From e6d3ee715fb00e10cba3126c9d28d5d42982b0ed Mon Sep 17 00:00:00 2001 From: j-adamczyk Date: Sat, 1 Feb 2025 12:22:25 +0100 Subject: [PATCH 1/6] Allow Python 3.13 --- pyproject.toml | 4 ++-- src/e3fp/__init__.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e534749..faf6e0b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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 = [ diff --git a/src/e3fp/__init__.py b/src/e3fp/__init__.py index a53298a..e461c93 100644 --- a/src/e3fp/__init__.py +++ b/src/e3fp/__init__.py @@ -1,4 +1,4 @@ import importlib.metadata from .util import E3FPWarning, E3FPDeprecationWarning -__version__ = importlib.metadata.version("e3fp") +# __version__ = importlib.metadata.version("e3fp") From 216286bbf4196e76fb4911436883292c138227ad Mon Sep 17 00:00:00 2001 From: Jakub Adamczyk Date: Sun, 2 Feb 2025 21:00:57 +0100 Subject: [PATCH 2/6] Update __init__.py --- src/e3fp/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/e3fp/__init__.py b/src/e3fp/__init__.py index e461c93..a53298a 100644 --- a/src/e3fp/__init__.py +++ b/src/e3fp/__init__.py @@ -1,4 +1,4 @@ import importlib.metadata from .util import E3FPWarning, E3FPDeprecationWarning -# __version__ = importlib.metadata.version("e3fp") +__version__ = importlib.metadata.version("e3fp") From 8e88e8b93fd48a2630c23afceb6e0fa0e3a9b3be Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Sun, 2 Feb 2025 22:45:13 +0100 Subject: [PATCH 3/6] Add Python 3.13 classifier --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index faf6e0b..1be8d35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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", From 84c58c2b44b5e9cc9a22220341cc3ab8131b2ebe Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Sun, 2 Feb 2025 22:46:07 +0100 Subject: [PATCH 4/6] Resolve dependencies separately for each Python version --- pyproject.toml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 1be8d35..ddf9956 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -76,3 +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'", +] From c88f9ac904721472eaba564f51b8ec2f8a69075b Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Sun, 2 Feb 2025 22:46:56 +0100 Subject: [PATCH 5/6] Run GA and RTD workflows with Python 3.13 --- .github/workflows/ci.yml | 2 +- .github/workflows/publish.yml | 2 +- .readthedocs.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7103476..6719642 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -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 diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index f6e7908..f2196f5 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -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 diff --git a/.readthedocs.yml b/.readthedocs.yml index 48b749c..c82a604 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -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 From 971d1fbe3dc6a620eccc95f86c072f92f68b91a1 Mon Sep 17 00:00:00 2001 From: Seth Axen Date: Sun, 2 Feb 2025 23:03:55 +0100 Subject: [PATCH 6/6] Make doctest work for recent SciPy versions --- src/e3fp/fingerprint/db.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/e3fp/fingerprint/db.py b/src/e3fp/fingerprint/db.py index 0124071..3ecd56b 100644 --- a/src/e3fp/fingerprint/db.py +++ b/src/e3fp/fingerprint/db.py @@ -105,9 +105,8 @@ class FingerprintDatabase(object): Alternatively, the underlying `scipy.sparse.csr_matrix` may be accessed. - >>> db.array - <3x1024 sparse matrix of type '' - ...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],