InsightSoftwareConsortium · thewtex · Jul 14, 2024 · Jul 14, 2024 · Jul 15, 2024 · Jul 15, 2024
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true
diff --git a/.gitignore b/.gitignore
@@ -94,3 +94,6 @@ cypress/videos/
 packages/core/typescript/itk-wasm/dist
 
 CMakePresets.json
+# pixi environments
+.pixi
+*.egg-info
diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ ITK-Wasm
 [![npm version](https://badge.fury.io/py/itkwasm.svg)](https://pypi.org/project/itkwasm/)
 [![npm version](https://badge.fury.io/py/itk-webassemblyinterface.svg)](https://pypi.org/project/itk-webassemblyinterface/)
 
-[![DOI](https://zenodo.org/badge/45812381.svg)](https://zenodo.org/badge/latestdoi/45812381)
+[![DOI](https://zenodo.org/badge/45812381.svg)](https://zenodo.org/doi/10.5281/zenodo.3688880)
 
 ![License](https://img.shields.io/github/license/InsightSoftwareConsortium/ITK-Wasm) ![GitHub commit activity](https://img.shields.io/github/commit-activity/y/InsightSoftwareConsortium/ITK-Wasm)
 

diff --git a/docs/_static/packages/compare-images.png b/docs/_static/packages/compare-images.png
diff --git a/docs/_static/packages/compress-stringify.png b/docs/_static/packages/compress-stringify.png
diff --git a/docs/_static/packages/dicom.png b/docs/_static/packages/dicom.png
diff --git a/docs/_static/packages/downsample.png b/docs/_static/packages/downsample.png
diff --git a/docs/_static/packages/elastix.png b/docs/_static/packages/elastix.png
diff --git a/docs/_static/packages/htj2k.png b/docs/_static/packages/htj2k.png
diff --git a/docs/_static/packages/image-io.png b/docs/_static/packages/image-io.png
diff --git a/docs/_static/packages/mesh-io.png b/docs/_static/packages/mesh-io.png
diff --git a/docs/_static/packages/morphological-contour-interpolation.png b/docs/_static/packages/morphological-contour-interpolation.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -42,9 +42,9 @@
 }
 
 html_theme = 'furo'
-html_static_path = ['_static']
-html_logo = "_static/logo-white.svg"
-html_favicon = "_static/icon/favicon.png"
+htmlstatic_path = ['static']
+html_logo = "static/logo-white.svg"
+html_favicon = "static/icon/favicon.png"
 html_title = f"{project} documentation"
 html_baseurl = os.environ.get("SPHINX_BASE_URL", "")
 

diff --git a/docs/cxx/interface_types.md b/docs/cxx/interface_types.md
@@ -45,9 +45,8 @@ int main(argc, char * argv[])
 }
 ```
 
-<dl>
-  <dt><b><code>itk::wasm::InputTextStream</code></b><dt><dd>A string. To reader this data type in C++, using the resulting  <a href="https://www.cplusplus.com/reference/istream/istream/">std::istream</a>.</dd>
-</dl>
+`itk::wasm::InputTextStream`
+: A string. To reader this data type in C++, using the resulting [`std::istream`](https://www.cplusplus.com/reference/istream/istream/).
 
 *todo: document remaining CLI11 input and output classes.*
 

diff --git a/docs/cxx/tutorial/debugging.md b/docs/cxx/tutorial/debugging.md
@@ -51,29 +51,29 @@ add_executable(DebugMe DebugMe.cxx)
 
 with standard CMake commands,
 
-![Native build](/_static/tutorial/debugging/native-build.png)
+![Native build](../../static/tutorial/debugging/native-build.png)
 
 The native binary can then be debugged in the standard way. For example, with `gdb` on Linux:
 
-![Native debug Linux](/_static/tutorial/debugging/native-debug-linux.png)
+![Native debug Linux](../../static/tutorial/debugging/native-debug-linux.png)
 
 ## WASI
 
 The most direct way to debug WebAssembly is through the [WebAssembly System Interface (WASI)](https://wasi.dev/). In itk-wasm we can build to WASI with the [WASI SDK](https://github.com/WebAssembly/wasi-sdk) by specifying the `itkwasm/wasi` toolchain image. A backtrace can quickly be obtained with the `itk-wasm` CLI. Or, a fully fledged debugger session can be started with LLDB.
 
 First, build to WASI WebAssembly with debugging symbols available:
 
-![WASI debug build](/_static/tutorial/debugging/wasi-build-debug.png)
+![WASI debug build](../../static/tutorial/debugging/wasi-build-debug.png)
 
 Then, the `itk-wasm` CLI can conveniently run the Wasm binary with the included WASI runtime:
 
-![Run WASI debug](/_static/tutorial/debugging/run-wasi-debug.png)
+![Run WASI debug](../../static/tutorial/debugging/run-wasi-debug.png)
 
 We can see that `abort` is called in the `main` function at line 13 in `DebugMe.cxx`.
 
 A full debugging session is also possible after [LLDB](https://lldb.llvm.org/) >= 13 and [Wasmtime](https://wasmtime.dev/) are installed.
 
-![LLDB WASI debug](/_static/tutorial/debugging/lldb-wasi-debug.png)
+![LLDB WASI debug](../../static/tutorial/debugging/lldb-wasi-debug.png)
 
 **Note:** when calling `wasmtime` directly and passing local files into a pipeline, `--dir` arguments must be set. This gives `wasmtime` permission to access the directories containing the files. This is required due to WASI's [capability-based security](https://en.wikipedia.org/wiki/Capability-based_security) model. For example, if a file path starts with `./`, then add `--dir ./` arguments to the `wasmtime` invocation. `--dir` can be specified multiple times.
 
@@ -85,31 +85,31 @@ As with native builds, this builds debugging symbols, the human-readable names o
 
 When built with the default `Release` build type:
 
-![Emscripten build Release](/_static/tutorial/debugging/emscripten-build-release.png)
+![Emscripten build Release](../../static/tutorial/debugging/emscripten-build-release.png)
 
 the JavaScript support code is minified, and difficult to debug:
 
-![Run Node Release](/_static/tutorial/debugging/run-node-release.png)
+![Run Node Release](../../static/tutorial/debugging/run-node-release.png)
 
 However, when built with the `Debug` build type:
 
-![Emscripten build Debug](/_static/tutorial/debugging/emscripten-build-debug.png)
+![Emscripten build Debug](../../static/tutorial/debugging/emscripten-build-debug.png)
 
 a useful backtrace can be obtained:
 
-![Run Node Debug](/_static/tutorial/debugging/run-node-debug.png)
+![Run Node Debug](../../static/tutorial/debugging/run-node-debug.png)
 
 In order to run a debugger with Node, add the `--inspect-brk` flag when invoking `node`:
 
-![Node inspect](/_static/tutorial/debugging/node-inspect.png)
+![Node inspect](../../static/tutorial/debugging/node-inspect.png)
 
 This will pause execution on start a debugging remote interface. To connect to the remote interface with a Chromium browser, visit `chrome://inspect` and click the *inspect* link on the corresponding *Remote Target*:
 
-![Node inspect Remote Target](/_static/tutorial/debugging/node-inspect-remote-target.png)
+![Node inspect Remote Target](../../static/tutorial/debugging/node-inspect-remote-target.png)
 
 This will open the Chrome Dev Tools debugger:
 
-![Node inspect Chrome DevTools](/_static/tutorial/debugging/node-inspect-chrome-dev-tools.png)
+![Node inspect Chrome DevTools](../../static/tutorial/debugging/node-inspect-chrome-dev-tools.png)
 
 Other debugger interfaces [are also available](https://nodejs.org/en/docs/inspector), like a CLI debugger or the VSCode debugger.
 
@@ -127,21 +127,21 @@ Next, enable it in DevTools.
 
   Open DevTools -> Click the *gear (⚙)* icon in the top right corner -> go to the *Experiments* panel -> and tick *WebAssembly Debugging: Enable DWARF support*.
 
-![Enable Wasm Debugging](/_static/tutorial/debugging/enable-chrome-wasm-debugging.png)
+![Enable Wasm Debugging](../../static/tutorial/debugging/enable-chrome-wasm-debugging.png)
 
 After exitting Settings, you will be prompted to reload DevTools -- reload.
 
 Next, open the options for Chrome WebAssembly Debugging extension:
 
-![Wasm Debugging Options](/_static/tutorial/debugging/devtools-options.png)
+![Wasm Debugging Options](../../static/tutorial/debugging/devtools-options.png)
 
 Since itk-wasm performs builds in a clean Docker environment, the debugging source paths in the Docker environment are different than the paths on the host system. The debugging extension has a path substitution system that can account for these differences. In the Docker image, the directory where `itk-wasm` is invoked is mounted as `/work`. Substitute `/work` with the directory where the `itk-wasm` CLI is invoked. For example, if `itk-wasm` was invoked at `/home/matt/src/itk-wasm/examples/Debugging`, then:
 
-![Path substitution](/_static/tutorial/debugging/path-substitution.png)
+![Path substitution](../../static/tutorial/debugging/path-substitution.png)
 
 Build the project with itk-wasm and the `Debug` `CMAKE_BUILD_TYPE` to include DWARF debugging information:
 
-![Emscripten build Debug](/_static/tutorial/debugging/emscripten-build-debug.png)
+![Emscripten build Debug](../../static/tutorial/debugging/emscripten-build-debug.png)
 
 Here we load and run the WebAssembly with a simple HTML file and server:
 
@@ -167,8 +167,8 @@ Here we load and run the WebAssembly with a simple HTML file and server:
 </html>
 ```
 
-![HTTP Server](/_static/tutorial/debugging/http-server.png)
+![HTTP Server](../../static/tutorial/debugging/http-server.png)
 
 And we can debug the C++ code in Chrome's DevTools debugger along side the executing JavaScript!
 
-![Debug C++ DevTools](/_static/tutorial/debugging/debug-cxx-devtools.png)
+![Debug C++ DevTools](../../static/tutorial/debugging/debug-cxx-devtools.png)
diff --git a/docs/cxx/tutorial/hello_pipeline.md b/docs/cxx/tutorial/hello_pipeline.md
@@ -151,7 +151,7 @@ Check the generated help output:
 npx itk-wasm run hello-pipeline.wasi.wasm -- -- --help
 ```
 
-![Hello pipeline help](/_static/tutorial/hello_pipeline.png)
+![Hello pipeline help](../../static/tutorial/hello_pipeline.png)
 
 The two `--`'s are to separate arguments for the Wasm module from arguments to the `itk-wasm` CLI and the WebAssembly interpreter.
 

diff --git a/docs/cxx/tutorial/hello_world.md b/docs/cxx/tutorial/hello_world.md
@@ -146,13 +146,13 @@ Create an HTML file named `index.html` that will call the Wasm module through Ja
 
 Serve the web page and Wasm module with an http server:
 
-```sh
+```shell
 npm install http-server
 http-server .
 ```
 
 And point your browser to `http://127.0.0.1:8080/`.
 
-![Hello Wasm World!](/_static/tutorial/hello_wasm_world.png)
+![Hello Wasm World!](../../static/tutorial/hello_wasm_world.png)
 
 Congratulations! You just executed a C++ program in your web browser. 🎉
diff --git a/docs/cxx/tutorial/index.md b/docs/cxx/tutorial/index.md
@@ -12,13 +12,3 @@ This tutorial will walk you through the process of *creating WebAssembly scienti
 
 This [Jupyter notebook
 tutorial](https://github.com/InsightSoftwareConsortium/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/blob/master/10_Create_Scientific_WebAssembly_Pipelines.ipynb) also provides an interactive walkthrough.
-
-```{toctree}
-:maxdepth: 2
-:caption: 📖 Tutorial Steps
-
-hello_world.md
-hello_pipeline.md
-inputs_outputs.md
-debugging.md
-```
diff --git a/docs/cxx/tutorial/inputs_outputs.md b/docs/cxx/tutorial/inputs_outputs.md
@@ -84,7 +84,7 @@ Parse the command line arguments with the `ITK_WASM_PARSE` macro:
 
 The `-h` and `--help` flags are automatically generated from pipeline arguments to print usage information.
 
-![inputs-outputs help](/_static/tutorial/inputs_outputs_help.png)
+![inputs-outputs help](../../static/tutorial/inputs_outputs_help.png)
 
 Finally, process our data: 
 ```cpp
@@ -157,11 +157,11 @@ npx itk-wasm -b wasi-build run inputs-outputs.wasi.wasm -- -- --radius 2 cthead1
 
 The input image:
 
-![input image](/_static/tutorial/cthead1.png)
+![input image](../../static/tutorial/cthead1.png)
 
 has been smoothed:
 
-![smoothed](/_static/tutorial/smoothed.png)
+![smoothed](../../static/tutorial/smoothed.png)
 
 ## Run in Node.js
 

diff --git a/docs/index.md b/docs/index.md
@@ -5,14 +5,14 @@ ITK-Wasm
 
 <div align="center">
 
-![itk-wasm](_static/itk-webassembly.png)
+![itk-wasm](static/itk-webassembly.png)
 
 [![Examples](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/examples.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/examples.yml) [![Toolchains](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/toolchains.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/toolchains.yml) [![JavaScript, TypeScript](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/javascript-typescript.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/javascript-typescript.yml) [![Python WASM](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/python-wasm.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/python-wasm.yml) [![C++,Native Python](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/cxx-python.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/cxx-python.yml) [![WASI](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/wasi.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/wasi.yml) [![Documentation](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/documentation.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/documentation.yml)
 
 [![npm version](https://badge.fury.io/js/itk-wasm.svg)](https://www.npmjs.com/package/itk-wasm)
 [![itkwasm version](https://badge.fury.io/py/itkwasm.svg)](https://pypi.org/project/itkwasm/)
 
-[![DOI](https://zenodo.org/badge/45812381.svg)](https://zenodo.org/badge/latestdoi/45812381)
+[![DOI](https://zenodo.org/badge/45812381.svg)](https://zenodo.org/doi/10.5281/zenodo.3688880)
 
 ![License](https://img.shields.io/github/license/InsightSoftwareConsortium/ITK-Wasm) ![GitHub commit activity](https://img.shields.io/github/commit-activity/y/InsightSoftwareConsortium/ITK-Wasm)
 </div>
@@ -26,55 +26,4 @@ The project provides tools to
 - transfer data efficiently in and out of the WebAssembly runtime.
 - perform asynchronous, parallel execution of processing pipelines in a worker pool.
 
-*ITK-Wasm* can be used to execute [ITK](https://www.itk.org/) or arbitrary C++ codes in the browser, on the command line, and in languages like Python via [WASI](https://wasi.dev/) and [Emscripten](https://emscripten.org) runtimes.
-
-```{toctree}
-:hidden:
-:maxdepth: 3
-:caption: 👋 Introduction
-
-introduction/packages.md
-introduction/parts.md
-model/index.md
-introduction/file_formats/index.md
-```
-
-```{toctree}
-:hidden:
-:maxdepth: 3
-:caption: 🌐 JavaScript/TypeScript
-
-typescript/interface_types/index.md
-typescript/index.md
-typescript/distribution/index.md
-```
-
-```{toctree}
-:hidden:
-:maxdepth: 3
-:caption: 🐍 Python
-
-python/introduction.md
-python/numpy.md
-python/itk_python.md
-apidocs/index.rst
-```
-
-```{toctree}
-:hidden:
-:maxdepth: 3
-:caption: 📖 C++ Wasm Processing Pipelines
-
-cxx/installation.md
-cxx/tutorial/index.md
-cxx/interface_types.md
-```
-
-```{toctree}
-:hidden:
-:maxdepth: 3
-:caption: 🔨 ITK-Wasm Development
-
-development/hacking_itk_wasm.md
-development/itk_js_to_itk_wasm_migration_guide.md
-```
+*ITK-Wasm* can be used to execute [ITK](https://www.itk.org/) or arbitrary C++ codes in the browser, on the command line, and in languages like Python via [WASI](https://wasi.dev/) and [Emscripten](https://emscripten.org) runtimes.
diff --git a/docs/introduction/file_formats/index.md b/docs/introduction/file_formats/index.md
@@ -14,17 +14,8 @@ ITK-Wasm formats can be output in a directory or bundled in a single `.cbor` fil
 
 ITK-Wasm file formats are available in ITK-Wasm IO functions but also in C++ via the *WebAssemblyInterface* ITK module. This module can be enabled in an ITK build by setting the `-DModule_WebAssemblyInterface:BOOL=ON` flag in CMake. And, loading and conversion is also available native-binary Python bindings via the [*itk-webassemblyinterface* Python package](https://pypi.org/project/itk-webassemblyinterface/).
 
-<dl>
-  <dt><b>ITK-Wasm Image (.iwi, .iwi.cbor, .iwi.cbor.zst)</b><dt><dd>Serialization of an <a href="../../typescript/interface_types/Image.html"><code>Image</code></a>.</dd>
-  <dt><b>ITK-Wasm Mesh (.iwm, .iwm.cbor, .iwm.cbor.zst)</b><dt><dd>Serialization of a <a href="../../typescript/interface_types/Mesh.html"><code>Mesh</code></a>, or <a href="../../typescript/interface_types/PolyData.html"><code>PolyData</code></a>.</dd>
-</dl>
+ITK-Wasm Image (.iwi, .iwi.cbor, .iwi.cbor.zst)
+: Serialization of an [Image](../../model/Image).
 
-
-```{toctree}
-:hidden:
-:maxdepth: 3
-
-images.md
-meshes.md
-dicom.md
-```
+ITK-Wasm Mesh (.iwm, .iwm.cbor, .iwm.cbor.zst)
+: Serialization of a [Mesh](../../model/Mesh) or [PolyData](../../model/PolyData).