Merge pull request #265 from kephale/scijava-repl

Add a REPL widget that supports the SciJava ScriptREPL
imagej · Oct 1, 2024 · 3a0fe0b · 3a0fe0b
2 parents 7052365 + 4dbbc62
commit 3a0fe0b
Show file tree

Hide file tree

Showing 27 changed files with 567 additions and 333 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -122,7 +122,7 @@ jobs:
           # Create env with dev packages
           auto-update-conda: true
           python-version: "3.10"
-          miniforge-variant: Mambaforge
+          miniforge-version: latest
           environment-file: dev-environment.yml
           # Activate napari-imagej-dev environment
           activate-environment: napari-imagej-dev

diff --git a/bin/test.sh b/bin/test.sh
@@ -6,7 +6,7 @@ cd "$dir/.."
 modes="
 | Testing ImageJ2 + original ImageJ |NAPARI_IMAGEJ_INCLUDE_IMAGEJ_LEGACY=TRUE
 |    Testing ImageJ2 standalone     |NAPARI_IMAGEJ_INCLUDE_IMAGEJ_LEGACY=FALSE
-|  Testing Fiji Is Just ImageJ(2)   |NAPARI_IMAGEJ_IMAGEJ_DIRECTORY_OR_ENDPOINT=sc.fiji:fiji:2.13.1
+|  Testing Fiji Is Just ImageJ(2)   |NAPARI_IMAGEJ_IMAGEJ_DIRECTORY_OR_ENDPOINT=sc.fiji:fiji:2.15.0
 "
 
 echo "$modes" | while read mode

diff --git a/doc/Usage.rst b/doc/Usage.rst
@@ -57,3 +57,13 @@ Note that these buttons are only enabled when there is a ``Layer`` that can be t
     Using the |advanced export| button, users can provide metadata for richer data transfer to the ImageJ UI
 
 The |import| button can be used to transfer the **active** ImageJ window back into the napari application.
+
+Using the SciJava REPL
+--------------------------------
+
+You can use the SciJava REPL to interactively run SciJava code. This makes it possible to do things like paste existing SciJava scripts into the REPL. More information on scripting in SciJava can be found `here <https://imagej.net/scripting/interpreter>`_.
+
+.. figure:: https://media.imagej.net/napari-imagej/0.2.0/script_repl.png
+
+    The REPL can be shown/hidden by clicking on the command prompt icon.
+
diff --git a/src/napari_imagej/__init__.py b/src/napari_imagej/__init__.py
@@ -20,5 +20,9 @@
 
 import scyjava as sj
 
+from napari_imagej.model import NapariImageJ
+
 __author__ = "ImageJ2 developers"
 __version__ = sj.get_version("napari-imagej")
+
+nij = NapariImageJ()