- some workarounds to get jars and shared libs in the right place for python

- add most ndbioimage python code and use rs code as bfread

build.rs

@@ -1,21 +1,58 @@
-// copied from https://github.com/AzHicham/bioformats-rs
-
+#[cfg(not(feature = "python"))]
 use j4rs::{errors::J4RsError, JvmBuilder, MavenArtifact, MavenArtifactRepo, MavenSettings};
+
+#[cfg(not(feature = "python"))]
 use retry::{delay, delay::Exponential, retry};
 
+#[cfg(feature = "python")]
+use j4rs::Jvm;
+
 fn main() -> anyhow::Result<()> {
     println!("cargo:rerun-if-changed=build.rs");
 
-    if std::env::var("DOCS_RS").is_ok() {
-        Ok(())
-    } else {
-        Ok(retry(
+    #[cfg(not(feature = "python"))]
+    if std::env::var("DOCS_RS").is_err() {
+        retry(
             Exponential::from_millis(1000).map(delay::jitter).take(4),
             deploy_java_artifacts,
-        )?)
+        )?
     }
+
+    #[cfg(feature = "python")]
+    {
+        let py_src_path = std::env::current_dir()?.join("py").join("ndbioimage");
+        let py_jassets_path = py_src_path.join("jassets");
+        let py_deps_path = py_src_path.join("deps");
+        if py_jassets_path.exists() {
+            std::fs::remove_dir_all(&py_jassets_path)?;
+        }
+        if py_deps_path.exists() {
+            std::fs::remove_dir_all(&py_deps_path)?;
+        }
+
+        Jvm::copy_j4rs_libs_under(py_src_path.to_str().unwrap())?;
+
+        // rename else maturin will ignore them
+        for file in std::fs::read_dir(&py_deps_path)? {
+            let f = file?.path().to_str().unwrap().to_string();
+            if !f.ends_with("_") {
+                std::fs::rename(&f, std::format!("{f}_"))?;
+            }
+        }
+
+        // remove so we don't include too much accidentally
+        for file in std::fs::read_dir(&py_jassets_path)? {
+            let f = file?.path();
+            if !f.file_name().unwrap().to_str().unwrap().starts_with("j4rs") {
+                std::fs::remove_file(&f)?;
+            }
+        }
+    }
+
+    Ok(())
 }
 
+#[cfg(not(feature = "python"))]
 fn deploy_java_artifacts() -> Result<(), J4RsError> {
     let jvm = JvmBuilder::new()
         .with_maven_settings(MavenSettings::new(vec![MavenArtifactRepo::from(
@@ -23,10 +60,10 @@ fn deploy_java_artifacts() -> Result<(), J4RsError> {
         )]))
         .build()?;
 
-    jvm.deploy_artifact(&MavenArtifact::from("ome:bioformats_package:8.0.1"))?;
+    jvm.deploy_artifact(&MavenArtifact::from("ome:bioformats_package:8.1.0"))?;
 
     #[cfg(feature = "gpl-formats")]
-    jvm.deploy_artifact(&MavenArtifact::from("ome:formats-gpl:8.0.1"))?;
+    jvm.deploy_artifact(&MavenArtifact::from("ome:formats-gpl:8.1.0"))?;
 
     Ok(())
 }