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Drop Python 3.9 support #178

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merged 6 commits into from
Jan 9, 2025
Merged

Drop Python 3.9 support #178

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7011550
Remove setup.py
AntObi Jan 9, 2025
87b7451
Port setup.py to pyproject.toml
AntObi Jan 9, 2025
73d7b72
Drop 3.9, add 3.13 and use uv
AntObi Jan 9, 2025
70f691d
Run pre-commit
AntObi Jan 9, 2025
be26a4b
Remove 3.13
AntObi Jan 9, 2025
e5ada19
Fix uv installation
AntObi Jan 9, 2025
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11 changes: 6 additions & 5 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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}}
Expand All @@ -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
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63 changes: 61 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -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"
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💡 Codebase verification

Dependencies not ready for Python 3.13

While the project declares Python 3.13 support, several key dependencies don't explicitly support Python 3.13 yet:

  • pymatgen (up to 3.12)
  • seaborn (up to 3.12)
  • umap-learn (up to 3.12)
  • llvmlite (up to 3.12)
  • adjustText (no version info)
  • openTSNE (generic Python 3)

Consider removing Python 3.13 from classifiers until these dependencies add support for it.

🔗 Analysis chain

Verify Python version compatibility

The Python version requirement and classifiers align with dropping Python 3.9 support. However, ensure all dependencies support Python 3.13.

Run this script to check dependency compatibility with Python 3.13:

Also applies to: 16-21

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check dependency compatibility with Python 3.13
# Test: Extract dependencies and check their Python version support

# Get all dependencies
rg '^    "[^"]+[>=<]+[0-9.]+' pyproject.toml | while read -r dep; do
    pkg=$(echo "$dep" | sed 's/^    "\([^"]*\)[>=<].*/\1/')
    echo "Checking $pkg..."
    curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.classifiers[] | select(contains("Programming Language :: Python"))'
done

Length of output: 3305

Script:

#!/bin/bash
# Description: Check dependency compatibility with Python 3.13 (fixed version)
# Get all dependencies including optional ones
rg '^    "[^"]+"' pyproject.toml | sed 's/^    "\([^"]*\).*/\1/' | while read -r pkg; do
    # Skip empty lines and section headers
    if [[ -z "$pkg" || "$pkg" == "["* ]]; then
        continue
    fi
    echo "Checking $pkg..."
    curl -s "https://pypi.org/pypi/${pkg%,}/json" | jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3"))'
done

Length of output: 32163

Script:

#!/bin/bash
# Description: Check dependency compatibility with Python 3.13 (improved version)
# Get dependencies section only
echo "Main dependencies:"
rg '^\[project\.dependencies\]' -A 50 pyproject.toml | while read -r line; do
    if [[ $line == "["* && $line != "[project.dependencies]" ]]; then
        break
    fi
    if [[ $line =~ ^\"([^\"]+)\" ]]; then
        pkg="${BASH_REMATCH[1]}"
        echo "Checking $pkg..."
        curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3"))'
        echo "---"
    fi
done

Length of output: 116

Script:

#!/bin/bash
# First, let's see the content structure
echo "File content:"
cat pyproject.toml
echo -e "\n=== Now checking dependencies ===\n"
# Extract dependencies using a simpler pattern
cat pyproject.toml | awk '/^dependencies = \[/,/\]/' | grep '"' | tr -d '", ' | while read -r pkg; do
    if [[ $pkg == *"="* ]]; then
        pkg=${pkg%%=*}
    fi
    if [[ -n $pkg ]]; then
        echo "Checking $pkg..."
        curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3"))'
        echo "---"
    fi
done

Length of output: 11297

Script:

#!/bin/bash
# Check main dependencies for Python 3.13 support
echo "Checking core dependencies for Python 3.13 support:"
for pkg in numpy scipy pymatgen seaborn matplotlib scikit-learn umap-learn adjustText openTSNE typing-extensions llvmlite; do
    echo "=== Checking $pkg ==="
    curl -s "https://pypi.org/pypi/$pkg/json" | jq -r '.info.classifiers[] | select(contains("Programming Language :: Python :: 3"))'
    echo "---"
done

Length of output: 5712

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

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82 changes: 0 additions & 82 deletions setup.py
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This file was deleted.

2 changes: 1 addition & 1 deletion src/elementembeddings/_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/elementembeddings/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion src/elementembeddings/plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))]
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