Merge branch 'master' of github.com:materialsproject/pymatgen

.github/workflows/lint.yml

@@ -16,29 +16,28 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.11'
           cache: pip
           cache-dependency-path: setup.py
+
       - name: Install dependencies
         run: |
-          pip install --upgrade pip
           pip install -e '.[dev]'
-      - name: pylint
+
+      - name: ruff
         run: |
-          pylint pymatgen
+          ruff --version
+          ruff check . --ignore 'D,SIM'
+
       - name: black
         run: |
           black --version
           black --check --diff --color pymatgen
-      - name: flake8
-        run: |
-          flake8 --version
-          flake8 --count --show-source --statistics pymatgen
-          # exit-zero treats all errors as warnings.
-          flake8 --count --exit-zero --max-complexity=20 --statistics pymatgen
+
       - name: mypy
         run: |
           mypy --version

.pre-commit-config.yaml

@@ -2,19 +2,14 @@ exclude: ^(docs|.*test_files|cmd_line|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [mypy, pylint, codespell, pydocstyle]
+  skip: [mypy, codespell]
 
 repos:
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.1
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.247
     hooks:
-      - id: autoflake
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+      - id: ruff
+        args: [--fix, --ignore, 'D,SIM']
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
@@ -24,38 +19,16 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: [--profile, black]
-
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
       - id: black
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-bugbear]
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.0.1
     hooks:
       - id: mypy
 
-  - repo: local
-    hooks:
-      - id: pylint
-        name: pylint
-        entry: pylint
-        language: python
-        types: [python]
-        args: [-sn, --rcfile=pylintrc]
-        additional_dependencies: [pylint]
-
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.2
     hooks:
@@ -64,12 +37,6 @@ repos:
         exclude_types: [html]
         args: [--ignore-words-list, 'titel,titels,reson,rute,pres,kno,coo']
 
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.3.0
-    hooks:
-      - id: pydocstyle
-        exclude: tests
-
   - repo: https://github.com/MarcoGorelli/cython-lint
     rev: v0.12.4
     hooks:

ADMIN.md

@@ -1,42 +1,42 @@
 # Introduction
 
-This documentation provides a guide for pymatgen administrators. The
-following assumes you are using miniconda or Anaconda.
+This documentation provides a guide for `pymatgen` administrators. The
+following assumes you are using `miniconda` or Anaconda.
 
 ## Releases
 
-The general procedure to releasing pymatgen comprises the following
+The general procedure to releasing `pymatgen` comprises the following
 steps:
 
 1. Make sure all CI checks are green. We don't want to release known bugs.
 2. Update and edit change log.
 3. Release PyPI versions + doc.
-4. Release conda versions.
+4. Release `conda` versions.
 5. Release Dash documentation.
 
 ## Initial setup
 
-Install some conda tools first:
+Install some `conda` tools first:
 
 ```sh
 conda install --yes conda-build anaconda-client
 ```
 
-Pymatgen uses [invoke](http://www.pyinvoke.org/) to automate releases.
+Pymatgen uses [invoke](http://pyinvoke.org) to automate releases.
 You will also need sphinx and doc2dash. Install these using:
 
 ```sh
 pip install --upgrade invoke sphinx doc2dash
 ```
 
-Create environment for py38 using conda:
+Create environment for py38 using `conda`:
 
 ```sh
 conda create --yes -n py38 python=3.8
 ```
 
-For each env, install some packages using conda followed by dev install
-for pymatgen:
+For each env, install some packages using `conda` followed by dev install
+for `pymatgen`:
 
 ```sh
 conda install --yes numpy scipy sympy matplotlib cython
@@ -105,7 +105,7 @@ generated by Appveyor.
 
 Fork and clone the
 [materials.sh](https://github.com/materialsvirtuallab/materials.sh).
-This repo contains the conda skeletons to build the conda versions for
+This repo contains the `conda` skeletons to build the `conda` versions for
 various matsci codes on the Anaconda [matsci
 channel](https://anaconda.org/matsci).
 

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -293,7 +293,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 exit()
         # 2. Optimization of the permutations
         print(f"Getting explicit optimized permutations for geometry {cg.name!r} (symbol : {cg_symbol!r})\n")
-        perms_used_algos = [dict() for algo in cg.algorithms]
+        perms_used_algos = [{} for algo in cg.algorithms]
 
         # Loop on algorithms
         for ialgo, algo in enumerate(cg.algorithms):
@@ -357,7 +357,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 points_perfect = lgf.perfect_geometry.points_wcs_ctwcc()
 
                 # Loop on the facets
-                separation_permutations = list()
+                separation_permutations = []
                 for iplane, plane_point_indices in enumerate(all_planes_point_indices):
                     prt2(
                         string=f"In plane {iplane:d} ({'-'.join(str(pp) for pp in plane_point_indices)})",

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -287,11 +287,11 @@ def get_weights(self, weights_options):
     alldeltacsmmins = []
     all_cn_pairs = []
     for ii in range(1, 14):
-        self_weight_max_csms_per_cn[str(ii)] = list()
+        self_weight_max_csms_per_cn[str(ii)] = []
         for jj in range(ii + 1, 14):
             cn_pair = f"{ii:d}_{jj:d}"
-            self_weight_max_csms[cn_pair] = list()
-            delta_csm_mins[cn_pair] = list()
+            self_weight_max_csms[cn_pair] = []
+            delta_csm_mins[cn_pair] = []
             all_cn_pairs.append(cn_pair)
     for ce_pair_dict in ce_pairs:
         ce1 = ce_pair_dict["initial_environment_symbol"]

dev_scripts/chemenv/test_algos_all_geoms.py

@@ -46,10 +46,7 @@
         symbol_name_mapping = allcg.get_symbol_name_mapping(coordination=coordination)
 
         if perms_def == "standard":
-            if coordination > 6:
-                test = "500"
-            else:
-                test = "all"
+            test = "500" if coordination > 6 else "all"
         elif perms_def == "ndefined":
             test = nperms  # type: ignore[assignment]
         else:

dev_scripts/update_pt_data.py

@@ -11,8 +11,8 @@
 import re
 from itertools import product
 
-import ruamel.yaml as yaml
 from monty.serialization import dumpfn, loadfn
+from ruamel import yaml
 
 from pymatgen.core import Element
 from pymatgen.core.periodic_table import get_el_sp
@@ -176,16 +176,13 @@ def parse_shannon_radii():
             el = sheet[f"A{i}"].value
         if sheet[f"B{i}"].value:
             charge = int(sheet[f"B{i}"].value)
-            radii[el][charge] = dict()
+            radii[el][charge] = {}
         if sheet[f"C{i}"].value:
             cn = sheet[f"C{i}"].value
             if cn not in radii[el][charge]:
-                radii[el][charge][cn] = dict()
+                radii[el][charge][cn] = {}
 
-        if sheet[f"D{i}"].value is not None:
-            spin = sheet[f"D{i}"].value
-        else:
-            spin = ""
+        spin = sheet[f"D{i}"].value if sheet[f"D{i}"].value is not None else ""
 
         radii[el][charge][cn][spin] = {
             "crystal_radius": float(sheet[f"E{i}"].value),
@@ -300,10 +297,7 @@ def add_ionization_energies():
         if row:
             Z = int(row[0])
             val = re.sub(r"\s", "", row[8].strip("()[]"))
-            if val == "":
-                val = None
-            else:
-                val = float(val)
+            val = None if val == "" else float(val)
             data[Z].append(val)
     print(data)
     print(data[51])

docs_rst/conf-docset.py

@@ -9,10 +9,13 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
+from __future__ import annotations
 
 import os
 import sys
 
+from pymatgen.core import __author__, __version__
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -21,7 +24,6 @@
 sys.path.insert(0, os.path.dirname("../pymatgen"))
 sys.path.insert(0, os.path.dirname("../.."))
 
-from pymatgen.core import __author__, __version__
 
 # -- General configuration -----------------------------------------------------
 

docs_rst/conf-normal.py

@@ -9,10 +9,13 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
+from __future__ import annotations
 
 import os
 import sys
 
+from pymatgen.core import __author__, __file__, __version__
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -21,8 +24,6 @@
 sys.path.insert(0, os.path.dirname("../pymatgen"))
 sys.path.insert(0, os.path.dirname("../.."))
 
-from pymatgen.core import __author__, __file__, __version__
-
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -318,9 +319,11 @@
 # Allow duplicate toc entries.
 # epub_tocdup = True
 
-# Resolve function for the linkcode extension.
-# Thanks to https://github.com/Lasagne/Lasagne/blob/master/docs/conf.py
+
 def linkcode_resolve(domain, info):
+    # Resolve function for the linkcode extension.
+    # Thanks to https://github.com/Lasagne/Lasagne/blob/master/docs/conf.py
+
     def find_source():
         # try to find the file and line number, based on code from numpy:
         # https://github.com/numpy/numpy/blob/master/doc/source/conf.py#L286

docs_rst/conf.py

@@ -9,10 +9,13 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
+from __future__ import annotations
 
 import os
 import sys
 
+from pymatgen.core import __author__, __file__, __version__
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -21,7 +24,6 @@
 sys.path.insert(0, os.path.dirname("../pymatgen"))
 sys.path.insert(0, os.path.dirname("../.."))
 
-from pymatgen.core import __author__, __file__, __version__
 
 # -- General configuration -----------------------------------------------------
 
@@ -346,5 +348,4 @@ def find_source():
         # no need to be relative to core here as module includes full path.
         filename = info["module"].replace(".", "/") + ".py"
 
-    tag = "v" + __version__
-    return f"https://github.com/materialsproject/pymatgen/blob/{tag}/{filename}"
+    return f"https://github.com/materialsproject/pymatgen/blob/v{__version__}/{filename}"