Squashed 'lib/foldseek/' changes from fbf7df07..19800e92

19800e92 change modelNameMode to auto
b2e48ff8 Merge pull request #437 from sooyoung-cha/master
77ca7109 Merge branch 'master' of https://github.com/steineggerlab/foldseek
97f9fd57 Fix sort
7e800905 Merge commit 'b0815f7d045b99edf726d8d0bc36d00be3d10870'
b0815f7d Squashed 'lib/mmseqs/' changes from e49a41dd06..eddbd48a40
4890860a Merge commit 'ab7771690bac41376c262236e36db071712f95f0'
ab777169 Squashed 'lib/foldcomp/' changes from 881ae5aab..60a79b1f6
50011e26 Add target multi-threaded tmalign
c15be6ee update LocalParameters
2062c282 made model name mode parameter
ffdb9b9b lookup and header name is same

git-subtree-dir: lib/foldseek
git-subtree-split: 19800e921de4dcadd646feac40d83b4114137515

Author: milot-mirdita

.github/foldmason_logo.png

@@ -3,17 +3,19 @@ name: Create and publish a Docker image
 on:
   push:
     branches:
-      - "main"
+      - "master"
   release:
     types: [published]
   workflow_dispatch:
     inputs:
       tag:
         required: true
         type: string
+        description: "Docker tag"
       latest:
         default: false
         type: boolean
+        description: "Mark as latest"
 
 
 env:
@@ -45,7 +47,7 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
@@ -77,4 +79,63 @@ jobs:
             ${{ steps.dispatch_tag.outputs.tag }}
             ${{ steps.dispatch_tag.outputs.latest }}
           labels: ${{ steps.meta.outputs.labels }}
+  build-and-push-gpu-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # - name: Set up QEMU
+      #   uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          flavor: |
+            suffix=-cuda12,onlatest=true
+
+      - name: Tag for workflow_dispatch
+        id: dispatch_tag
+        run: |
+          if [ x"$TAG" != x"" ];then
+            echo "::set-output name=tag::${FULL_TAG}"
+          fi
+          if [ x"$LATEST" = x"true" ]; then
+            echo "::set-output name=latest::${LATEST_TAG}"
+          fi
+        env:
+          FULL_TAG: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.event.inputs.tag }}
+          LATEST_TAG: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest
+          TAG: ${{ github.event.inputs.tag }}
+          LATEST: ${{ github.event.inputs.latest }}
 
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          platforms: linux/amd64
+          push: true
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          build-args: |
+            GPU=1
+          tags: |
+            ${{ steps.meta.outputs.tags }}
+            ${{ steps.dispatch_tag.outputs.tag }}
+            ${{ steps.dispatch_tag.outputs.latest }}
+          labels: ${{ steps.meta.outputs.labels }}

lib/foldseek/.github/foldseek.png .github/foldseek.pnglib/foldseek/.github/foldseek.png renamed to .github/foldseek.png

@@ -8,16 +8,20 @@ on:
 
 jobs:
   build:
-    runs-on: [self-hosted, macOS, ARM64]
+    runs-on: macos-latest
     steps:
       - uses: actions/checkout@v3
         with:
           submodules: true
 
+      - name: Dependencies
+        run: |
+          brew install -f --overwrite cmake libomp rustup
+          rustup-init --profile minimal -q -y
+
       - name: Build
         run: |
           mkdir -p build
-          rustup update
           cd build
           LIBOMP=$(brew --prefix libomp)
           cmake \

.github/html.gif

@@ -1,8 +1,11 @@
 [submodule "util/regression"]
-	path = lib/foldseek/lib/mmseqs/util/regression
+	path = lib/mmseqs/util/regression
 	url = https://github.com/soedinglab/MMseqs2-Regression.git
 	update = none
+[submodule "lib/prostt5/ggml/src/ggml-kompute/kompute"]
+	path = lib/prostt5/ggml/src/ggml-kompute/kompute
+	url =
+	update = none
 [submodule "regression"]
-	path = lib/foldseek/regression
+	path = regression
 	url = https://github.com/steineggerlab/foldseek-regression
-	update = none