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magnusuMETmagnusuMET
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Merge pull request #56 from magnusuMET/vendor
Option for building netCDF from source
2 parents 97cff73 + 0c10ba6 commit 0d79e65

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Lines changed: 256 additions & 75 deletions

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‎.github/workflows/ci.yml‎

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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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with: {submodules: true}
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- name: Install netCDF
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run: sudo apt-get install libnetcdf-dev
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- name: Install rust
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uses: actions-rs/toolchain@v1
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with:
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- name: Check formatting
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run: cargo fmt -- --check
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- name: Documentation
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run: cargo doc --workspace
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run: cargo doc --workspace --exclude netcdf-src
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- name: Clippy
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run: cargo clippy --workspace -- -D warnings
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run: cargo clippy --workspace --exclude netcdf-src -- -D warnings
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test:
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name: test
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runs-on: ${{ matrix.os }}
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test_apt:
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name: test apt
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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build:
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- nightly
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include:
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- build: stable
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os: ubuntu-18.04
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rust: stable
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- build: beta
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os: ubuntu-18.04
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rust: beta
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- build: nightly
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os: ubuntu-18.04
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rust: nightly
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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with: {submodules: false}
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- name: Install netcdf
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run: sudo apt-get install libnetcdf-dev
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override: true
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- name: Build
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run: cargo build --verbose --workspace
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run: cargo build --verbose --workspace --exclude netcdf-src
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- name: Test
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run: cargo test --verbose --workspace
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run: cargo test --verbose --workspace --exclude netcdf-src
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if: matrix.os == 'ubuntu-18.04'
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tarpaulin:
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name: tarpaulin
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runs-on: ubuntu-18.04
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conda:
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name: conda
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runs-on: ${{matrix.os}}-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- {os: ubuntu, channel: conda-forge, rust: stable}
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- {os: windows, channel: conda-forge, rust: stable}
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- {os: macos, channel: conda-forge, rust: stable}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install netcdf
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run: sudo apt-get install libnetcdf-dev
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- name: Install rust
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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profile: minimal
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override: true
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- name: Install tarpaulin
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uses: actions-rs/install@v0.1
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with:
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crate: cargo-tarpaulin
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version: latest
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use-tool-cache: true
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- name: Tarpaulin
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run: cargo tarpaulin --verbose --out Xml --ignore-tests
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- name: Checkout repository
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uses: actions/checkout@v2
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with: {submodules: true}
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- name: Install Rust (${{matrix.rust}})
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uses: actions-rs/toolchain@v1
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with: {toolchain: '${{matrix.rust}}', profile: minimal, override: true}
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- name: Install conda
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uses: goanpeca/setup-miniconda@v1
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with: {auto-update-conda: false, activate-environment: testenv}
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- name: Install netCDF
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run: conda install -y -c ${{matrix.channel}} libnetcdf=4.7.4
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- name: Build and test
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run: |
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export HDF5_DIR="$CONDA_PREFIX"
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[ "${{runner.os}}" != "Windows" ] && export RUSTFLAGS="-C link-args=-Wl,-rpath,$CONDA_PREFIX/lib"
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cargo test -vv --workspace --exclude netcdf-src
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- name: Upload to codecov
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uses: codecov/codecov-action@v1.0.2
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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static_builds:
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name: static builds
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runs-on: ${{matrix.os}}-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- {os: ubuntu, rust: stable}
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- {os: windows, rust: stable-msvc}
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- {os: windows, rust: stable-gnu}
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- {os: macos, rust: stable}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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with: {submodules: true}
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- name: Install Rust (${{matrix.rust}})
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uses: actions-rs/toolchain@v1
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with: {toolchain: '${{matrix.rust}}', profile: minimal, override: true}
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- name: Build and test
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run: cargo test -vv --workspace --features static

‎.github/workflows/codecov.yml‎

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name: codecov
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on: [push]
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env:
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CARGO_TERM_COLOR: always
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jobs:
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tarpaulin:
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name: tarpaulin
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runs-on: ubuntu-18.04
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Install netcdf
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run: sudo apt-get install libnetcdf-dev
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- name: Install rust
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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profile: minimal
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override: true
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- name: Install tarpaulin
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uses: actions-rs/install@v0.1
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with:
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crate: cargo-tarpaulin
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version: latest
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use-tool-cache: true
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- name: Tarpaulin
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run: cargo tarpaulin --verbose --out Xml --ignore-tests
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- name: Upload to codecov
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uses: codecov/codecov-action@v1.0.2
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with:
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token: ${{ secrets.CODECOV_TOKEN }}

‎.gitmodules‎

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[submodule "netcdf-sys/source"]
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path = netcdf-src/source
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url = https://github.com/Unidata/netcdf-c.git

‎Cargo.toml‎

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[features]
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default = ["ndarray"]
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memory = ["netcdf-sys/memio"]
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static = ["netcdf-sys/static"]
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[dependencies]
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lazy_static = "1.4.0"
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[workspace]
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members = [
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"netcdf-sys",
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"netcdf-src",
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]

‎Dockerfile‎

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This file was deleted.

‎README.md‎

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<!-- [![dependency status](https://deps.rs/repo/github/georust/netcdf/status.svg)](https://deps.rs/repo/github/georust/netcdf) -->
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Medium-level [netCDF](http://www.unidata.ucar.edu/software/netcdf/) bindings for Rust, allowing easy reading and writing of array-like structures to a file.
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netCDF can read and write `hdf5` files, which is a commonly used file format in scientific computing.
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## Status
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## Building
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This crate depends on libnetcdf. The Travis build runs on Ubuntu 16.04 Xenial and installs libnetcdf via apt, which results in netcdf v.4.4.0. netcdf is not widely tested on other versions of netcdf.
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This crate depends on `libnetcdf`, but a static build from source is also supported, which can be enabled using the `static` feature.
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You can build the library and run the tests via Docker like this:
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The crate is built on several platforms using github actions, and is currently known to build form from source on all major platforms (linux, macos, windows (gnu+msvc)), and through the package installers `conda` and `apt`.
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```
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docker build . -t netcdf
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docker run -it --rm netcdf
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```
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## Documentation
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‎netcdf-src/Cargo.toml‎

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[package]
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name = "netcdf-src"
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version = "0.1.0"
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authors = ["Magnus Ulimoen <magnusu@met.no>"]
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edition = "2018"
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description = "Build scripts for building `netCDF` from source"
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build = "build.rs"
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repository = "https://github.com/georust/netcdf"
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license-file = "source/COPYRIGHT"
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links = "netcdfsrc"
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exclude = [
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"source/unit_test/**",
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"source/NUG/**",
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"source/dap4_test/**",
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"source/examples/**",
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"source/nc_test/**",
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"source/h5_test/**",
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"source/nc_perf/**",
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"source/ncdump/**",
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"source/hdf4_test/**",
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"source/ncgen/**",
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"source/ncgen3/**",
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"source/nctest/**",
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]
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[features]
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dap = []
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[dependencies]
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hdf5-sys = { version = "0.7.0", features = ["hl", "deprecated", "zlib"] }
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[build-dependencies]
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cmake = "0.1.44"

‎netcdf-src/build.rs‎

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macro_rules! feature {
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($feature:expr) => {
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std::env::var(concat!("CARGO_FEATURE_", $feature))
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};
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}
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fn main() {
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println!("cargo:rerun-if-changed=build.rs");
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let hdf5_incdir = std::env::var("DEP_HDF5_INCLUDE").unwrap();
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let hdf5_lib = std::env::var("DEP_HDF5_LIBRARY").unwrap();
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let hdf5_hl_lib = std::env::var("DEP_HDF5_HL_LIBRARY").unwrap();
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let mut netcdf_config = cmake::Config::new("source");
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netcdf_config
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.define("BUILD_SHARED_LIBS", "OFF")
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.define("NC_FIND_SHARED_LIBS", "OFF")
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.define("BUILD_UTILITIES", "OFF")
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.define("ENABLE_EXAMPLES", "OFF")
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.define("ENABLE_DAP_REMOTE_TESTS", "OFF")
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.define("ENABLE_TESTS", "OFF")
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.define("ENABLE_EXTREME_NUMBERS", "OFF")
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.define("ENABLE_PARALLEL_TESTS", "OFF")
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.define("ENABLE_FILTER_TESTING", "OFF")
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.define("ENABLE_BASH_SCRIPT_TESTING", "OFF")
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//
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.define("HDF5_C_LIBRARY", &hdf5_lib)
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.define("HDF5_HL_LIBRARY", &hdf5_hl_lib)
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.define("HDF5_INCLUDE_DIR", hdf5_incdir)
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//
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.define("ENABLE_DAP", "OFF") // TODO: feature flag, requires curl
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//
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.profile("RelWithDebInfo"); // TODO: detect opt-level
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if feature!("DAP").is_ok() {
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netcdf_config.define("ENABLE_DAP", "ON");
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}
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let netcdf = netcdf_config.build();
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println!("cargo:lib={}", "netcdf");
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let search_path = format!("{}/lib", netcdf.display());
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if std::path::Path::new(&search_path).exists() {
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println!("cargo:search={}", search_path);
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} else {
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let search_path = format!("{}/lib64", netcdf.display());
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println!("cargo:search={}", search_path);
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}
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}

‎netcdf-src/source‎

Submodule source added at 26fba54

‎netcdf-src/src/lib.rs‎

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//! Dummy crate for building `netCDF` from source
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//!
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//! The current pinned version is 4.7.4

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