From c8fc32ae41ccbfd213a7168cddb2e0900c64b2d7 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Wed, 29 Apr 2026 05:52:32 +0000 Subject: [PATCH 1/3] chore: update dependencies --- environment.yml | 32 ++++++++++++++++---------------- pyproject.toml | 26 +++++++++++++------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/environment.yml b/environment.yml index 4361834a..9c28badd 100644 --- a/environment.yml +++ b/environment.yml @@ -3,16 +3,16 @@ channels: - conda-forge dependencies: - adjusttext=1.3.0 - - bioconda::snakemake-minimal=9.6.2 + - bioconda::snakemake-minimal=9.19.0 # Conda refers to pypi/docker as docker-py. - docker-py=7.1.0 - - matplotlib=3.10.3 - - networkx=3.5 - - pandas=2.3.0 - - pydantic=2.11.7 - - numpy=2.3.1 - - requests=2.32.4 - - scikit-learn=1.7.0 + - matplotlib=3.10.9 + - networkx=3.6.1 + - pandas=3.0.2 + - pydantic=2.13.3 + - numpy=2.4.4 + - requests=2.33.1 + - scikit-learn=1.8.0 - seaborn=0.13.2 - spython=0.3.14 @@ -24,16 +24,16 @@ dependencies: - tabulate=0.9.0 # toolchain deps - - pip=25.3 + - pip=26.1 # This should be the same as requires-python minus the >=. - - python=3.11 + - python=3.13 # development dependencies - - pre-commit=4.2.0 - - pytest=8.4.1 - - pytest-split=0.10.0 - - sphinx=7.4.7 - - sphinx-rtd-theme=2.0.0 + - pre-commit=4.6.0 + - pytest=9.0.3 + - pytest-split=0.11.0 + - sphinx=9.1.0 + - sphinx-rtd-theme=3.1.0 - pip: - - dsub==0.4.13 + - dsub==0.5.2 diff --git a/pyproject.toml b/pyproject.toml index bfc602c6..46166ca8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,29 +18,29 @@ classifiers = [ ] requires-python = ">=3.11" dependencies = [ - "adjusttext==0.7.3", - "snakemake==9.6.2", + "adjusttext==1.3.0", + "snakemake==9.19.0", "docker==7.1.0", - "matplotlib==3.10.3", - "networkx==3.5", - "pandas==2.3.0", - "pydantic==2.11.7", - "numpy==2.3.1", - "requests==2.32.4", - "scikit-learn==1.7.0", + "matplotlib==3.10.9", + "networkx==3.6.1", + "pandas==3.0.2", + "pydantic==2.13.3", + "numpy==2.4.4", + "requests==2.33.1", + "scikit-learn==1.8.0", "seaborn==0.13.2", "spython==0.3.14", # toolchain deps - "pip==25.3", + "pip==26.1", ] [project.optional-dependencies] dev = [ # Only required for development - "pre-commit==4.2.0", - "pytest==8.4.1", - "pytest-split==0.10.0", + "pre-commit==4.6.0", + "pytest==9.0.3", + "pytest-split==0.11.0", ] [project.urls] From 7b3e383853676c0c7471b8962f34010cb280de9e Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Thu, 30 Apr 2026 21:24:31 +0000 Subject: [PATCH 2/3] fix: bump python to 3.13 --- .pre-commit-config.yaml | 2 +- .readthedocs.yaml | 2 +- environment.yml | 10 +++++----- pyproject.toml | 6 +++--- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fe010814..3b0581af 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # See https://pre-commit.com/hooks.html for more hooks default_language_version: # Match this to the version specified in environment.yml - python: python3.11 + python: python3.13 repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.4.0 # Use the ref you want to point at diff --git a/.readthedocs.yaml b/.readthedocs.yaml index cd6d3883..612c1d92 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,7 +8,7 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.11" + python: "3.13" # Build documentation in the "docs/" directory with Sphinx sphinx: diff --git a/environment.yml b/environment.yml index 9c28badd..197fe214 100644 --- a/environment.yml +++ b/environment.yml @@ -18,13 +18,13 @@ dependencies: # conda-specific for dsub - python-dateutil=2.9.0 - - pytz=2025.2 - - pyyaml=6.0.2 - - tenacity=9.1.2 - - tabulate=0.9.0 + - pytz=2026.1 + - pyyaml=6.0.3 + - tenacity=9.1.4 + - tabulate=0.10.0 # toolchain deps - - pip=26.1 + - pip=26.0.1 # This should be the same as requires-python minus the >=. - python=3.13 diff --git a/pyproject.toml b/pyproject.toml index 46166ca8..45f9b572 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ classifiers = [ "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics", ] -requires-python = ">=3.11" +requires-python = ">=3.13" dependencies = [ "adjusttext==1.3.0", "snakemake==9.19.0", @@ -32,7 +32,7 @@ dependencies = [ "spython==0.3.14", # toolchain deps - "pip==26.1", + "pip==26.0.1", ] [project.optional-dependencies] @@ -52,7 +52,7 @@ requires = ["setuptools>=64.0"] build-backend = "setuptools.build_meta" [tool.ruff] -target-version = "py311" +target-version = "py313" # Autofix errors when possible fix = true # Select categories or specific rules from https://beta.ruff.rs/docs/rules/ From 641df788aee2d954f631b8e91bc7bc3b05c87c5b Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Thu, 30 Apr 2026 21:26:35 +0000 Subject: [PATCH 3/3] fix: bump SPRAS image to Python 3.13 --- docker-wrappers/SPRAS/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-wrappers/SPRAS/Dockerfile b/docker-wrappers/SPRAS/Dockerfile index 3d69943c..4bb0d660 100644 --- a/docker-wrappers/SPRAS/Dockerfile +++ b/docker-wrappers/SPRAS/Dockerfile @@ -4,7 +4,7 @@ FROM almalinux:9 RUN dnf update -y && \ dnf install -y epel-release && \ dnf install -y gcc gcc-c++ \ - python3.11 python3.11-pip python3.11-devel \ + python3.13 python3.13-pip python3.13-devel \ docker apptainer && \ dnf clean all @@ -13,4 +13,4 @@ RUN chmod -R 777 /spras WORKDIR /spras # Install spras into the container -RUN pip3.11 install . +RUN pip3.13 install .