MSRV to 1.65,updated fitsio and fitsio-sys,mwalib Python lib now has …

…typing and docstrings,added cfitsio CI tests

.github/workflows/coverage.yml

@@ -11,8 +11,7 @@ on:
 env:
   RUST_BACKTRACE: 1  
   CARGO_TERM_COLOR: always
-  CARGO_INCREMENTAL: 0
-  MWALIB_LINK_STATIC_CFITSIO: 1
+  CARGO_INCREMENTAL: 0  
 
 jobs:
   generate_coverage:

.github/workflows/run_cfitsio_tests.yml

@@ -0,0 +1,111 @@
+name: cfitsio tests
+
+on:
+  push:
+    tags-ignore:
+      - '**'
+    branches:
+      - '**'
+  pull_request:
+
+env:
+  RUST_BACKTRACE: 1
+  CARGO_TERM_COLOR: always
+  CARGO_INCREMENTAL: 0
+
+jobs:
+  test_cfitsio_3:
+    name: Test cfitsio 3.49 on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # see https://github.com/actions/runner-images?tab=readme-ov-file#available-images for runner types
+        os: [ubuntu-latest, macos-13, macos-14, macos-15] # macos-13 is x86_64, macos-14 & 15 are Arm64
+    steps:
+    - name: Checkout sources
+      uses: actions/checkout@v4
+
+    - name: (macos) install automake and autoconf
+      if: ${{ startsWith(matrix.os, 'macOS') }}
+      run: |
+        brew install automake autoconf    
+          
+    - name: Install stable minimal toolchain
+      uses: dtolnay/rust-toolchain@v1
+      with:          
+          toolchain: stable
+
+    - name: Install cfitsio 3.49
+      run: |
+        curl "https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-3.49.tar.gz" -o cfitsio.tar.gz
+        tar -xf cfitsio.tar.gz
+        rm cfitsio.tar.gz
+        cd cfitsio-3.49
+        # Enabling SSE2/SSSE3 could cause portability problems, but it's unlikely that anyone
+        # is using such a CPU...
+        # https://stackoverflow.com/questions/52858556/most-recent-processor-without-support-of-ssse3-instructions
+        # Disabling curl just means you cannot fits_open() using a URL.
+        CFLAGS="-O3" ./configure --prefix=/usr/local --enable-reentrant --enable-sse2 --enable-ssse3 --disable-curl
+
+        if [[ "$OSTYPE" == "linux-gnu"* ]]; then    
+            make -j
+            sudo make install
+            sudo ldconfig    
+
+        elif [[ "$OSTYPE" == "darwin"* ]]; then    
+            sudo make shared
+            sudo make install    
+        fi
+
+        cd ..
+
+    - name: Run tests run on latest stable rust
+      run: cargo test --features examples
+
+  test_cfitsio_4:
+    name: Test cfitsio 4.5.0 on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # see https://github.com/actions/runner-images?tab=readme-ov-file#available-images for runner types
+        os: [ubuntu-latest, macos-13, macos-14, macos-15] # macos-13 is x86_64, macos-14 & 15 are Arm64
+    steps:
+    - name: Checkout sources
+      uses: actions/checkout@v4
+
+    - name: (macos) install automake and autoconf
+      if: ${{ startsWith(matrix.os, 'macOS') }}
+      run: |
+        brew install automake autoconf    
+          
+    - name: Install stable minimal toolchain
+      uses: dtolnay/rust-toolchain@v1
+      with:          
+          toolchain: stable
+
+    - name: Install cfitsio 4.5.0
+      run: |
+        curl "https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-4.5.0.tar.gz" -o cfitsio.tar.gz
+        tar -xf cfitsio.tar.gz
+        rm cfitsio.tar.gz
+        cd cfitsio-4.5.0
+        # Enabling SSE2/SSSE3 could cause portability problems, but it's unlikely that anyone
+        # is using such a CPU...
+        # https://stackoverflow.com/questions/52858556/most-recent-processor-without-support-of-ssse3-instructions
+        # Disabling curl just means you cannot fits_open() using a URL.
+        CFLAGS="-O3" ./configure --prefix=/usr/local --enable-reentrant --enable-sse2 --enable-ssse3 --disable-curl
+
+        if [[ "$OSTYPE" == "linux-gnu"* ]]; then    
+            make -j
+            sudo make install
+            sudo ldconfig    
+
+        elif [[ "$OSTYPE" == "darwin"* ]]; then    
+            sudo make
+            sudo make install    
+        fi
+
+        cd ..
+
+    - name: Run tests run on latest stable rust
+      run: cargo test --features examples

.github/workflows/run_tests.yml

@@ -42,4 +42,4 @@ jobs:
       run: |
         MIN_RUST=$(grep -m1 "rust-version" Cargo.toml | sed 's|.*\"\(.*\)\"|\1|')
         ~/.cargo/bin/rustup install $MIN_RUST --profile minimal          
-        cargo +${MIN_RUST} test --features cfitsio-static, examples
+        cargo +${MIN_RUST} test --features cfitsio-static,examples

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 Changes in each release are listed below.
 
+## 1.7.0 23-Oct-2024
+
+* Bumped MSRV to 1.65.
+* Update fitsio to 0.21 and fitsio-sys to 0.5.
+* Removed Rust Report Card from README status badges. Looks like this service is abandonded.
+* Added Python .pyi stub generation to provide mwalib Python users with type and docstring information. The mwalib.pyi should get baked into the python wheels released to github and Pypi. See `bin/README.md` for caveats and more details.
+* Added CI to test compilation against cfitsio 3.x and 4.x when not using the `cfitsio-static` feature.
+
 ## 1.6.0 18-Oct-2024
 
 * Updated ndarray to 0.16

Cargo.toml

@@ -1,36 +1,44 @@
 [package]
 name = "mwalib"
-version = "1.6.0"
+version = "1.7.0"
 homepage = "https://github.com/MWATelescope/mwalib"
 repository = "https://github.com/MWATelescope/mwalib"
 readme = "README.md"
 authors = ["Greg Sleap <[email protected]>",
            "Christopher H. Jordan <[email protected]>"]
 edition = "2021"
-rust-version = "1.64"
+rust-version = "1.65"
 description = "A library to simplify reading Murchison Widefield Array (MWA) raw visibilities, voltages and metadata."
 license = "MPL-2.0"
 keywords = ["radioastronomy", "mwa", "astronomy"]
 categories = ["science","parsing"]
 exclude = ["test_files/*", "tools/*",".github/*"]
 
+[[bin]]
+name = "stub_gen"
+path = "bin/stub_gen.rs"
+doc = false
+required-features = ["python"]
+
 # Make a rust library, as well as static and C-compatible dynamic libraries
 # available as "libmwalib.a" and "libmwalib.so".
 [lib]
 crate-type = ["rlib", "staticlib", "cdylib"]
 
 [features]
+# default
+default = ["cfitsio-static", "examples"]
 # Compile cfitsio from source and link it statically.
 cfitsio-static = ["fitsio-sys/fitsio-src"]
 # Enable optional features needed by examples.
 examples = ["anyhow", "clap", "env_logger"]
 # Enable python
-python = ["pyo3", "numpy", "ndarray"]
+python = ["anyhow", "env_logger", "ndarray", "numpy", "pyo3", "pyo3-stub-gen", "pyo3-stub-gen-derive"]
 
 [dependencies]
 chrono = "0.4.38"
-fitsio = "~0.20"
-fitsio-sys = "~0.4"
+fitsio = "~0.21"
+fitsio-sys = "~0.5"
 lazy_static = "~1.5"
 libc = "~0.2"
 log = "~0.4"
@@ -40,15 +48,19 @@ rayon = "~1.10"
 regex = "~1.9"
 thiserror = "~1.0"
 
-# "python" feature.
-pyo3 = { version = "~0.22", features = ["chrono", "extension-module"], optional = true }
-numpy = { version = "~0.22", optional = true }
+# "python" and examples features
+anyhow = { version = "~1.0", optional = true }
+env_logger = { version = "~0.10", optional = true }
+
+# "python" feature
 ndarray = { version = "~0.16", optional = true }
+numpy = { version = "~0.22", optional = true }
+pyo3 = { version = "~0.22", features = ["chrono", "extension-module", "macros"], optional = true }
+pyo3-stub-gen = { version = "~0.6", optional = true }
+pyo3-stub-gen-derive = { version = "~0.6", optional = true }
 
 # "examples" feature.
-anyhow = { version = "~1.0", optional = true }
 clap = { version = "~4.1", features = ["derive"], optional = true }
-env_logger = { version = "~0.10", optional = true }
 
 [dev-dependencies]
 csv = "~1.3"
@@ -85,4 +97,4 @@ required-features = ["examples"]
 
 [[example]]
 name = "mwalib-sum-first-fine-channel-gpubox-hdus"
-required-features = ["examples"]
+required-features = ["examples"]

README.md

@@ -12,7 +12,6 @@
 ![Crates.io](https://img.shields.io/crates/d/mwalib)
 ![Crates.io](https://img.shields.io/crates/l/mwalib)
 [![docs](https://docs.rs/mwalib/badge.svg)](https://docs.rs/crate/mwalib/latest)
-[![Rust Report Card](https://rust-reportcard.xuri.me/badge/github.com/MWATelescope/mwalib)](https://rust-reportcard.xuri.me/report/github.com/MWATelescope/mwalib)
 
 mwalib is an MWA library to read raw visibilities, voltages and metadata into a common structure.
 mwalib supports the existing "legacy" MWA correlator, as well as the "MWAX" correlator observations. This library

bin/README.md

@@ -0,0 +1,20 @@
+# mwalib python pyi stub generation
+
+## How it works
+
+1. Build mwalib using: `cargo build --all-features`
+2. Run the stub generator: `target/debug/stub_gen`
+3. At this point you can view the `mwalib.pyi` file and see what Python stubs were generated.
+4. To test, build a python wheel to test with: `maturin build --all-features --out dist`.
+5. In a freah Python environment install the wheel: `pip install dist/mwalib-1.7.0-cp313-cp313-manylinux_2_34_x86_64.whl`.
+6. Open a python file in your IDE and hopefully you have some type info and some doc strings.
+
+## Caveats
+
+* Due to [this issue](https://github.com/Jij-Inc/pyo3-stub-gen/issues/93) and [this issue](https://github.com/PyO3/pyo3/issues/780), the codem as of mwalib 1.7.0 does NOT produce a full mwalib.pyi file, due to the fact that the stub generation requires the `python` feature and to get all the struct members to appear in the stub you need to decorate each member with `#[pyo3(get,set)]` but this decorator does not work with the `#[cfg_attr(feature = "python", pyo3(get,set))]` syntax needed to allow mwalib to be compiled without the `python` feature! So to get past this, I have removed the `#[cfg_attr(feature = "python", pyo3(get,set))]` syntax from all struct members and changed `#[cfg_attr(feature = "python", pyo3::pyclass]` on each struct to `#[cfg_attr(feature = "python", pyo3::pyclass(get_all, set_all))]` which will still create the python bindings but none of the struct members will be emitted when generating the stub file!
+
+* Docstrings for `#[new]` methods on structs/classes do not get generated.
+
+* `__enter__` method for a class gets the wrong generated stub so I have to override it (see below).
+
+* Some other manual fixes can be seen in `bin/stubgen.rs`. Hacky but we live in an imperfect world!