Merge branch 'materialsproject:master' into master

.github/workflows/jekyll-gh-pages.yml

@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Pages
         uses: actions/configure-pages@v3
       - name: Build with Jekyll

.gitignore

@@ -40,4 +40,3 @@ venv/
 ENV/
 env.bak/
 venv.bak/
-docs/tokens.py

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.1.5
     hooks:
       - id: ruff
         args: [--fix]
@@ -56,3 +56,9 @@ repos:
         # MD041: first line in a file should be a top-level heading
         # MD025: single title
         args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        args: [--drop-empty-cells, --keep-output]

README.md

@@ -33,7 +33,6 @@ Pymatgen is free to use. However, we also welcome your help to improve this libr
 - Code contributions via [pull request] are welcome.
 - For questions that are not bugs or feature requests, please use the `pymatgen` [MatSci forum](https://matsci.org/pymatgen) or open a [GitHub discussion].
 - [`matgenb`](https://github.com/materialsvirtuallab/matgenb#introduction) provides some example Jupyter notebooks that demonstrate how to use `pymatgen` functionality.
-- Follow us on [Twitter](https://twitter.com/pymatgen) to get news and tips.
 
 [pull request]: https://github.com/materialsproject/pymatgen/pulls
 [github issue]: https://github.com/materialsproject/pymatgen/issues
@@ -87,10 +86,10 @@ If you use `pymatgen` in your research, please consider citing the following wor
 
 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 the [`pymatgen` docs] on how to cite them.
 
-### Soliciting contributions to an updated pymatgen paper
+### Soliciting contributions to 2nd `pymatgen` paper
 
 If you are a long-standing `pymatgen` contributor and would like to be involved in working on an updated `pymatgen` publication,
-please contact the maintainers [@shyuep, @mkhorton and @janosh](mailto:[email protected],[email protected],[email protected]?subject=Contributing%20to%20updated%20pymatgen%20paper).
+please fill out this [co-author registration form](https://docs.google.com/forms/d/e/1FAIpQLSecIhD2YjdPGldrRTM8Go3VxVg_vjKjZAOXtIKDG7qckHLYaQ/viewform) or contact [@shyuep, @mkhorton and @janosh](mailto:[email protected],[email protected],[email protected]?subject=Contributing%20to%20updated%20pymatgen%20paper) with questions.
 
 ## License
 

dev_scripts/chemenv/explicit_permutations.py

@@ -91,8 +91,7 @@ class Algo:
         if len(cg.algorithms) != 1:
             raise ValueError("Multiple algorithms !")
         cg._algorithms = [ExplicitPermutationsAlgorithm(permutations=explicit_permutations)]
-        newgeom_dir = "new_geometry_files"
-        if not os.path.exists(newgeom_dir):
-            os.makedirs(newgeom_dir)
-        with open(f"{newgeom_dir}/{cg_symbol}.json", "w") as f:
+        new_geom_dir = "new_geometry_files"
+        os.makedirs(new_geom_dir, exist_ok=True)
+        with open(f"{new_geom_dir}/{cg_symbol}.json", "w") as f:
             json.dump(cg.as_dict(), f)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -431,7 +431,6 @@ def random_permutations_iterator(initial_permutation, n_permutations):
         )
         if test == "y":
             new_geom_dir = "new_geometry_files"
-            if not os.path.exists(new_geom_dir):
-                os.makedirs(new_geom_dir)
+            os.makedirs(new_geom_dir, exist_ok=True)
             with open(f"{new_geom_dir}/{cg_symbol}.json", "w") as file:
                 json.dump(cg.as_dict(), file)

dev_scripts/regen_libxcfunc.py

@@ -12,6 +12,7 @@
 import json
 import os
 import sys
+from copy import deepcopy
 
 
 def parse_libxc_docs(path):
@@ -46,8 +47,6 @@ def parse_section(section):
 
 def write_libxc_docs_json(xcfuncs, jpath):
     """Write json file with libxc metadata to path jpath."""
-    from copy import deepcopy
-
     xcfuncs = deepcopy(xcfuncs)
 
     # Remove XC_FAMILY from Family and XC_ from Kind to make strings more human-readable.

dev_scripts/update_pt_data.py

@@ -7,34 +7,36 @@
 
 from __future__ import annotations
 
+import collections
 import json
 import re
 from itertools import product
 
+import requests
+from bs4 import BeautifulSoup
 from monty.serialization import dumpfn, loadfn
 from ruamel import yaml
 
-from pymatgen.core import Element
-from pymatgen.core.periodic_table import get_el_sp
+from pymatgen.core import Element, get_el_sp
 
 
 def test_yaml():
-    with open("periodic_table.yaml") as f:
-        data = yaml.load(f)
+    with open("periodic_table.yaml") as file:
+        data = yaml.load(file)
         print(data)
 
 
 def test_json():
-    with open("periodic_table.json") as f:
-        data = json.load(f)
+    with open("periodic_table.json") as file:
+        data = json.load(file)
         print(data)
 
 
 def parse_oxi_state():
-    with open("periodic_table.yaml") as f:
-        data = yaml.load(f)
-    with open("oxidation_states.txt") as f:
-        oxi_data = f.read()
+    with open("periodic_table.yaml") as file:
+        data = yaml.load(file)
+    with open("oxidation_states.txt") as file:
+        oxi_data = file.read()
     oxi_data = re.sub("[\n\r]", "", oxi_data)
     patt = re.compile("<tr>(.*?)</tr>", re.MULTILINE)
 
@@ -65,8 +67,8 @@ def parse_oxi_state():
             data[el]["Common oxidation states"] = common_oxi
         else:
             print(el)
-    with open("periodic_table2.yaml", "w") as f:
-        yaml.dump(data, f)
+    with open("periodic_table2.yaml", "w") as file:
+        yaml.dump(data, file)
 
 
 def parse_ionic_radii():
@@ -161,7 +163,6 @@ def update_ionic_radii():
 def parse_shannon_radii():
     with open("periodic_table.yaml") as f:
         data = yaml.load(f)
-    import collections
 
     from openpyxl import load_workbook
 
@@ -251,10 +252,8 @@ def gen_iupac_ordering():
 
 def add_electron_affinities():
     """Update the periodic table data file with electron affinities."""
-    import requests
-    from bs4 import BeautifulSoup
 
-    req = requests.get("https://en.wikipedia.org/wiki/Electron_affinity_(data_page)")
+    req = requests.get("https://wikipedia.org/wiki/Electron_affinity_(data_page)")
     soup = BeautifulSoup(req.text, "html.parser")
     for t in soup.find_all("table"):
         if "Hydrogen" in t.text:
@@ -277,9 +276,6 @@ def add_electron_affinities():
 
 def add_ionization_energies():
     """Update the periodic table data file with ground level and ionization energies from NIST."""
-    import collections
-
-    from bs4 import BeautifulSoup
 
     with open("NIST Atomic Ionization Energies Output.html") as f:
         soup = BeautifulSoup(f.read(), "html.parser")