- implement shape in Rust

- implement more readers
- fix downloading of bioformats jar
- (mostly) compatible with python version

Cargo.toml

@@ -1,20 +1,19 @@
 [package]
 name = "ndbioimage"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2024"
-rust-version = "1.87.0"
-authors = ["Wim Pomp <w.pomp@nki.nl>"]
-license = "MIT"
+rust-version = "1.94.0"
+authors = ["Wim Pomp <w.pomp@nki.nl>", "opencode"]
+license = "MIT OR Apache-2.0"
 description = "Read bio image formats using the bio-formats java package."
-homepage = "https://git.wimpomp.nl/wim/ndbioimage/src/branch/rs"
-repository = "https://git.wimpomp.nl/wim/ndbioimage/src/branch/rs"
+homepage = "https://git.pomppervova.nl/wim/ndbioimage/src/branch/rs"
+repository = "https://git.pomppervova.nl/wim/ndbioimage/src/branch/rs"
 documentation = "https://docs.rs/ndbioimage"
 readme = "README.md"
 keywords = ["bioformats", "imread", "ndarray", "metadata"]
 categories = ["multimedia::images", "science"]
 exclude = ["/tests"]
 
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
 name = "ndbioimage"
 crate-type = ["cdylib", "rlib"]
@@ -22,50 +21,65 @@ crate-type = ["cdylib", "rlib"]
 [dependencies]
 clap = { version = "4", features = ["derive"] }
 color-eyre = { version = "0.6", optional = true }
+console = { version = "0.16", optional = true }
+downloader = { version = "0.2", optional = true }
 ffmpeg-sidecar = { version = "2", optional = true }
-itertools = "0.14"
+itertools = "0.15"
 indexmap = { version = "2", features = ["serde"] }
 indicatif = { version = "0.18", features = ["rayon"], optional = true }
-j4rs = "0.24"
+j4rs = { version = "0.25", optional = true }
+libczirw-sys = { path = "../libczirw-sys", optional = true }
 ndarray = { version = "0.17", features = ["serde"] }
 num = "0.4"
-numpy = { version = "0.28", optional = true }
-ordered-float = "5"
+numpy = { version = "0.29", optional = true }
+ome-metadata = { path = "../ome-metadata/ome-metadata" }
+ordered-float = { version = "5", optional = true }
+phf = { version = "0.14", features = ["macros"] }
+postcard = { version = "1", features = ["use-std"], optional = true }
+pyo3 = { version = "0.29", features = ["abi3-py310", "eyre", "anyhow", "generate-import-lib"], optional = true }
+pyo3-stub-gen = { version = "0.23", optional = true }
 rayon = { version = "1", optional = true }
-serde = { version = "1", features = ["rc"] }
-serde_json = { version = "1", optional = true }
+regex = "1"
+serde = { version = "1", features = ["rc", "derive"] }
+serde_yaml = { version = "0.9", optional = true }
 serde_with = "3"
-tiffwrite = { version = ">=2026.1.1, <2026.2.0", optional = true}
-thread_local = "1"
-ome-metadata = "0.4"
-lazy_static = "1"
+strum = { version = "0.28", features = ["derive"] }
 thiserror = "2"
-
-[dependencies.pyo3]
-version = "0.28"
-features = ["extension-module", "abi3-py310", "eyre", "generate-import-lib"]
-optional = true
+tiff = { version = "0.11", features = ["zstd"], optional = true }
+tiffwrite = { version = "2026.6.0", optional = true }
+tokio = { version = "1", features = ["rt", "rt-multi-thread"], optional = true }
+thread_local = { version = "1", optional = true }
+xmltree = { version = "0.12", optional = true }
+bioformats = { version = "0.1", optional = true }
 
 [dev-dependencies]
-downloader = "0.2"
 rayon = "1"
 regex = "1"
-reqwest = { version = "0.13", features = ["blocking"] }
 
 [build-dependencies]
-j4rs = "0.24"
+j4rs = "0.25"
 ffmpeg-sidecar = "2"
 retry = "2"
+toml = "1"
 
 [features]
-# Enables formats for which code in bioformats with a GPL license is needed
+default = []
+all = ["bioformats_java", "bioformats_rust", "czi", "gpl-formats", "movie", "tiffseq", "tiffwrite", "tiff"]
 gpl-formats = []
-# Enables python ffi using pyO3
-python = ["dep:pyo3", "dep:numpy", "dep:serde_json", "dep:color-eyre"]
-# Enables writing as tiff
-tiff = ["dep:tiffwrite", "dep:indicatif", "dep:rayon"]
-# Enables writing as mp4 using ffmpeg
-movie = ["dep:ffmpeg-sidecar"]
+python = ["dep:pyo3", "dep:numpy", "dep:color-eyre", "dep:pyo3-stub-gen", "dep:postcard", "ome-metadata/python"]
+czi = ["dep:libczirw-sys", "dep:xmltree", "dep:thread_local"]
+bioformats_rust = ["dep:bioformats", "dep:thread_local"]
+bioformats_java = ["dep:j4rs", "dep:thread_local", "dep:downloader"]
+tiffwrite = ["dep:tiffwrite", "dep:indicatif", "dep:console", "dep:rayon"]
+tiffseq = ["dep:tiff", "dep:serde_yaml"]
+tiff = ["dep:tiff", "dep:thread_local"]
+movie = ["dep:ffmpeg-sidecar", "dep:tokio", "dep:ordered-float", "dep:indicatif", "dep:console"]
 
 [package.metadata.docs.rs]
-features = ["gpl-formats", "tiff", "movie"]
+features = ["bioformats", "gpl-formats", "czi", "tiff", "movie"]
+
+[profile.test]
+inherits = "release"
+
+[profile.dev.package.backtrace]
+opt-level = 3