Merge pull request #18 from fmi-faim/scyjava

Replace deprecated bioformats_jar dependency

bioio_bioformats/tests/test_reader.py

@@ -196,7 +196,7 @@
             (1, 3, 1, 1024, 1024),
             np.uint16,
             dimensions.DEFAULT_DIMENSION_ORDER,
-            ["Channel:0:0", "Channel:0:1", "Channel:0:2"],
+            ["Red", "Green", "Blue"],
             (0.001, 1.2059374999999999, 1.2059570312500014),
         ),
         (

bioio_bioformats/utils.py

@@ -10,9 +10,8 @@
 
 import jpype
 import numpy as np
-from bioformats_jar import get_loci
+import scyjava
 from bioio_base import dimensions, types
-from jgo.jgo import ExecutableNotFound
 from ome_types import OME
 
 ###############################################################################
@@ -662,8 +661,9 @@ def _hide_memoization_warning() -> None:
 
 def _try_get_loci() -> jpype.JPackage:
     try:
-        return get_loci()
-    except ExecutableNotFound as e:
-        raise RuntimeError(MAVEN_ERROR_MSG) from e
+        scyjava.config.endpoints.append("ome:formats-gpl:6.7.0")
+        scyjava.start_jvm()
+        loci = jpype.JPackage("loci")
+        return loci
     except jpype.JVMNotFoundException as e:
         raise RuntimeError(JAVA_ERROR_MSG) from e

pyproject.toml

@@ -28,12 +28,12 @@ classifiers = [
 dynamic = ["version"]
 dependencies = [
   "bioio-base>=0.3.0",
-  "bioformats_jar", 
   "dask[array]>=2021.4.1",
   "fsspec>=2022.8.0",
   "numpy>=1.21",
   "ome-types>=0.3.4",
   "resource-backed-dask-array>=0.1.0",
+  "scyjava",
 ]
 
 [project.urls]
@@ -110,7 +110,7 @@ show_error_codes = true
 # https://gitlab.com/durko/flake8-pyprojecttoml
 [tool.flake8]
 max-line-length = 88
-ignore = "E203,E402,W291,W503"
+ignore = "E203,E231,E402,W291,W503"
 min-python-version = "3.9.0"
 per-file-ignores = [
   "__init__.py:F401",