Features & build cleanups (#189)

* make bindgen optional
* test prebuilt bindings
* use correct htslib
* update prebuilt linux bindings
* add pre-built osx bindings
* fix optional bindgen branch
* better setup for optional features. build with cc rather than Make
* fixed up support for libdeflate
* use url of temp libdeflater
* add support for gcs and s3
* need direct dep on openssl
* run version.sh and write version.h
* use new -sys setup in libdeflate
* restore rerun directives for header files
* add test for http access
* don't use bindgen by default

Co-authored-by: Roman Valls Guimera <[email protected]>

.github/workflows/rust.yml

@@ -68,14 +68,26 @@ jobs:
       - name: Run cargo-tarpaulin
         uses: actions-rs/[email protected]
         with:
-          args: '--out Lcov -- --test-threads 1'
+          args: '--out Lcov --exclude-files hts-sys/*_prebuilt_bindings.rs -- --test-threads 1'
 
       - name: Upload coverage
         uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
 
+      - name: Test standard build without default features
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --no-default-features
+
+      - name: Test standard build with all features
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --all-features
+
       - name: Test musl build without default features
         env:
            CFLAGS: -I/usr/local/musl/include
@@ -92,5 +104,4 @@ jobs:
         with:
           use-cross: true  
           command: build
-          args: --target x86_64-unknown-linux-musl --all-features
-
+          args: --target x86_64-unknown-linux-musl --all-features

Cargo.toml

@@ -35,9 +35,13 @@ hts-sys = { version = "^1.10", path = "hts-sys", default-features = false }
 default = ["bzip2", "lzma", "curl"]
 bzip2 = ["hts-sys/bzip2"]
 lzma = ["hts-sys/lzma"]
+bindgen = ["hts-sys/bindgen"]
 curl = ["hts-sys/curl"]
+libdeflate = ["hts-sys/libdeflate-sys"]
+s3 = ["hts-sys/s3"]
+gcs = ["hts-sys/gcs"]
+static = ["hts-sys/static"]
 serde = ["serde_base", "serde_bytes"]
-static = []
 
 [dev-dependencies]
 tempdir = "0.3"

README.md

@@ -19,7 +19,11 @@ If you only want to use the library, there is no need to clone the repository. G
 
 ## Requirements
 
-To compile this crate you need docker and cross:
+rust-htslib comes with pre-built bindings to htslib for Mac and Linux. You will need a C toolchain compatible with the `cc` crate. The build script for this crate will automatically build a link htslib.
+
+
+### MUSL build
+To compile this for MUSL crate you need docker and cross:
 
 ```shell
 $ cargo install cross
@@ -62,7 +66,16 @@ with these compression methods, you can deactivate these features to reduce you
 rust-htslib = { version = "*", default-features = false }
 ```
 
-`rust-htslib` also has optional support for `serde`, to allow (de)serialization of `bam::Record` via any serde-supported format:
+`rust-htslib` has optional support for `serde`, to allow (de)serialization of `bam::Record` via any serde-supported format.
+
+Http access to files is available with the `curl` feature.
+
+Beta-level S3 and Google Cloud Storge support is available with the `s3` and `gcs` features.
+
+`rust-htslib` can optionally use `bindgen` to generate bindings to htslib. This can slow down the build substantially. Enabling the `bindgen` feature will 
+cause `hts-sys` to use a create a binding file for your architecture. Pre-built bindings are supplied for Mac and Linux. The `bindgen` feature on Windows is untested - please file a bug if you need help.
+
+
 
 ```toml
 [dependencies]

hts-sys/Cargo.toml

@@ -18,20 +18,25 @@ tag-message = "Version {{version}} of Rust-HTSlib."
 
 [dependencies]
 libz-sys = { version = "1.0.25", features = ["static"] }
-# https://github.com/alexcrichton/bzip2-rs/issues/56
 bzip2-sys = { version = "0.1.8", optional = true }
 lzma-sys = { version = "0.1.16", optional = true, features = ["static"] }
-curl-sys = { version = "0.4.31", optional = true, features = ["static-curl", "static-ssl"] }
+curl-sys = { version = "0.4.31", optional = true, features = ["static-curl", "static-ssl", "protocol-ftp"] }
+libdeflate-sys = { version = "0.5", optional = true }
+
+[target.'cfg(all(unix, not(target_os = "macos")))'.dependencies]
+openssl-sys = { version = "0.9", optional = true }
 
 [features]
-default = ["bzip2", "lzma"]
+default = ["bzip2", "lzma", "curl"]
 bzip2 = ["bzip2-sys"]
 lzma = ["lzma-sys"]
-curl = ["curl-sys"]
-static = []
+curl = ["curl-sys", "openssl-sys"]
+gcs = ["curl"] # Google Cloud Storage support
+s3 = ["curl"] # Amazon S3 support
+static = [] # Don't dynamically link to other libraries
 
 [build-dependencies]
 fs-utils = "1.1"
-bindgen = { version = "0.53.2", default-features = false, features = ["runtime"] }
-cc = "1.0"
+bindgen = { version = "0.53.2", default-features = false, features = ["runtime"], optional = true }
+cc = { version = "1.0", features = ["parallel"] }
 glob = "0.3.0"