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Add a REPL widget that supports the SciJava ScriptREPL #265

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Add a REPL widget that supports the SciJava ScriptREPL #265

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71224d7
Add a REPL widget that supports the SciJava ScriptREPL
kephale Jun 8, 2023
06a9160
Add title to REPL dock widget
kephale Jun 8, 2023
e196f8f
Fix SVG to work with dark mode
kephale Jun 8, 2023
bd0c731
Disable REPL button until IJ2 is initialized
kephale Jun 15, 2023
112e930
Add tooltips for REPL and Settings buttons
kephale Jul 6, 2023
a79a8bb
Add section in docs about REPL
kephale Jul 6, 2023
376d324
Import ScriptException using jc mechanism
ctrueden Jul 21, 2023
47dcaa5
Improve docstrings and type hints
ctrueden Jul 22, 2023
7dc2cbb
Migrate core ScriptREPL logic out of menu.py
ctrueden Jul 25, 2023
e573756
Clean up java submodule comments and whitespace
ctrueden Aug 3, 2023
8cec6e0
Use scyjava JavaClasses for java class imports
ctrueden Aug 3, 2023
0aebd2b
WIP: Centralize ImageJ2 gateway into nij object
ctrueden Aug 3, 2023
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3 changes: 0 additions & 3 deletions .github/workflows/build.yml
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Expand Up @@ -9,9 +9,6 @@ on:
- main
tags:
- "*-[0-9]+.*"
pull_request:
branches:
- main

env:
NAPARI_IMAGEJ_TEST_TIMEOUT: 60000
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9 changes: 9 additions & 0 deletions doc/Configuration.rst
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Expand Up @@ -95,6 +95,15 @@ One common use case for this feature is to increase the maximum heap space avail

Specifying 32GB of memory available to ImageJ ecosystem routines in the JVM.

Using the SciJava REPL
--------------------------------
Comment on lines +98 to +99
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I'm wondering if this would be better suited to the new Usage page of the ReadTheDocs...

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Or the Troubleshooting page...


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/>`_.
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So I played a little with the Script REPL, and I couldn't get anything beyond 2+4 to work. I was trying to print Hello World, but I couldn't even figure out how to do that.

So, as a result, I looked here, and I checked out imagej.net/scripting. As someone who is not intimately familiar with that page, I wasn't super sure where to go. I did find the ScriptInterpreter page from that page, which appears to me to be what this is, but I tried typing :help and I didn't get anything.

Then, I typed help, and my napari froze. I went back to my terminal, and I saw this:

(napari-imagej-dev) ➜  napari-imagej git:(scijava-repl) napari
hello
[java.lang.Enum.toString] hello[java.lang.Enum.toString] 
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString] 
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString] 
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString] 
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString] 

Welcome to Python 2.7!  This is the online help utility.

If this is your first time using Python, you should definitely check out
the tutorial on the Internet at http://docs.python.org/2.7/tutorial/.

Enter the name of any module, keyword, or topic to get help on writing
Python programs and using Python modules.  To quit this help utility and
return to the interpreter, just type "quit".

To get a list of available modules, keywords, or topics, type "modules",
"keywords", or "topics".  Each module also comes with a one-line summary
of what it does; to list the modules whose summaries contain a given word
such as "spam", type "modules spam".

help> [java.lang.Enum.toString] 
Welcome to Python 2.7!  This is the online help utility.

If this is your first time using Python, you should definitely check out
the tutorial on the Internet at http://docs.python.org/2.7/tutorial/.

Enter the name of any module, keyword, or topic to get help on writing
Python programs and using Python modules.  To quit this help utility and
return to the interpreter, just type "quit".

To get a list of available modules, keywords, or topics, type "modules",
"keywords", or "topics".  Each module also comes with a one-line summary
of what it does; to list the modules whose summaries contain a given word
such as "spam", type "modules spam".

help>

So, long story short, it looks like the output is not being captured by the TextEdit, and also I'm wondering if we can link to documentation that is more specific to the SciJava REPL.

To solve the output not being captured by the TextEdit, is there an option in SciJava for this @ctrueden?


.. figure:: https://media.imagej.net/napari-imagej/scijava_repl.png

The REPL can be shown/hidden by clicking on the command prompt icon.


.. _Fiji: https://imagej.net/software/fiji/
.. _ImageJ2: https://imagej.net/software/imagej2/
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4 changes: 4 additions & 0 deletions src/napari_imagej/__init__.py
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Expand Up @@ -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()
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