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some bindgen wrapper.c objects fail with htslib 1.11 upgrade #275

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Merged
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Nov 15, 2020
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938d0d4
That is no longer the case, I encouraged @FiloSottile to bottle it up…
brainstorm Jun 3, 2020
7c34d57
Merge branch 'master' of github.com:rust-bio/rust-htslib
brainstorm Sep 7, 2020
b9f9136
Merge branch 'master' of github.com:rust-bio/rust-htslib
brainstorm Sep 7, 2020
155f9f0
Fix for OSX compilation
brainstorm Sep 24, 2020
f92367a
point to my htslib fork
brainstorm Sep 24, 2020
d841e10
Merge branch 'master' of github.com:rust-bio/rust-htslib into htslib_…
brainstorm Sep 25, 2020
98bac7f
Point submodule to upstream now that OSX compilation got fixed
brainstorm Sep 25, 2020
678ba88
fixes #274
brainstorm Sep 25, 2020
12372cc
Bump version of Github Actions cargo to (hopefully) fix https://githu…
brainstorm Sep 25, 2020
e39a117
Actually test (and build), not just build...
brainstorm Sep 25, 2020
f8d2a0f
Merge branch 'master' into htslib_1.11_osx_fix_upstream
brainstorm Nov 6, 2020
37e1867
Thanks @mbargull for the suggestion... :facepalm:
brainstorm Nov 6, 2020
16d1a75
Merge branch 'htslib_1.11_osx_fix_upstream' of github.com:brainstorm/…
brainstorm Nov 6, 2020
73ec23a
Also test OSX without default features
brainstorm Nov 6, 2020
7166312
Container action is only supported on Linux (by textbook/git-checkout…
brainstorm Nov 6, 2020
4ffc3d7
Docker is not supported in Github Actions runners: https://github.com…
brainstorm Nov 6, 2020
e496b79
Go full in into OSX native GitHub actions testing instead of using cr…
brainstorm Nov 6, 2020
ed44403
Is musl-gcc installed? Yes it is: https://github.com/rust-bio/rust-ht…
brainstorm Nov 6, 2020
eaa8419
According to build.rs:180,80, config.h does not seem to be found, whi…
brainstorm Nov 6, 2020
7f730d5
Is it a musl-specific issue or affects all targets?
brainstorm Nov 6, 2020
bbe3814
Bump htslib up to the last memory leak fix
brainstorm Nov 6, 2020
7c757c2
Submodule update
brainstorm Nov 6, 2020
37452f2
This might need a bit more clang/LLVM gymnastics, go back to MUSL and…
brainstorm Nov 6, 2020
dbf0266
Switch submodule to develop upstream branch
brainstorm Nov 6, 2020
4b562c8
Submodule update
brainstorm Nov 7, 2020
7b6aeb3
Try with (possibly broken) regenerated OSX bindgen
brainstorm Nov 9, 2020
c68d548
Revert OSX bindings generation
brainstorm Nov 9, 2020
949f23d
Regenerate OSX bindings, thanks @pmarks
brainstorm Nov 12, 2020
adec558
Just test the build for Intel OSX instead of MUSL, works locally
brainstorm Nov 12, 2020
fc353bd
Wrong submodule fix, disable thousand warnings coming from upstream's…
brainstorm Nov 12, 2020
31de837
Some stray commits on submodule?
brainstorm Nov 13, 2020
39207d0
Merge branch 'master' into htslib_1.11_osx_fix_upstream
brainstorm Nov 15, 2020
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61 changes: 58 additions & 3 deletions .github/workflows/rust.yml
Original file line number Diff line number Diff line change
Expand Up @@ -92,19 +92,74 @@ jobs:
uses: actions-rs/cargo@v1
with:
use-cross: true
command: build
command: test
args: --release --target x86_64-unknown-linux-musl --no-default-features

- name: Test musl build with all features
uses: actions-rs/cargo@v1
with:
use-cross: true
command: build
command: test
args: --release --target x86_64-unknown-linux-musl --all-features --verbose

- name: Test musl build with all features and debug symbols (non --release)
uses: actions-rs/cargo@v1
with:
use-cross: true
command: build
command: test
args: --target x86_64-unknown-linux-musl --all-features --verbose

Testing-OSX:
needs: Formatting
runs-on: macOS-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2.3.4
with:
submodules: true

- name: Install htslib dependencies
run: brew install bzip2 zlib xz curl-openssl

# Test for Intel OSX
- uses: actions-rs/toolchain@v1
with:
toolchain: stable
target: x86_64-apple-darwin
override: true

- name: Test build without default features for the default x86_64 OSX target
uses: actions-rs/cargo@v1.0.1
with:
use-cross: false # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
command: test
args: --release --all-features --verbose

# Test MUSL builds on OSX
#
# - uses: actions-rs/toolchain@v1
# with:
# toolchain: stable
# target: x86_64-unknown-linux-musl
# override: true

# - name: Install OSX musl-cross
# run: brew install FiloSottile/musl-cross/musl-cross

# # https://github.com/FiloSottile/homebrew-musl-cross/issues/16
# - name: Provide musl-gcc symlink for the right musl arch
# run: ln -sf /usr/local/opt/musl-cross/libexec/bin/x86_64-linux-musl-gcc /usr/local/bin/musl-gcc

# - name: Test musl build without default features
# uses: actions-rs/cargo@v1
# with:
# use-cross: false # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
# command: test
# args: --release --target x86_64-unknown-linux-musl --no-default-features

# - name: Test musl build with all features and debug symbols (non --release) on OSX
# uses: actions-rs/cargo@v1.0.1
# with:
# use-cross: false
# command: test
# args: --target x86_64-unknown-linux-musl --all-features --verbose
6 changes: 3 additions & 3 deletions hts-sys/build.rs
Original file line number Diff line number Diff line change
Expand Up @@ -83,9 +83,9 @@ fn main() {
let want_static = cfg!(feature = "static") || env::var("HTS_STATIC").is_ok();

if want_static {
cfg.warnings(true).static_flag(true).pic(true);
cfg.warnings(false).static_flag(true).pic(true);
} else {
cfg.warnings(true).static_flag(false).pic(true);
cfg.warnings(false).static_flag(false).pic(true);
}

if let Ok(z_inc) = env::var("DEP_Z_INCLUDE") {
Expand Down Expand Up @@ -252,4 +252,4 @@ fn main() {
// Note: config.h is a function of the cargo features. Any feature change will
// cause build.rs to re-run, so don't re-run on that change.
//println!("cargo:rerun-if-changed=htslib/config.h");
}
}
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