Merge pull request #358 from daisybio/update_versions

Update versions

Author: JudithBernett

Dockerfile

@@ -4,7 +4,7 @@
 # The builder image, used to build the virtual environment
 FROM python:3.13-bookworm AS builder
 
-RUN pip install poetry==2.2.1
+RUN pip install poetry==2.3.1
 
 # POETRY_CACHE_DIR: When removing the cache folder, make sure this is done in the same RUN command. If it’s done in a
 # separate RUN command, the cache will still be part of the previous Docker layer (the one containing poetry install )

docs/conf.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """Configuration file for the Sphinx documentation builder."""
+
 # mypy: ignore-errors
 # drevalpy documentation build configuration file
 #
@@ -56,9 +57,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "1.4.1"
+version = "1.4.2"
 # The full version, including alpha/beta/rc tags.
-release = "1.4.1"
+release = "1.4.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

drevalpy/datasets/featurizer/create_molgnet_embeddings.py

@@ -4,6 +4,7 @@
 Creates MolGNet embeddings for molecules given their SMILES strings. This module needs torch_scatter.
     python create_molgnet_embeddings.py dataset_name --checkpoint meta/MolGNet.pt --data_path data
 """
+
 import argparse
 import math
 import os

drevalpy/models/MOLIR/molir.py

@@ -183,13 +183,13 @@ def predict(
             cell_line_input=cell_line_input,
             drug_input=drug_input,
         )
-        (gene_expression, mutations, cnvs) = (
+        gene_expression, mutations, cnvs = (
             input_data["gene_expression"],
             input_data["mutations"],
             input_data["copy_number_variation_gistic"],
         )
 
-        (gene_expression, mutations, cnvs) = filter_and_sort_omics(
+        gene_expression, mutations, cnvs = filter_and_sort_omics(
             model=self, gene_expression=gene_expression, mutations=mutations, cnvs=cnvs, cell_line_input=cell_line_input
         )
 

drevalpy/models/SuperFELTR/superfeltr.py

@@ -237,7 +237,7 @@ def predict(
         mutations = input_data["mutations"]
         cnvs = input_data["copy_number_variation_gistic"]
 
-        (gene_expression, mutations, cnvs) = filter_and_sort_omics(
+        gene_expression, mutations, cnvs = filter_and_sort_omics(
             model=self, gene_expression=gene_expression, mutations=mutations, cnvs=cnvs, cell_line_input=cell_line_input
         )
 

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "drevalpy"
-version = "1.4.1"
+version = "1.4.2"
 description = "Drug response evaluation of cancer cell line drug response models in a fair setting"
 authors = ["DrEvalPy development team"]
 license = "GPL-3.0"

pyproject.toml

@@ -1,6 +1,7 @@
 aiohappyeyeballs==2.6.1 ; python_version >= "3.11" and python_version < "3.14"
 aiohttp==3.13.3 ; python_version >= "3.11" and python_version < "3.14"
 aiosignal==1.4.0 ; python_version >= "3.11" and python_version < "3.14"
+annotated-types==0.7.0 ; python_version >= "3.11" and python_version < "3.14"
 anyio==4.12.1 ; python_version >= "3.11" and python_version < "3.14"
 attrs==25.4.0 ; python_version >= "3.11" and python_version < "3.14"
 backports-tarfile==1.2.0 ; python_version == "3.11"
@@ -11,21 +12,26 @@ certifi==2026.1.4 ; python_version >= "3.11" and python_version < "3.14"
 cffi==2.0.0 ; python_version >= "3.11" and python_version < "3.14" and (platform_python_implementation != "PyPy" or sys_platform == "darwin") and (sys_platform == "linux" or sys_platform == "darwin")
 charset-normalizer==3.4.4 ; python_version >= "3.11" and python_version < "3.14"
 cleo==2.1.0 ; python_version >= "3.11" and python_version < "3.14"
+click==8.3.1 ; python_version >= "3.11" and python_version < "3.14"
 colorama==0.4.6 ; python_version >= "3.11" and python_version < "3.14" and (platform_system == "Windows" or sys_platform == "win32" or os_name == "nt")
 contourpy==1.3.3 ; python_version >= "3.11" and python_version < "3.14"
 crashtest==0.4.1 ; python_version >= "3.11" and python_version < "3.14"
 cryptography==46.0.3 ; python_version >= "3.11" and python_version < "3.14" and sys_platform == "linux"
+cuda-bindings==12.9.4 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
+cuda-pathfinder==1.3.3 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
 curve-curator==0.6.0 ; python_version >= "3.11" and python_version < "3.14"
 cycler==0.12.1 ; python_version >= "3.11" and python_version < "3.14"
 distlib==0.4.0 ; python_version >= "3.11" and python_version < "3.14"
-dulwich==0.24.10 ; python_version >= "3.11" and python_version < "3.14"
+dulwich==0.25.2 ; python_version >= "3.11" and python_version < "3.14"
 fastjsonschema==2.21.2 ; python_version >= "3.11" and python_version < "3.14"
 filelock==3.20.3 ; python_version >= "3.11" and python_version < "3.14"
 findpython==0.7.1 ; python_version >= "3.11" and python_version < "3.14"
 flaky==3.8.1 ; python_version >= "3.11" and python_version < "3.14"
 fonttools==4.61.1 ; python_version >= "3.11" and python_version < "3.14"
 frozenlist==1.8.0 ; python_version >= "3.11" and python_version < "3.14"
 fsspec==2026.1.0 ; python_version >= "3.11" and python_version < "3.14"
+gitdb==4.0.12 ; python_version >= "3.11" and python_version < "3.14"
+gitpython==3.1.46 ; python_version >= "3.11" and python_version < "3.14"
 h11==0.16.0 ; python_version >= "3.11" and python_version < "3.14"
 httpcore==1.0.9 ; python_version >= "3.11" and python_version < "3.14"
 httpx==0.28.1 ; python_version >= "3.11" and python_version < "3.14"
@@ -45,6 +51,7 @@ kiwisolver==1.4.9 ; python_version >= "3.11" and python_version < "3.14"
 lightning-utilities==0.15.2 ; python_version >= "3.11" and python_version < "3.14"
 markupsafe==3.0.3 ; python_version >= "3.11" and python_version < "3.14"
 matplotlib==3.10.8 ; python_version >= "3.11" and python_version < "3.14"
+mock==5.2.0 ; python_version >= "3.11" and python_version < "3.14"
 more-itertools==10.8.0 ; python_version >= "3.11" and python_version < "3.14"
 mpmath==1.3.0 ; python_version >= "3.11" and python_version < "3.14"
 msgpack==1.1.2 ; python_version >= "3.11" and python_version < "3.14"
@@ -65,23 +72,26 @@ nvidia-cusparse-cu12==12.5.8.93 ; python_version >= "3.11" and python_version <
 nvidia-cusparselt-cu12==0.7.1 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
 nvidia-nccl-cu12==2.27.5 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
 nvidia-nvjitlink-cu12==12.8.93 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
-nvidia-nvshmem-cu12==3.3.20 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
+nvidia-nvshmem-cu12==3.4.5 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
 nvidia-nvtx-cu12==12.8.90 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
-packaging==25.0 ; python_version >= "3.11" and python_version < "3.14"
+packaging==26.0 ; python_version >= "3.11" and python_version < "3.14"
 pandas==2.3.3 ; python_version >= "3.11" and python_version < "3.14"
 patsy==1.0.2 ; python_version >= "3.11" and python_version < "3.14"
-pbs-installer==2025.12.17 ; python_version >= "3.11" and python_version < "3.14"
+pbs-installer==2026.1.14 ; python_version >= "3.11" and python_version < "3.14"
 pillow==12.1.0 ; python_version >= "3.11" and python_version < "3.14"
 pkginfo==1.12.1.2 ; python_version >= "3.11" and python_version < "3.14"
 platformdirs==4.5.1 ; python_version >= "3.11" and python_version < "3.14"
-plotly==6.5.1 ; python_version >= "3.11" and python_version < "3.14"
+plotly==6.5.2 ; python_version >= "3.11" and python_version < "3.14"
 pluggy==1.6.0 ; python_version >= "3.11" and python_version < "3.14"
-poetry-core==2.2.1 ; python_version >= "3.11" and python_version < "3.14"
-poetry==2.2.1 ; python_version >= "3.11" and python_version < "3.14"
+poetry-core==2.3.0 ; python_version >= "3.11" and python_version < "3.14"
+poetry==2.3.1 ; python_version >= "3.11" and python_version < "3.14"
 propcache==0.4.1 ; python_version >= "3.11" and python_version < "3.14"
+protobuf==6.33.4 ; python_version >= "3.11" and python_version < "3.14"
 psutil==7.2.1 ; python_version >= "3.11" and python_version < "3.14"
-pycparser==2.23 ; python_version >= "3.11" and python_version < "3.14" and implementation_name != "PyPy" and (platform_python_implementation != "PyPy" or sys_platform == "darwin") and (sys_platform == "linux" or sys_platform == "darwin")
-pyparsing==3.3.1 ; python_version >= "3.11" and python_version < "3.14"
+pycparser==3.0 ; python_version >= "3.11" and python_version < "3.14" and implementation_name != "PyPy" and (platform_python_implementation != "PyPy" or sys_platform == "darwin") and (sys_platform == "linux" or sys_platform == "darwin")
+pydantic-core==2.41.5 ; python_version >= "3.11" and python_version < "3.14"
+pydantic==2.12.5 ; python_version >= "3.11" and python_version < "3.14"
+pyparsing==3.3.2 ; python_version >= "3.11" and python_version < "3.14"
 pyproject-hooks==1.2.0 ; python_version >= "3.11" and python_version < "3.14"
 pytest==7.4.4 ; python_version >= "3.11" and python_version < "3.14"
 python-dateutil==2.9.0.post0 ; python_version >= "3.11" and python_version < "3.14"
@@ -97,26 +107,31 @@ scikit-posthocs==0.11.4 ; python_version >= "3.11" and python_version < "3.14"
 scipy==1.17.0 ; python_version >= "3.11" and python_version < "3.14"
 seaborn==0.13.2 ; python_version >= "3.11" and python_version < "3.14"
 secretstorage==3.5.0 ; python_version >= "3.11" and python_version < "3.14" and sys_platform == "linux"
-setuptools==80.9.0 ; python_version >= "3.11" and python_version < "3.14"
+sentry-sdk==2.50.0 ; python_version >= "3.11" and python_version < "3.14"
+setuptools==80.10.1 ; python_version >= "3.11" and python_version < "3.14"
 shellingham==1.5.4 ; python_version >= "3.11" and python_version < "3.14"
 six==1.17.0 ; python_version >= "3.11" and python_version < "3.14"
-starlette==0.51.0 ; python_version >= "3.11" and python_version < "3.14"
+smmap==5.0.2 ; python_version >= "3.11" and python_version < "3.14"
+starlette==0.52.1 ; python_version >= "3.11" and python_version < "3.14"
 statsmodels==0.14.6 ; python_version >= "3.11" and python_version < "3.14"
+subword-nmt==0.3.8 ; python_version >= "3.11" and python_version < "3.14"
 sympy==1.14.0 ; python_version >= "3.11" and python_version < "3.14"
 threadpoolctl==3.6.0 ; python_version >= "3.11" and python_version < "3.14"
 toml==0.10.2 ; python_version >= "3.11" and python_version < "3.14"
 tomlkit==0.14.0 ; python_version >= "3.11" and python_version < "3.14"
 torch-geometric==2.7.0 ; python_version >= "3.11" and python_version < "3.14"
-torch==2.9.1 ; python_version >= "3.11" and python_version < "3.14"
+torch==2.10.0 ; python_version >= "3.11" and python_version < "3.14"
 torchmetrics==1.8.2 ; python_version >= "3.11" and python_version < "3.14"
 tornado==6.5.4 ; python_version >= "3.11" and python_version < "3.14" and sys_platform != "emscripten"
 tqdm==4.67.1 ; python_version >= "3.11" and python_version < "3.14"
-triton==3.5.1 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
-trove-classifiers==2026.1.12.15 ; python_version >= "3.11" and python_version < "3.14"
+triton==3.6.0 ; python_version >= "3.11" and python_version < "3.14" and platform_system == "Linux" and platform_machine == "x86_64"
+trove-classifiers==2026.1.14.14 ; python_version >= "3.11" and python_version < "3.14"
 typing-extensions==4.15.0 ; python_version >= "3.11" and python_version < "3.14"
+typing-inspection==0.4.2 ; python_version >= "3.11" and python_version < "3.14"
 tzdata==2025.3 ; python_version >= "3.11" and python_version < "3.14"
 urllib3==2.6.3 ; python_version >= "3.11" and python_version < "3.14"
 virtualenv==20.36.1 ; python_version >= "3.11" and python_version < "3.14"
+wandb==0.24.0 ; python_version >= "3.11" and python_version < "3.14"
 xattr==1.3.0 ; python_version >= "3.11" and python_version < "3.14" and sys_platform == "darwin"
 xxhash==3.6.0 ; python_version >= "3.11" and python_version < "3.14"
 xyzservices==2025.11.0 ; python_version >= "3.11" and python_version < "3.14"