Merge remote-tracking branch 'upstream/main' into feature/classificat…

…ion_evaluation

.github/workflows/code_checks.yml

@@ -26,19 +26,19 @@ jobs:
   run-code-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@v4.2.1
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - uses: actions/setup-python@v5.1.1
+      - uses: actions/setup-python@v5.2.0
         with:
-          python-version: '3.9'
+          python-version: '3.10'
           cache: 'poetry'
       - name: Install dependencies and check code
         run: |
-          poetry env use '3.9'
+          poetry env use '3.10'
           source .venv/bin/activate
           poetry install --with test --all-extras
           pre-commit run --all-files

.github/workflows/integration_tests.yml

@@ -32,15 +32,15 @@ jobs:
   integration-tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.1
+      - uses: actions/checkout@v4.2.1
       - name: Install poetry
         run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/setup-python@v5.0.0
+      - uses: actions/setup-python@v5.2.0
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - name: Install dependencies and check code
         run: |
-          poetry env use '3.9'
+          poetry env use '3.10'
           source $(poetry env info --path)/bin/activate
           poetry install --with test
           pytest -m integration_test

.github/workflows/publish.yml

@@ -18,12 +18,12 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install libcurl4-openssl-dev libssl-dev
-      - uses: actions/checkout@v4.1.1
+      - uses: actions/checkout@v4.2.1
       - name: Install poetry
         run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/setup-python@v5.1.1
+      - uses: actions/setup-python@v5.2.0
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - name: Build package
         run: poetry build
       - name: Publish package

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0  # Use the ref you want to point at
+    rev: v5.0.0  # Use the ref you want to point at
     hooks:
       - id: trailing-whitespace
       - id: check-ast
@@ -22,7 +22,7 @@ repos:
         args: [--lock]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -31,13 +31,13 @@ repos:
         types_or: [ python, pyi, jupyter ]
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.23.6
+    rev: v1.26.0
     hooks:
       - id: typos
         args: []
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         entry: mypy
@@ -46,7 +46,7 @@ repos:
         exclude: tests|projects
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.7
+    rev: 1.9.0
     hooks:
       - id: nbqa-ruff
         args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -9,7 +9,7 @@ experimentation and research for new techniques.
 ## Quick Start
 ### Installation
 #### Prerequisites
-The library requires Python 3.9 or later. We recommend using a virtual environment to manage dependencies. You can create
+The library requires Python 3.10 or later. We recommend using a virtual environment to manage dependencies. You can create
 a virtual environment using the following command:
 ```bash
 python3 -m venv /path/to/new/virtual/environment

mmlearn/conf/__init__.py

@@ -1,6 +1,7 @@
 """Hydra/Hydra-zen-based configurations."""
 
 import functools
+import os
 import warnings
 from dataclasses import dataclass, field
 from enum import Enum
@@ -29,7 +30,7 @@
 
 def _get_default_ckpt_dir() -> Any:
     """Get the default checkpoint directory."""
-    return SI("/checkpoint/${oc.env:USER}/${oc.env:SLURM_JOB_ID}")
+    return SI("${hydra:runtime.output_dir}/checkpoints")
 
 
 _DataLoaderConf = builds(

mmlearn/datasets/chexpert.py

@@ -105,7 +105,7 @@ def __getitem__(self, idx: int) -> Example:
 
         return Example(
             {
-                Modalities.RGB: image,
+                Modalities.RGB.name: image,
                 Modalities.RGB.target: label,
                 "qid": entry["qid"],
                 EXAMPLE_INDEX_KEY: idx,

mmlearn/datasets/core/data_collator.py

@@ -2,12 +2,12 @@
 
 from collections.abc import Mapping
 from dataclasses import dataclass
-from typing import Any, Callable, Optional, Union
+from typing import Any, Callable, Optional
 
 from torch.utils.data import default_collate
 
 from mmlearn.datasets.core.example import Example
-from mmlearn.datasets.core.modalities import Modalities, Modality
+from mmlearn.datasets.core.modalities import Modalities
 
 
 @dataclass
@@ -43,9 +43,9 @@ def __call__(self, examples: list[Example]) -> dict[str, Any]:
 
         if self.batch_processors is not None:
             for key, processor in self.batch_processors.items():
-                batch_key: Union[str, Modality] = key
+                batch_key: str = key
                 if Modalities.has_modality(key):
-                    batch_key = Modalities.get_modality(key)
+                    batch_key = Modalities.get_modality(key).name
 
                 if batch_key in batch:
                     batch_processed = processor(batch[batch_key])