chore: update dependencies

.github/workflows/release.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3

.github/workflows/test-spras.yml

@@ -12,13 +12,13 @@ jobs:
         os: [macos-latest, windows-latest]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: spras
           environment-file: environment.yml
-          auto-activate-base: false
+          auto-activate: false
           miniconda-version: 'latest'
       - name: Log conda environment
         # Log conda environment contents
@@ -49,11 +49,11 @@ jobs:
           sudo docker image prune --all --force
           sudo docker builder prune -a
       - name: Install conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: spras
           environment-file: environment.yml
-          auto-activate-base: false
+          auto-activate: false
           miniconda-version: 'latest'
       - name: Install spras in conda env
         # Install spras in the environment using pip
@@ -85,11 +85,11 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
       - name: Install conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: spras
           environment-file: environment.yml
-          auto-activate-base: false
+          auto-activate: false
           miniconda-version: 'latest'
       # Install spras in the environment using pip
       - name: Install spras in conda env
@@ -110,11 +110,11 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v3
       - name: Install conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: spras
           environment-file: environment.yml
-          auto-activate-base: false
+          auto-activate: false
           miniconda-version: 'latest'
       - name: Run pre-commit
         shell: bash --login {0}

.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=9.20.0
   # 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

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==9.20.0",
     "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/

spras/dataset.py

@@ -1,7 +1,7 @@
 import os
 import pickle as pkl
 import warnings
-from typing import Union
+from typing import Self, Union
 
 import pandas as pd
 
@@ -60,9 +60,8 @@ def to_file(self, file: LoosePathLike):
         with open(file, "wb") as f:
             pkl.dump(self, f)
 
-    # NOTE: When we bump to Python 3.13, we can use the reference Dataset instead of the literal "Dataset" for typing.
     @classmethod
-    def from_file(cls, file: Union[LoosePathLike, "Dataset"]):
+    def from_file(cls, file: Union[LoosePathLike, Self]):
         """
         Loads dataset object from a pickle file or another `Dataset` object.
         Usage: dataset = Dataset.from_file(pickle_file)

spras/prm.py

@@ -1,6 +1,7 @@
 import os
 from abc import ABC, abstractmethod
 from pathlib import Path
+from types import get_original_bases
 from typing import Any, Generic, Mapping, Optional, TypeVar, cast, get_args
 
 from pydantic import BaseModel
@@ -52,10 +53,22 @@ def get_params_generic(cls) -> type[T]:
         For example, on `class PathLinker(PRM[PathLinkerParams])`,
         calling `PathLinker.get_params_generic()` returns `PathLinkerParams`.
         """
-        # TODO: use the type-safe get_original_bases when we bump to >= Python 3.12
-        # This is hacky reflection from https://stackoverflow.com/a/71720366/7589775
-        # which grabs the class of type T by the definition of `__orig_bases__`.
-        return get_args(cast(Any, cls).__orig_bases__[0])[0]
+        # This gives us (PRM[PathLinkerParams], )
+        original_bases = get_original_bases(cls)
+
+        # Since we just used reflection, we provide a few mountain-dewey error messages here
+        # to protect against any developer confusion.
+        assert len(original_bases) == 1, f"{cls} inherits from several classes, when precisely one is required."
+        original_bases_args = get_args(original_bases[0])
+        assert len(original_bases_args) == 1, "There were several generics passed into PRM, when precisely one is required."
+        T_class, = original_bases_args
+
+        if not issubclass(T_class, BaseModel):
+            raise RuntimeError("The generic passed into PRM is not a pydantic.BaseModel.")
+
+        # Finally, we cast, since issubclass overeagerly restricts T_class to type[BaseModel]
+        # instead of type[T] without imposing the restriction that T inherits from BaseModel
+        return cast(type[T], T_class)
 
     # This is used in `runner.py` to avoid a dependency diamond when trying
     # to import the actual algorithm schema.
@@ -66,11 +79,6 @@ def run_typeless(cls, inputs: dict[str, str | os.PathLike], output_file: str | o
         """
         T_class = cls.get_params_generic()
 
-        # Since we just used reflection, we provide a mountain-dewey error message here
-        # to protect against any developer confusion.
-        if not issubclass(T_class, BaseModel):
-            raise RuntimeError("The generic passed into PRM is not a pydantic.BaseModel.")
-
         # Validates our untyped `args` parameter against our parameter class of type T
         # using BaseModel.model_validate (https://docs.pydantic.dev/latest/api/base_model/#pydantic.BaseModel.model_validate)
         # (Pydantic already provides nice error messages, so we don't need to worry about catching this.)

spras/responsenet.py

@@ -136,7 +136,7 @@ def parse_output(raw_pathway_file, standardized_pathway_file, params):
         df = raw_pathway_df(raw_pathway_file, sep='\t', header=0)
         if not df.empty:
             df.columns = ['Node1', 'Node2', 'Flow']
-            df = df.drop(columns=['Flow'], axis=1)
+            df = df.drop(columns=['Flow'])
             df = add_rank_column(df)
             # ResponseNet's outputs should be treated as undirected outputs.
             df = reinsert_direction_col_undirected(df)