Update environment YAML

6bf5c8ce · Matthew W. Thompson · 2300f672 · 6bf5c8ce
Commit 6bf5c8ce authored Oct 23, 2023 by Matthew W. Thompson
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environment.yml environment.yml +21 -21

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--- a/environment.yml
+++ b/environment.yml
@@ -2,30 +2,30 @@ name: openfold_venv
 channels:
  - conda-forge
  - bioconda
-  - pytorch
 dependencies:
-  - conda-forge::python=3.9
+  - python=3.9
-  - conda-forge::setuptools=59.5.0
+  - setuptools=59.5.0
-  - conda-forge::pip
+  - pip
-  - conda-forge::openmm=7.5.1
+  - openmm=7.7
-  - conda-forge::pdbfixer
+  - pdbfixer
-  - conda-forge::cudatoolkit==11.3.*
+  - cudatoolkit==11.3.*
-  - bioconda::hmmer==3.3.2
+  - pytorch=1.12.*
-  - bioconda::hhsuite==3.3.0
+  - pytorch_lightning==1.5.10
-  - bioconda::kalign2==2.04
-  - pytorch::pytorch=1.12.*
-  - pip:
  - biopython==1.79
-      - deepspeed==0.5.10
+  - numpy==1.21
-      - dm-tree==0.1.6
-      - ml-collections==0.1.0
-      - numpy==1.21.2
  - PyYAML==5.4.1
-      - requests==2.26.0
+  - requests
-      - scipy==1.7.1
+  - scipy==1.7
  - tqdm==4.62.2
-      - typing-extensions==3.10.0.2
+  - typing-extensions==3.10
-      - pytorch_lightning==1.5.10
  - wandb==0.12.21
  - modelcif==0.7
+  - bioconda::hmmer==3.3.2
+  - bioconda::hhsuite==3.3.0
+  - bioconda::kalign2==2.04
+  - pip:
+      - deepspeed==0.5.10  # can this be updated?
+      - dm-tree==0.1.6  # 0.1.6 yanked from conda-forge - update?
+      - ml-collections==0.1.0  # 0.1.1 is oldest available on conda-forge - update?
      - git+https://github.com/NVIDIA/dllogger.git
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8bef