Merge pull request #29 from aldanor/feature/bindgen-pubconf

Rewrite build system, fix hbool_t, remove libhdf5-lib crate

Author: aldanor

.travis.yml

@@ -1,9 +1,56 @@
 sudo: false
 language: rust
-rust:
-- stable
-- beta
-- nightly
+notifications:
+  email:
+    on_success: never
+addons:
+  apt:
+    packages:
+      - pkg-config
+
+matrix:
+  include:
+    - name: xenial-stable-conda-1.10.4
+      os: linux
+      dist: xenial
+      rust: stable
+      env:
+        - H5_CONDA=1.10.4
+    - name: xenial-beta-apt-1.8.13
+      os: linux
+      dist: xenial
+      rust: beta
+      addons:
+        apt:
+          packages:
+            - libhdf5-dev
+      env:
+        - HDF5_VERSION=1.8.16
+    - name: trusty-nightly-apt-1.8.11
+      os: linux
+      dist: trusty
+      rust: nightly
+      addons:
+        apt:
+          packages:
+            - libhdf5-serial-dev
+    - name: macos-stable-brew-1.10.*
+      os: osx
+      rust: stable
+      env:
+        - H5_BREW=1.8
+    - name: macos-beta-brew-1.8.*
+      os: osx
+      rust: beta
+      env:
+        - H5_BREW=1.10
+    - name: macos-nightly-conda-1.8.9
+      os: osx
+      rust: nightly
+      env:
+        - H5_CONDA=1.8.9
+        - HDF5_VERSION=1.8.9
+
 before_script:
 - |
   if [ $TRAVIS_RUST_VERSION = "nightly" ]; then
@@ -18,32 +65,48 @@ script:
     fi
   fi
 - cargo clean
-- cargo test -v -p hdf5-derive
-- cargo clean
-- cargo build -v
+- cargo build -vv
 - cargo test -v --no-run --all --exclude hdf5-derive
 - cargo test -v --all --exclude hdf5-derive
+- cargo clean
+- cargo test -v -p hdf5-derive
 - |
-  if [ $TRAVIS_RUST_VERSION = "stable" ] && [ `uname` = "Linux" ]; then
+  if [ $TRAVIS_RUST_VERSION = "stable" ] && [ `uname` = "Linux" ] &&\
+     [ $TRAVIS_BRANCH = "master" ] && [ $TRAVIS_PULL_REQUEST = "false" ]; then
+    cargo clean;
     cargo doc --no-deps;
   fi
-addons:
-  apt:
-    packages:
-    - libhdf5-serial-dev
-    - pkg-config
-notifications:
-  email:
-    on_success: never
-os:
-- linux
-- osx
 before_install:
-- if [ `uname` = "Darwin" ]; then
+- |
+  if [ `uname` = "Darwin" ] && [ ! -z "$H5_BREW" ]; then
     brew update >/dev/null;
     brew tap homebrew/science;
-    brew install hdf5;
+    brew install hdf5@${H5_BREW};
+  fi
+- |
+  if [ ! -z "$H5_CONDA" ]; then
+    if [ `uname` = "Darwin" ]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+      # note: this is only required for older HDF5 installations on OS X
+      export DYLD_FALLBACK_LIBRARY_PATH="$HOME/miniconda/envs/testenv/lib";
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+    bash miniconda.sh -b -p $HOME/miniconda;
+    export PATH="$HOME/miniconda/bin:$PATH";
+    hash -r;
+    conda config --set always_yes yes --set changeps1 no;
+    conda info -a;
+    conda create -q -n testenv hdf5=${H5_CONDA};
+    export HDF5_DIR="$HOME/miniconda/envs/testenv";
+    export RUSTFLAGS="-C link-args=-Wl,-rpath,$HOME/miniconda/envs/testenv/lib";
+  fi
+- |
+  if [ $TRAVIS_OS_NAME = "linux" ]; then
+    pkg-config hdf5 --modversion || true;
   fi
+- find /usr -name '*hdf5*' || true
+- find /usr -name 'H5*.h' || true
 after_success: |
   [ $TRAVIS_BRANCH = "master" ] &&
   [ $TRAVIS_PULL_REQUEST = "false" ] &&

Cargo.toml

@@ -4,7 +4,6 @@ members = [
     "hdf5-types",
     "hdf5-derive",
     "libhdf5-sys",
-    "libhdf5-lib",
 ]
 exclude = [
     "*.yml"

README.md

@@ -67,16 +67,18 @@ fn main() -> h5::Result<()> {
 
 ### Platforms
 
-`hdf5-rs` is known to run on these platforms:
-
-- Linux (tested on Travis CI, HDF5 v1.8.4)
-- OS X (tested on Travis CI, HDF5 v1.8.16)
-- Windows (tested on AppVeyor, MSVC target, HDF5 v1.8.16, VS2015 x64)
+`hdf5-rs` is known to run on these platforms: Linux, macOS, Windows (tested on Travis CI and 
+AppVeyor, HDF5 1.8 and 1.10, system installations and conda environments).
 
 ### Rust
 
-`hdf5-rs` is tested for all three official release channels, and requires Rust compiler
-of version 1.13 or newer.
+`hdf5-rs` is tested continuously for all three official release channels, and requires 
+a modern Rust compiler (e.g. of version 1.31 or later).
+
+### HDF5
+
+Required HDF5 version is 1.8.4 or newer. The library doesn't have to be built with
+threadsafe option enabled.
 
 ## Building
 
@@ -88,38 +90,56 @@ enabled or disabled at compile time. While this allows supporting multiple versi
 in a single codebase, this is something the library user should be aware of in case they
 choose to use the low level FFI bindings.
 
-### Linux, OS X
+### Environment variables
+
+If `HDF5_DIR` is set, the build script will look there (and nowhere else) for HDF5
+headers and binaries (i.e., it will look for headers under `$HDF5_DIR/include`).
+
+If `HDF5_VERSION` is set, the build script will check that the library version matches
+the specified version string; in some cases it may also be used by the build script to
+help locating the library (e.g. when both 1.8 and 1.10 are installed via Homebrew on macOS).
+
+### conda
+
+It is possible to link against `hdf5` conda package; a few notes and tips:
+
+- Point `HDF5_DIR` to conda environment root.
+- The build script knows about conda environment layout specifics and will adjust
+  paths accordingly (e.g. `Library` subfolder in Windows environments).
+- On Windows, environment's `bin` folder must be in `PATH` (or the environment can
+  be activated prior to running cargo).
+- On Linux / macOS, it is recommended to set rpath, e.g. by setting
+  `RUSTFLAGS="-C link-args=-Wl,-rpath,$HDF5_DIR/lib"`.
+- For old versions of HDF5 conda packages on macOS, it may also be necessary to set
+  `DYLD_FALLBACK_LIBRARY_PATH="$HDF5_DIR/lib"`.
 
-The build script of `libhdf5-lib` crate will try to use `pkg-config` if it's available
-to deduce HDF5 library location. This is sufficient for most standard setups.
+### Linux
 
-There are also two environment variables that may be of use if the library location and/or name
-is unconventional:
+The build script will attempt to use pkg-config first, which will likely work out without
+further tweaking for the more recent versions of HDF5. The build script will then also look 
+in some standard locations where HDF5 can be found after being apt-installed on Ubuntu.
 
-- `HDF5_LIBDIR` – added to library search path during the build step
-- `HDF5_LIBNAME` – library name (defaults to `hdf5`)
+### macOS
 
-Note that `cargo clean` is requred before rebuilding if any of those variables are changed.
+On macOS, the build script will attempt to locate HDF5 via Homebrew if it's available.
+If both 1.8 and 1.10 are installed and available, the default (1.10) will be used 
+unless `HDF5_VERSION` is set.
 
 ### Windows
 
 `hdf5-rs` fully supports MSVC toolchain, which allows using the
 [official releases](https://www.hdfgroup.org/downloads/index.html) of
-HDF5 and is generally the recommended way to go. That being said, previous experiments have shown
-that all tests pass on the `gnu` target as well, one just needs to be careful with building the
-HDF5 binary itself and configuring the build environment.
+HDF5 and is generally the recommended way to go. That being said, previous experiments have 
+shown that all tests pass on the `gnu` target as well, one just needs to be careful with 
+building the HDF5 binary itself and configuring the build environment.
 
 Few things to note when building on Windows:
 
 - `hdf5.dll` should be available in the search path at build time and runtime (both `gnu` and `msvc`).
   This normally requires adding the `bin` folder of HDF5 installation to `PATH`. If using an official
-  HDF5 release (`msvc` only), this will be done automatically by the installer.
-- If `HDF5_LIBDIR` or `HDF5_LIBNAME` change, `cargo clean` is required before rebuilding.
+  HDF5 release (`msvc` only), this will typically be done automatically by the installer.
 - `msvc`: installed Visual Studio version should match the HDF5 binary (2013 or 2015). Note that it
   is not necessary to run `vcvars` scripts; Rust build system will take care of that.
-- In most cases, it is not necessary to manually set `HDF5_LIBDIR` as it would be inferred from the
-  search path (both `gnu` and `msvc`). This also implies that the official releases should work
-  out of the box.
 - When building for either target, make sure that there are no conflicts in the search path (e.g.,
   some binaries from MinGW toolchain may shadow MSVS executables or vice versa).
 - The recommended platform for `gnu` target is [TDM distribution](http://tdm-gcc.tdragon.net/) of

appveyor.yml

@@ -3,30 +3,29 @@ platform:
   - x64
 os: Visual Studio 2015
 matrix:
-  fast_finish: true
+  fast_finish: false
 skip_tags: true
-build: false
+build: off
+init:
+- set CONDA=C:\Miniconda36-x64
+- set PATH=%CONDA%;%CONDA%\Scripts;%CONDA%\Library\bin;C:\Rust\bin;%PATH%
 
 environment:
-  TARGET: x86_64-pc-windows-msvc
-  HDF5_BINDIR: "C:\\Program Files\\HDF_Group\\HDF5\\1.8.17\\bin"
-  HDF5_URL: "https://support.hdfgroup.org/ftp/HDF5/prev-releases/hdf5-1.8/hdf5-1.8.17/bin/windows/extra/hdf5-1.8.17-win64-vs2015-shared.zip"
   matrix:
-    - CHANNEL: 1.31.0
+    - CHANNEL: 1.32.0
+      H5_VERSION: 1.8.21
+      H5_SOURCE: msi
     - CHANNEL: beta
+      H5_VERSION: 1.10.0
+      H5_SOURCE: msi
+      H5_PIN: yes
     - CHANNEL: nightly
+      H5_VERSION: 1.10.4
+      H5_SOURCE: conda
+
 install:
-  - ps: Start-FileDownload "https://static.rust-lang.org/dist/rust-${env:CHANNEL}-${env:TARGET}.msi"
-  - ps: Start-Process -FilePath msiexec -ArgumentList /i, rust-${env:CHANNEL}-${env:TARGET}.msi, INSTALLDIR="C:\Rust", /quiet -Wait
-  - set PATH=%PATH%;C:\Rust\bin;%HDF5_BINDIR%
-  - rustc -vV
-  - cargo -vV
-  - ps: Invoke-WebRequest ${env:HDF5_URL} -OutFile hdf5.zip
-  - 7z x hdf5.zip -y
-  - ps: Start-Process -FilePath msiexec -ArgumentList /i, "hdf5\HDF5-1.8.17-win64.msi", /quiet -Wait
+  - python scripts\appveyor.py install-rust
+  - python scripts\appveyor.py install-hdf5
 
 test_script:
-  - cd %APPVEYOR_BUILD_FOLDER%
-  - cargo build -v
-  - cargo test -v --no-run
-  - cargo test -v --all --exclude hdf5-derive
+  - python scripts\appveyor.py run-tests

hdf5-rs/Cargo.toml

@@ -22,7 +22,6 @@ parking_lot = "0.7"
 ndarray = "0.12"
 num-integer = "0.1"
 num-traits = "0.2"
-libhdf5-lib = { path = "../libhdf5-lib", version = "0.2.0" }
 libhdf5-sys = { path = "../libhdf5-sys", version = "0.2.0" }
 hdf5-types = { path = "../hdf5-types", version = "0.2.0" }
 hdf5-derive = { path = "../hdf5-derive", version = "0.2.0" }
@@ -34,4 +33,4 @@ scopeguard = "1.0"
 tempdir = "0.3"
 
 [build-dependencies]
-libhdf5-lib = { path = "../libhdf5-lib", version = "0.2.0" }
+libhdf5-sys = { path = "../libhdf5-sys", version = "0.2.0" }

hdf5-rs/build.rs

@@ -1,3 +1,3 @@
 fn main() {
-    libhdf5_lib::dump_build_flags();
+    libhdf5_sys::emit_cfg_flags();
 }

hdf5-rs/src/lib.rs

@@ -95,9 +95,14 @@ mod internal_prelude {
 #[cfg(test)]
 pub mod test;
 
-/// Returns the version of the HDF5 library that the crate was compiled against.
+/// Returns the runtime version of the HDF5 library.
 pub fn hdf5_version() -> (u8, u8, u8) {
-    h5lock!(libhdf5_lib::hdf5_version()).unwrap_or((0, 0, 0))
+    use self::internal_prelude::c_uint;
+    use libhdf5_sys::h5::H5get_libversion;
+    let mut v: (c_uint, c_uint, c_uint) = (0, 0, 0);
+    h5call!(H5get_libversion(&mut v.0, &mut v.1, &mut v.2))
+        .map(|_| (v.0 as _, v.1 as _, v.2 as _))
+        .unwrap_or((0, 0, 0))
 }
 
 #[cfg(test)]
@@ -106,6 +111,6 @@ pub mod tests {
 
     #[test]
     pub fn test_hdf5_version() {
-        assert!(hdf5_version() >= (1, 8, 0));
+        assert!(hdf5_version() >= (1, 8, 4));
     }
 }