[package]
name = "ndbioimage"
version.workspace = true
edition.workspace = true
rust-version.workspace = true
authors.workspace = true
license.workspace = true
description.workspace = true
repository.workspace = true
documentation.workspace = true
keywords.workspace = true
categories.workspace = true
readme = "../README.md"
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", version = "0.1", optional = true }
indexmap = { version = "2", features = ["serde"] }
indicatif = { version = "0.18", features = ["rayon"], optional = true }
j4rs = { version = "0.25", optional = true }
libczirw-sys = { version = "0.5.2", optional = true }
ndarray = { version = "0.17", features = ["serde"] }
num = "0.4"
numpy = { version = "0.29", optional = true }
ome-metadata = "0.6"
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", "multiple-pymethods"], 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 = { package = "ndbioimage-tiff", path = "../image-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 }
# "bioformats 0.1.8" is written for "zip 2.4.x", where zip::read::ZipFile has a single lifetime parameter.
# "zip >= 2.5" added a second "R: Read" generic (2.6.1 breaks bioformats), so the build fails.
zip = { version = "=2.4.2", optional = true, default-features = false }

[dev-dependencies]
rayon = "1"
regex = "1"
postcard = { version = "1", features = ["use-std"] }

[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", "dep:zip"]
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"]