigrid = gemmimtz.get_f_phi_on_grid("FMODEL", "PHIFMODEL", size=grid_size)
+        expected = gemmigrid.array
 
         # Requires rtol due to truncations applied in gemmi
         assert np.allclose(result, expected, rtol=1e-4)

reciprocalspaceship-1.0.3/reciprocalspaceship/VERSION

@@ -1 +0,0 @@
-1.0.3