- workflow updates

- python stubs

.github/workflows/cargo_test.yml

@@ -0,0 +1,52 @@
+name: PyTest
+
+on: [push, pull_request, workflow_call]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.12", "3.14"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Restore cache
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ~/.cargo
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Install Rust
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v rustc >/dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          else
+            rustup update
+          fi
+        shell: bash
+
+      - name: "cargo test"
+        run: |-
+          export PATH="$HOME/.cargo/bin:$PATH"
+          cargo test
+
+      - name: Store cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ~/.cargo
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile

.github/workflows/publish_crates.yml

@@ -8,8 +8,10 @@ permissions:
 jobs:
   publish_pytest:
     uses: ./.github/workflows/pytest.yml
+  publish_cargo_test:
+    uses: ./.github/workflows/cargo_test.yml
   crates_io_publish:
-    needs: [ publish_pytest ]
+    needs: [ publish_pytest, publish_cargo_test ]
     name: Publish (crates.io)
     runs-on: ubuntu-latest
     timeout-minutes: 25
@@ -50,7 +52,7 @@ jobs:
       # have passed.
       - name: "cargo release publish"
         run: |-
-          export PATH="$HOME/.osxcross/bin:$PATH"
+          export PATH="$HOME/.cargo/bin:$PATH"
           cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
           cargo release \
             publish \

.github/workflows/publish_pypi.yml

@@ -8,8 +8,10 @@ permissions:
 jobs:
   publish_pytest:
     uses: ./.github/workflows/pytest.yml
+  publish_cargo_test:
+    uses: ./.github/workflows/cargo_test.yml
   pypi_publish:
-    needs: [ publish_pytest ]
+    needs: [ publish_pytest, publish_cargo_test ]
     name: Publish (pypi.org)
     runs-on: ubuntu-latest
     steps:

.github/workflows/pytest.yml

@@ -42,7 +42,7 @@ jobs:
         run: |
           export PATH="$HOME/.cargo/bin:$PATH"
           python -m pip install --upgrade pip
-          pip install maturin ziglang
+          pip install maturin
           if ! command -v sccache >/dev/null 2>&1; then
             cargo install sccache || pip install sccache
           fi

Cargo.toml

@@ -29,10 +29,11 @@ ndarray = "0.17"
 num = "0.4"
 numpy = { version = "0.28", optional = true }
 pyo3 = { version = "0.28", features = ["abi3-py310", "eyre", "generate-import-lib", "multiple-pymethods"], optional = true }
+pyo3-stub-gen = { version = "0.22", optional = true }
 rayon = "1"
 thiserror = "2"
 tokio = { version = "1", features = ["fs", "rt", "rt-multi-thread", "time"] }
 zstd = "0.13"
 
 [features]
-python = ["dep:pyo3", "dep:numpy", "dep:color-eyre"]
+python = ["dep:pyo3", "dep:numpy", "dep:color-eyre", "dep:pyo3-stub-gen"]

README.md

@@ -1,4 +1,4 @@
-[![pytest](https://github.com/wimpomp/tiffwrite/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/tiffwrite/actions/workflows/pytest.yml)
+[![pytest](https://git.wimpomp.nl/wim/tiffwrite/actions/workflows/pytest.yml/badge.svg)](https://git.wimpomp.nl/wim/tiffwrite/actions/workflows/pytest.yml)
 
 # Tiffwrite
 Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel using Rust.

py/tiffwrite/__init__.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import sys
 from importlib.metadata import version
 from itertools import product
 from pathlib import Path
@@ -10,7 +11,7 @@ import numpy as np
 from numpy.typing import ArrayLike, DTypeLike
 from tqdm.auto import tqdm
 
-from . import tiffwrite_rs as rs  # noqa
+from . import tiffwrite_rs as rs
 
 __all__ = ["IJTiffFile", "IJTiffParallel", "FrameInfo", "Tag", "tiffwrite"]
 
@@ -236,3 +237,16 @@ try:
 
 except ImportError:
     IJTiffParallel = None
+
+
+def tiffwrite_generate_stub():
+    if len(sys.argv) > 1:
+        path = Path(sys.argv[1]).resolve()
+    else:
+        path = Path.cwd().resolve()
+    if (path / "py" / "tiffwrite" / "__init__.py").exists():
+        rs.generate_stub(str(path))  # noqa
+        (path / "py" / "tiffwrite_rs" / "__init__.pyi").rename(path / "py" / "tiffwrite" / "tiffwrite_rs.pyi")
+        (path / "py" / "tiffwrite_rs").rmdir()
+    else:
+        raise ModuleNotFoundError(str(path / "py" / "tiffwrite" / "__init__.py"))

py/tiffwrite/tiffwrite_rs.pyi

@@ -0,0 +1,101 @@
+# This file is automatically generated by pyo3_stub_gen
+# ruff: noqa: E501, F401, F403, F405
+
+import builtins
+import typing
+
+import numpy
+import numpy.typing
+
+__all__ = [
+    "IJTiffFile",
+    "Tag",
+]
+
+class IJTiffFile:
+    @property
+    def colors(self) -> typing.Optional[builtins.list[builtins.list[builtins.int]]]: ...
+    @colors.setter
+    def colors(self, value: typing.Sequence[builtins.str]) -> None: ...
+    @property
+    def colormap(self) -> typing.Optional[builtins.list[builtins.list[builtins.int]]]: ...
+    @colormap.setter
+    def colormap(self, value: builtins.str) -> None: ...
+    @property
+    def px_size(self) -> typing.Optional[builtins.float]: ...
+    @px_size.setter
+    def px_size(self, value: builtins.float) -> None: ...
+    @property
+    def delta_z(self) -> typing.Optional[builtins.float]: ...
+    @delta_z.setter
+    def delta_z(self, value: builtins.float) -> None: ...
+    @property
+    def time_interval(self) -> typing.Optional[builtins.float]: ...
+    @time_interval.setter
+    def time_interval(self, value: builtins.float) -> None: ...
+    @property
+    def comment(self) -> typing.Optional[builtins.str]: ...
+    @comment.setter
+    def comment(self, value: builtins.str) -> None: ...
+    def __new__(cls, path: builtins.str) -> IJTiffFile: ...
+    def set_compression(self, compression: builtins.int, level: builtins.int) -> None:
+        r"""
+        set zstd compression level: -7 ..= 22
+        """
+    def append_extra_tag(
+        self, tag: Tag, czt: typing.Optional[tuple[builtins.int, builtins.int, builtins.int]] = None
+    ) -> None: ...
+    def get_tags(
+        self, czt: typing.Optional[tuple[builtins.int, builtins.int, builtins.int]] = None
+    ) -> builtins.list[Tag]: ...
+    def close(self) -> None: ...
+    def save_f64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u16(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_f32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u8(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i16(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i8(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+
+class Tag:
+    @staticmethod
+    def byte(code: builtins.int, byte: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def ascii(code: builtins.int, ascii: builtins.str) -> Tag: ...
+    @staticmethod
+    def short(code: builtins.int, short: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def long(code: builtins.int, long: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def rational(code: builtins.int, rational: typing.Sequence[builtins.float]) -> Tag: ...
+    @staticmethod
+    def sbyte(code: builtins.int, sbyte: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def sshort(code: builtins.int, sshort: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def slong(code: builtins.int, slong: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def srational(code: builtins.int, srational: typing.Sequence[builtins.float]) -> Tag: ...
+    @staticmethod
+    def float(code: builtins.int, float: typing.Sequence[builtins.float]) -> Tag: ...
+    @staticmethod
+    def double(code: builtins.int, double: typing.Sequence[builtins.float]) -> Tag: ...
+    @staticmethod
+    def ifd(code: builtins.int, ifd: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def unicode(code: builtins.int, unicode: builtins.str) -> Tag: ...
+    @staticmethod
+    def complex(code: builtins.int, complex: typing.Sequence[tuple[builtins.float, builtins.float]]) -> Tag: ...
+    @staticmethod
+    def long8(code: builtins.int, long8: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def slong8(code: builtins.int, slong8: typing.Sequence[builtins.int]) -> Tag: ...
+    @staticmethod
+    def ifd8(code: builtins.int, ifd8: typing.Sequence[builtins.int]) -> Tag: ...
+    def count(self) -> builtins.int:
+        r"""
+        get the number of values in the tag
+        """

pyproject.toml

@@ -33,6 +33,9 @@ test = ["pytest", "tifffile", "imagecodecs"]
 homepage = "https://github.com/wimpomp/tiffwrite"
 repository = "https://github.com/wimpomp/tiffwrite"
 
+[project.scripts]
+tiffwrite_generate_stub = "tiffwrite:tiffwrite_generate_stub"
+
 [tool.maturin]
 python-source = "py"
 features = ["pyo3/extension-module", "python"]

src/py.rs

@@ -3,6 +3,9 @@ use num::{Complex, FromPrimitive, Rational32};
 use numpy::{AllowTypeChange, PyArrayLike2};
 use pyo3::exceptions::PyValueError;
 use pyo3::prelude::*;
+use pyo3_stub_gen::derive::{gen_stub_pyclass, gen_stub_pymethods};
+use pyo3_stub_gen::{StubGenConfig, StubInfo};
+use std::path::PathBuf;
 
 impl From<crate::error::Error> for PyErr {
     fn from(err: crate::error::Error) -> PyErr {
@@ -10,6 +13,7 @@ impl From<crate::error::Error> for PyErr {
     }
 }
 
+#[gen_stub_pyclass]
 #[pyclass(name = "Tag", module = "tiffwrite_rs", subclass, from_py_object)]
 #[derive(Clone, Debug)]
 struct PyTag {
@@ -17,6 +21,7 @@ struct PyTag {
 }
 
 /// Tiff tag, use one of the constructors to get a tag of a specific type
+#[gen_stub_pymethods]
 #[pymethods]
 impl PyTag {
     #[staticmethod]
@@ -162,12 +167,14 @@ impl PyTag {
     }
 }
 
+#[gen_stub_pyclass]
 #[pyclass(name = "IJTiffFile", module = "tiffwrite_rs", subclass)]
 #[derive(Debug)]
 struct PyIJTiffFile {
     ijtifffile: Option<IJTiffFile>,
 }
 
+#[gen_stub_pymethods]
 #[pymethods]
 impl PyIJTiffFile {
     #[new]
@@ -333,10 +340,12 @@ impl PyIJTiffFile {
 macro_rules! impl_save {
     ($($T:ty: $t:ident $(,)?)*) => {
         $(
+            #[gen_stub_pymethods]
             #[pymethods]
             impl PyIJTiffFile {
                 fn $t(
                     &mut self,
+                    #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy", "numpy.typing")))]
                     frame: PyArrayLike2<$T, AllowTypeChange>,
                     c: usize,
                     t: usize,
@@ -365,11 +374,28 @@ impl_save! {
     f64: save_f64,
 }
 
+/// generates tiffwrite/tiffwrite_rs.pyi
+#[pyfunction]
+fn generate_stub(dest_path: String) -> PyResult<()> {
+    StubInfo::from_project_root(
+        "tiffwrite_rs".to_string(),
+        PathBuf::from(dest_path).join("py"),
+        true,
+        StubGenConfig::default(),
+    )
+    .map_err(|e| PyValueError::new_err(format!("{:?}", e)))?
+    .generate()
+    .map_err(|e| PyValueError::new_err(format!("{:?}", e)))
+}
+
 #[pymodule]
 #[pyo3(name = "tiffwrite_rs")]
 mod tiffwrite_rs {
     use pyo3::prelude::*;
 
+    #[pymodule_export]
+    use super::generate_stub;
+
     #[pymodule_export]
     use super::PyTag;