Updates in tests

refresh-bio · Nov 25, 2024 · e98e257 · e98e257
1 parent 43f8263
commit e98e257
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Showing 4 changed files with 24 additions and 29 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -31,7 +31,7 @@ jobs:
 
     - name: make
       run: | 
-        gmake -j CXX=g++-12 CC=gcc-12
+        gmake -j CXX=g++-12 CC=gcc-12 STATIC_LINK=true
 
     - name: tar artifacts
       run: tar -cvf kmer-db.tar ./test/virus -C ./bin kmer-db

diff --git a/.github/workflows/self-hosted.yml b/.github/workflows/self-hosted.yml
@@ -35,9 +35,8 @@ jobs:
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
         compiler: [11, 12, 13]
-        force_zlib: [true, false]
         include:
-        - {machine: x64_linux, platform: avx2, compiler: 14, force_zlib: false}
+        - {machine: x64_linux, platform: avx2, compiler: 14}
         - {machine: x64_linux, platform: avx2}
         - {machine: arm64_linux, platform: arm8}
         - {machine: x64_mac, platform: avx2}
@@ -48,10 +47,10 @@ jobs:
     runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']  
 
     steps:
-    - name: make (${{matrix.compiler}}, FORCE_ZLIB=${{matrix.force_zlib}}, PLATFORM=${{ matrix.platform}})
+    - name: make (${{matrix.compiler}}, PLATFORM=${{ matrix.platform}})
       run: | 
-        gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} FORCE_ZLIB=${{matrix.force_zlib}} PLATFORM=${{ matrix.platform }}
-        cp ./bin/kmer-db ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
+        gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} STATIC_LINK=true
+        cp ./bin/kmer-db ./kmer-db-${{matrix.compiler}}
         gmake clean
         
 ########################################################################################
@@ -63,29 +62,28 @@ jobs:
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
         compiler: [11, 12, 13]
-        force_zlib: [false, true]
         mode: [unknown_mode]
         exclude:
         - {machine: arm64_linux, compiler: 13}
         include:
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: all2all}
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: all2all-parts} 
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: all2all-sp} 
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: new2all} 
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: one2all} 
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: distance} 
-        - {machine: x64_linux, compiler: 14, force_zlib: false, mode: minhash} 
+        - {machine: x64_linux, compiler: 14, mode: all2all}
+        - {machine: x64_linux, compiler: 14, mode: all2all-parts} 
+        - {machine: x64_linux, compiler: 14, mode: all2all-sp} 
+        - {machine: x64_linux, compiler: 14, mode: new2all} 
+        - {machine: x64_linux, compiler: 14, mode: one2all} 
+        - {machine: x64_linux, compiler: 14, mode: distance} 
+        - {machine: x64_linux, compiler: 14, mode: minhash} 
 
     runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']
 
     env: 
-      EXEC: ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
+      EXEC: ./kmer-db-${{matrix.compiler}}
 
     steps:
     - name: help (${{matrix.compiler}}, ${{matrix.mode}})
       run: ${EXEC} ${{matrix.mode}} -help
 
-    - name: run (${{matrix.compiler}})
+    - name: version (${{matrix.compiler}})
       run: ${EXEC} -version  
 
 
@@ -98,18 +96,16 @@ jobs:
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
         compiler: [11, 12, 13]
-        force_zlib: [false]
         include:
-        - {machine: x64_linux, compiler: 14, force_zlib: false}
+        - {machine: x64_linux, compiler: 14}
         exclude:
         - {machine: arm64_linux, compiler: 13}
 
     runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']
 
     env: 
       INPUT_DIR: ./test/synth
-      EXEC: ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
-
+      EXEC: ./kmer-db-${{matrix.compiler}}
     steps:
 
     - name: build 
@@ -223,12 +219,11 @@ jobs:
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
         compiler: [11, 12, 13]
-        force_zlib: [false]
         threads: [1, 2, 16]
         include:
-        - {machine: x64_linux, compiler: 14, force_zlib: false, threads: 1}
-        - {machine: x64_linux, compiler: 14, force_zlib: false, threads: 2}
-        - {machine: x64_linux, compiler: 14, force_zlib: false, threads: 16}
+        - {machine: x64_linux, compiler: 14, threads: 1}
+        - {machine: x64_linux, compiler: 14, threads: 2}
+        - {machine: x64_linux, compiler: 14, threads: 16}
         exclude:
         - {machine: arm64_linux, compiler: 13}
 
@@ -237,7 +232,7 @@ jobs:
 
     env: 
       INPUT_DIR: ./test/virus
-      EXEC: ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
+      EXEC: ./kmer-db-${{matrix.compiler}}
 
     steps:
 

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (inde
 
 ```bash
 git clone --recurse-submodules https://github.com/refresh-bio/kmer-db
-cd kmer-db && make
+cd kmer-db && gmake
 
 INPUT=./test/virus
 OUTPUT=./output
@@ -79,7 +79,7 @@ conda install -c bioconda kmer-db
 For detailed instructions how to set up Bioconda, please refer to the [Bioconda manual](https://bioconda.github.io/user/install.html#install-conda).
 Kmer-db can be also built from the sources distributed as:
 
-* MAKE project (C++-20-compatible compiler required, e.g., g++-11) for Linux and macOS,
+* GNU Make project for Linux and macOS (gmake 4.3 and gcc/g++ 11 or newer required),
 * Visual Studio 2022 solution for Windows.
 
 

diff --git a/refresh.mk b/refresh.mk
@@ -1,4 +1,4 @@
-### REFRESH group macros - v.1.0.8 (2024-11-19)
+### REFRESH group macros - v.1.0.9 (2024-11-25)
 
 ### Macros for initialization
 define INIT_GLOBALS
@@ -291,7 +291,7 @@ define SET_STATIC
 			$(eval STATIC_LFLAGS:=-static-libgcc -static-libstdc++ -pthread), \
 			$(if $(filter x86_64,$(ARCH_TYPE)), \
 				$(eval STATIC_LFLAGS:=-static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive), \
-				$(eval STATIC_LFLAGS:=-static-libgcc -static-libstdc++ -lpthread) \
+				$(eval STATIC_LFLAGS:=-static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive) \
 			)
 		)
 	)