Bump version to 0.1.0a0.dev6 (#24)

Author: fcogidi

.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]

mmlearn/conf/__init__.py

@@ -151,7 +151,7 @@ class MMLearnConf:
         metadata={"help": "Configuration for torch.jit.compile."},
     )
     hydra: HydraConf = HydraConf(
-        searchpath=["pkg://mmlearn/conf"],
+        searchpath=["pkg://mmlearn.conf"],
         run=RunDir(
             dir=SI("./outputs/${experiment_name}/${now:%Y-%m-%d}/${now:%H-%M-%S}")
         ),

poetry.lock

@@ -80,6 +80,6 @@ results we obtained from our experiments.
 
 There are 3 values for each metric in the table. The first value is the original result from the paper. The second value is the
 average result we obtained from running the experiment with LoRA applied only to the query and value embeddings. The third value is
-the average result we obtained from running the experiment with LoRA applied to both the query, key and value embeddings.
+the average result we obtained from running the experiment with LoRA applied to all three  query, key, and value matrices.
 
 </details>

projects/bioscan_clip/README.md

@@ -1,17 +1,18 @@
 import io
-from typing import Literal, Union, Optional
+from typing import Literal, Optional, Union
+
 import h5py
 import numpy as np
 import pandas as pd
 from PIL import Image
 from torch.utils.data import Dataset
 from torchvision import transforms
 
-from mmlearn.datasets.core import Example, Modalities
 from mmlearn.constants import EXAMPLE_INDEX_KEY
-
+from mmlearn.datasets.core import Example, Modalities
 from projects.bioscan_clip.dna_tokenizer import DNAProcessor
 
+
 # NOTE: this module must be imported before any use of Modalities.DNA anywhere
 # else in the code
 Modalities.register_modality("dna")

projects/bioscan_clip/dataset.py

@@ -1,4 +1,5 @@
 import itertools
+
 from tokenizers import Tokenizer
 from tokenizers.models import WordLevel
 from tokenizers.processors import TemplateProcessing

projects/bioscan_clip/dna_tokenizer.py

@@ -1,11 +1,11 @@
-from typing import Any, Dict, List, Optional, Union
 import warnings
+from typing import Any, Dict, List, Optional, Union
 
-from peft import PeftConfig
 import torch
+from peft import PeftConfig
 from torch import nn
-from transformers.modeling_outputs import BaseModelOutput
 from transformers import BertConfig, BertForMaskedLM
+from transformers.modeling_outputs import BaseModelOutput
 
 from mmlearn import hf_utils
 from mmlearn.datasets.core.modalities import Modalities, Modality