Leiden algorithm included in precompiled macOS binaries

refresh-bio · Oct 14, 2024 · 93a364b · 93a364b
1 parent b79a6f1
commit 93a364b
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Showing 7 changed files with 70 additions and 603 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -41,19 +41,18 @@ jobs:
         machine: [x64_linux]
         platform: [avx2]
         compiler: [14]
-        leiden: [true]
         include:
-        - {machine: arm64_linux, platform: arm8, compiler: 12, leiden: true}
-        - {machine: x64_mac, platform: avx2, compiler: 12, leiden: false}
-        - {machine: arm64_mac, platform: m1, compiler: 13, leiden: false}
+        - {machine: arm64_linux, platform: arm8, compiler: 12}
+        - {machine: x64_mac, platform: avx2, compiler: 12}
+        - {machine: arm64_mac, platform: m1, compiler: 12}
 
     runs-on: [self-hosted, vclust, '${{ matrix.machine }}'] 
     env:
       DIR: vclust-${{ github.event.release.tag_name }}-${{matrix.machine}}
 
     steps:
     - name: make
-      run: make -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }} LEIDEN=${{ matrix.leiden }}
+      run: make -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} LEIDEN=true
     - name: tar artifacts
       run: | 
         mkdir ${DIR}

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,4 +1,4 @@
-name: GitHub Actions CI
+name: Build and tests
 
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         machine: [ubuntu-latest, macOS-12]
-        compiler: [g++-12]
+        compiler: [12]
     runs-on: ['${{ matrix.machine }}']   
 
     steps:
@@ -26,7 +26,7 @@ jobs:
 
     - name: make
       run: | 
-        make -j32 CXX=${{matrix.compiler}} 
+        make -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}}
     - name: tar artifacts
       run: tar -cvf vclust.tar ./vclust.py ./test.py ./example ./bin/kmer-db ./bin/lz-ani ./bin/clusty ./bin/multi-fasta-split
 
@@ -43,7 +43,6 @@ jobs:
       fail-fast: false
       matrix:
         machine: [ubuntu-latest, macOS-12]
-        compiler: [g++-11]
 
     runs-on: ['${{ matrix.machine }}']    
 

diff --git a/.github/workflows/self-hosted.yml b/.github/workflows/self-hosted.yml
@@ -41,21 +41,20 @@ jobs:
         machine: [x64_linux]
         platform: [avx2]
         compiler: [14]
-        leiden: [true]
         include:
-        - {machine: arm64_linux, platform: arm8, compiler: 12, leiden: true}
-        - {machine: x64_mac, platform: avx2, compiler: 12, leiden: false}
-        - {machine: arm64_mac, platform: m1, compiler: 13, leiden: false}
+        - {machine: arm64_linux, platform: arm8, compiler: 12}
+        - {machine: x64_mac, platform: avx2, compiler: 12}
+        - {machine: arm64_mac, platform: m1, compiler: 12}
 
     runs-on: [self-hosted, vclust, '${{ matrix.machine }}'] 
 
     steps:
     - name: make
-      run: make -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }} LEIDEN=${{ matrix.leiden }}
+      run: make -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} LEIDEN=true
 
 ########################################################################################
-  pipeline:
-    name: Pipeline
+  pipeline-linux:
+    name: Pipeline (linux)
     needs: make
     strategy:
       fail-fast: false
@@ -64,7 +63,23 @@ jobs:
     runs-on: [self-hosted, vclust, '${{ matrix.machine }}']
 
     steps:
-
     - name: run pipeline
       run: |
         pytest test.py
+
+  ########################################################################################
+  pipeline-macos:
+    name: Pipeline (macOS)
+    needs: make
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [x64_mac, arm64_mac]
+    runs-on: [self-hosted, vclust, '${{ matrix.machine }}']
+
+    steps:
+
+    - name: run pipeline
+      run: |
+        source /Users/agudys/agudys-env/bin/activate
+        pytest test.py     
diff --git a/3rd_party/clusty b/3rd_party/clusty
+7 −17		.github/workflows/deploy.yml
+8 −5		.github/workflows/main.yml
+45 −108		.github/workflows/self-hosted.yml
+11 −4		README.md
+5 −5		makefile
+1 −1		src/params.cpp
+18 −16		src/version.h