v2023.5.8

update CHANGES.rst fix shadowed python built-ins sort pyproject.toml arrays alphabetically
molmd · May 8, 2023 · 92f89f0 · 92f89f0
1 parent 1baa8ad
commit 92f89f0
Show file tree

Hide file tree

Showing 3 changed files with 129 additions and 24 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,6 +1,110 @@
 Change log
 ==========
 
+v2023.5.8
+---------
+* PR #2959 from @materialsproject dependabot/github_actions/pypa/cibuildwheel-2.12.3
+    Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.4 to 2.12.3.
+    <details>
+    <summary>Release notes</summary>
+    <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
+    <blockquote>
+    <h2>v2.12.3</h2>
+    <ul>
+    <li>🐛 Fix an import error when running on Python 3.7. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1479">#1479</a>)</li>
+    </ul>
+    <h2>v2.12.2</h2>
+    <ul>
+    <li>🐛 Fix a bug that caused an extra empty config-setting to be passed to the backend when CIBW_BUILD_FRONTEND is set to <code>build</code>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1474">#1474</a>)</li>
+    <li>🐛 Fix a crash that occurred when overwriting an existing wheel on Windows. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1464">#1464</a>)</li>
+    <li>🛠 Pinned version updates, including CPython 3.10.11, 3.11.3, pip 23.1 and wheel 0.40.0.</li>
+    </ul>
+    <h2>v2.12.1</h2>
+    <ul>
+    <li>🐛 Fix a bug that prevented the use of CIBW_CONFIG_SETTINGS with the 'pip' build backend. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>)</li>
+    </ul>
+    <h2>v2.12.0</h2>
+    <ul>
+    <li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
+    <li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
+    </ul>
+    </blockquote>
+    </details>
+    <details>
+    <summary>Changelog</summary>
+    <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
+    <blockquote>
+    <h3>v2.12.3</h3>
+    <p><em>19 April 2023</em></p>
+    <ul>
+    <li>🐛 Fix an import error when running on Python 3.7. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1479">#1479</a>)</li>
+    </ul>
+    <h3>v2.12.2</h3>
+    <p><em>18 April 2023</em></p>
+    <ul>
+    <li>🐛 Fix a bug that caused an extra empty config-setting to be passed to the backend when CIBW_BUILD_FRONTEND is set to <code>build</code>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1474">#1474</a>)</li>
+    <li>🐛 Fix a crash that occurred when overwriting an existing wheel on Windows. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1464">#1464</a>)</li>
+    <li>🛠 Pinned version updates, including CPython 3.10.11, 3.11.3, pip 23.1 and wheel 0.40.0.</li>
+    </ul>
+    <h3>v2.12.1</h3>
+    <p><em>11 March 2023</em></p>
+    <ul>
+    <li>🐛 Fix a bug that prevented the use of CIBW_CONFIG_SETTINGS with the 'pip' build backend. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>)</li>
+    </ul>
+    <h3>v2.12.0</h3>
+    <p><em>16 Jan 2023</em></p>
+    <ul>
+    <li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
+    <li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
+    </ul>
+    </blockquote>
+    </details>
+    <details>
+    <summary>Commits</summary>
+    <ul>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/5e15bb25b428e1bf2daf2215f173d2b40135f56f"><code>5e15bb2</code></a> Bump version: v2.12.3</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/52572ccdd01fcde11603283bcfda090086a7d11c"><code>52572cc</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1479">#1479</a> from henryiii/henryiii/fix/py37</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/c6027e4fc72eee01851e06b1cd173aabeb3abfe0"><code>c6027e4</code></a> docs: fix options.md typos (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1477">#1477</a>)</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/aff6dd5adc49114f1ee49c82bcb386a142fc614a"><code>aff6dd5</code></a> refactor: tomllib in _compat</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/31bd9c91743e09f5b48c4def38c255c14c00d1af"><code>31bd9c9</code></a> refactor: restore typing for non-backports</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/d996af554ae21435028e538e417e403e8db7433e"><code>d996af5</code></a> fix: restore Python 3.7 support</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/e42f243b523a93352f0686ba2f4a62b7bf5f7d34"><code>e42f243</code></a> ci: add Python 3.7</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/9f18d385cbb38b9c24f46a2c798f361ecea8fd5c"><code>9f18d38</code></a> Bump version: v2.12.2</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/dfbc6c3902b689c250f9d9dd10ce8f88db8e2b7b"><code>dfbc6c3</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1476">#1476</a> from henryiii/henryiii/chore/ruff_ex</li>
+    <li><a href="https://github.com/pypa/cibuildwheel/commit/8c5f89c035ba6ac81794ed5a5d6cd2110957f181"><code>8c5f89c</code></a> chore: update typing to be generic on function args</li>
+    <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.11.4...v2.12.3">compare view</a></li>
+    </ul>
+    </details>
+    <br />
+    [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=pypa/cibuildwheel&package-manager=github_actions&previous-version=2.11.4&new-version=2.12.3)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
+    Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
+    [//]: # (dependabot-automerge-start)
+    [//]: # (dependabot-automerge-end)
+    ---
+    <details>
+    <summary>Dependabot commands and options</summary>
+    <br />
+    You can trigger Dependabot actions by commenting on this PR:
+    - `@dependabot rebase` will rebase this PR
+    - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
+    - `@dependabot merge` will merge this PR after your CI passes on it
+    - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
+    - `@dependabot cancel merge` will cancel a previously requested merge and block automerging
+    - `@dependabot reopen` will reopen this PR if it is closed
+    - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
+    - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
+    - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
+    - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
+    </details>
+* PR #2935 from @materialsproject pandas-v2-fixes
+    Closes #2914.
+    Replace calls to df.append() with pd.concat() and df.iteritems() with df.items().
+* PR #2925 from @jmmshn master
+    ## Allow proper versioning for forked repos
+    I'm not 100% sure how the current version numbering is updated for `pymatgen` but it's not able to update the number properly for forks.  The forks seem to keep a much older version number (from before the forking)
+    This creates problems if you have the forked repo as a dependency in a requirement.txt file.
+    This should fix that issue.
+
 v2023.3.23
 ----------
 * Misc bug fixes.

diff --git a/pymatgen/symmetry/maggroups.py b/pymatgen/symmetry/maggroups.py
@@ -11,6 +11,7 @@
 from fractions import Fraction
 
 import numpy as np
+from git import Sequence
 from monty.design_patterns import cached_class
 
 from pymatgen.core.lattice import Lattice
@@ -32,7 +33,7 @@ class MagneticSpaceGroup(SymmetryGroup):
     Representation of a magnetic space group.
     """
 
-    def __init__(self, id, setting_transformation="a,b,c;0,0,0"):
+    def __init__(self, label, setting_transformation="a,b,c;0,0,0"):
         """
         Initializes a MagneticSpaceGroup from its Belov, Neronova and
         Smirnova (BNS) number supplied as a list or its label supplied
@@ -106,14 +107,14 @@ def __init__(self, id, setting_transformation="a,b,c;0,0,0"):
         # retrieve raw data
         db = sqlite3.connect(MAGSYMM_DATA)
         c = db.cursor()
-        if isinstance(id, str):
-            id = "".join(id.split())  # remove any white space
-            c.execute("SELECT * FROM space_groups WHERE BNS_label=?;", (id,))
-        elif isinstance(id, list):
-            c.execute("SELECT * FROM space_groups WHERE BNS1=? AND BNS2=?;", (id[0], id[1]))
-        elif isinstance(id, int):
+        if isinstance(label, str):
+            label = "".join(label.split())  # remove any white space
+            c.execute("SELECT * FROM space_groups WHERE BNS_label=?;", (label,))
+        elif isinstance(label, list):
+            c.execute("SELECT * FROM space_groups WHERE BNS1=? AND BNS2=?;", (label[0], label[1]))
+        elif isinstance(label, int):
             # OG3 index is a 'master' index, going from 1 to 1651
-            c.execute("SELECT * FROM space_groups WHERE OG3=?;", (id,))
+            c.execute("SELECT * FROM space_groups WHERE OG3=?;", (label,))
         raw_data = list(c.fetchone())
 
         # Jones Faithful transformation
@@ -132,10 +133,10 @@ def __init__(self, id, setting_transformation="a,b,c;0,0,0"):
 
         def _get_point_operator(idx):
             """Retrieve information on point operator (rotation matrix and Seitz label)."""
-            hex = self._data["bns_number"][0] >= 143 and self._data["bns_number"][0] <= 194
+            is_hex = self._data["bns_number"][0] >= 143 and self._data["bns_number"][0] <= 194
             c.execute(
                 "SELECT symbol, matrix FROM point_operators WHERE idx=? AND hex=?;",
-                (idx - 1, hex),
+                (idx - 1, is_hex),
             )
             op = c.fetchone()
             op = {
@@ -281,7 +282,7 @@ def _parse_transformation(b):
         db.close()
 
     @classmethod
-    def from_og(cls, id):
+    def from_og(cls, label: Sequence[int] | str) -> MagneticSpaceGroup:
         """
         Initialize from Opechowski and Guccione (OG) label or number.
 
@@ -291,12 +292,12 @@ def from_og(cls, id):
         """
         db = sqlite3.connect(MAGSYMM_DATA)
         c = db.cursor()
-        if isinstance(id, str):
-            c.execute("SELECT BNS_label FROM space_groups WHERE OG_label=?", (id,))
-        elif isinstance(id, list):
+        if isinstance(label, str):
+            c.execute("SELECT BNS_label FROM space_groups WHERE OG_label=?", (label,))
+        elif isinstance(label, list):
             c.execute(
                 "SELECT BNS_label FROM space_groups WHERE OG1=? and OG2=? and OG3=?",
-                (id[0], id[1], id[2]),
+                (label[0], label[1], label[2]),
             )
         bns_label = c.fetchone()[0]
         db.close()

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,9 +1,9 @@
 [build-system]
 requires = [
   # pin NumPy version used in the build
+  "Cython>=0.29.23",
   "oldest-supported-numpy",
   "setuptools>=65.0.0",
-  "Cython>=0.29.23",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -29,9 +29,10 @@ select = [
   "B",   # flake8-bugbear
   "C40", # flake8-comprehensions
   "D",   # pydocstyle
-  "E",   # pycodestyle
+  "E",   # pycodestyle error
   "F",   # pyflakes
   "I",   # isort
+  "PD",  # pandas-vet
   "PIE", # flake8-pie
   "PL",  # pylint
   "PT",  # flake8-pytest-style
@@ -40,9 +41,8 @@ select = [
   "SIM", # flake8-simplify
   "TID", # tidy imports
   "UP",  # pyupgrade
-  "W",   # pycodestyle
+  "W",   # pycodestyle warning
   "YTT", # flake8-2020
-  "PD",  # pandas-vet
 ]
 ignore = [
   "B018",    # Found useless expression. Either assign it to a variable or remove it.
@@ -89,15 +89,15 @@ relative_files = true
 
 [tool.coverage.report]
 exclude_lines = [
-  "pragma: no cover",
+  "@deprecated",
   "def __repr__",
+  "if 0:",
+  "if __name__ == .__main__.:",
   "if self.debug:",
   "if settings.DEBUG",
+  "pragma: no cover",
   "raise AssertionError",
   "raise NotImplementedError",
-  "if 0:",
-  "if __name__ == .__main__.:",
-  "@deprecated",
   "show_plot",
 ]
 
@@ -108,7 +108,7 @@ explicit_package_bases = true
 no_implicit_optional = false
 
 [[tool.mypy.overrides]]
-module = ["tabulate.*", "requests.*"]
+module = ["requests.*", "tabulate.*"]
 ignore_missing_imports = true
 
 [tool.codespell]