Merge pull request #300 from mims-harvard/fix_dgl_and_build

fix dgl and builds

.github/workflows/conda-tests.yml

@@ -8,9 +8,6 @@ on:
   push:
     branches:
       - main
-      - avelez-cellxgene-dev
-      - avelez-dev
-      - avelez-cellxgene-dev
       - '*'
   pull_request:
     branches: [ "main" ]
@@ -36,7 +33,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: "latest"
-          channels: bioconda, conda-forge, defaults
+          channels: bioconda, conda-forge, defaults, dgl
           use-only-tar-bz2: true  
           auto-update-conda: true
           auto-activate-base: true

environment.yml

@@ -3,14 +3,10 @@ channels:
   - bioconda
   - conda-forge
   - defaults
-  - dglteam
-  - pyg
-  - pytorch
 dependencies:
   - anndata=0.6.22
   - biopython=1.78
   - dataclasses=0.8
-  - dgl=2.1.0
   - fuzzywuzzy=0.18.0
   - huggingface_hub=0.20.3
   - mygene=3.2.2
@@ -19,28 +15,30 @@ dependencies:
   - python=3.9.13
   - pip=23.3.1
   - pandas=2.1.4
-  - pyg=2.5.0
-  - pytorch=2.2.1
-  - pyg=2.5.0
-  - pytorch=2.2.1
   - requests=2.31.0
   - scikit-learn=1.2.2
   - seaborn=0.12.2
   - tqdm=4.65.0
-  - torchaudio=2.2.1
-  - torchvision=0.17.1
-  - torchaudio=2.2.1
-  - torchvision=0.17.1
   - pip:
-    - cellxgene-census==1.10.2 
+    - accelerate==0.33.0
+    - cellxgene-census==1.15.0 
+    - datasets==2.20.0
+    - dgl==1.1.3
+    - evaluate==0.4.2
     - gget==0.28.4
     - pydantic==2.6.3
     - gget==0.28.4
     - pydantic==2.6.3
     - gget==0.28.4
     - pydantic==2.6.3
+    - pytest==8.3.2
     - rdkit==2023.9.5
-    - tiledbsoma==1.7.2
+    - tiledbsoma==1.11.4
+    - torch==2.1.1
+    - torch_geometric==2.5.3
+    - torchvision==0.16.1
+    - transformers==4.43.4
     - yapf==0.40.2
+
 variables:
   KMP_DUPLICATE_LIB_OK: "TRUE"

requirements.txt

@@ -1,5 +1,8 @@
+accelerate==0.33.0
 biopython>=1.78,<2.0
 dataclasses>=0.6,<1.0
+datasets==2.20.0
+evaluate==0.4.2
 fuzzywuzzy>=0.18.0,<1.0
 huggingface_hub>=0.20.3,<1.0
 mygene>=3.2.2,<4.0.0
@@ -11,7 +14,8 @@ requests>=2.31.0,<3.0.0
 scikit-learn==1.2.2
 seaborn>=0.12.2,<1.0.0
 tqdm>=4.65.0,<5.0.0
-cellxgene-census>=1.10.2,<2.0.0
+transformers==4.43.4
+cellxgene-census==1.15.0
 gget>=0.28.4,<1.0.0
 pydantic>=2.6.3,<3.0.0
 rdkit>=2023.9.5,<2024.3.1