Skip to content

Commit e98e257

Browse files
agudysagudys
committed
Updates in tests
1 parent 43f8263 commit e98e257

File tree

4 files changed

+24
-29
lines changed

4 files changed

+24
-29
lines changed

‎.github/workflows/main.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ jobs:
3131

3232
- name: make
3333
run: |
34-
gmake -j CXX=g++-12 CC=gcc-12
34+
gmake -j CXX=g++-12 CC=gcc-12 STATIC_LINK=true
3535
3636
- name: tar artifacts
3737
run: tar -cvf kmer-db.tar ./test/virus -C ./bin kmer-db

‎.github/workflows/self-hosted.yml

Lines changed: 19 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -35,9 +35,8 @@ jobs:
3535
matrix:
3636
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
3737
compiler: [11, 12, 13]
38-
force_zlib: [true, false]
3938
include:
40-
- {machine: x64_linux, platform: avx2, compiler: 14, force_zlib: false}
39+
- {machine: x64_linux, platform: avx2, compiler: 14}
4140
- {machine: x64_linux, platform: avx2}
4241
- {machine: arm64_linux, platform: arm8}
4342
- {machine: x64_mac, platform: avx2}
@@ -48,10 +47,10 @@ jobs:
4847
runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']
4948

5049
steps:
51-
- name: make (${{matrix.compiler}}, FORCE_ZLIB=${{matrix.force_zlib}}, PLATFORM=${{ matrix.platform}})
50+
- name: make (${{matrix.compiler}}, PLATFORM=${{ matrix.platform}})
5251
run: |
53-
gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} FORCE_ZLIB=${{matrix.force_zlib}} PLATFORM=${{ matrix.platform }}
54-
cp ./bin/kmer-db ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
52+
gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} STATIC_LINK=true
53+
cp ./bin/kmer-db ./kmer-db-${{matrix.compiler}}
5554
gmake clean
5655
5756
########################################################################################
@@ -63,29 +62,28 @@ jobs:
6362
matrix:
6463
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
6564
compiler: [11, 12, 13]
66-
force_zlib: [false, true]
6765
mode: [unknown_mode]
6866
exclude:
6967
- {machine: arm64_linux, compiler: 13}
7068
include:
71-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: all2all}
72-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: all2all-parts}
73-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: all2all-sp}
74-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: new2all}
75-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: one2all}
76-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: distance}
77-
- {machine: x64_linux, compiler: 14, force_zlib: false, mode: minhash}
69+
- {machine: x64_linux, compiler: 14, mode: all2all}
70+
- {machine: x64_linux, compiler: 14, mode: all2all-parts}
71+
- {machine: x64_linux, compiler: 14, mode: all2all-sp}
72+
- {machine: x64_linux, compiler: 14, mode: new2all}
73+
- {machine: x64_linux, compiler: 14, mode: one2all}
74+
- {machine: x64_linux, compiler: 14, mode: distance}
75+
- {machine: x64_linux, compiler: 14, mode: minhash}
7876

7977
runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']
8078

8179
env:
82-
EXEC: ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
80+
EXEC: ./kmer-db-${{matrix.compiler}}
8381

8482
steps:
8583
- name: help (${{matrix.compiler}}, ${{matrix.mode}})
8684
run: ${EXEC} ${{matrix.mode}} -help
8785

88-
- name: run (${{matrix.compiler}})
86+
- name: version (${{matrix.compiler}})
8987
run: ${EXEC} -version
9088

9189

@@ -98,18 +96,16 @@ jobs:
9896
matrix:
9997
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
10098
compiler: [11, 12, 13]
101-
force_zlib: [false]
10299
include:
103-
- {machine: x64_linux, compiler: 14, force_zlib: false}
100+
- {machine: x64_linux, compiler: 14}
104101
exclude:
105102
- {machine: arm64_linux, compiler: 13}
106103

107104
runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']
108105

109106
env:
110107
INPUT_DIR: ./test/synth
111-
EXEC: ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
112-
108+
EXEC: ./kmer-db-${{matrix.compiler}}
113109
steps:
114110

115111
- name: build
@@ -223,12 +219,11 @@ jobs:
223219
matrix:
224220
machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
225221
compiler: [11, 12, 13]
226-
force_zlib: [false]
227222
threads: [1, 2, 16]
228223
include:
229-
- {machine: x64_linux, compiler: 14, force_zlib: false, threads: 1}
230-
- {machine: x64_linux, compiler: 14, force_zlib: false, threads: 2}
231-
- {machine: x64_linux, compiler: 14, force_zlib: false, threads: 16}
224+
- {machine: x64_linux, compiler: 14, threads: 1}
225+
- {machine: x64_linux, compiler: 14, threads: 2}
226+
- {machine: x64_linux, compiler: 14, threads: 16}
232227
exclude:
233228
- {machine: arm64_linux, compiler: 13}
234229

@@ -237,7 +232,7 @@ jobs:
237232

238233
env:
239234
INPUT_DIR: ./test/virus
240-
EXEC: ./kmer-db-${{matrix.compiler}}-${{matrix.force_zlib}}
235+
EXEC: ./kmer-db-${{matrix.compiler}}
241236

242237
steps:
243238

‎README.md

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (inde
1717

1818
```bash
1919
git clone --recurse-submodules https://github.com/refresh-bio/kmer-db
20-
cd kmer-db && make
20+
cd kmer-db && gmake
2121

2222
INPUT=./test/virus
2323
OUTPUT=./output
@@ -79,7 +79,7 @@ conda install -c bioconda kmer-db
7979
For detailed instructions how to set up Bioconda, please refer to the [Bioconda manual](https://bioconda.github.io/user/install.html#install-conda).
8080
Kmer-db can be also built from the sources distributed as:
8181

82-
* MAKE project (C++-20-compatible compiler required, e.g., g++-11) for Linux and macOS,
82+
* GNU Make project for Linux and macOS (gmake 4.3 and gcc/g++ 11 or newer required),
8383
* Visual Studio 2022 solution for Windows.
8484

8585

‎refresh.mk

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
### REFRESH group macros - v.1.0.8 (2024-11-19)
1+
### REFRESH group macros - v.1.0.9 (2024-11-25)
22

33
### Macros for initialization
44
define INIT_GLOBALS
@@ -291,7 +291,7 @@ define SET_STATIC
291291
$(eval STATIC_LFLAGS:=-static-libgcc -static-libstdc++ -pthread), \
292292
$(if $(filter x86_64,$(ARCH_TYPE)), \
293293
$(eval STATIC_LFLAGS:=-static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive), \
294-
$(eval STATIC_LFLAGS:=-static-libgcc -static-libstdc++ -lpthread) \
294+
$(eval STATIC_LFLAGS:=-static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive) \
295295
)
296296
)
297297
)

0 commit comments

Comments
 (0)