diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index c88b26f..2d8a3ef 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -3,7 +3,6 @@ on: push: branches: - main - - tests jobs: build: diff --git a/.github/workflows/pytest-multiversion.yml b/.github/workflows/pytest-multiversion.yml index a9d24ef..9b0779f 100644 --- a/.github/workflows/pytest-multiversion.yml +++ b/.github/workflows/pytest-multiversion.yml @@ -36,3 +36,4 @@ jobs: - name: Test with pytest run: | pytest -v --alluredir=allure_results --cov-report=html --cov --cov-config=.coveragerc --random-order + coverage report -m diff --git a/README.md b/README.md index 4bb0d11..3a9e52b 100644 --- a/README.md +++ b/README.md @@ -109,7 +109,7 @@ The dataset is tabular, where each row corresponds to a labelled MS2 spectra. The intensity values of the MS2 spectrum For example, the DataFrame for the -[Nine-Species excluding Yeast](https://huggingface.co/datasets/InstaDeepAI/instanovo_ninespecies_exclude_yeast) +[Nine-Species excluding Yeast](https://huggingface.co/datasets/InstaDeepAI/ms_ninespecies_benchmark) dataset look as follows: | | sequence | modified_sequence | precursor_mz | precursor_charge | mz_array | intensity_array | diff --git a/notebooks/getting_started_with_instanovo.ipynb b/notebooks/getting_started_with_instanovo.ipynb index c6f560c..f0556c1 100644 --- a/notebooks/getting_started_with_instanovo.ipynb +++ b/notebooks/getting_started_with_instanovo.ipynb @@ -317,10 +317,10 @@ "from datasets import load_dataset\n", "\n", "# Only evaluate on a subset of the data for demo\n", - "dataset = load_dataset(\"InstaDeepAI/instanovo_ninespecies_exclude_yeast\", split=\"test[:10%]\")\n", + "dataset = load_dataset(\"InstaDeepAI/ms_ninespecies_benchmark\", split=\"test[:10%]\")\n", "\n", "# Otherwise evaluate on the full test set\n", - "# dataset = load_dataset(\"InstaDeepAI/instanovo_ninespecies_exclude_yeast\", split=\"test\")" + "# dataset = load_dataset(\"InstaDeepAI/ms_ninespecies_benchmark\", split=\"test\")" ] }, { diff --git a/requirements-docs.txt b/requirements-docs.txt index 4ee1125..2638393 100644 --- a/requirements-docs.txt +++ b/requirements-docs.txt @@ -7,4 +7,4 @@ mkdocs-material==8.5.6 mkdocs-pymdownx-material-extras==2.2.1 mkdocstrings==0.23.0 mkdocstrings-python==1.7.1 -pymdown-extensions==9.5 +pymdown-extensions==10.7 diff --git a/tests/conftest.py b/tests/conftest.py index 7461d40..157bf58 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -52,7 +52,7 @@ def dataset() -> DatasetDict | Dataset | IterableDatasetDict | IterableDataset: Loads a specific subset (1% of test data) from the 'instanovo_ninespecies_exclude_yeast' dataset. """ - return load_dataset("InstaDeepAI/instanovo_ninespecies_exclude_yeast", split="test[:1%]") + return load_dataset("InstaDeepAI/ms_ninespecies_benchmark", split="test[:1%]") @pytest.fixture(scope="session")