Rebase conda branch to latest upstream

.github/workflows/ci.yml

@@ -2,6 +2,8 @@ name: CI
 
 on:
   push:
+    branches:
+      - master
   pull_request:
     branches:
       - master
@@ -33,7 +35,19 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: ${{matrix.command}}
-          args: "${{matrix.command == 'fmt' && '--all -- --check' || '-- -D warnings'}}"
+          args: "${{matrix.command == 'fmt' && '--all -- --check' || '--workspace --exclude hdf5-src -- -D warnings -D clippy::cargo'}}"
+
+  doc: # This task should mirror the procedure on docs.rs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with: {submodules: true}
+      - name: Install Rust (${{matrix.rust}})
+        uses: actions-rs/toolchain@v1
+        with: {toolchain: nightly, profile: minimal, override: true}
+      - name: Document workspace
+        run: env RUSTDOCFLAGS="--cfg docsrs" cargo doc --features hdf5-sys/static,hdf5-sys/zlib,blosc,lzf
 
   brew:
     name: brew
@@ -80,9 +94,11 @@ jobs:
           - {os: macos, version: 1.10.5, mpi: openmpi, channel: conda-forge, rust: beta}
           - {os: ubuntu, version: 1.10.6, channel: anaconda, rust: stable}
           - {os: ubuntu, version: 1.10.6, mpi: mpich, channel: conda-forge, rust: nightly}
+          # - {os: ubuntu, version: 1.10.8, channel: conda-forge, rust: stable}
           - {os: ubuntu, version: 1.12.0, mpi: openmpi, channel: conda-forge, rust: stable}
           - {os: macos, version: 1.12.0, channel: conda-forge, rust: stable}
           - {os: windows, version: 1.12.0, channel: conda-forge, rust: stable}
+          - {os: ubuntu, version: 1.12.1, channel: conda-forge, rust: stable}
     defaults:
       run:
         shell: bash -l {0}
@@ -94,7 +110,7 @@ jobs:
         uses: actions-rs/toolchain@v1
         with: {toolchain: '${{matrix.rust}}', profile: minimal, override: true}
       - name: Install conda
-        uses: goanpeca/setup-miniconda@v1
+        uses: conda-incubator/setup-miniconda@v2
         with: {auto-update-conda: false, activate-environment: testenv}
       - name: Install HDF5 (${{matrix.version}}${{matrix.mpi && '-' || ''}}${{matrix.mpi}})
         run: |
@@ -129,6 +145,39 @@ jobs:
         with: {toolchain: '${{matrix.rust}}', profile: minimal, override: true}
       - name: Build and test all crates
         run: cargo test --workspace -v --features hdf5-sys/static,hdf5-sys/zlib --exclude hdf5-derive
+      - name: Build and test with filters
+        run: cargo test --workspace -v --features hdf5-sys/static,hdf5-sys/zlib,lzf,blosc --exclude hdf5-derive
+        if: matrix.rust != 'stable-gnu'
+      - name: Run examples
+        run: |
+          cargo r --example simple --features hdf5-sys/static,hdf5-sys/zlib,lzf,blosc
+          cargo r --example chunking --features hdf5-sys/static,hdf5-sys/zlib,lzf,blosc
+        if: matrix.rust != 'stable-gnu'
+
+  conda_dl:
+    name: static
+    runs-on: ${{matrix.os}}-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {os: ubuntu, rust: stable}
+          - {os: windows, rust: stable-msvc}
+          - {os: windows, rust: stable-gnu}
+          - {os: macos, rust: stable}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with: {submodules: true}
+      - name: Change to older toolchain
+        if: matrix.os == 'macos'
+        run: sudo xcode-select -s "/Applications/Xcode_11.7.app"
+      - name: Install Rust (${{matrix.rust}})
+        uses: actions-rs/toolchain@v1
+        with: {toolchain: '${{matrix.rust}}', profile: minimal, override: true}
+      - name: Build and test all crates
+        run: cargo test --workspace -v --features conda --exclude hdf5-derive
+
 
   apt:
     name: apt
@@ -137,7 +186,6 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {ubuntu: 16.04, mpi: serial, rust: nightly}
           - {ubuntu: 18.04, mpi: mpich, rust: beta}
           - {ubuntu: 20.04, mpi: openmpi, rust: stable}
     steps:
@@ -157,6 +205,12 @@ jobs:
         run: |
           [ "${{matrix.mpi}}" != "serial" ] && FEATURES=mpio
           cargo test -vv --features="$FEATURES"
+      - name: Test crate for locking on synchronisation
+        run: |
+          [ "${{matrix.mpi}}" != "serial" ] && FEATURES=mpio
+          cargo test -vv --features="$FEATURES" -- lock_part
+          cargo test -vv --features="$FEATURES" -- lock_part
+          cargo test -vv --features="$FEATURES" -- lock_part
 
   msi:
     name: msi
@@ -165,7 +219,7 @@ jobs:
       fail-fast: false
       matrix:
         rust: [stable]
-        version: [1.8, '1.10']
+        version: ["1.8", "1.10", "1.12", "1.13"]
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -176,18 +230,26 @@ jobs:
       - name: Configure environment
         shell: bash
         run: |
-          if [ "${{matrix.version}}" == "1.8" ]; then
+          if [[ "${{matrix.version}}" == "1.8" ]]; then
             VERSION=1.8.21
             DL_PATH=hdf5-1.8.21-Std-win7_64-vs14.zip
-            echo ::set-env name=MSI_PATH::hdf\\HDF5-1.8.21-win64.msi
-          else
+            echo "MSI_PATH=hdf\\HDF5-1.8.21-win64.msi" >> $GITHUB_ENV
+          elif [[ "${{matrix.version}}" == "1.10" ]]; then
             VERSION=1.10.0
             DL_PATH=windows/extra/hdf5-1.10.0-win64-VS2015-shared.zip
-            echo ::set-env name=MSI_PATH::hdf5\\HDF5-1.10.0-win64.msi
+            echo "MSI_PATH=hdf5\\HDF5-1.10.0-win64.msi" >> $GITHUB_ENV
+          elif [[ "${{matrix.version}}" == "1.12" ]]; then
+            VERSION=1.12.0
+            DL_PATH=hdf5-1.12.0-Std-win10_64-vs16.zip
+            echo "MSI_PATH=hdf\\HDF5-1.12.0-win64.msi" >> $GITHUB_ENV
+          else
+            VERSION=1.13.0
+            DL_PATH=windows/hdf5-1.13.0-Std-win10_64-vs16.zip
+            echo "MSI_PATH=hdf\\HDF5-1.13.0-win64.msi" >> $GITHUB_ENV
           fi
           BASE_URL=https://support.hdfgroup.org/ftp/HDF5/prev-releases
-          echo ::set-env name=DL_URL::$BASE_URL/hdf5-${{matrix.version}}/hdf5-$VERSION/bin/$DL_PATH
-          echo ::add-path::C:\\Program Files\\HDF_Group\\HDF5\\$VERSION\\bin
+          echo "DL_URL=$BASE_URL/hdf5-${{matrix.version}}/hdf5-$VERSION/bin/$DL_PATH" >> $GITHUB_ENV
+          echo "C:\\Program Files\\HDF_Group\\HDF5\\$VERSION\\bin" >> $GITHUB_PATH
       - name: Install HDF5 (${{matrix.version}})
         shell: pwsh
         run: |
@@ -196,3 +258,46 @@ jobs:
           msiexec /i ${{env.MSI_PATH}} /quiet /qn /norestart
       - name: Build and test all crates
         run: cargo test -vv
+
+  msrv:
+    name: Minimal Supported Rust Version
+    runs-on: ubuntu-18.04
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with: {submodules: true}
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with: {toolchain: 1.51, profile: minimal, override: true}
+      - name: Build and test all crates
+        run:
+          cargo test --workspace -vv --features=hdf5-sys/static --exclude=hdf5-derive
+
+  wine:
+    name: wine
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with: {submodules: true}
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with: {toolchain: stable, target: x86_64-pc-windows-gnu, profile: minimal, override: true}
+      - name: Install dependencies
+        run: sudo apt-get update && sudo apt install wine64 mingw-w64
+      - name: Build and test
+        run: env CARGO_TARGET_X86_64_PC_WINDOWS_GNU_RUNNER=wine64 cargo test --features hdf5-sys/static --target x86_64-pc-windows-gnu -- --skip test_compile_fail
+  addr_san:
+    name: Address sanitizer
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with: {submodules: true}
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with: {toolchain: nightly, profile: minimal, override: true}
+      - name: Run test with sanitizer
+        run: env RUSTFLAGS="-Z sanitizer=address" cargo test --features hdf5-sys/static --target x86_64-unknown-linux-gnu --workspace --exclude hdf5-derive