- use a fork of the tiff crate to open RGBPalette tiffs

Cargo.toml

@@ -1,7 +1,11 @@
-[package]
-name = "ndbioimage"
+[workspace]
+resolver = "3"
+members = ["ndbioimage", "image-tiff", "image-registration"]
+
+[workspace.package]
 version = "0.2.0"
 edition = "2024"
+# the workspace must satisfy every member, so this is the highest `rust-version` of the members
 rust-version = "1.94.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "MIT OR Apache-2.0"
@@ -9,77 +13,13 @@ description = "Read bio image formats using the bio-formats java package."
 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"
+# inherited paths are resolved relative to the workspace root, not the member, so this has to point
+# at the member's readme
+readme = "ndbioimage/README.md"
 keywords = ["bioformats", "imread", "ndarray", "metadata"]
 categories = ["multimedia::images", "science"]
-exclude = ["/tests"]
-
-[lib]
-name = "ndbioimage"
-crate-type = ["cdylib", "rlib"]
-
-[dependencies]
-bioformats = { version = "0.1", optional = true, default-features = false, features = ["zarr", "tissuefaxs"] }
-clap = { version = "4", features = ["derive"] }
-console = { version = "0.16", optional = true }
-downloader = { version = "0.2", optional = true, default-features = false, features = ["rustls-tls"] }
-ffmpeg-sidecar = { version = "2", optional = true }
-itertools = "0.15"
-image-registration = { path = "../image-registration", optional = true }
-indexmap = { version = "2", features = ["serde"] }
-indicatif = { version = "0.18", features = ["rayon"], optional = true }
-j4rs = { version = "0.25", optional = true }
-libczirw-sys = { version = "0.5", optional = true }
-ndarray = { version = "0.17", features = ["serde"] }
-num = "0.4"
-numpy = { version = "0.29", optional = true }
-ome-metadata = "0.5"
-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", "anyhow", "generate-import-lib"], optional = true }
-pyo3-stub-gen = { version = "0.23", optional = true }
-rayon = { version = "1", optional = true }
-regex = "1"
-serde = { version = "1", features = ["rc", "derive"] }
-serde_with = "3"
-strum = { version = "0.28", features = ["derive"] }
-thiserror = "2"
-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 }
-yaml_serde = { version = "0.10", optional = true }
-
-[dev-dependencies]
-rayon = "1"
-regex = "1"
-
-[build-dependencies]
-j4rs = "0.25"
-ffmpeg-sidecar = "2"
-retry = "2"
-toml = "1"
-
-[features]
-default = ["bioformats_java", "gpl-formats", "czi", "tiff", "tiffseq", "movie", "tiffwrite"]
-all = ["bioformats_java", "bioformats_rust", "czi", "gpl-formats", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
-gpl-formats = []
-python = ["dep:pyo3", "dep:numpy", "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:yaml_serde"]
-tiff = ["dep:tiff", "dep:thread_local"]
-movie = ["dep:ffmpeg-sidecar", "dep:tokio", "dep:ordered-float", "dep:indicatif", "dep:console"]
-transforms = ["dep:image-registration", "dep:yaml_serde"]
-
-[package.metadata.docs.rs]
-no-default-features = true
-features = ["bioformats_java", "bioformats_rust", "czi", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
 
+# profiles are only honoured in the workspace root manifest
 [profile.test]
 inherits = "release"
 
@@ -87,4 +27,4 @@ inherits = "release"
 debug = true
 
 [profile.dev.package.backtrace]
-opt-level = 3
+opt-level = 3