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- bump bioformats to 8.3.0

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- rust: command line binary, save as mp4, save as tiff, ome metadata, more methods for View, bugfixes, less unsafe code
- python: ome as dict
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Wim Pomp
2025-08-21 19:45:02 +02:00
parent 24af64ac7e
commit 3dc8e6af04
17 changed files with 2317 additions and 1261 deletions
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39
Cargo.toml
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@@ -1,8 +1,8 @@
[package]
name = "ndbioimage"
version = "2025.4.1"
edition = "2021"
rust-version = "1.78.0"
version = "2025.8.0"
edition = "2024"
rust-version = "1.85.1"
authors = ["Wim Pomp <w.pomp@nki.nl>"]
license = "MIT"
description = "Read bio image formats using the bio-formats java package."
@@ -19,20 +19,28 @@ name = "ndbioimage"
crate-type = ["cdylib", "rlib"]
[dependencies]
anyhow = "1.0.98"
anyhow = { version = "1.0.99", features = ["backtrace"] }
clap = { version = "4.5.45", features = ["derive"] }
ffmpeg-sidecar = { version = "2.1.0", optional = true }
itertools = "0.14.0"
indexmap = { version = "2.9.0", features = ["serde"] }
indexmap = { version = "2.0.0", features = ["serde"] }
indicatif = { version = "0.18.0", features = ["rayon"], optional = true }
j4rs = "0.22.0"
ndarray = { version = "0.16.1", features = ["serde"] }
ndarray = { version = "0.16.1", features = ["serde"] }
num = "0.4.3"
numpy = { version = "0.24.0", optional = true }
numpy = { version = "0.25.0", optional = true }
ordered-float = "5.0.0"
rayon = { version = "1.11.0", optional = true }
serde = { version = "1.0.219", features = ["rc"] }
serde_json = { version = "1.0.140", optional = true }
serde_json = { version = "1.0.143", optional = true }
serde_with = "3.12.0"
thread_local = "1.1.8"
tiffwrite = { version = "2025.5.0", optional = true}
thread_local = "1.1.9"
ome-metadata = "0.2.2"
lazy_static = "1.5.0"
[dependencies.pyo3]
version = "0.24.2"
version = "0.25.1"
features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
optional = true
@@ -40,10 +48,17 @@ optional = true
rayon = "1.10.0"
[build-dependencies]
anyhow = "1.0.98"
anyhow = "1.0.99"
j4rs = "0.22.0"
ffmpeg-sidecar = "2.1.0"
retry = "2.1.0"
[features]
# Enables formats for which code in bioformats with a GPL license is needed
gpl-formats = []
# Enables python ffi using pyO3
python = ["dep:pyo3", "dep:numpy", "dep:serde_json"]
gpl-formats = []
# Enables writing as tiff
tiff = ["dep:tiffwrite", "dep:indicatif", "dep:rayon"]
# Enables writing as mp4 using ffmpeg
movie = ["dep:ffmpeg-sidecar"]