From 53d7c8bd40a85f4240231103bba287cd02a2e897 Mon Sep 17 00:00:00 2001 From: Benoit Putzeys Date: Wed, 19 Feb 2025 10:24:43 +0100 Subject: [PATCH 1/3] Bump to ubuntu 24 --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d231be7f..9385aac0 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -10,7 +10,7 @@ permissions: jobs: fresh-install: - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 steps: - name: Checkout repository uses: actions/checkout@v2 From 09c6705bfc74e24a3462fedd629f9c192f24f31b Mon Sep 17 00:00:00 2001 From: Benoit Putzeys Date: Wed, 19 Feb 2025 10:37:34 +0100 Subject: [PATCH 2/3] Fix typo in HyendaDNA Inference notebook --- README.md | 1 - docs/index.md | 1 - examples/notebooks/Hyena-DNA-Inference.ipynb | 4 ++-- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index b28cfd37..9975a35c 100644 --- a/README.md +++ b/README.md @@ -121,7 +121,6 @@ Within the `examples/notebooks` folder, open the notebook of your choice. We rec |[Cell-Type-Classification-Fine-Tuning.ipynb](./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb)|An example how to fine-tune different models on classification tasks.|[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb) | |[HyenaDNA-Fine-Tuning.ipynb](./examples/notebooks/HyenaDNA-Fine-Tuning.ipynb)|An example of how to fine-tune the HyenaDNA model on downstream benchmarks.|[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/HyenaDNA-Fine-Tuning.ipynb) | |[Cell-Gene-Cls-embedding-generation.ipynb](./examples/notebooks/Cell-Gene-Cls-embedding-generation.ipynb)|A notebook explaining the different embedding modes of single cell RNA models.|[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Cell-Gene-Cls-embedding-generation.ipynb) | -| Coming Soon | New models such as SCimilarity, scVI; benchmarking scripts; new use cases; others | ## Stuck somewhere ? Other ideas ? We are eager to help you and interact with you. Reach out via support@helical-ai.com. diff --git a/docs/index.md b/docs/index.md index 5b3ac1d1..49caa486 100644 --- a/docs/index.md +++ b/docs/index.md @@ -99,7 +99,6 @@ Within the `example/notebooks` folder, open the notebook of your choice. We reco |[Cell-Type-Classification-Fine-Tuning.ipynb](./notebooks/Cell-Type-Classification-Fine-Tuning.ipynb)|An example how to fine-tune different models on classification tasks.|[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb) | |[HyenaDNA-Fine-Tuning.ipynb](./notebooks/HyenaDNA-Fine-Tuning.ipynb)|An example of how to fine-tune the HyenaDNA model on downstream benchmarks.|[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/HyenaDNA-Fine-Tuning.ipynb) | |[Cell-Gene-Cls-embedding-generation.ipynb](./examples/notebooks/Cell-Gene-Cls-embedding-generation.ipynb)|A notebook explaining the different embedding modes of single cell RNA models.|[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/helicalAI/helical/blob/main/examples/notebooks/Cell-Gene-Cls-embedding-generation.ipynb) | -| Coming Soon | New models such as SCimilarity, scVI; benchmarking scripts; new use cases; others | ## Stuck somewhere ? Other ideas ? We are eager to help you and interact with you. Reach out via support@helical-ai.com. diff --git a/examples/notebooks/Hyena-DNA-Inference.ipynb b/examples/notebooks/Hyena-DNA-Inference.ipynb index 1719ba55..9eee7cf8 100644 --- a/examples/notebooks/Hyena-DNA-Inference.ipynb +++ b/examples/notebooks/Hyena-DNA-Inference.ipynb @@ -501,8 +501,8 @@ ], "source": [ "X_unseen, y_unseen = get_model_inputs(dataset[\"test\"])\n", - "#np.save(f\"data/test/x_{label}_norm_256.npy\")\n", - "#np.save(f\"data/test/y_{label}_norm_256.npy\")" + "#np.save(f\"data/test/x_{label}_norm_256.npy\", X_unseen)\n", + "#np.save(f\"data/test/y_{label}_norm_256.npy\", y_unseen)" ] }, { From 0604ce87e586e9e9502e1d5305beb53505aa22f2 Mon Sep 17 00:00:00 2001 From: Benoit Putzeys Date: Wed, 19 Feb 2025 10:42:17 +0100 Subject: [PATCH 3/3] bump version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5392551f..977865d4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "helical" -version = "0.0.1a22" +version = "0.0.1a23" authors = [ { name="Helical Team", email="support@helical-ai.com" }, ]