Bring main to release

ci/tests/test_caduceus/test_caduceus_model.py

@@ -3,7 +3,7 @@
 import torch
 
 try:
-    from helical import Caduceus, CaduceusConfig
+    from helical.models.caduceus import Caduceus, CaduceusConfig
 
     caduceus_unavailable = False  # only run tests if able to import the package
 except:

ci/tests/test_geneformer/test_geneformer_model.py

@@ -1,5 +1,9 @@
 import pytest
-from helical import GeneformerConfig, Geneformer, GeneformerFineTuningModel
+from helical.models.geneformer import (
+    GeneformerConfig,
+    Geneformer,
+    GeneformerFineTuningModel,
+)
 from anndata import AnnData
 import torch
 import pandas as pd

ci/tests/test_helix_mrna/test_helix_mrna_fine_tuning.py

@@ -1,6 +1,6 @@
 import pytest
 import torch
-from helical import HelixmRNAConfig, HelixmRNAFineTuningModel
+from helical.models.helix_mrna import HelixmRNAConfig, HelixmRNAFineTuningModel
 
 
 class TestHelixmRNAFineTuning:

ci/tests/test_helix_mrna/test_helix_mrna_model.py

@@ -1,4 +1,4 @@
-from helical import HelixmRNA, HelixmRNAConfig
+from helical.models.helix_mrna import HelixmRNA, HelixmRNAConfig
 import pytest
 from pandas import DataFrame
 import torch

ci/tests/test_hyena_dna/test_hyena_dna_fine_tuning.py

@@ -1,6 +1,6 @@
 import pytest
 import torch
-from helical import HyenaDNAConfig, HyenaDNAFineTuningModel
+from helical.models.hyena_dna import HyenaDNAConfig, HyenaDNAFineTuningModel
 
 
 class TestHyenaDNAFineTuning:

ci/tests/test_hyena_dna/test_hyena_dna_model.py

@@ -1,6 +1,5 @@
-from helical.models.hyena_dna.model import HyenaDNAConfig
+from helical.models.hyena_dna import HyenaDNAConfig, HyenaDNA
 import pytest
-from helical.models.hyena_dna.model import HyenaDNA
 import numpy as np
 from pandas import DataFrame
 

ci/tests/test_mamba2_mrna/test_mamba2_mrna_fine_tuning.py

@@ -1,6 +1,6 @@
 import pytest
 import torch
-from helical import Mamba2mRNAConfig, Mamba2mRNAFineTuningModel
+from helical.models.mamba2_mrna import Mamba2mRNAConfig, Mamba2mRNAFineTuningModel
 
 
 class TestHelixmRNAFineTuning:

ci/tests/test_mamba2_mrna/test_mamba2_mrna_model.py

@@ -1,4 +1,4 @@
-from helical import Mamba2mRNA, Mamba2mRNAConfig
+from helical.models.mamba2_mrna import Mamba2mRNA, Mamba2mRNAConfig
 import pytest
 import torch
 

ci/tests/test_scgpt/test_scgpt_model.py

@@ -1,5 +1,4 @@
-from helical.models.scgpt.model import scGPT, scGPTConfig
-from helical.models.scgpt.fine_tuning_model import scGPTFineTuningModel
+from helical.models.scgpt import scGPT, scGPTConfig, scGPTFineTuningModel
 from anndata import AnnData
 import pytest
 import anndata as ad

ci/tests/test_uce/test_uce_config.py

@@ -1,4 +1,4 @@
-from helical.models.uce.model import UCEConfig
+from helical.models.uce import UCEConfig
 import pytest
 
 

examples/fine_tune_models/fine_tune_UCE.py

@@ -1,4 +1,4 @@
-from helical import UCEConfig, UCEFineTuningModel
+from helical.models.uce import UCEConfig, UCEFineTuningModel
 from helical.utils import get_anndata_from_hf_dataset
 from datasets import load_dataset
 import anndata as ad

examples/fine_tune_models/fine_tune_caduceus.py

@@ -1,4 +1,4 @@
-from helical import CaduceusFineTuningModel, CaduceusConfig
+from helical.models.caduceus import CaduceusFineTuningModel, CaduceusConfig
 import hydra
 from omegaconf import DictConfig
 

examples/fine_tune_models/fine_tune_geneformer.py

@@ -1,4 +1,4 @@
-from helical import GeneformerConfig, GeneformerFineTuningModel
+from helical.models.geneformer import GeneformerConfig, GeneformerFineTuningModel
 from helical.utils import get_anndata_from_hf_dataset
 from datasets import load_dataset
 import anndata as ad

examples/fine_tune_models/fine_tune_helix_mrna.py

@@ -1,4 +1,4 @@
-from helical import HelixmRNAFineTuningModel, HelixmRNAConfig
+from helical.models.helix_mrna import HelixmRNAFineTuningModel, HelixmRNAConfig
 import hydra
 from omegaconf import DictConfig
 

examples/fine_tune_models/fine_tune_hyena_dna.py

@@ -1,4 +1,4 @@
-from helical import HyenaDNAFineTuningModel, HyenaDNAConfig
+from helical.models.hyena_dna import HyenaDNAFineTuningModel, HyenaDNAConfig
 import hydra
 from omegaconf import DictConfig
 

examples/fine_tune_models/fine_tune_mamba2_mrna.py

@@ -1,4 +1,4 @@
-from helical import Mamba2mRNAFineTuningModel, Mamba2mRNAConfig
+from helical.models.mamba2_mrna import Mamba2mRNAFineTuningModel, Mamba2mRNAConfig
 import hydra
 from omegaconf import DictConfig
 

examples/fine_tune_models/fine_tune_scgpt.py

@@ -1,4 +1,4 @@
-from helical import scGPTConfig, scGPTFineTuningModel
+from helical.models.scgpt import scGPTConfig, scGPTFineTuningModel
 from helical.utils import get_anndata_from_hf_dataset
 from datasets import load_dataset
 import anndata as ad

examples/notebooks/Cell-Gene-Cls-embedding-generation.ipynb

@@ -28,7 +28,7 @@
     }
    ],
    "source": [
-    "from helical import scGPT, scGPTConfig\n",
+    "from helical.models.scgpt import scGPT, scGPTConfig\n",
     "import torch\n",
     "import anndata\n",
     "from pathlib import Path\n",

examples/notebooks/Cell-Type-Annotation.ipynb

@@ -78,8 +78,8 @@
     "from torch import nn\n",
     "from scipy.sparse import lil_matrix\n",
     "import torch.optim as optim\n",
-    "from helical.models.scgpt.model import scGPT, scGPTConfig\n",
-    "from helical.models.geneformer.model import Geneformer, GeneformerConfig\n",
+    "from helical.models.scgpt import scGPT, scGPTConfig\n",
+    "from helical.models.geneformer import Geneformer, GeneformerConfig\n",
     "from copy import deepcopy   \n",
     "from torch.nn.functional import one_hot"
    ]
@@ -1147,7 +1147,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 0
 }

examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb

@@ -38,7 +38,8 @@
    ],
    "source": [
     "from helical.utils import get_anndata_from_hf_dataset\n",
-    "from helical import GeneformerConfig, GeneformerFineTuningModel, scGPTConfig, scGPTFineTuningModel\n",
+    "from helical.models.geneformer import GeneformerConfig, GeneformerFineTuningModel\n",
+    "from helical.models.scgpt import scGPTConfig, scGPTFineTuningModel\n",
     "import torch\n",
     "import numpy as np\n",
     "from sklearn.metrics import confusion_matrix, ConfusionMatrixDisplay, classification_report\n",

examples/notebooks/Evo-2.ipynb

@@ -1196,9 +1196,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "np.savez(\"train_embeddings.npz\", embeddings=np.array(evo_mean_train_embeddings[\"embeddings\"]), original_lengths=np.array(evo_mean_train_embeddings[\"original_lengths\"]))\n",
-    "np.savez(\"eval_embeddings.npz\", embeddings=np.array(evo_mean_eval_embeddings[\"embeddings\"]), original_lengths=np.array(evo_mean_eval_embeddings[\"original_lengths\"]))\n",
-    "np.savez(\"test_embeddings.npz\", embeddings=np.array(evo_mean_test_embeddings[\"embeddings\"]), original_lengths=np.array(evo_mean_test_embeddings[\"original_lengths\"]))\n",
+    "np.savez(\"train_embeddings.npz\", embeddings=evo_mean_train_embeddings)\n",
+    "np.savez(\"eval_embeddings.npz\", embeddings=evo_mean_eval_embeddings)\n",
+    "np.savez(\"test_embeddings.npz\", embeddings=evo_mean_test_embeddings)\n",
     "print(\"Embeddings saved successfully\")"
    ]
   },

examples/notebooks/Geneformer-vs-UCE.ipynb

@@ -78,7 +78,8 @@
     "warnings.filterwarnings(\"ignore\")\n",
     "\n",
     "# Import Geneformer & UCE from the Helical package\n",
-    "from helical import Geneformer,GeneformerConfig, UCE, UCEConfig\n"
+    "from helical.models.geneformer import Geneformer,GeneformerConfig\n",
+    "from helical.models.uce import UCE, UCEConfig\n"
    ]
   },
   {

examples/notebooks/Genegpt-sample-run.ipynb

@@ -42,7 +42,7 @@
     "import os\n",
     "os.environ[\"CUDA_VISIBLE_DEVICES\"] = \"1\"\n",
     "from transformers import AutoTokenizer, AutoModelForCausalLM,AutoModel\n",
-    "from helical.models.genept.genept_config import GenePTConfig\n",
+    "from helical.models.genept import GenePTConfig\n",
     "\n",
     "import umap\n",
     "import matplotlib.pyplot as plt\n",