Faff

docs_rst/introduction.rst

@@ -97,7 +97,7 @@ One of the ways you can contribute is to fork the matgenb repo and add your own
 
 Below are a quick look at some of the graphical output possible.
 
-.. figure:: _static/examples.png
+.. figure:: _static/phase_diagram.png
    :width: 100%
    :alt: Examples
    :align: center

docs_rst/team.rst

@@ -60,11 +60,18 @@ Lead Maintainers
 
 | **Janosh Riebesell** |janosh|
 | University of Cambridge
+| Materials Project Staff
 .. |janosh| image:: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/mark-github.svg
    :target: https://github.com/materialsproject/pymatgen/pulls?q=is:pr+author:janosh
    :width: 16
    :height: 16
-   :alt: GitHub profile for janosh
+   :alt: janosh GitHub profile
+
+.. |janosh.dev| image:: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/browser.svg
+   :target: https://janosh.dev
+   :width: 16
+   :height: 16
+   :alt: janosh homepage
 
 Newest Contributors
 ===================

docs_rst/usage.rst

@@ -62,16 +62,16 @@ which is a general python supplementary library arising from pymatgen.
 The output from an as_dict method is always json/yaml serializable. So if you
 want to save a structure, you may do the following::
 
-    with open('structure.json','w') as f:
-        json.dump(structure.as_dict(), f)
+    with open('structure.json', 'w') as file:
+        json.dump(structure.as_dict(), file)
 
 Similarly, to get the structure back from a json, you can do the following to
-restore the structure (or any object with a as_dict method) from the json as
+restore the structure (or any object with an as_dict method) from the json as
 follows::
 
-    with open('structure.json', 'r') as f:
-        d = json.load(f)
-        structure = Structure.from_dict(d)
+    with open('structure.json') as file:
+        dct = json.load(file)
+        structure = Structure.from_dict(dct)
 
 You may replace any of the above json commands with yaml in the PyYAML package
 to create a yaml file instead. There are certain tradeoffs between the two

pymatgen/analysis/local_env.py

@@ -3856,25 +3856,25 @@ def get_nn_info(self, structure: Structure, n: int) -> list[dict]:
                 to the coordination number (1 or smaller), 'site_index' gives index of
                 the corresponding site in the original structure.
         """
-        nndata = self.get_nn_data(structure, n)
+        nn_data = self.get_nn_data(structure, n)
 
         if not self.weighted_cn:
-            max_key = max(nndata.cn_weights, key=lambda k: nndata.cn_weights[k])
-            nn = nndata.cn_nninfo[max_key]
+            max_key = max(nn_data.cn_weights, key=lambda k: nn_data.cn_weights[k])
+            nn = nn_data.cn_nninfo[max_key]
             for entry in nn:
                 entry["weight"] = 1
             return nn
 
-        for entry in nndata.all_nninfo:
+        for entry in nn_data.all_nninfo:
             weight = 0
-            for cn in nndata.cn_nninfo:
-                for cn_entry in nndata.cn_nninfo[cn]:
+            for cn in nn_data.cn_nninfo:
+                for cn_entry in nn_data.cn_nninfo[cn]:
                     if entry["site"] == cn_entry["site"]:
-                        weight += nndata.cn_weights[cn]
+                        weight += nn_data.cn_weights[cn]
 
             entry["weight"] = weight
 
-        return nndata.all_nninfo
+        return nn_data.all_nninfo
 
     def get_nn_data(self, structure: Structure, n: int, length=None):
         """
@@ -3887,9 +3887,9 @@ def get_nn_data(self, structure: Structure, n: int, length=None):
 
         Returns:
             a namedtuple (NNData) object that contains:
-                - all near neighbor sites with weights
-                - a dict of CN -> weight
-                - a dict of CN -> associated near neighbor sites
+            - all near neighbor sites with weights
+            - a dict of CN -> weight
+            - a dict of CN -> associated near neighbor sites
         """
         length = length or self.fingerprint_length
 
@@ -4082,23 +4082,23 @@ def _semicircle_integral(dist_bins, idx):
         return (area1 - area2) / (0.25 * math.pi * r**2)
 
     @staticmethod
-    def transform_to_length(nndata, length):
+    def transform_to_length(nn_data, length):
         """
         Given NNData, transforms data to the specified fingerprint length
         Args:
-            nndata: (NNData)
+            nn_data: (NNData)
             length: (int) desired length of NNData
         """
         if length is None:
-            return nndata
+            return nn_data
 
         if length:
             for cn in range(length):
-                if cn not in nndata.cn_weights:
-                    nndata.cn_weights[cn] = 0
-                    nndata.cn_nninfo[cn] = []
+                if cn not in nn_data.cn_weights:
+                    nn_data.cn_weights[cn] = 0
+                    nn_data.cn_nninfo[cn] = []
 
-        return nndata
+        return nn_data
 
 
 def _get_default_radius(site):

pymatgen/analysis/tests/test_local_env.py

@@ -1317,9 +1317,9 @@ def test_weighted_cn_no_oxid(self):
 
     def test_fixed_length(self):
         cnn = CrystalNN(fingerprint_length=30)
-        nndata = cnn.get_nn_data(self.lifepo4, 0)
-        assert len(nndata.cn_weights) == 30
-        assert len(nndata.cn_nninfo) == 30
+        nn_data = cnn.get_nn_data(self.lifepo4, 0)
+        assert len(nn_data.cn_weights) == 30
+        assert len(nn_data.cn_nninfo) == 30
 
     def test_cation_anion(self):
         cnn = CrystalNN(weighted_cn=True, cation_anion=True)

pymatgen/core/__init__.py

@@ -10,21 +10,21 @@
 
 from ruamel.yaml import YAML
 
-from .composition import Composition as Composition
-from .lattice import Lattice as Lattice
-from .operations import SymmOp as SymmOp
-from .periodic_table import DummySpecies as DummySpecies
-from .periodic_table import Element as Element
-from .periodic_table import Species as Species
-from .sites import PeriodicSite as PeriodicSite
-from .sites import Site as Site
-from .structure import IMolecule as IMolecule
-from .structure import IStructure as IStructure
-from .structure import Molecule as Molecule
-from .structure import Structure as Structure
-from .units import ArrayWithUnit as ArrayWithUnit
-from .units import FloatWithUnit as FloatWithUnit
-from .units import Unit as Unit
+from pymatgen.core.composition import Composition as Composition
+from pymatgen.core.lattice import Lattice as Lattice
+from pymatgen.core.operations import SymmOp as SymmOp
+from pymatgen.core.periodic_table import DummySpecies as DummySpecies
+from pymatgen.core.periodic_table import Element as Element
+from pymatgen.core.periodic_table import Species as Species
+from pymatgen.core.sites import PeriodicSite as PeriodicSite
+from pymatgen.core.sites import Site as Site
+from pymatgen.core.structure import IMolecule as IMolecule
+from pymatgen.core.structure import IStructure as IStructure
+from pymatgen.core.structure import Molecule as Molecule
+from pymatgen.core.structure import Structure as Structure
+from pymatgen.core.units import ArrayWithUnit as ArrayWithUnit
+from pymatgen.core.units import FloatWithUnit as FloatWithUnit
+from pymatgen.core.units import Unit as Unit
 
 __author__ = "Pymatgen Development Team"
 __email__ = "pymatgen@googlegroups.com"

pymatgen/util/coord.py

@@ -289,18 +289,7 @@ def lattice_points_in_supercell(supercell_matrix):
     Returns:
         numpy array of the fractional coordinates
     """
-    diagonals = np.array(
-        [
-            [0, 0, 0],
-            [0, 0, 1],
-            [0, 1, 0],
-            [0, 1, 1],
-            [1, 0, 0],
-            [1, 0, 1],
-            [1, 1, 0],
-            [1, 1, 1],
-        ]
-    )
+    diagonals = np.array([[0, 0, 0], [0, 0, 1], [0, 1, 0], [0, 1, 1], [1, 0, 0], [1, 0, 1], [1, 1, 0], [1, 1, 1]])
     d_points = np.dot(diagonals, supercell_matrix)
 
     mins = np.min(d_points, axis=0)

tasks.py

@@ -30,29 +30,29 @@ def make_doc(ctx):
 
     :param ctx:
     """
-    with open("CHANGES.rst") as f:
-        contents = f.read()
+    with open("CHANGES.rst") as file:
+        contents = file.read()
 
     toks = re.split(r"\-{3,}", contents)
     n = len(toks[0].split()[-1])
     changes = [toks[0]]
     changes.append("\n" + "\n".join(toks[1].strip().split("\n")[0:-1]))
     changes = ("-" * n).join(changes)
 
-    with open("docs_rst/latest_changes.rst", "w") as f:
-        f.write(changes)
+    with open("docs_rst/latest_changes.rst", "w") as file:
+        file.write(changes)
 
     with cd("docs_rst"):
         ctx.run("cp ../CHANGES.rst change_log.rst")
         ctx.run("rm pymatgen.*.rst", warn=True)
         ctx.run("sphinx-apidoc --implicit-namespaces --separate -d 7 -o . -f ../pymatgen")
         ctx.run("rm *.tests.*rst")
-        for f in glob("*.rst"):
-            if f.startswith("pymatgen") and f.endswith("rst"):
+        for file in glob("*.rst"):
+            if file.startswith("pymatgen") and file.endswith("rst"):
                 new_output = []
                 sub_output = []
                 sub_package = False
-                with open(f) as fid:
+                with open(file) as fid:
                     for line in fid:
                         clean = line.strip()
                         if clean == "Subpackages":
@@ -67,7 +67,7 @@ def make_doc(ctx):
                                 sub_package = False
                                 sub_output = []
 
-                with open(f, "w") as fid:
+                with open(file, "w") as fid:
                     fid.write("".join(new_output))
         ctx.run("make html")
 
@@ -109,16 +109,6 @@ def make_dash(ctx):
     with open(plist, "w") as file:
         file.write("\n".join(xml))
     ctx.run('tar --exclude=".DS_Store" -cvzf pymatgen.tgz pymatgen.docset')
-    # xml = []
-    # with open("docs/pymatgen.xml") as f:
-    #     for l in f:
-    #         l = l.strip()
-    #         if l.startswith("<version>"):
-    #             xml.append(f"<version>{version}</version>")
-    #         else:
-    #             xml.append(l)
-    # with open("docs/pymatgen.xml", "wt") as f:
-    #     f.write("\n".join(xml))
     ctx.run("rm -r pymatgen.docset")
     ctx.run("cp docs_rst/conf-normal.py docs_rst/conf.py")
 
@@ -128,11 +118,11 @@ def contribute_dash(ctx, version):
     make_dash(ctx)
     ctx.run("cp pymatgen.tgz ../Dash-User-Contributions/docsets/pymatgen/pymatgen.tgz")
     with cd("../Dash-User-Contributions/docsets/pymatgen"):
-        with open("docset.json") as f:
-            data = json.load(f)
+        with open("docset.json") as file:
+            data = json.load(file)
             data["version"] = version
-        with open("docset.json", "w") as f:
-            json.dump(data, f, indent=4)
+        with open("docset.json", "w") as file:
+            json.dump(data, file, indent=4)
         ctx.run(f'git commit --no-verify -a -m "Update to v{version}"')
         ctx.run("git push")
     ctx.run("rm pymatgen.tgz")
@@ -181,19 +171,19 @@ def publish(ctx):
 
 @task
 def set_ver(ctx, version):
-    with open("pymatgen/core/__init__.py") as f:
-        contents = f.read()
+    with open("pymatgen/core/__init__.py") as file:
+        contents = file.read()
         contents = re.sub(r"__version__ = .*\n", f"__version__ = {version!r}\n", contents)
 
-    with open("pymatgen/core/__init__.py", "w") as f:
-        f.write(contents)
+    with open("pymatgen/core/__init__.py", "w") as file:
+        file.write(contents)
 
-    with open("setup.py") as f:
-        contents = f.read()
+    with open("setup.py") as file:
+        contents = file.read()
         contents = re.sub(r"version=([^,]+),", f"version={version!r},", contents)
 
-    with open("setup.py", "w") as f:
-        f.write(contents)
+    with open("setup.py", "w") as file:
+        file.write(contents)
 
 
 @task
@@ -203,12 +193,12 @@ def release_github(ctx, version):
 
     :param ctx:
     """
-    with open("CHANGES.rst") as f:
-        contents = f.read()
-    toks = re.split(r"\-+", contents)
-    desc = toks[1].strip()
-    toks = desc.split("\n")
-    desc = "\n".join(toks[:-1]).strip()
+    with open("CHANGES.rst") as file:
+        contents = file.read()
+    tokens = re.split(r"\-+", contents)
+    desc = tokens[1].strip()
+    tokens = desc.split("\n")
+    desc = "\n".join(tokens[:-1]).strip()
     payload = {
         "tag_name": f"v{version}",
         "target_commitish": "master",