- 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

src/bioformats.rs

@@ -10,11 +10,51 @@ thread_local! {
 /// Ensure 1 jvm per thread
 fn jvm() -> Rc<Jvm> {
     JVM.with(|cell| {
-        cell.get_or_init(move || Rc::new(JvmBuilder::new().build().expect("Failed to build JVM")))
-            .clone()
+        cell.get_or_init(move || {
+            #[cfg(feature = "python")]
+            let path = crate::py::ndbioimage_file().unwrap();
+
+            #[cfg(not(feature = "python"))]
+            let path = std::env::current_exe()
+                .unwrap()
+                .parent()
+                .unwrap()
+                .to_path_buf();
+
+            let class_path = path.parent().unwrap();
+            Rc::new(
+                JvmBuilder::new()
+                    .with_base_path(class_path.to_str().unwrap())
+                    .build()
+                    .expect("Failed to build JVM"),
+            )
+        })
+        .clone()
     })
 }
 
+#[cfg(feature = "python")]
+pub(crate) fn download_bioformats(gpl_formats: bool) -> Result<()> {
+    let path = crate::py::ndbioimage_file().unwrap();
+    let class_path = path.parent().unwrap();
+    let jvm = JvmBuilder::new()
+        .with_base_path(class_path.to_str().unwrap())
+        .with_maven_settings(j4rs::MavenSettings::new(vec![
+            j4rs::MavenArtifactRepo::from(
+                "openmicroscopy::https://artifacts.openmicroscopy.org/artifactory/ome.releases",
+            ),
+        ]))
+        .build()?;
+
+    jvm.deploy_artifact(&j4rs::MavenArtifact::from("ome:bioformats_package:8.1.0"))?;
+
+    if gpl_formats {
+        jvm.deploy_artifact(&j4rs::MavenArtifact::from("ome:formats-gpl:8.1.0"))?;
+    }
+
+    Ok(())
+}
+
 macro_rules! method_return {
     ($R:ty$(|c)?) => { Result<$R> };
     () => { Result<()> };
@@ -113,7 +153,7 @@ impl ImageReader {
         Ok(jvm()
             .chain(&mds)?
             .cast("loci.formats.ome.OMEPyramidStore")?
-            .invoke("dumpXML", &[])?
+            .invoke("dumpXML", InvocationArg::empty())?
             .to_rust()?)
     }