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Allow Python 3.13 #89

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Merged
sethaxen merged 6 commits into from
Feb 4, 2025
Merged

Allow Python 3.13 #89

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e6d3ee7
Allow Python 3.13
j-adamczyk Feb 1, 2025
216286b
Update __init__.py
j-adamczyk Feb 2, 2025
8e88e8b
Add Python 3.13 classifier
sethaxen Feb 2, 2025
84c58c2
Resolve dependencies separately for each Python version
sethaxen Feb 2, 2025
c88f9ac
Run GA and RTD workflows with Python 3.13
sethaxen Feb 2, 2025
971d1fb
Make doctest work for recent SciPy versions
sethaxen Feb 2, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ jobs:
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest"]
python-version: ["3.9", "3.12"]
python-version: ["3.9", "3.13"]
fail-fast: false
steps:
- uses: actions/checkout@v2
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2 changes: 1 addition & 1 deletion .github/workflows/publish.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
runs-on: ubuntu-latest
env:
uv_version: "0.5.2"
python_version: "3.12"
python_version: "3.13"
steps:
- uses: actions/checkout@v2
- name: Setup MPI
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2 changes: 1 addition & 1 deletion .readthedocs.yml
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Expand Up @@ -3,7 +3,7 @@ version: 2
build:
os: "ubuntu-22.04"
tools:
python: "3.12"
python: "3.13"
commands:
- asdf plugin add uv
- asdf install uv latest
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13 changes: 11 additions & 2 deletions pyproject.toml
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Expand Up @@ -4,8 +4,8 @@ build-backend = "flit_core.buildapi"

[project]
name = "e3fp"
version = "1.2.6"
requires-python = ">=3.9, <3.13"
version = "1.2.7"
requires-python = ">=3.9, <3.14"
description = "Molecular 3D fingerprinting"
readme = "README.rst"
authors = [
Expand All @@ -19,6 +19,7 @@ classifiers = [
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
"Operating System :: OS Independent",
"Development Status :: 4 - Beta",
Expand Down Expand Up @@ -75,3 +76,11 @@ testpaths = ["e3fp/test"]
# https://github.com/astral-sh/uv/issues/6281
[tool.uv]
constraint-dependencies = ["numba>=0.60.0"]
# Resolve dependencies separately for each Python version
environments = [
"python_version>='3.13'",
"python_version=='3.12'",
"python_version=='3.11'",
"python_version=='3.10'",
"python_version=='3.9'",
]
5 changes: 2 additions & 3 deletions src/e3fp/fingerprint/db.py
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Expand Up @@ -105,9 +105,8 @@ class FingerprintDatabase(object):

Alternatively, the underlying `scipy.sparse.csr_matrix` may be accessed.

>>> db.array
<3x1024 sparse matrix of type '<class 'numpy.bool'>'
...with 327 stored elements in Compressed Sparse Row format>
>>> db.array # doctest: +ELLIPSIS
<...sparse matrix...with 327 stored elements...>
>>> db.array.toarray()
array([[False, False, False, ..., False, False, False],
[False, False, False, ..., False, False, False],
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