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Make btllib an external dependency #464

Merged
merged 82 commits into from
Apr 28, 2023
Merged

Make btllib an external dependency #464

merged 82 commits into from
Apr 28, 2023

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lcoombe
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@lcoombe lcoombe commented Apr 28, 2023

  • btllib is currently packaged within ABySS, and required for Rresolver
  • This PR separates out the btllib code so that it is a dependency vs. packaged within ABySS
    • Better code separation, and easier to adapt to newer btllib release versions
  • Ported the tests to Azure pipelines only, removed circleCI
    • Consistent with most of our other repositories
    • Some older tests were removed due to btllib version requirements

Johnathan Wong and others added 30 commits April 28, 2023 14:10
@lcoombe
remove btllib header files
8b9ed58
@lcoombe
RAlgorithmsShort.cpp: use ssytem btllib
d8a76a0
@lcoombe
RResolver/Makefile.am: compiled with system btllib
8b3f09c
@lcoombe
configure.ac: set up btllib compile
532ee9f
@lcoombe
azure: use conda to compile
f6f2b07
@jwcodee @lcoombe
gtest-1.7.0/Makefile.am: disable specific warning
dbc2a54
@jwcodee @lcoombe
azure: download and compile btllib on the fly
7ef73c2
@jwcodee @lcoombe
azure: remove ninja
8789a73
@jwcodee @lcoombe
azure: remove security
a748f09
@jwcodee @lcoombe
azure: old install
a1e26fb
@jwcodee @lcoombe
azure: use full btllib path
874a444
@jwcodee @lcoombe
azure: export dist check fig
051bc3f
@jwcodee @lcoombe
azure: compile btllib with specific version of gxx
8f623ac
@jwcodee @lcoombe
azure: set up env variable for btllib
28ccf95
@jwcodee @lcoombe
azure: export gxx variable
d1775f7
@jwcodee @lcoombe
azure: compile with non-deprecated gxx
d73fd5c
@jwcodee @lcoombe
azure: macOS with default clang and gxx
6175eb0
@jwcodee @lcoombe
azure: update btllib path for macOS
cf96528
@jwcodee @lcoombe
azure: install via brew
932147c
@jwcodee @lcoombe
azure: use container
63b5453
@jwcodee @lcoombe
azure: remove pool for gcc-12
4c6792c
@jwcodee @lcoombe
azure: change job parameter
62580ea
@jwcodee @lcoombe
azure: try unbuntu 22.04
e90054a
@jwcodee @lcoombe
azure: install via apt
dd23387
@jwcodee @lcoombe
azure: install ABySS with clang
edc73af
@jwcodee @lcoombe
azure: add cmake to installation
78ab2c3
@jwcodee @lcoombe
azure: export cmake flags
f7c77a2
@jwcodee @lcoombe
azure: fix export syntax
43589d8
@jwcodee @lcoombe
azure: correct export statement
2fc8849
@jwcodee @lcoombe
azure: install llvm
9e36e1f
@lcoombe
Fix naming for compilers-12 and macos_default_clang dependencies
915a58c
@lcoombe
compilers-12 - activate conda environment
994847a
@lcoombe
Add CXXFLAG for ubuntu-latest, print message for macos_default_clang
f100c73
@lcoombe
Try btllib brew install for macos_default_clang, add libomp to macos_…
22d22d4 
…def_gcc
@lcoombe
tap brewsci/bio
57551e2
@lcoombe
Organize and only retain needed/important tests
54e7cbd 
* For mac, move away from using brew for most tests
@lcoombe
Formatting fixes
0cc58ce
@lcoombe
Move clang-format to gcc-10, add paths to mac_gcc install
1c3d213
@lcoombe
Troubleshooting mac gcc
e1c19a3
@lcoombe
Fix for sparsehash
73a2c57
@lcoombe
Fix for sparsehash
c5eaa74
@lcoombe
Test sparsehash
2c4077c
@lcoombe
test
b04d7f8
@lcoombe
Test
55d5a5d
@lcoombe
Test
38bad9f
@lcoombe
Test
6b61de8
@lcoombe
Test
713eb6c
@lcoombe
Test
ecb4cac
@lcoombe
Test
10758b4
@lcoombe
Test
c624918
@lcoombe
See if btllib path is wrong
a9a2445
@lcoombe
Fix path to btllib install
9bf2386
@lcoombe
Add DISTCHECK flags
23bcfd0
@lcoombe
Change VM image for mac
aa31cfd
@lcoombe
Clean-up azure-pipelines.yml, remove circleCI tests, update README.md
c6665f2
@lcoombe lcoombe requested a review from jwcodee April 28, 2023 21:33
@lcoombe lcoombe self-assigned this Apr 28, 2023
jwcodee
jwcodee approved these changes Apr 28, 2023
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Thanks

@lcoombe lcoombe merged commit d8ff33f into master Apr 28, 2023
@lcoombe lcoombe deleted the conda_btllib_v5 branch April 28, 2023 22:20
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