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Nomerge/first cwl files #135

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Nomerge/first cwl files #135

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83a453b
fix: update seqan3 submodule
SGSSGene May 3, 2023
75a7cae
patch: replace seqan3::argument_parser with sharg
SGSSGene May 3, 2023
dcaef64
fix: update cmake env version in ci
SGSSGene May 3, 2023
def94d5
fix: ci: force using c++20
SGSSGene May 3, 2023
ea9b04b
fix: newest version, that still works with gcc10
SGSSGene May 3, 2023
fcdc4d8
fix: remove duplicate default message and mark entries with todos tha…
SGSSGene May 3, 2023
fa2cdec
fix: update needle_options_test
SGSSGene May 3, 2023
d870b6c
feat: adding cwl files
SGSSGene May 3, 2023
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6 changes: 5 additions & 1 deletion .github/workflows/ci_linux.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ concurrency:
cancel-in-progress: true

env:
CMAKE_VERSION: 3.10.3
CMAKE_VERSION: 3.16.9
SEQAN3_NO_VERSION_CHECK: 1
TZ: Europe/Berlin

Expand All @@ -32,22 +32,26 @@ jobs:
- name: "Coverage gcc12"
cxx: "g++-12"
cc: "gcc-12"
cxx_flags: "-std=c++20"
build: coverage
build_type: Coverage

- name: "gcc12"
cxx: "g++-12"
cc: "gcc-12"
cxx_flags: "-std=c++20"
build_type: Release

- name: "gcc11"
cxx: "g++-11"
cc: "gcc-11"
cxx_flags: "-std=c++20"
build_type: Release

- name: "gcc10"
cxx: "g++-10"
cc: "gcc-10"
cxx_flags: "-std=c++20"
build_type: Release

steps:
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5 changes: 4 additions & 1 deletion .github/workflows/ci_macos.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ concurrency:
cancel-in-progress: true

env:
CMAKE_VERSION: 3.10.3
CMAKE_VERSION: 3.16.9
SEQAN3_NO_VERSION_CHECK: 1
TZ: Europe/Berlin

Expand All @@ -32,16 +32,19 @@ jobs:
- name: "gcc12"
cxx: "g++-12"
cc: "gcc-12"
cxx_flags: "-std=c++20"
build_type: Release

- name: "gcc11"
cxx: "g++-11"
cc: "gcc-11"
cxx_flags: "-std=c++20"
build_type: Release

- name: "gcc10"
cxx: "g++-10"
cc: "gcc-10"
cxx_flags: "-std=c++20"
build_type: Release

steps:
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3 changes: 2 additions & 1 deletion .github/workflows/ci_misc.yml
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Expand Up @@ -30,9 +30,10 @@ jobs:
include:
- name: "Documentation"
build: documentation
cxx_flags: "-std=c++20"
build_threads: 2
test_threads: 2
cmake: 3.10.3
cmake: 3.16.9
doxygen: 1.9.4
requires_toolchain: false
requires_ccache: false
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3 changes: 3 additions & 0 deletions .gitmodules
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Expand Up @@ -5,3 +5,6 @@
[submodule "lib/robin-hood-hashing"]
path = lib/robin-hood-hashing
url = https://github.com/martinus/robin-hood-hashing
[submodule "lib/sharg-parser"]
path = lib/sharg-parser
url = https://github.com/seqan/sharg-parser.git
3 changes: 3 additions & 0 deletions CMakeLists.txt
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Expand Up @@ -27,6 +27,9 @@ set (FontReset "${Esc}[m")
# Dependency: SeqAn3.
find_package (SeqAn3 QUIET REQUIRED HINTS lib/seqan3/build_system)

# Dependency: sharg
find_package (sharg QUIET REQUIRED HINTS lib/sharg-parser/build_system)

# Use ccache.
include ("${SEQAN3_CLONE_DIR}/test/cmake/seqan3_require_ccache.cmake")
seqan3_require_ccache ()
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2 changes: 1 addition & 1 deletion lib/seqan3
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Submodule seqan3 updated 329 files
1 change: 1 addition & 0 deletions lib/sharg-parser
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Submodule sharg-parser added at 285f6a
9 changes: 6 additions & 3 deletions src/CMakeLists.txt
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Expand Up @@ -2,9 +2,12 @@ cmake_minimum_required (VERSION 3.9)

find_package(OpenMP REQUIRED)
add_library ("${PROJECT_NAME}_lib" STATIC ibf.cpp estimate.cpp)
target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan3::seqan3)
target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC robin_hood)
target_link_libraries("${PROJECT_NAME}_lib" PUBLIC OpenMP::OpenMP_CXX)
target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC
seqan3::seqan3
robin_hood
OpenMP::OpenMP_CXX
sharg::sharg
)

target_include_directories ("${PROJECT_NAME}_lib" PUBLIC ../include)

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