Merge remote-tracking branch 'mattwthompson/ci' into installation-upd…

…ates

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/docker-image.yml

@@ -10,6 +10,6 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Build the Docker image
       run: docker build . --file Dockerfile --tag openfold:$(date +%s)

Dockerfile

@@ -13,15 +13,15 @@ RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/
 
 RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git
 RUN wget -P /tmp \
-    "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \
-    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
-    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
+    "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" \
+    && bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda \
+    && rm /tmp/Miniforge3-Linux-x86_64.sh
 ENV PATH /opt/conda/bin:$PATH
 
 COPY environment.yml /opt/openfold/environment.yml
 
 # installing into the base environment since the docker container wont do anything other than run openfold
-RUN conda env update -n base --file /opt/openfold/environment.yml && conda clean --all
+RUN mamba env update -n base --file /opt/openfold/environment.yml && mamba clean --all
 
 COPY openfold /opt/openfold/openfold
 COPY scripts /opt/openfold/scripts

environment.yml

@@ -2,35 +2,32 @@ 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::cudatoolkit==11.3.*
-  - conda-forge::openmm=7.7.0
-  - conda-forge::pdbfixer
-  - conda-forge::awscli
-  - conda-forge::biopython==1.79
-  - conda-forge::ninja
-  - conda-forge::numpy==1.21.2
-  - conda-forge::scipy==1.7.1
-  - conda-forge::pyyaml==5.4.1
-  - conda-forge::packaging
-  - conda-forge::tqdm==4.62.2
-  - conda-forge::typing-extensions==3.10.0.2
+  - 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
+  - awscli
+  - bioconda::aria2
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04
-  - bioconda::aria2
-  - pytorch::pytorch=1.12.*
   - pip:
-      - deepspeed==0.5.10
-      - dm-tree==0.1.6
-      - ml-collections==0.1.0
-      - requests==2.26.0
-      - 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
+      - git+https://github.com/Dao-AILab/flash-attention.git@5b838a8