Merge pull request #178 from WMD-group/bump_python

Drop Python 3.9 support

.github/workflows/ci.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     runs-on: ${{matrix.os}}
@@ -30,12 +30,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
-          python -m pip install -e ".[dev]"
+          python -m pip install --upgrade uv
+          uv pip install -e ".[dev]" --system
       - name: Check package versions
         run: |
-          pip show -V elementembeddings
-          pip show -V pytest
-          pip show -V matplotlib
+          uv pip show -V elementembeddings
+          uv pip show -V pytest
+          uv pip show -V matplotlib
 
       - name: Run tests
         run: python -m pytest --mpl --mpl-baseline-path=src/elementembeddings/tests/baseline --cov=src/elementembeddings --cov-report=xml -v

pyproject.toml

@@ -1,14 +1,73 @@
 [build-system]
 # Minimum requirements for the build system to execute.
-requires = ["setuptools"]  # PEP 508 specifications.
+requires = ["setuptools>=65.0.0"]  # PEP 508 specifications.
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "ElementEmbeddings"
+version = "0.6.1"
+description = "Element Embeddings"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+authors = [
+    { name = "Anthony O. Onwuli", email = "[email protected]" }
+]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "License :: OSI Approved :: MIT License",
+]
+dependencies = [
+    "numpy>=1.23.3,<3",
+    "scipy>=1.10.1",
+    "pymatgen>2022.9.21",
+    "seaborn>=0.13.0",
+    "matplotlib>=3.7.1",
+    "scikit-learn>=1.3.0",
+    "umap-learn>=0.5.3",
+    "adjustText>=0.8",
+    "openTSNE>=1.0.0",
+    "typing-extensions",
+    "llvmlite>=0.40",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pre-commit",
+    "black",
+    "isort",
+    "pytest",
+    "pytest-subtests",
+    "nbqa",
+    "flake8",
+    "pyupgrade",
+    "autopep8",
+    "pytest-cov",
+    "pytest-mpl",
+]
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocstrings",
+    "mkdocstrings-python",
+    "mike",
+    "mkdocs-jupyter",
+]
+
 [tool.semantic_release]
 version_variable = "setup.py:__version__"
 version_source = "tag"
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 line-length = 120
 force-exclude = true
 

src/elementembeddings/_base.py

@@ -167,7 +167,7 @@ def standardise(self, inplace: bool = False):
             embeddings_copy = self.embeddings.copy()
             embeddings_array = np.array(list(embeddings_copy.values()))
             embeddings_array = StandardScaler().fit_transform(embeddings_array)
-            for el, emb in zip(embeddings_copy.keys(), embeddings_array):
+            for el, emb in zip(embeddings_copy.keys(), embeddings_array, strict=False):
                 embeddings_copy[el] = emb
             if inplace:
                 self.embeddings = embeddings_copy

src/elementembeddings/core.py

@@ -255,7 +255,7 @@ def standardise(self, inplace: bool = False):
             embeddings_copy = self.embeddings.copy()
             embeddings_array = np.array(list(embeddings_copy.values()))
             embeddings_array = StandardScaler().fit_transform(embeddings_array)
-            for el, emb in zip(embeddings_copy.keys(), embeddings_array):
+            for el, emb in zip(embeddings_copy.keys(), embeddings_array, strict=False):
                 embeddings_copy[el] = emb
 
             if inplace:

src/elementembeddings/plotter.py

@@ -176,7 +176,7 @@ def dimension_plotter(
 
             species_labels = [
                 rf"$\mathregular{{{element}^{{{abs(charge)}{sign}}}}}$"
-                for (element, charge), sign in zip(parsed_species, signs)
+                for (element, charge), sign in zip(parsed_species, signs, strict=False)
             ]
 
             texts = [ax.text(df["x"][i], df["y"][i], species_labels[i], fontsize=12) for i in range(len(df))]