Merge remote-tracking branch 'trunk/master'

.github/workflows/test.yml

@@ -27,19 +27,23 @@ jobs:
       matrix:
         # maximize CI coverage of different platforms and python versions while minimizing the
         # total number of jobs. We run all pytest splits with the oldest supported python
-        # version (currently 3.9) on windows (seems most likely to surface errors) and with
+        # version (currently 3.10) on windows (seems most likely to surface errors) and with
         # newest version (currently 3.12) on ubuntu (to get complete coverage on unix).
         config:
           - os: windows-latest
-            python: "3.9"
+            python: "3.10"
             resolution: highest
             extras: ci,optional
+          - os: windows-latest
+            python: "3.10"
+            resolution: highest
+            extras: ci,optional,numpy1  # Test NP1 on Windows (quite buggy ATM)
           - os: ubuntu-latest
-            python: ">3.9"
+            python: ">3.10"
             resolution: lowest-direct
             extras: ci,optional
           - os: macos-latest
-            python: "3.10"
+            python: "3.11"
             resolution: lowest-direct
             extras: ci # test with only required dependencies installed
 

ADMIN.md

@@ -16,7 +16,7 @@ The general procedure for releasing `pymatgen` comprises the following steps:
 
 ## Initial setup
 
-Pymatgen uses [invoke](http://pyinvoke.org) to automate releases.
+Pymatgen uses [invoke](https://pyinvoke.org) to automate releases.
 You will also need `sphinx` and `doc2dash`.
 
 ```sh

CITATION.cff

@@ -5,7 +5,7 @@ message: |
 
   In addition, some of pymatgen's functionality is based on scientific advances
   / principles developed by the computational materials scientists in our team.
-  Please refer to pymatgen's docs at http://pymatgen.org on how to cite them.
+  Please refer to pymatgen's docs at https://pymatgen.org on how to cite them.
 authors:
 - family-names: Ong
   given-names: Shyue Ping

CONTRIBUTING.md

@@ -78,7 +78,7 @@ Given that `pymatgen` is intended to be a long-term code base, we adopt very str
     pre-commit run --all-files  # ensure your entire codebase passes linters
    ```
 
-1. **Python 3**. We only support Python 3.9+.
+1. **Python 3**. We only support Python 3.10+.
 1. **Documentation** is required for all modules, classes and methods. In particular, the method doc strings should make clear the arguments expected and the return values. For complex algorithms (e.g., an Ewald summation), a summary of the algorithm should be provided and preferably with a link to a publication outlining the method in detail.
 
 For the above, if in doubt, please refer to the core classes in `pymatgen` for examples of what is expected.

README.md

@@ -12,7 +12,7 @@ height="70">
 [![codecov](https://codecov.io/gh/materialsproject/pymatgen/branch/master/graph/badge.svg?token=XC47Un1LV2)](https://codecov.io/gh/materialsproject/pymatgen)
 [![PyPI Downloads](https://img.shields.io/pypi/dm/pymatgen?logo=pypi&logoColor=white&color=blue&label=PyPI)](https://pypi.org/project/pymatgen)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/pymatgen?logo=condaforge&color=blue&label=Conda)](https://anaconda.org/conda-forge/pymatgen)
-[![Requires Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
+[![Requires Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 [![Paper](https://img.shields.io/badge/J.ComMatSci-2012.10.028-blue?logo=elsevier&logoColor=white)](https://doi.org/10.1016/j.commatsci.2012.10.028)
 
 </h4>
@@ -63,7 +63,7 @@ If you'd like to use the latest unreleased changes on the main branch, you can i
 pip install -U git+https://github.com/materialsproject/pymatgen
 ```
 
-The minimum Python version is 3.9. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
+The minimum Python version is 3.10. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
 
 ## Change Log
 

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -44,16 +44,14 @@
             raise ValueError("Should all be separation plane")
 
         perms_on_file = f"Permutations on file in this algorithm ({len(sep_plane_algo._permutations)}) "
-        print(perms_on_file)
-        print(sep_plane_algo._permutations)
+        print(f"{perms_on_file}\n{sep_plane_algo._permutations}")
         permutations = sep_plane_algo.safe_separation_permutations(
             ordered_plane=sep_plane_algo.ordered_plane, ordered_point_groups=sep_plane_algo.ordered_point_groups
         )
 
         sep_plane_algo._permutations = permutations
 
-        print(f"Test permutations ({len(permutations)}) :")
-        print(permutations)
+        print(f"Test permutations ({len(permutations)}):\n{permutations}")
 
         lgf = LocalGeometryFinder()
         lgf.setup_parameters(structure_refinement=lgf.STRUCTURE_REFINEMENT_NONE)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -398,9 +398,10 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                         perms_used[some_perm] += 1
                     else:
                         perms_used[some_perm] = 1
-                tcurrent = time.process_time()
-                assert n_permutations is not None
-                time_left = (n_permutations - idx_perm) * (tcurrent - t0) / idx_perm
+                t_now = time.process_time()
+                if n_permutations is None:
+                    raise ValueError(f"{n_permutations=}")
+                time_left = (n_permutations - idx_perm) * (t_now - t0) / idx_perm
                 time_left = f"{time_left:.1f}"
                 idx_perm += 1
             print(

dev_scripts/nist_codata.txt

@@ -2,7 +2,7 @@
              Fundamental Physical Constants --- Complete Listing
 
 
-  From:  http://physics.nist.gov/constants
+  From:  https://physics.nist.gov/cuu/Constants/index.html
 
 
 

dev_scripts/regen_libxcfunc.py

@@ -34,10 +34,12 @@ def parse_section(section):
                 section += [line]
             else:
                 num, entry = parse_section(section)
-                assert num not in dct
+                if num in dct:
+                    raise RuntimeError(f"{num=} should not be present in {dct=}.")
                 dct[num] = entry
                 section = []
-        assert section == []
+        if section:
+            raise RuntimeError(f"Expected empty section, got {section=}")
 
     return dct
 

dev_scripts/update_pt_data.py

@@ -20,11 +20,11 @@
 except ImportError:
     BeautifulSoup = None
 
-ptable_yaml_path = "periodic_table.yaml"
+PTABLE_YAML_PATH = "periodic_table.yaml"
 
 
 def parse_oxi_state():
-    data = loadfn(ptable_yaml_path)
+    data = loadfn(PTABLE_YAML_PATH)
     with open("oxidation_states.txt") as file:
         oxi_data = file.read()
     oxi_data = re.sub("[\n\r]", "", oxi_data)
@@ -62,7 +62,7 @@ def parse_oxi_state():
 
 
 def parse_ionic_radii():
-    data = loadfn(ptable_yaml_path)
+    data = loadfn(PTABLE_YAML_PATH)
     with open("ionic_radii.csv") as file:
         radii_data = file.read()
     radii_data = radii_data.split("\r")
@@ -92,7 +92,7 @@ def parse_ionic_radii():
 
 
 def parse_radii():
-    data = loadfn(ptable_yaml_path)
+    data = loadfn(PTABLE_YAML_PATH)
     with open("radii.csv") as file:
         radii_data = file.read()
     radii_data = radii_data.split("\r")
@@ -128,7 +128,7 @@ def parse_radii():
 
 
 def update_ionic_radii():
-    data = loadfn(ptable_yaml_path)
+    data = loadfn(PTABLE_YAML_PATH)
 
     for dct in data.values():
         if "Ionic_radii" in dct:
@@ -147,7 +147,7 @@ def update_ionic_radii():
 
 
 def parse_shannon_radii():
-    data = loadfn(ptable_yaml_path)
+    data = loadfn(PTABLE_YAML_PATH)
 
     from openpyxl import load_workbook
 
@@ -179,13 +179,13 @@ def parse_shannon_radii():
         if el in data:
             data[el]["Shannon radii"] = dict(radii[el])
 
-    dumpfn(data, ptable_yaml_path)
+    dumpfn(data, PTABLE_YAML_PATH)
     with open("../pymatgen/core/periodic_table.json", mode="w") as file:
         json.dump(data, file)
 
 
 def gen_periodic_table():
-    data = loadfn(ptable_yaml_path)
+    data = loadfn(PTABLE_YAML_PATH)
 
     with open("../pymatgen/core/periodic_table.json", mode="w") as file:
         json.dump(data, file)
@@ -217,14 +217,16 @@ def gen_iupac_ordering():
         ([17], range(6, 1, -1)),
     ]  # At -> F
 
-    order = sum((list(product(x, y)) for x, y in order), [])  # noqa: RUF017
-    iupac_ordering_dict = dict(zip([Element.from_row_and_group(row, group) for group, row in order], range(len(order))))
+    order = [item for sublist in (list(product(x, y)) for x, y in order) for item in sublist]
+    iupac_ordering_dict = dict(
+        zip([Element.from_row_and_group(row, group) for group, row in order], range(len(order)), strict=True)
+    )
 
     # first clean periodic table of any IUPAC ordering
     for el in periodic_table:
         periodic_table[el].pop("IUPAC ordering", None)
 
-    # now add iupac ordering
+    # now add IUPAC ordering
     for el in periodic_table:
         if "IUPAC ordering" in periodic_table[el]:
             # sanity check that we don't cover the same element twice
@@ -237,7 +239,7 @@ def gen_iupac_ordering():
 def add_electron_affinities():
     """Update the periodic table data file with electron affinities."""
 
-    req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)", timeout=600)
+    req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)", timeout=60)
     soup = BeautifulSoup(req.text, "html.parser")
     table = None
     for table in soup.find_all("table"):
@@ -251,23 +253,26 @@ def add_electron_affinities():
         data += [row]
     data.pop(0)
 
-    ea = {}
+    element_electron_affinities = {}
     max_Z = max(Element(element).Z for element in Element.__members__)
     for r in data:
         # don't want superheavy elements or less common isotopes
-        if int(r[0]) > max_Z or r[2] in ea:
+        if int(r[0]) > max_Z or r[2] in element_electron_affinities:
             continue
         temp_str = re.sub(r"[\s\(\)]", "", r[3].strip("()[]"))
         # hyphen-like characters used that can't be parsed by .float
         bytes_rep = temp_str.encode("unicode_escape").replace(b"\\u2212", b"-")
-        ea[r[2]] = float(bytes_rep.decode("unicode_escape"))
-
-    Z_set = {Element.from_name(element).Z for element in ea}
-    assert Z_set.issuperset(range(1, 93))  # Ensure that we have data for up to U.
-    print(ea)
+        element_electron_affinities[r[2]] = float(bytes_rep.decode("unicode_escape"))
+
+    Z_set = {Element.from_name(element).Z for element in element_electron_affinities}
+    # Ensure that we have data for up to Uranium
+    if not Z_set.issuperset(range(1, 93)):
+        missing_electron_affinities = set(range(1, 93)) - Z_set
+        raise ValueError(f"{missing_electron_affinities=}")
+    print(element_electron_affinities)
     pt = loadfn("../pymatgen/core/periodic_table.json")
     for key, val in pt.items():
-        val["Electron affinity"] = ea.get(Element(key).long_name)
+        val["Electron affinity"] = element_electron_affinities.get(Element(key).long_name)
     dumpfn(pt, "../pymatgen/core/periodic_table.json")
 
 
@@ -282,15 +287,17 @@ def add_ionization_energies():
             break
     data = defaultdict(list)
     for row in table.find_all("tr"):
-        row = [td.get_text().strip() for td in row.find_all("td")]
-        if row:
+        if row := [td.get_text().strip() for td in row.find_all("td")]:
             Z = int(row[0])
             val = re.sub(r"\s", "", row[8].strip("()[]"))
             val = None if val == "" else float(val)
             data[Z] += [val]
     print(data)
-    print(data[51])
-    assert set(data).issuperset(range(1, 93))  # Ensure that we have data for up to U.
+
+    # Ensure that we have data for up to U.
+    if not set(data).issuperset(range(1, 93)):
+        raise RuntimeError("Failed to get data up to Uranium")
+
     pt = loadfn("../pymatgen/core/periodic_table.json")
     for key, val in pt.items():
         del val["Ionization energy"]