From a73278908f05a12144d24b3516de49244d989004 Mon Sep 17 00:00:00 2001 From: Alejandro Velez-Arce Date: Tue, 6 Aug 2024 13:34:37 -0400 Subject: [PATCH 1/6] fix dgl and builds --- environment.yml | 25 +++++++++++-------------- requirements.txt | 6 +++++- 2 files changed, 16 insertions(+), 15 deletions(-) diff --git a/environment.yml b/environment.yml index 17b2eb88..5d1f34db 100644 --- a/environment.yml +++ b/environment.yml @@ -3,14 +3,12 @@ channels: - bioconda - conda-forge - defaults - - dglteam - - pyg - - pytorch + - dgl dependencies: - anndata=0.6.22 - biopython=1.78 - dataclasses=0.8 - - dgl=2.1.0 + - dgl=1.1.3 - fuzzywuzzy=0.18.0 - huggingface_hub=0.20.3 - mygene=3.2.2 @@ -19,28 +17,27 @@ 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 + - pytorch=2.1.2 - 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 + - torchvision=0.16.1 - pip: - - cellxgene-census==1.10.2 + - accelerate==0.33.0 + - cellxgene-census==1.15.0 + - datasets==2.20.0 + - 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 + - transformers==4.43.4 - yapf==0.40.2 variables: KMP_DUPLICATE_LIB_OK: "TRUE" diff --git a/requirements.txt b/requirements.txt index 347a1f49..ae980929 100644 --- a/requirements.txt +++ b/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 From 66811e475b2487de299573407b8f98033673a816 Mon Sep 17 00:00:00 2001 From: Alejandro Velez-Arce Date: Tue, 6 Aug 2024 13:45:32 -0400 Subject: [PATCH 2/6] mend --- .github/workflows/conda-tests.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/conda-tests.yml b/.github/workflows/conda-tests.yml index de2277d4..f6dc88b1 100644 --- a/.github/workflows/conda-tests.yml +++ b/.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 From c7a44962acdbe0b674a1a17ddeaea8ed9c8545b5 Mon Sep 17 00:00:00 2001 From: Alejandro Velez-Arce Date: Tue, 6 Aug 2024 13:53:44 -0400 Subject: [PATCH 3/6] install torch and dgl from source... --- environment.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 5d1f34db..1fcd96f4 100644 --- a/environment.yml +++ b/environment.yml @@ -3,12 +3,10 @@ channels: - bioconda - conda-forge - defaults - - dgl dependencies: - anndata=0.6.22 - biopython=1.78 - dataclasses=0.8 - - dgl=1.1.3 - fuzzywuzzy=0.18.0 - huggingface_hub=0.20.3 - mygene=3.2.2 @@ -17,12 +15,10 @@ dependencies: - python=3.9.13 - pip=23.3.1 - pandas=2.1.4 - - pytorch=2.1.2 - requests=2.31.0 - scikit-learn=1.2.2 - seaborn=0.12.2 - tqdm=4.65.0 - - torchvision=0.16.1 - pip: - accelerate==0.33.0 - cellxgene-census==1.15.0 @@ -39,5 +35,9 @@ dependencies: - tiledbsoma==1.11.4 - transformers==4.43.4 - yapf==0.40.2 + - https://pypi.tuna.tsinghua.edu.cn/packages/b0/a7/64b37abff0296753cb890f50c5a2eda1d957f64bf2dce36a3b4f99bcacf0/dgl-1.1.3-cp39-cp39-manylinux1_x86_64.whl#sha256=9dcb8ac172960851cc513409d35073f69c19d9548d04f8dc1c36cc01294bbbae + - https://download.pytorch.org/whl/cpu/torch-2.1.2%2Bcpu-cp39-cp39-linux_x86_64.whl#sha256=10df25736edb00852eca6041941e99d13502e65773d5c6164372eaaab83d976b + - https://download.pytorch.org/whl/cpu/torchvision-0.16.1%2Bcpu-cp39-cp39-linux_x86_64.whl#sha256=048b029410bc4c7ce87b1f2b621fd8b88249c68350ee773c3152faa088e9fcca + variables: KMP_DUPLICATE_LIB_OK: "TRUE" From 5b706c175e7e846598d97725391aacb363bbb805 Mon Sep 17 00:00:00 2001 From: Alejandro Velez-Arce Date: Tue, 6 Aug 2024 13:58:58 -0400 Subject: [PATCH 4/6] use traditional pip --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 1fcd96f4..41dd84b6 100644 --- a/environment.yml +++ b/environment.yml @@ -23,6 +23,7 @@ dependencies: - 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 @@ -33,11 +34,10 @@ dependencies: - pytest==8.3.2 - rdkit==2023.9.5 - tiledbsoma==1.11.4 + - torch==2.1.2 + - torchvision==0.16.1 - transformers==4.43.4 - yapf==0.40.2 - - https://pypi.tuna.tsinghua.edu.cn/packages/b0/a7/64b37abff0296753cb890f50c5a2eda1d957f64bf2dce36a3b4f99bcacf0/dgl-1.1.3-cp39-cp39-manylinux1_x86_64.whl#sha256=9dcb8ac172960851cc513409d35073f69c19d9548d04f8dc1c36cc01294bbbae - - https://download.pytorch.org/whl/cpu/torch-2.1.2%2Bcpu-cp39-cp39-linux_x86_64.whl#sha256=10df25736edb00852eca6041941e99d13502e65773d5c6164372eaaab83d976b - - https://download.pytorch.org/whl/cpu/torchvision-0.16.1%2Bcpu-cp39-cp39-linux_x86_64.whl#sha256=048b029410bc4c7ce87b1f2b621fd8b88249c68350ee773c3152faa088e9fcca variables: KMP_DUPLICATE_LIB_OK: "TRUE" From c4f8af1d6d849e64805d6762882d610b6eaf62b1 Mon Sep 17 00:00:00 2001 From: Alejandro Velez-Arce Date: Tue, 6 Aug 2024 15:20:22 -0400 Subject: [PATCH 5/6] pytoch change --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 41dd84b6..b8735ce4 100644 --- a/environment.yml +++ b/environment.yml @@ -34,7 +34,7 @@ dependencies: - pytest==8.3.2 - rdkit==2023.9.5 - tiledbsoma==1.11.4 - - torch==2.1.2 + - torch==2.1.1 - torchvision==0.16.1 - transformers==4.43.4 - yapf==0.40.2 From b5b7a27fb5e9e7944107b01d7a7c4b9e80a6fddf Mon Sep 17 00:00:00 2001 From: Alejandro Velez-Arce Date: Tue, 6 Aug 2024 15:39:43 -0400 Subject: [PATCH 6/6] pyg --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index b8735ce4..c71bcc05 100644 --- a/environment.yml +++ b/environment.yml @@ -35,6 +35,7 @@ dependencies: - rdkit==2023.9.5 - 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