Fix project metadata and document usage

The name, description and inception year were inherited from
scripting-python. License headers are regenerated accordingly.

The README now explains how to write scripts, how environments are
managed, and how inputs and outputs are passed to and from Python.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Author: ctrueden

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2021 - 2025, SciJava developers.
+Copyright (c) 2026, SciJava developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

README.md

@@ -2,20 +2,69 @@
 
 # Python Scripting with Appose
 
-This library provides a
-[JSR-223-compliant](https://en.wikipedia.org/wiki/Scripting_for_the_Java_Platform)
-scripting plugin for the [Python](https://python.org/) language, built on
-the [appose](https://github.com/apposed/appose-python) Python package.
-
-It is implemented as a `ScriptLanguage` plugin for the [SciJava
-Common](https://github.com/scijava/scijava-common) platform, which means that
-in addition to being usable directly as a `javax.script.ScriptEngineFactory`,
-it also provides some functionality on top.
-
-For a complete list of scripting languages available as part of the SciJava
-platform, see the
-[Scripting](https://github.com/scijava/scijava-common/wiki/Scripting) page on
-the SciJava Common wiki.
-
-See also:
-* [Python Scripting](https://imagej.net/scripting/python) on the ImageJ wiki.
+This library provides a `ScriptLanguage` plugin for the
+[SciJava Common](https://github.com/scijava/scijava-common) platform that runs
+scripts in [CPython](https://python.org/) (not Jython!), each in its own
+Python environment, using [Appose](https://github.com/apposed/appose).
+
+Scripts are ordinary SciJava scripts: they declare
+[script parameters](https://imagej.net/scripting/parameters) and can be run
+from the Script Editor or menus of ImageJ2/Fiji like any other script.
+
+## Writing a script
+
+```python
+#!appose-python
+#@script(env="myenv.toml")
+
+#@ Img image
+#@ double sigma
+#@output Img blurred
+
+from scipy.ndimage import gaussian_filter
+
+print(f"Blurring image of shape {image.shape}")
+blurred = gaussian_filter(image, sigma)
+```
+
+* The `#!appose-python` line selects this script language, rather than
+  another language handling `.py` files, such as Jython.
+* The `env` attribute points to an environment configuration file, resolved
+  relative to the script's location. Any format Appose supports works:
+  `pixi.toml`, `environment.yml`, `requirements.txt` or `pyproject.toml`.
+  An optional `scheme` attribute (e.g. `scheme="pixi.toml"`) sets the format
+  explicitly, which is useful when the file name does not reveal it.
+* The environment must include the `appose` Python package, plus `numpy` if
+  the script uses images.
+
+See the `StarDist_cellcast.py` template for a complete example.
+
+## Environments
+
+The environment is built the first time a script needs it, which may take a
+while. Afterward, it is reused, both within the running application and across
+restarts. Environments are stored in the Appose environments directory
+(`~/.local/share/appose` by default), named after the configuration file.
+Scripts that share a configuration file share an environment. Editing the file
+causes the environment to be updated on the next run.
+
+Each script run starts a fresh Python process.
+
+## Inputs and outputs
+
+* Images (anything convertible to an Appose `NDArray`, such as an ImgLib2
+  `Img`) are passed via shared memory and appear in Python as
+  NumPy arrays. Axes are in NumPy's usual order, which is the reverse of
+  ImgLib2's: an image with X×Y dimensions `512×384` has NumPy shape
+  `(384, 512)`.
+* Numbers, strings, booleans, lists and maps are passed as the corresponding
+  Python values; files are passed as path strings.
+* Outputs are read from the Python variables of the same names after the
+  script finishes. NumPy arrays are converted back to images; NumPy scalars
+  become plain numbers. Outputs the script never assigns are left empty.
+* If the script declares no outputs and ends with an expression, its value
+  becomes the script's result.
+
+Text printed to stdout and stderr appears in the Script Editor's output
+panes. Errors are reported with a Python traceback that refers to the
+script's own line numbers.

pom.xml

@@ -12,10 +12,10 @@
 	<artifactId>scripting-appose-python</artifactId>
 	<version>0.1.0-SNAPSHOT</version>
 
-	<name>SciJava Scripting: Python</name>
-	<description>Python scripting language plugin to be used via scyjava.</description>
+	<name>SciJava Scripting: Appose Python</name>
+	<description>Python scripting language plugin backed by Appose.</description>
 	<url>https://github.com/scijava/scripting-appose-python</url>
-	<inceptionYear>2021</inceptionYear>
+	<inceptionYear>2026</inceptionYear>
 	<organization>
 		<name>SciJava</name>
 		<url>https://scijava.org/</url>

src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptEngine.java

@@ -1,18 +1,18 @@
 /*
  * #%L
- * Python scripting language plugin to be used via scyjava.
+ * Python scripting language plugin backed by Appose.
  * %%
- * Copyright (C) 2021 - 2025 SciJava developers.
+ * Copyright (C) 2026 SciJava developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptLanguage.java

@@ -1,8 +1,8 @@
 /*
  * #%L
- * Python scripting language plugin to be used via scyjava.
+ * Python scripting language plugin backed by Appose.
  * %%
- * Copyright (C) 2021 - 2025 SciJava developers.
+ * Copyright (C) 2026 SciJava developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

src/main/java/org/scijava/plugins/scripting/appose/python/ApposePythonScriptSyntaxHighlighter.java

@@ -1,8 +1,8 @@
 /*
  * #%L
- * Python scripting language plugin to be used via scyjava.
+ * Python scripting language plugin backed by Appose.
  * %%
- * Copyright (C) 2021 - 2025 SciJava developers.
+ * Copyright (C) 2026 SciJava developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

src/main/java/org/scijava/plugins/scripting/appose/python/NDArrayToImgConverter.java

@@ -1,18 +1,18 @@
 /*
  * #%L
- * Python scripting language plugin to be used via scyjava.
+ * Python scripting language plugin backed by Appose.
  * %%
- * Copyright (C) 2021 - 2025 SciJava developers.
+ * Copyright (C) 2026 SciJava developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

src/main/java/org/scijava/plugins/scripting/appose/python/RAIToNDArrayConverter.java

@@ -1,18 +1,18 @@
 /*
  * #%L
- * Python scripting language plugin to be used via scyjava.
+ * Python scripting language plugin backed by Appose.
  * %%
- * Copyright (C) 2021 - 2025 SciJava developers.
+ * Copyright (C) 2026 SciJava developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

src/main/resources/org/scijava/plugins/scripting/appose/python/wrapper.py

@@ -1,3 +1,31 @@
+###
+# #%L
+# Python scripting language plugin backed by Appose.
+# %%
+# Copyright (C) 2026 SciJava developers.
+# %%
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# 
+# 1. Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+# #L%
+###
 # Appose task script that runs a SciJava appose-python script.
 #
 # The Java side passes the following task inputs, alongside the script's own

src/test/java/org/scijava/plugins/scripting/appose/python/ApposePythonIntegrationTest.java

@@ -1,18 +1,18 @@
 /*
  * #%L
- * Python scripting language plugin to be used via scyjava.
+ * Python scripting language plugin backed by Appose.
  * %%
- * Copyright (C) 2021 - 2025 SciJava developers.
+ * Copyright (C) 2026 SciJava developers.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE