chore: update dependencies

.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

.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:

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 .

environment.yml

@@ -3,37 +3,37 @@ 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
 
   # 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=25.3
+  - pip=26.0.1
   # 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

pyproject.toml

@@ -16,31 +16,31 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.13"
 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==26.0.1",
 ]
 
 [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]
@@ -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/