Update environment YAML

environment.yml

@@ -2,30 +2,30 @@ name: openfold_venv
 channels:
   - conda-forge
   - bioconda
-  - pytorch
 dependencies:
-  - conda-forge::python=3.9
-  - conda-forge::setuptools=59.5.0
-  - conda-forge::pip
-  - conda-forge::openmm=7.5.1
-  - conda-forge::pdbfixer
-  - conda-forge::cudatoolkit==11.3.*
+  - python=3.9
+  - setuptools=59.5.0
+  - pip
+  - openmm=7.7
+  - pdbfixer
+  - cudatoolkit==11.3.*
+  - pytorch=1.12.*
+  - pytorch_lightning==1.5.10
+  - biopython==1.79
+  - numpy==1.21
+  - PyYAML==5.4.1
+  - requests
+  - scipy==1.7
+  - tqdm==4.62.2
+  - typing-extensions==3.10
+  - wandb==0.12.21
+  - modelcif==0.7
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
-  - pytorch::pytorch=1.12.*
   - pip:
-      - biopython==1.79
-      - deepspeed==0.5.10
-      - dm-tree==0.1.6
-      - ml-collections==0.1.0
-      - numpy==1.21.2
-      - PyYAML==5.4.1
-      - requests==2.26.0
-      - scipy==1.7.1
-      - tqdm==4.62.2
-      - typing-extensions==3.10.0.2
-      - pytorch_lightning==1.5.10
-      - wandb==0.12.21
-      - modelcif==0.7
+      - 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