10_Create_Scientific_WebAssembly_Pipelines.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Create Scientific WebAssembly Pipelines\n",
    "\n",
    "### Learning Objectives\n",
    "\n",
    "- Gain experience **building** an **[ITK-Wasm](https://wasm.itk.org)** C++ scientific processing pipeline.\n",
    "- Learn about the concept of **wasm interface types**.\n",
    "- Learn how to **add custom processing code** to an ITK-Wasm pipeline.\n",
    "- Learn how to build, run, and test **generated TypeScript and Python binding packages.**  "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Build a custom ITK-Wasm project\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "### Why ITK-Wasm?\n",
    "\n",
    "ITK-Wasm provides a **simple, powerful, and interoperable** tooling to *create C++-based wasm scientific processing pipelines*. This tooling is compatible with wasm and open-source scientific community standards can easily be customized to meet your needs.\n",
    "\n",
    "Specifically, [ITK-Wasm provides the ability](https://wasm.itk.org/en/latest/introduction/parts.html):\n",
    "\n",
    "- To **easily and reproducibly build scientific C++ codebases** to wasm with the Emscripten or WASI toolchains\n",
    "- To build the same C++ code *without any modifications* to **native binaries** for debugging or deployment of native binaries\n",
    "- To create **CLI tests** that can be run on both native and wasm binaries without modification\n",
    "- To generate **TypeScript / JavaScript bindings and packages**\n",
    "- To generate a zero-install web application that provides a **live API demo**\n",
    "- To generate **Python bindings and packages**\n",
    "- To **manage testing data** shared across CLI and language binding tests\n",
    "- To **drive the build and testing process** for these constituent parts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create an ITK-Wasm project that provides an N-dimensional median image filter\n",
    "\n",
    "In this tutorial, we will create an ITK-Wasm project that provides an N-dimensional median image filter.\n",
    "\n",
    "*Note:* Cells in this notebook are shell commands that run on a Jupyter bash kernel. Follow the tutorial [installation instructions](./README.md) to install the bash kernel and required command line executables.\n",
    "\n",
    "ITK-Wasm projects are intended to be developed in standalone source code repositories, as subdirectories in source code repositories, or as package in a [JavaScript project monorepo](https://www.robinwieruch.de/javascript-monorepos/).\n",
    "\n",
    "Example ITK-Wasm projects can be found in the [packages/* directory of the *itk-wasm* repository](https://github.com/InsightSoftwareConsortium/itk-wasm/tree/main/packages).\n",
    "\n",
    "We will start with a project in the tutorial repository *wasm-median/* directory. This contains the skeleton of our ITK-Wasm project. Work is in progress so this skeleton can be generated interactively with the command:\n",
    "\n",
    "```sh\n",
    "pnpm create itk-wasm\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CMakeLists.txt\t median-image-filter  pnpm-workspace.yaml\n",
      "environment.yml  package.json\t      README.md\n"
     ]
    }
   ],
   "source": [
    "cd wasm-median/\n",
    "ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The skeleton contains the following files:\n",
    "\n",
    "### *README.md*\n",
    "\n",
    "A description of the project for the repository."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# median\n",
      "\n",
      "Apply a median filter to a 2D or 3D spatial image.\n"
     ]
    }
   ],
   "source": [
    "cat README.md"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "### *CMakeLists.txt*\n",
    "\n",
    "A top level *CMakeLists.txt* [CMake](https://cmake.org) C++ build system configuration file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cmake_minimum_required(VERSION 3.16)\n",
      "project(median LANGUAGES CXX)\n",
      "\n",
      "set(CMAKE_CXX_STANDARD 17)\n",
      "\n",
      "find_package(ITK REQUIRED COMPONENTS\n",
      "  WebAssemblyInterface\n",
      ")\n",
      "include(${ITK_USE_FILE})\n",
      "\n",
      "enable_testing()\n",
      "\n",
      "# Begin create-itk-wasm added pipelines.\n",
      "add_subdirectory(median-image-filter)\n",
      "# End create-itk-wasm added pipelines.\n"
     ]
    }
   ],
   "source": [
    "cat CMakeLists.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### *median-image-filter/CMakeLists.txt*\n",
    "\n",
    "A *CMakeLists.txt* CMake configuration file for the `median-image-filter` pipeline. This describes how to build the pipeline and adds a default test that produces the CLI help output."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "add_executable(median-image-filter median-image-filter.cxx)\n",
      "target_link_libraries(median-image-filter PUBLIC ${ITK_LIBRARIES})\n",
      "\n",
      "add_test(NAME median-image-filter-help COMMAND median-image-filter --help)\n"
     ]
    }
   ],
   "source": [
    "cat median-image-filter/CMakeLists.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### median-image-filter/median-image-filter.cxx\n",
    "\n",
    "This is the C++ source code for the WebAssembly module.\n",
    "\n",
    "The source contains a command line interface for a processing pipeline executable. Command line arguments are parsed with an extension to the  modern C++ argument parser, [CLI11](https://github.com/CLIUtils/CLI11), `itk::wasm::Pipeline`. From this interface, and `itk::wasm` **interface types**, we can:\n",
    "\n",
    "- Build and run as a native executable on the command line.\n",
    "- Build and run as a wasm module the command on the command line.\n",
    "- Generate bindings and packages for programming languages."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/*=========================================================================\n",
      "\n",
      " *  Copyright NumFOCUS\n",
      " *\n",
      " *  Licensed under the Apache License, Version 2.0 (the \"License\");\n",
      " *  you may not use this file except in compliance with the License.\n",
      " *  You may obtain a copy of the License at\n",
      " *\n",
      " *         https://www.apache.org/licenses/LICENSE-2.0.txt\n",
      " *\n",
      " *  Unless required by applicable law or agreed to in writing, software\n",
      " *  distributed under the License is distributed on an \"AS IS\" BASIS,\n",
      " *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
      " *  See the License for the specific language governing permissions and\n",
      " *  limitations under the License.\n",
      " *\n",
      " *=========================================================================*/\n",
      "\n",
      "#include \"itkPipeline.h\"\n",
      "#include \"itkInputImage.h\"\n",
      "#include \"itkOutputImage.h\"\n",
      "#include \"itkSupportInputImageTypes.h\"\n",
      "\n",
      "template <typename TImage>\n",
      "int MedianFilter(itk::wasm::Pipeline &pipeline, const TImage *inputImage)\n",
      "{\n",
      "  using ImageType = TImage;\n",
      "\n",
      "  pipeline.get_option(\"input-image\")->required()->type_name(\"INPUT_IMAGE\");\n",
      "\n",
      "  using OutputImageType = itk::wasm::OutputImage<ImageType>;\n",
      "  OutputImageType outputImage;\n",
      "  pipeline.add_option(\"output-image\", outputImage, \"The output image\")->required()->type_name(\"OUTPUT_IMAGE\");\n",
      "\n",
      "  unsigned int radius = 1;\n",
      "  pipeline.add_option(\"-r,--radius\", radius, \"Kernel radius in pixels\");\n",
      "\n",
      "  ITK_WASM_PARSE(pipeline);\n",
      "\n",
      "  // Pipeline code goes here\n",
      "\n",
      "  return EXIT_SUCCESS;\n",
      "}\n",
      "\n",
      "template <typename TImage>\n",
      "class PipelineFunctor\n",
      "{\n",
      "public:\n",
      "  int operator()(itk::wasm::Pipeline &pipeline)\n",
      "  {\n",
      "    using ImageType = TImage;\n",
      "\n",
      "    using InputImageType = itk::wasm::InputImage<ImageType>;\n",
      "    InputImageType inputImage;\n",
      "    pipeline.add_option(\"input-image\", inputImage, \"The input image\");\n",
      "\n",
      "    ITK_WASM_PRE_PARSE(pipeline);\n",
      "\n",
      "    typename ImageType::ConstPointer image = inputImage.Get();\n",
      "    return MedianImageFilter<ImageType>(pipeline, image);\n",
      "  }\n",
      "};\n",
      "\n",
      "int main(int argc, char *argv[])\n",
      "{\n",
      "  itk::wasm::Pipeline pipeline(\"median-image-filter\", \"Computes an image where a given pixel is the median value of the the pixels in a neighborhood about the corresponding input pixel.\", argc, argv);\n",
      "\n",
      "  return itk::wasm::SupportInputImageTypes<PipelineFunctor,\n",
      "                                           uint8_t,\n",
      "                                           float>::Dimensions<2U, 3U>(\"input-image\", pipeline);\n",
      "\n",
      "  return EXIT_SUCCESS;\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "cat median-image-filter/median-image-filter.cxx"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### *environment.yml*\n",
    "\n",
    "An *environment.yml* provides the conda environment configuration to build and test Python packages.\n",
    "\n",
    "In the future, this may also include packages to support development and testing of bindings and packages for other languages such as Java, C#, and Rust. \n",
    "\n",
    "At build time, [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) is downloaded and a conda environment, a conda environment is created from this configuration, and Python packages are built and tested with this environment's tools."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "name: median\n",
      "channels:\n",
      "  - conda-forge\n",
      "dependencies:\n",
      "  - pytest\n",
      "  - python=3.11\n",
      "  - pip\n",
      "  - pip:\n",
      "    - hatch\n"
     ]
    }
   ],
   "source": [
    "cat environment.yml"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### *package.json* and *pnpm-workspace.yaml*\n",
    "\n",
    "The build and test process is driven by [`pnpm`](https://pnpm.io/), the fast, disk-space efficient package manager.\n",
    "\n",
    "This process is configured by the *package.json* Node Package Manager (NPM) configuration file and *pnpm-workspace.yml*.\n",
    "\n",
    "`pnpm` uses the `itk-wasm` pnpm build scripts to build the project in parallel following build stage dependencies. WebAssembly binaries are built before bindings are generated, etc."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "packages:\n",
      "  - 'typescript'\n",
      "{\n",
      "  \"name\": \"median-build\",\n",
      "  \"version\": \"0.1.0\",\n",
      "  \"private\": true,\n",
      "  \"packageManager\": \"pnpm@8.15.1\",\n",
      "  \"description\": \"Scripts to generate median itk-wasm artifacts.\",\n",
      "  \"type\": \"module\",\n",
      "  \"itk-wasm\": {\n",
      "    \"package-description\": \"Apply a median filter to a 2D or 3D spatial image.\",\n",
      "    \"typescript-package-name\": \"@itk-wasm/median\",\n",
      "    \"python-package-name\": \"itkwasm-median\",\n",
      "    \"repository\": \"https://github.com/InsightSoftwareConsortium/itk-wasm\"\n",
      "  },\n",
      "  \"license\": \"Apache-2.0\",\n",
      "  \"scripts\": {\n",
      "    \"build\": \"pnpm build:gen:typescript && pnpm build:gen:python\",\n",
      "    \"build:emscripten\": \"itk-wasm pnpm-script build:emscripten\",\n",
      "    \"build:emscripten:debug\": \"itk-wasm pnpm-script build:emscripten:debug\",\n",
      "    \"build:wasi\": \"itk-wasm pnpm-script build:wasi\",\n",
      "    \"build:wasi:debug\": \"itk-wasm pnpm-script build:wasi:debug\",\n",
      "    \"build:python:wasi\": \"itk-wasm pnpm-script build:python:wasi\",\n",
      "    \"bindgen:typescript\": \"itk-wasm pnpm-script bindgen:typescript\",\n",
      "    \"bindgen:python\": \"itk-wasm pnpm-script bindgen:python\",\n",
      "    \"build:gen:typescript\": \"itk-wasm pnpm-script build:gen:typescript\",\n",
      "    \"build:gen:python\": \"itk-wasm pnpm-script build:gen:python\",\n",
      "    \"build:micromamba\": \"itk-wasm pnpm-script build:micromamba\",\n",
      "    \"build:python:versionSync\": \"itk-wasm pnpm-script build:python:versionSync\",\n",
      "    \"publish:python\": \"itk-wasm pnpm-script publish:python\",\n",
      "    \"test\": \"pnpm test:data:download && pnpm build:gen:python && pnpm test:python\",\n",
      "    \"test:data:download\": \"dam download test/data test/data.tar.gz bafkreigpkk3pqcoqzjzcauogw6dml52yig3ksmcrobau5pkoictymizzri https://github.com/InsightSoftwareConsortium/itk-wasm/releases/download/itk-wasm-v1.0.0-b.163/create-itk-wasm-test-data.tar.gz https://bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca.ipfs.w3s.link/ipfs/bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca/create-itk-wasm-test-data.tar.gz https://ipfs.filebase.io/ipfs/QmcxyvUKnaoTTwUqEPXwp1sdcbrFh3XnnwckLKVRpctJx9\",\n",
      "    \"test:data:pack\": \"dam pack test/data test/data.tar.gz\",\n",
      "    \"test:python:wasi\": \"itk-wasm pnpm-script test:python:wasi\",\n",
      "    \"test:python:emscripten\": \"itk-wasm pnpm-script test:python:emscripten\",\n",
      "    \"test:python:dispatch\": \"itk-wasm pnpm-script test:python:emscripten\",\n",
      "    \"test:python\": \"itk-wasm pnpm-script test:python\",\n",
      "    \"test:wasi\": \"itk-wasm pnpm-script test:wasi\"\n",
      "  },\n",
      "  \"devDependencies\": {\n",
      "    \"@itk-wasm/dam\": \"^1.1.1\",\n",
      "    \"@thewtex/setup-micromamba\": \"^1.9.7\",\n",
      "    \"itk-wasm\": \"1.0.0-b.166\"\n",
      "  },\n",
      "  \"author\": \"Insight Software Consortium\",\n",
      "  \"repository\": {\n",
      "    \"type\": \"git\",\n",
      "    \"url\": \"https://github.com/InsightSoftwareConsortium/itk-wasm\"\n",
      "  }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "cat pnpm-workspace.yaml\n",
    "cat package.json"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Build the skeleton\n",
    "\n",
    "To install the dependencies specified in the *package.json* file, run `pnpm install`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Progress: resolved \u001b[96m1\u001b[39m, reused \u001b[96m0\u001b[39m, downloaded \u001b[96m0\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m3\u001b[39m, reused \u001b[96m2\u001b[39m, downloaded \u001b[96m0\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m35\u001b[39m, reused \u001b[96m34\u001b[39m, downloaded \u001b[96m0\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m90\u001b[39m, reused \u001b[96m88\u001b[39m, downloaded \u001b[96m1\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m93\u001b[39m, reused \u001b[96m91\u001b[39m, downloaded \u001b[96m2\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m116\u001b[39m, reused \u001b[96m113\u001b[39m, downloaded \u001b[96m2\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m130\u001b[39m, reused \u001b[96m125\u001b[39m, downloaded \u001b[96m3\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m134\u001b[39m, reused \u001b[96m129\u001b[39m, downloaded \u001b[96m5\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m169\u001b[39m, reused \u001b[96m158\u001b[39m, downloaded \u001b[96m9\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m173\u001b[39m, reused \u001b[96m162\u001b[39m, downloaded \u001b[96m11\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m197\u001b[39m, reused \u001b[96m184\u001b[39m, downloaded \u001b[96m13\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m200\u001b[39m, reused \u001b[96m186\u001b[39m, downloaded \u001b[96m13\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1A\u001b[43m\u001b[30m WARN \u001b[39m\u001b[49m \u001b[31m1 deprecated subdependencies found:\u001b[39m uuid@3.4.0\u001b[0K\n",
      "Progress: resolved \u001b[96m200\u001b[39m, reused \u001b[96m186\u001b[39m, downloaded \u001b[96m13\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1APackages: \u001b[32m+201\u001b[39m\u001b[0K\n",
      "\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\u001b[32m+\u001b[39m\n",
      "Progress: resolved \u001b[96m200\u001b[39m, reused \u001b[96m186\u001b[39m, downloaded \u001b[96m13\u001b[39m, added \u001b[96m0\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m201\u001b[39m, reused \u001b[96m187\u001b[39m, downloaded \u001b[96m14\u001b[39m, added \u001b[96m176\u001b[39m\n",
      "\u001b[1AProgress: resolved \u001b[96m201\u001b[39m, reused \u001b[96m187\u001b[39m, downloaded \u001b[96m14\u001b[39m, added \u001b[96m201\u001b[39m, done\n",
      "\u001b[90mnode_modules/.pnpm/protobufjs@7.2.6/node_modules/\u001b[39mprotobufjs: Running postinstall script...\n",
      "\u001b[1A\u001b[90mnode_modules/.pnpm/protobufjs@7.2.6/node_modules/\u001b[39mprotobufjs: Running postinstall script, done in 48ms\n",
      "\n",
      "\u001b[96mdevDependencies:\u001b[39m\n",
      "\u001b[32m+\u001b[39m @itk-wasm/dam \u001b[90m1.1.1\u001b[39m\n",
      "\u001b[32m+\u001b[39m @thewtex/setup-micromamba \u001b[90m1.9.7\u001b[39m\n",
      "\u001b[32m+\u001b[39m itk-wasm \u001b[90m1.0.0-b.166\u001b[39m\n",
      "\n",
      "Done in 3.2s\n"
     ]
    }
   ],
   "source": [
    "pnpm install"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "Run the `pnpm build` target.\n",
    "\n",
    "This runs `build` script, building Emscripten and WASI wasm modules, TypeScript and Python bindings, and Typescript and Python package configurations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "> median-build@0.1.0 build /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> pnpm build:gen:typescript && pnpm build:gen:python\n",
      "\n",
      "\n",
      "> median-build@0.1.0 build:gen:typescript /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:gen:typescript\n",
      "\n",
      ">> pnpm -c exec pnpm build:emscripten && pnpm bindgen:typescript && pnpm install && pnpm -r build\n",
      "\n",
      "> median-build@0.1.0 build:emscripten /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:emscripten\n",
      "\n",
      ">> pnpm -c exec itk-wasm build -i itkwasm/emscripten:20231217-40780708\n",
      "Not searching for unused variables given on the command line.\n",
      "-- Configuring done\n",
      "-- Generating done\n",
      "-- Build files have been written to: /work/emscripten-build\n",
      "ninja: Entering directory `emscripten-build'\n",
      "[2/2] Linking CXX executable median-image-filter/median-image-filter.js\u001b[Kcxx.o\u001b[K\n",
      "cache:INFO: generating system asset: symbol_lists/c824dc42a311ced7c4de2a6267617f2f158d990a.json... (this will be cached in \"/emsdk/upstream/emscripten/cache/symbol_lists/c824dc42a311ced7c4de2a6267617f2f158d990a.json\" for subsequent builds)\n",
      "cache:INFO:  - ok\n",
      "/work/emscripten-build/median-image-filter/median-image-filter.wasm : 31.78%   (   649 KiB =>    206 KiB, /work/emscripten-build/median-image-filter/median-image-filter.wasm.zst) \n",
      "\n",
      "> median-build@0.1.0 bindgen:typescript /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script bindgen:typescript\n",
      "\n",
      ">> pnpm -c exec itk-wasm -b emscripten-build bindgen --interface typescript --output-dir typescript --package-name @itk-wasm/median --package-description Apply a median filter to a 2D or 3D spatial image. --repository https://github.com/InsightSoftwareConsortium/itk-wasm\n",
      "Scope: all 2 workspace projects\n",
      "Lockfile is up to date, resolution step is skipped\n",
      "Already up to date\n",
      "Done in 395ms\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> pnpm build:tsc && pnpm build:browser:workerEmbedded && pnpm build:browser:workerEmbeddedMin && pnpm build:demo\n",
      "\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:tsc /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> tsc --pretty\n",
      "\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:browser:workerEmbedded /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> esbuild --loader:.worker.js=dataurl --bundle --format=esm --outfile=./dist/bundle/index-worker-embedded.js ./src/index-worker-embedded.ts\n",
      "\n",
      "\n",
      "  \u001b[37mdist/bundle/\u001b[0m\u001b[1mindex-worker-embedded.js\u001b[0m  \u001b[36m263.7kb\u001b[0m\n",
      "\n",
      "⚡ \u001b[32mDone in 8ms\u001b[0m\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:browser:workerEmbeddedMin /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> esbuild --minify --loader:.worker.js=dataurl --bundle --format=esm --outfile=./dist/bundle/index-worker-embedded.min.js ./src/index-worker-embedded.min.ts\n",
      "\n",
      "\n",
      "  \u001b[37mdist/bundle/\u001b[0m\u001b[1mindex-worker-embedded.min.js\u001b[0m  \u001b[36m134.7kb\u001b[0m\n",
      "\n",
      "⚡ \u001b[32mDone in 8ms\u001b[0m\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:demo /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> pnpm copyShoelaceAssets && vite build\n",
      "\n",
      "\n",
      "> @itk-wasm/median@0.1.0 copyShoelaceAssets /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> shx mkdir -p test/browser/demo-app/public && shx cp -r node_modules/@shoelace-style/shoelace/dist/assets test/browser/demo-app/public/\n",
      "\n",
      "\u001b[36mvite v4.5.2 \u001b[32mbuilding for production...\u001b[36m\u001b[39m\n",
      "\u001b[2K\u001b[1Gtransforming (1) \u001b[2mindex.html\u001b[22m\u001b[2K\u001b[1Gtransforming (81) \u001b[2m../../../../node_modules/.pnpm/@shoelace-style+shoelace@2\u001b[2K\u001b[1Gtransforming (174) \u001b[2m../../../../node_modules/.pnpm/itk-wasm@1.0.0-b.165/node\u001b[2K\u001b[1Gtransforming (237) \u001b[2m../../../../node_modules/.pnpm/@itk-wasm+image-io@1.1.0/\u001b[2K\u001b[1Gtransforming (297) \u001b[2m../../../../node_modules/.pnpm/itk-wasm@1.0.0-b.166/node\u001b[2K\u001b[1Gtransforming (349) \u001b[2m../../../../node_modules/.pnpm/@shoelace-style+shoelace@\u001b[2K\u001b[1G\u001b[32m✓\u001b[39m 352 modules transformed.\n",
      "\u001b[2K\u001b[1Grendering chunks (1)...\u001b[2K\u001b[1G\u001b[2K\u001b[1Gcomputing gzip size (0)...\u001b[2K\u001b[1Gcomputing gzip size (1)...\u001b[2K\u001b[1Gcomputing gzip size (2)...\u001b[2K\u001b[1Gcomputing gzip size (3)...\u001b[2K\u001b[1Gcomputing gzip size (4)...\u001b[2K\u001b[1Gcomputing gzip size (5)...\u001b[2K\u001b[1Gcomputing gzip size (6)...\u001b[2K\u001b[1G\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mtypescript-logo-336a54a4.svg          \u001b[39m\u001b[1m\u001b[2m  0.91 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  0.53 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mjavascript-logo-35328c60.svg          \u001b[39m\u001b[1m\u001b[2m  1.07 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  0.60 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mlogo-964238ba.svg                     \u001b[39m\u001b[1m\u001b[2m  2.95 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  1.38 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[32mindex.html                                   \u001b[39m\u001b[1m\u001b[2m  5.24 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  2.14 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mitk-wasm-pipeline.worker-21bb29ff.js  \u001b[39m\u001b[1m\u001b[2m 89.96 kB\u001b[22m\u001b[1m\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[35mindex-1a3477e4.css                    \u001b[39m\u001b[1m\u001b[2m 36.99 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  6.85 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[36mindex-0df74da5.js                     \u001b[39m\u001b[1m\u001b[2m326.52 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip: 75.83 kB\u001b[22m\n",
      "\u001b[36m[vite-plugin-static-copy]\u001b[39m \u001b[32mCopied 201 items.\u001b[39m\n",
      "\u001b[32m✓ built in 1.08s\u001b[39m\n",
      "\n",
      "> median-build@0.1.0 build:gen:python /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:gen:python\n",
      "\n",
      ">> pnpm -c exec pnpm build:wasi && pnpm bindgen:python && pnpm build:micromamba && pnpm build:python:wasi\n",
      "\n",
      "> median-build@0.1.0 build:wasi /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:wasi\n",
      "\n",
      ">> pnpm -c exec itk-wasm build -i itkwasm/wasi:20231217-40780708\n",
      "Not searching for unused variables given on the command line.\n",
      "-- The CXX compiler identification is Clang 16.0.6\n",
      "-- Detecting CXX compiler ABI info\n",
      "-- Detecting CXX compiler ABI info - failed\n",
      "-- Check for working CXX compiler: /usr/local/bin/clang++-wasi-sysroot.sh\n",
      "-- Check for working CXX compiler: /usr/local/bin/clang++-wasi-sysroot.sh - works\n",
      "-- Detecting CXX compile features\n",
      "-- Detecting CXX compile features - done\n",
      "-- Configuring done\n",
      "-- Generating done\n",
      "-- Build files have been written to: /work/wasi-build\n",
      "ninja: Entering directory `wasi-build'\n",
      "[6/6] Linking CXX executable median-image-filter/median-image-filter.wasi.wasm\u001b[KK\n",
      "\n",
      "> median-build@0.1.0 bindgen:python /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script bindgen:python\n",
      "\n",
      ">> pnpm -c exec itk-wasm -b wasi-build bindgen --interface python --output-dir python --package-name itkwasm-median --package-description Apply a median filter to a 2D or 3D spatial image. --repository https://github.com/InsightSoftwareConsortium/itk-wasm\n",
      "\n",
      "> median-build@0.1.0 build:micromamba /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:micromamba\n",
      "\n",
      ">> pnpm -c exec setup-micromamba --micromamba-binary-path ./micromamba/micromamba --micromamba-root-path micromamba --init-shell none --create-environment true --environment-file environment.yml --log-level info --run-command clean -fya\n",
      "\u001b[47m\u001b[30m ▼ \u001b[39m\u001b[49m Install micromamba\n",
      "::debug::Downloading https://github.com/mamba-org/micromamba-releases/releases/latest/download/micromamba-linux-64\n",
      "::debug::Destination /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba\n",
      "::debug::download complete\n",
      "  \u001b[44m\u001b[37m I \u001b[39m\u001b[49m micromamba installed to /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba\n",
      "\u001b[44m\u001b[37m I \u001b[39m\u001b[49m Adding conda-forge to condarc channels ...\n",
      "\u001b[47m\u001b[30m ▼ \u001b[39m\u001b[49m Install environment `median`\n",
      "[command]/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba create -y -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba -f environment.yml  --log-level info --rc-file /home/matt/micromamba-bin/.condarc\n",
      "info     libmamba Parsing MatchSpec pytest\n",
      "info     libmamba Parsing MatchSpec python=3.11\n",
      "info     libmamba Parsing MatchSpec pip\n",
      "info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/linux-64/repodata.json'\n",
      "info     libmamba No valid cache found\n",
      "info     libmamba Using OpenSSL backend\n",
      "info     libmamba Searching index cache file for repo 'https://conda.anaconda.org/conda-forge/noarch/repodata.json'\n",
      "info     libmamba No valid cache found\n",
      "info     libmamba All targets to download are cached\n",
      "info     libmamba Starting to download targets\n",
      "info     libmamba Transfer done for 'conda-forge/noarch'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/repodata.json.zst] 13522877 bytes\n",
      "info     libmamba Transfer done for 'conda-forge/linux-64'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/repodata.json.zst] 32418808 bytes\n",
      "info     libmamba Reading cache files '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/cache/497deca9.json.*' for repo index 'conda-forge/linux-64'\n",
      "info     libmamba Reading repodata.json file \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/cache/497deca9.json\" for repo conda-forge/linux-64\n",
      "info     libmamba Writing libsolv solv file \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/cache/497deca9.solv\" for repo conda-forge/linux-64\n",
      "info     libmamba Reading cache files '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/cache/09cdf8bf.json.*' for repo index 'conda-forge/noarch'\n",
      "info     libmamba Reading repodata.json file \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/cache/09cdf8bf.json\" for repo conda-forge/noarch\n",
      "info     libmamba Writing libsolv solv file \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/cache/09cdf8bf.solv\" for repo conda-forge/noarch\n",
      "info     libmamba Adding package record to repo __archspec\n",
      "info     libmamba Adding package record to repo __cuda\n",
      "info     libmamba Adding package record to repo __glibc\n",
      "info     libmamba Adding package record to repo __linux\n",
      "info     libmamba Adding package record to repo __unix\n",
      "info     libmamba Parsing MatchSpec pytest\n",
      "info     libmamba Parsing MatchSpec pytest\n",
      "info     libmamba Adding job: pytest\n",
      "info     libmamba Parsing MatchSpec python=3.11\n",
      "info     libmamba Parsing MatchSpec python=3.11\n",
      "info     libmamba Adding job: python=3.11\n",
      "info     libmamba Parsing MatchSpec pip\n",
      "info     libmamba Parsing MatchSpec pip\n",
      "info     libmamba Adding job: pip\n",
      "info     libmamba Problem count: 0\n",
      "info     libmamba Found python version in packages to be installed 3.11.7\n",
      "\n",
      "Transaction\n",
      "\n",
      "  Prefix: /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median\n",
      "\n",
      "  Updating specs:\n",
      "\n",
      "   - pytest\n",
      "   - python=3.11\n",
      "   - pip\n",
      "\n",
      "\n",
      "  Package              Version  Build               Channel          Size\n",
      "───────────────────────────────────────────────────────────────────────────\n",
      "  Install:\n",
      "───────────────────────────────────────────────────────────────────────────\n",
      "\n",
      "  + _libgcc_mutex          0.1  conda_forge         conda-forge       3kB\n",
      "  + ld_impl_linux-64      2.40  h41732ed_0          conda-forge     705kB\n",
      "  + ca-certificates   2024.2.2  hbcca054_0          conda-forge     155kB\n",
      "  + libgomp             13.2.0  h807b86a_5          conda-forge     420kB\n",
      "  + _openmp_mutex          4.5  2_gnu               conda-forge      24kB\n",
      "  + libgcc-ng           13.2.0  h807b86a_5          conda-forge     771kB\n",
      "  + openssl              3.2.1  hd590300_0          conda-forge       3MB\n",
      "  + libxcrypt           4.4.36  hd590300_1          conda-forge     100kB\n",
      "  + libzlib             1.2.13  hd590300_5          conda-forge      62kB\n",
      "  + libffi               3.4.2  h7f98852_5          conda-forge      58kB\n",
      "  + bzip2                1.0.8  hd590300_5          conda-forge     254kB\n",
      "  + ncurses                6.4  h59595ed_2          conda-forge     884kB\n",
      "  + libuuid             2.38.1  h0b41bf4_0          conda-forge      34kB\n",
      "  + libnsl               2.0.1  hd590300_0          conda-forge      33kB\n",
      "  + libexpat             2.5.0  hcb278e6_1          conda-forge      78kB\n",
      "  + xz                   5.2.6  h166bdaf_0          conda-forge     418kB\n",
      "  + tk                  8.6.13  noxft_h4845f30_101  conda-forge       3MB\n",
      "  + libsqlite           3.45.1  h2797004_0          conda-forge     859kB\n",
      "  + readline               8.2  h8228510_1          conda-forge     281kB\n",
      "  + tzdata               2024a  h0c530f3_0          conda-forge     120kB\n",
      "  + python              3.11.7  hab00c5b_1_cpython  conda-forge      31MB\n",
      "  + wheel               0.42.0  pyhd8ed1ab_0        conda-forge      58kB\n",
      "  + setuptools          69.0.3  pyhd8ed1ab_0        conda-forge     471kB\n",
      "  + pip                   24.0  pyhd8ed1ab_0        conda-forge       1MB\n",
      "  + tomli                2.0.1  pyhd8ed1ab_0        conda-forge      16kB\n",
      "  + iniconfig            2.0.0  pyhd8ed1ab_0        conda-forge      11kB\n",
      "  + exceptiongroup       1.2.0  pyhd8ed1ab_2        conda-forge      21kB\n",
      "  + packaging             23.2  pyhd8ed1ab_0        conda-forge      49kB\n",
      "  + colorama             0.4.6  pyhd8ed1ab_0        conda-forge      25kB\n",
      "  + pluggy               1.4.0  pyhd8ed1ab_0        conda-forge      23kB\n",
      "  + pytest               8.0.0  pyhd8ed1ab_0        conda-forge     252kB\n",
      "\n",
      "  Summary:\n",
      "\n",
      "  Install: 31 packages\n",
      "\n",
      "  Total download: 45MB\n",
      "\n",
      "───────────────────────────────────────────────────────────────────────────\n",
      "\n",
      "\n",
      "info     libmamba Cleaned 0 .mamba_trash files. 0 remaining.\n",
      "\n",
      "Transaction starting\n",
      "info     libmamba Starting to download targets\n",
      "info     libmamba Transfer done for 'ca-certificates'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda] 155432 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/ca-certificates-2024.2.2-hbcca054_0.conda'\n",
      "info     libmamba Transfer done for '_libgcc_mutex'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2] 2562 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/_libgcc_mutex-0.1-conda_forge.tar.bz2'\n",
      "info     libmamba Transfer done for 'libgomp'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_5.conda] 419751 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libgomp-13.2.0-h807b86a_5.conda'\n",
      "info     libmamba Transfer done for 'ld_impl_linux-64'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda] 704696 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/ld_impl_linux-64-2.40-h41732ed_0.conda'\n",
      "info     libmamba Transfer done for 'libnsl'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda] 33408 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libnsl-2.0.1-hd590300_0.conda'\n",
      "info     libmamba Transfer done for 'bzip2'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda] 254228 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/bzip2-1.0.8-hd590300_5.conda'\n",
      "info     libmamba Transfer done for 'tzdata'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda] 119815 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/tzdata-2024a-h0c530f3_0.conda'\n",
      "info     libmamba Transfer done for 'iniconfig'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda] 11101 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/iniconfig-2.0.0-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'tk'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda] 3318875 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/tk-8.6.13-noxft_h4845f30_101.conda'\n",
      "info     libmamba Transfer done for 'setuptools'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/setuptools-69.0.3-pyhd8ed1ab_0.conda] 470548 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/setuptools-69.0.3-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'libgcc-ng'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_5.conda] 770506 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libgcc-ng-13.2.0-h807b86a_5.conda'\n",
      "info     libmamba Transfer done for 'colorama'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2] 25170 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2'\n",
      "info     libmamba Transfer done for '_openmp_mutex'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2] 23621 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/_openmp_mutex-4.5-2_gnu.tar.bz2'\n",
      "info     libmamba Transfer done for 'libuuid'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda] 33601 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libuuid-2.38.1-h0b41bf4_0.conda'\n",
      "info     libmamba Transfer done for 'readline'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda] 281456 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/readline-8.2-h8228510_1.conda'\n",
      "info     libmamba Transfer done for 'libsqlite'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.1-h2797004_0.conda] 859346 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libsqlite-3.45.1-h2797004_0.conda'\n",
      "info     libmamba Transfer done for 'exceptiongroup'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda] 20551 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda'\n",
      "info     libmamba Transfer done for 'xz'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2] 418368 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/xz-5.2.6-h166bdaf_0.tar.bz2'\n",
      "info     libmamba Transfer done for 'pytest'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/pytest-8.0.0-pyhd8ed1ab_0.conda] 251713 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/pytest-8.0.0-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'libffi'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2] 58292 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libffi-3.4.2-h7f98852_5.tar.bz2'\n",
      "info     libmamba Transfer done for 'pluggy'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/pluggy-1.4.0-pyhd8ed1ab_0.conda] 23384 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/pluggy-1.4.0-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'libexpat'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda] 77980 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libexpat-2.5.0-hcb278e6_1.conda'\n",
      "info     libmamba Transfer done for 'ncurses'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda] 884434 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/ncurses-6.4-h59595ed_2.conda'\n",
      "info     libmamba Transfer done for 'pip'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda] 1398245 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/pip-24.0-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'wheel'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda] 57553 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/wheel-0.42.0-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'openssl'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda] 2863069 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/openssl-3.2.1-hd590300_0.conda'\n",
      "info     libmamba Transfer done for 'libxcrypt'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda] 100393 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libxcrypt-4.4.36-hd590300_1.conda'\n",
      "info     libmamba Transfer done for 'packaging'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/packaging-23.2-pyhd8ed1ab_0.conda] 49452 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/packaging-23.2-pyhd8ed1ab_0.conda'\n",
      "info     libmamba Transfer done for 'tomli'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2] 15940 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2'\n",
      "info     libmamba Transfer done for 'libzlib'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda] 61588 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/libzlib-1.2.13-hd590300_5.conda'\n",
      "info     libmamba Transfer done for 'python'\n",
      "info     libmamba Transfer finalized, status: 200 [https://conda.anaconda.org/conda-forge/linux-64/python-3.11.7-hab00c5b_1_cpython.conda] 30830615 bytes\n",
      "info     libmamba Download finished, validating '/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs/python-3.11.7-hab00c5b_1_cpython.conda'\n",
      "Linking _libgcc_mutex-0.1-conda_forge\n",
      "Linking ld_impl_linux-64-2.40-h41732ed_0\n",
      "Linking ca-certificates-2024.2.2-hbcca054_0\n",
      "Linking libgomp-13.2.0-h807b86a_5\n",
      "Linking _openmp_mutex-4.5-2_gnu\n",
      "Linking libgcc-ng-13.2.0-h807b86a_5\n",
      "Linking openssl-3.2.1-hd590300_0\n",
      "Linking libxcrypt-4.4.36-hd590300_1\n",
      "Linking libzlib-1.2.13-hd590300_5\n",
      "Linking libffi-3.4.2-h7f98852_5\n",
      "Linking bzip2-1.0.8-hd590300_5\n",
      "Linking ncurses-6.4-h59595ed_2\n",
      "Linking libuuid-2.38.1-h0b41bf4_0\n",
      "Linking libnsl-2.0.1-hd590300_0\n",
      "Linking libexpat-2.5.0-hcb278e6_1\n",
      "Linking xz-5.2.6-h166bdaf_0\n",
      "Linking tk-8.6.13-noxft_h4845f30_101\n",
      "Linking libsqlite-3.45.1-h2797004_0\n",
      "Linking readline-8.2-h8228510_1\n",
      "Linking tzdata-2024a-h0c530f3_0\n",
      "Linking python-3.11.7-hab00c5b_1_cpython\n",
      "info     libmamba New shebang path \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/bin/python3.11\"\n",
      "info     libmamba New shebang path \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/bin/python3.11\"\n",
      "info     libmamba New shebang path \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/bin/python3.11\"\n",
      "info     libmamba New shebang path \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/bin/python3.11\"\n",
      "Linking wheel-0.42.0-pyhd8ed1ab_0\n",
      "info     libmamba Running wrapped python compilation command /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/bin/python3.11 -Wi -u /tmp/mambafb63nWHdMl7\n",
      "info     libmamba Compiling 27 files to pyc\n",
      "Linking setuptools-69.0.3-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 221 files to pyc\n",
      "Linking pip-24.0-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 495 files to pyc\n",
      "Linking tomli-2.0.1-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 4 files to pyc\n",
      "Linking iniconfig-2.0.0-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 4 files to pyc\n",
      "Linking exceptiongroup-1.2.0-pyhd8ed1ab_2\n",
      "info     libmamba Compiling 6 files to pyc\n",
      "Linking packaging-23.2-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 14 files to pyc\n",
      "Linking colorama-0.4.6-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 13 files to pyc\n",
      "Linking pluggy-1.4.0-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 8 files to pyc\n",
      "Linking pytest-8.0.0-pyhd8ed1ab_0\n",
      "info     libmamba Compiling 72 files to pyc\n",
      "info     libmamba Waiting for pyc compilation to finish\n",
      "\n",
      "Transaction finished\n",
      "\n",
      "To activate this environment, use:\n",
      "\n",
      "    micromamba activate median\n",
      "\n",
      "Or to execute a single command in this environment, use:\n",
      "\n",
      "    micromamba run -n median mycommand\n",
      "\n",
      "info     libmamba Opening history file: \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/conda-meta/history\"\n",
      "\n",
      "Installing pip packages: hatch\n",
      "info     libmamba Calling: /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/bin/python -m pip install -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN --no-input\n",
      "Collecting hatch (from -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached hatch-1.9.3-py3-none-any.whl.metadata (5.2 kB)\n",
      "Collecting click>=8.0.6 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)\n",
      "Collecting hatchling>=1.21.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached hatchling-1.21.1-py3-none-any.whl.metadata (3.8 kB)\n",
      "Collecting httpx>=0.22.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached httpx-0.26.0-py3-none-any.whl.metadata (7.6 kB)\n",
      "Collecting hyperlink>=21.0.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached hyperlink-21.0.0-py2.py3-none-any.whl (74 kB)\n",
      "Collecting keyring>=23.5.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached keyring-24.3.0-py3-none-any.whl.metadata (20 kB)\n",
      "Requirement already satisfied: packaging>=21.3 in ./micromamba/envs/median/lib/python3.11/site-packages (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1)) (23.2)\n",
      "Collecting pexpect~=4.8 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)\n",
      "Collecting platformdirs>=2.5.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached platformdirs-4.2.0-py3-none-any.whl.metadata (11 kB)\n",
      "Collecting rich>=11.2.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached rich-13.7.0-py3-none-any.whl.metadata (18 kB)\n",
      "Collecting shellingham>=1.4.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)\n",
      "Collecting tomli-w>=1.0 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached tomli_w-1.0.0-py3-none-any.whl (6.0 kB)\n",
      "Collecting tomlkit>=0.11.1 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached tomlkit-0.12.3-py3-none-any.whl.metadata (2.7 kB)\n",
      "Collecting userpath~=1.7 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached userpath-1.9.1-py3-none-any.whl.metadata (3.0 kB)\n",
      "Collecting virtualenv>=20.16.2 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached virtualenv-20.25.0-py3-none-any.whl.metadata (4.5 kB)\n",
      "Collecting zstandard<1 (from hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached zstandard-0.22.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB)\n",
      "Collecting editables>=0.3 (from hatchling>=1.21.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached editables-0.5-py3-none-any.whl.metadata (3.1 kB)\n",
      "Collecting pathspec>=0.10.1 (from hatchling>=1.21.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached pathspec-0.12.1-py3-none-any.whl.metadata (21 kB)\n",
      "Requirement already satisfied: pluggy>=1.0.0 in ./micromamba/envs/median/lib/python3.11/site-packages (from hatchling>=1.21.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1)) (1.4.0)\n",
      "Collecting trove-classifiers (from hatchling>=1.21.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached trove_classifiers-2024.1.31-py3-none-any.whl.metadata (2.2 kB)\n",
      "Collecting anyio (from httpx>=0.22.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached anyio-4.2.0-py3-none-any.whl.metadata (4.6 kB)\n",
      "Collecting certifi (from httpx>=0.22.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)\n",
      "Collecting httpcore==1.* (from httpx>=0.22.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached httpcore-1.0.2-py3-none-any.whl.metadata (20 kB)\n",
      "Collecting idna (from httpx>=0.22.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)\n",
      "Collecting sniffio (from httpx>=0.22.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached sniffio-1.3.0-py3-none-any.whl (10 kB)\n",
      "Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx>=0.22.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached h11-0.14.0-py3-none-any.whl (58 kB)\n",
      "Collecting jaraco.classes (from keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached jaraco.classes-3.3.1-py3-none-any.whl.metadata (2.7 kB)\n",
      "Collecting importlib-metadata>=4.11.4 (from keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)\n",
      "Collecting SecretStorage>=3.2 (from keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached SecretStorage-3.3.3-py3-none-any.whl (15 kB)\n",
      "Collecting jeepney>=0.4.2 (from keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached jeepney-0.8.0-py3-none-any.whl (48 kB)\n",
      "Collecting ptyprocess>=0.5 (from pexpect~=4.8->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)\n",
      "Collecting markdown-it-py>=2.2.0 (from rich>=11.2.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)\n",
      "Collecting pygments<3.0.0,>=2.13.0 (from rich>=11.2.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)\n",
      "Collecting distlib<1,>=0.3.7 (from virtualenv>=20.16.2->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached distlib-0.3.8-py2.py3-none-any.whl.metadata (5.1 kB)\n",
      "Collecting filelock<4,>=3.12.2 (from virtualenv>=20.16.2->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)\n",
      "Collecting zipp>=0.5 (from importlib-metadata>=4.11.4->keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)\n",
      "Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich>=11.2.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)\n",
      "Collecting cryptography>=2.0 (from SecretStorage>=3.2->keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached cryptography-42.0.2-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (5.3 kB)\n",
      "Collecting more-itertools (from jaraco.classes->keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached more_itertools-10.2.0-py3-none-any.whl.metadata (34 kB)\n",
      "Collecting cffi>=1.12 (from cryptography>=2.0->SecretStorage>=3.2->keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached cffi-1.16.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB)\n",
      "Collecting pycparser (from cffi>=1.12->cryptography>=2.0->SecretStorage>=3.2->keyring>=23.5.0->hatch->-r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/mambafZ00rIbFDpN (line 1))\n",
      "  Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)\n",
      "Using cached hatch-1.9.3-py3-none-any.whl (110 kB)\n",
      "Using cached click-8.1.7-py3-none-any.whl (97 kB)\n",
      "Using cached hatchling-1.21.1-py3-none-any.whl (76 kB)\n",
      "Using cached httpx-0.26.0-py3-none-any.whl (75 kB)\n",
      "Using cached httpcore-1.0.2-py3-none-any.whl (76 kB)\n",
      "Using cached keyring-24.3.0-py3-none-any.whl (38 kB)\n",
      "Using cached pexpect-4.9.0-py2.py3-none-any.whl (63 kB)\n",
      "Using cached platformdirs-4.2.0-py3-none-any.whl (17 kB)\n",
      "Using cached rich-13.7.0-py3-none-any.whl (240 kB)\n",
      "Using cached shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)\n",
      "Using cached tomlkit-0.12.3-py3-none-any.whl (37 kB)\n",
      "Using cached userpath-1.9.1-py3-none-any.whl (9.1 kB)\n",
      "Using cached virtualenv-20.25.0-py3-none-any.whl (3.8 MB)\n",
      "Using cached zstandard-0.22.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)\n",
      "Using cached distlib-0.3.8-py2.py3-none-any.whl (468 kB)\n",
      "Using cached editables-0.5-py3-none-any.whl (5.1 kB)\n",
      "Using cached filelock-3.13.1-py3-none-any.whl (11 kB)\n",
      "Using cached idna-3.6-py3-none-any.whl (61 kB)\n",
      "Using cached importlib_metadata-7.0.1-py3-none-any.whl (23 kB)\n",
      "Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB)\n",
      "Using cached pathspec-0.12.1-py3-none-any.whl (31 kB)\n",
      "Using cached pygments-2.17.2-py3-none-any.whl (1.2 MB)\n",
      "Using cached anyio-4.2.0-py3-none-any.whl (85 kB)\n",
      "Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)\n",
      "Using cached jaraco.classes-3.3.1-py3-none-any.whl (6.8 kB)\n",
      "Using cached trove_classifiers-2024.1.31-py3-none-any.whl (13 kB)\n",
      "Using cached cryptography-42.0.2-cp39-abi3-manylinux_2_28_x86_64.whl (4.7 MB)\n",
      "Using cached zipp-3.17.0-py3-none-any.whl (7.4 kB)\n",
      "Using cached more_itertools-10.2.0-py3-none-any.whl (57 kB)\n",
      "Using cached cffi-1.16.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (464 kB)\n",
      "Installing collected packages: trove-classifiers, ptyprocess, distlib, zstandard, zipp, tomlkit, tomli-w, sniffio, shellingham, pygments, pycparser, platformdirs, pexpect, pathspec, more-itertools, mdurl, jeepney, idna, h11, filelock, editables, click, certifi, virtualenv, userpath, markdown-it-py, jaraco.classes, importlib-metadata, hyperlink, httpcore, hatchling, cffi, anyio, rich, httpx, cryptography, SecretStorage, keyring, hatch\n",
      "Successfully installed SecretStorage-3.3.3 anyio-4.2.0 certifi-2024.2.2 cffi-1.16.0 click-8.1.7 cryptography-42.0.2 distlib-0.3.8 editables-0.5 filelock-3.13.1 h11-0.14.0 hatch-1.9.3 hatchling-1.21.1 httpcore-1.0.2 httpx-0.26.0 hyperlink-21.0.0 idna-3.6 importlib-metadata-7.0.1 jaraco.classes-3.3.1 jeepney-0.8.0 keyring-24.3.0 markdown-it-py-3.0.0 mdurl-0.1.2 more-itertools-10.2.0 pathspec-0.12.1 pexpect-4.9.0 platformdirs-4.2.0 ptyprocess-0.7.0 pycparser-2.21 pygments-2.17.2 rich-13.7.0 shellingham-1.5.4 sniffio-1.3.0 tomli-w-1.0.0 tomlkit-0.12.3 trove-classifiers-2024.1.31 userpath-1.9.1 virtualenv-20.25.0 zipp-3.17.0 zstandard-0.22.0\n",
      "\u001b[44m\u001b[37m I \u001b[39m\u001b[49m Generating micromamba run shell.\n",
      "\u001b[47m\u001b[30m ▼ \u001b[39m\u001b[49m micromamba info\n",
      "[command]/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba info -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba -n median\n",
      "\n",
      "       libmamba version : 1.5.6\n",
      "     micromamba version : 1.5.6\n",
      "           curl version : libcurl/8.5.0 OpenSSL/3.2.0 zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.58.0\n",
      "     libarchive version : libarchive 3.7.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.5\n",
      "       envs directories : /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs\n",
      "          package cache : /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/pkgs\n",
      "                          /home/matt/.mamba/pkgs\n",
      "            environment : median\n",
      "           env location : /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median\n",
      "      user config files : /home/matt/.mambarc\n",
      " populated config files : \n",
      "       virtual packages : __unix=0=0\n",
      "                          __linux=6.5.0=0\n",
      "                          __glibc=2.38=0\n",
      "                          __archspec=1=x86_64-v4\n",
      "                          __cuda=12.2=0\n",
      "               channels : \n",
      "       base environment : /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba\n",
      "               platform : linux-64\n",
      "\u001b[47m\u001b[30m ▼ \u001b[39m\u001b[49m micromamba list\n",
      "[command]/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba list -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba -n median\n",
      "List of packages in environment: \"/home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median\"\n",
      "\n",
      "  Name              Version   Build               Channel    \n",
      "───────────────────────────────────────────────────────────────\n",
      "  _libgcc_mutex     0.1       conda_forge         conda-forge\n",
      "  _openmp_mutex     4.5       2_gnu               conda-forge\n",
      "  bzip2             1.0.8     hd590300_5          conda-forge\n",
      "  ca-certificates   2024.2.2  hbcca054_0          conda-forge\n",
      "  colorama          0.4.6     pyhd8ed1ab_0        conda-forge\n",
      "  exceptiongroup    1.2.0     pyhd8ed1ab_2        conda-forge\n",
      "  iniconfig         2.0.0     pyhd8ed1ab_0        conda-forge\n",
      "  ld_impl_linux-64  2.40      h41732ed_0          conda-forge\n",
      "  libexpat          2.5.0     hcb278e6_1          conda-forge\n",
      "  libffi            3.4.2     h7f98852_5          conda-forge\n",
      "  libgcc-ng         13.2.0    h807b86a_5          conda-forge\n",
      "  libgomp           13.2.0    h807b86a_5          conda-forge\n",
      "  libnsl            2.0.1     hd590300_0          conda-forge\n",
      "  libsqlite         3.45.1    h2797004_0          conda-forge\n",
      "  libuuid           2.38.1    h0b41bf4_0          conda-forge\n",
      "  libxcrypt         4.4.36    hd590300_1          conda-forge\n",
      "  libzlib           1.2.13    hd590300_5          conda-forge\n",
      "  ncurses           6.4       h59595ed_2          conda-forge\n",
      "  openssl           3.2.1     hd590300_0          conda-forge\n",
      "  packaging         23.2      pyhd8ed1ab_0        conda-forge\n",
      "  pip               24.0      pyhd8ed1ab_0        conda-forge\n",
      "  pluggy            1.4.0     pyhd8ed1ab_0        conda-forge\n",
      "  pytest            8.0.0     pyhd8ed1ab_0        conda-forge\n",
      "  python            3.11.7    hab00c5b_1_cpython  conda-forge\n",
      "  readline          8.2       h8228510_1          conda-forge\n",
      "  setuptools        69.0.3    pyhd8ed1ab_0        conda-forge\n",
      "  tk                8.6.13    noxft_h4845f30_101  conda-forge\n",
      "  tomli             2.0.1     pyhd8ed1ab_0        conda-forge\n",
      "  tzdata            2024a     h0c530f3_0          conda-forge\n",
      "  wheel             0.42.0    pyhd8ed1ab_0        conda-forge\n",
      "  xz                5.2.6     h166bdaf_0          conda-forge\n",
      "\u001b[44m\u001b[37m I \u001b[39m\u001b[49m Running micromamba command: clean\n",
      "Nothing to do.\n",
      "\n",
      "\n",
      "> median-build@0.1.0 build:python:wasi /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:python:wasi\n",
      "\n",
      ">> pnpm -c exec /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba -n median run --cwd python/itkwasm-median-wasi python -m pip install -e .\n",
      "Obtaining file:///home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/python/itkwasm-median-wasi\n",
      "  Installing build dependencies ... \u001b[?25ldone\n",
      "\u001b[?25h  Checking if build backend supports build_editable ... \u001b[?25ldone\n",
      "\u001b[?25h  Getting requirements to build editable ... \u001b[?25ldone\n",
      "\u001b[?25h  Preparing editable metadata (pyproject.toml) ... \u001b[?25ldone\n",
      "\u001b[?25hCollecting importlib-resources (from itkwasm-median-wasi==0.1.0)\n",
      "  Using cached importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB)\n",
      "Collecting itkwasm>=1.0.b145 (from itkwasm-median-wasi==0.1.0)\n",
      "  Using cached itkwasm-1.0b167-py3-none-any.whl.metadata (14 kB)\n",
      "Collecting numpy (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0)\n",
      "  Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)\n",
      "Requirement already satisfied: platformdirs in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0) (4.2.0)\n",
      "Collecting typing-extensions (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0)\n",
      "  Using cached typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)\n",
      "Collecting wasmtime>=13.0.2 (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0)\n",
      "  Using cached wasmtime-17.0.1-py3-none-manylinux1_x86_64.whl.metadata (7.3 kB)\n",
      "Using cached itkwasm-1.0b167-py3-none-any.whl (25 kB)\n",
      "Using cached importlib_resources-6.1.1-py3-none-any.whl (33 kB)\n",
      "Using cached wasmtime-17.0.1-py3-none-manylinux1_x86_64.whl (4.8 MB)\n",
      "Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB)\n",
      "Using cached typing_extensions-4.9.0-py3-none-any.whl (32 kB)\n",
      "Building wheels for collected packages: itkwasm-median-wasi\n",
      "  Building editable for itkwasm-median-wasi (pyproject.toml) ... \u001b[?25ldone\n",
      "\u001b[?25h  Created wheel for itkwasm-median-wasi: filename=itkwasm_median_wasi-0.1.0-py3-none-any.whl size=1677 sha256=acef4c0f039e84d85f3ba0713b81e75b4dee2e1626d67562a093fdf98bb76f79\n",
      "  Stored in directory: /tmp/pip-ephem-wheel-cache-_aoi0i7q/wheels/3f/55/34/ab9538a13bc5102bb09c5da30883cb9c71026e0334149bff2d\n",
      "Successfully built itkwasm-median-wasi\n",
      "Installing collected packages: wasmtime, typing-extensions, numpy, importlib-resources, itkwasm, itkwasm-median-wasi\n",
      "Successfully installed importlib-resources-6.1.1 itkwasm-1.0b167 itkwasm-median-wasi-0.1.0 numpy-1.26.4 typing-extensions-4.9.0 wasmtime-17.0.1\n"
     ]
    }
   ],
   "source": [
    "pnpm build"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The output includes *emscripten-build/* and *wasi-build/* directories, which contain the Emscripten and WASI builds, respectively.\n",
    "\n",
    "The *typescript/* and *python/* directories contain language bindings and package configurations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 128\n",
      "drwxrwxr-x 2 matt matt  4096 Feb 13 11:45 median-image-filter\n",
      "-rw-rw-r-- 1 matt matt    61 Feb 13 11:51 README.md\n",
      "-rw-rw-r-- 1 matt matt    27 Feb 13 11:51 pnpm-workspace.yaml\n",
      "-rw-rw-r-- 1 matt matt  2643 Feb 13 11:51 package.json\n",
      "-rw-rw-r-- 1 matt matt   109 Feb 13 11:51 environment.yml\n",
      "-rw-rw-r-- 1 matt matt 76836 Feb 13 12:15 pnpm-lock.yaml\n",
      "-rw-rw-r-- 1 matt matt   321 Feb 13 12:32 CMakeLists.txt\n",
      "drwxrwxr-x 5 matt matt  4096 Feb 13 12:33 python\n",
      "drwxrwxr-x 4 matt matt  4096 Feb 13 12:33 micromamba\n",
      "drwxrwxr-x 5 matt matt  4096 Feb 13 12:34 emscripten-build\n",
      "drwxrwxr-x 6 matt matt  4096 Feb 13 12:34 node_modules\n",
      "drwxrwxr-x 8 matt matt  4096 Feb 13 12:34 typescript\n",
      "drwxrwxr-x 3 matt matt  4096 Feb 13 12:34 test\n",
      "drwxrwxr-x 6 matt matt  4096 Feb 13 12:39 wasi-build\n"
     ]
    }
   ],
   "source": [
    "ls -ltr"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To list the available targets for `pnpm`, run `pnpm run`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Lifecycle scripts:\n",
      "  test\n",
      "    pnpm test:data:download && pnpm build:gen:python && pnpm test:python\n",
      "\n",
      "Commands available via \"pnpm run\":\n",
      "  build\n",
      "    pnpm build:gen:typescript && pnpm build:gen:python\n",
      "  build:emscripten\n",
      "    itk-wasm pnpm-script build:emscripten\n",
      "  build:emscripten:debug\n",
      "    itk-wasm pnpm-script build:emscripten:debug\n",
      "  build:wasi\n",
      "    itk-wasm pnpm-script build:wasi\n",
      "  build:wasi:debug\n",
      "    itk-wasm pnpm-script build:wasi:debug\n",
      "  build:python:wasi\n",
      "    itk-wasm pnpm-script build:python:wasi\n",
      "  bindgen:typescript\n",
      "    itk-wasm pnpm-script bindgen:typescript\n",
      "  bindgen:python\n",
      "    itk-wasm pnpm-script bindgen:python\n",
      "  build:gen:typescript\n",
      "    itk-wasm pnpm-script build:gen:typescript\n",
      "  build:gen:python\n",
      "    itk-wasm pnpm-script build:gen:python\n",
      "  build:micromamba\n",
      "    itk-wasm pnpm-script build:micromamba\n",
      "  build:python:versionSync\n",
      "    itk-wasm pnpm-script build:python:versionSync\n",
      "  publish:python\n",
      "    itk-wasm pnpm-script publish:python\n",
      "  test:data:download\n",
      "    dam download test/data test/data.tar.gz bafkreigpkk3pqcoqzjzcauogw6dml52yig3ksmcrobau5pkoictymizzri https://github.com/InsightSoftwareConsortium/itk-wasm/releases/download/itk-wasm-v1.0.0-b.163/create-itk-wasm-test-data.tar.gz https://bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca.ipfs.w3s.link/ipfs/bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca/create-itk-wasm-test-data.tar.gz https://ipfs.filebase.io/ipfs/QmcxyvUKnaoTTwUqEPXwp1sdcbrFh3XnnwckLKVRpctJx9\n",
      "  test:data:pack\n",
      "    dam pack test/data test/data.tar.gz\n",
      "  test:python:wasi\n",
      "    itk-wasm pnpm-script test:python:wasi\n",
      "  test:python:emscripten\n",
      "    itk-wasm pnpm-script test:python:emscripten\n",
      "  test:python:dispatch\n",
      "    itk-wasm pnpm-script test:python:emscripten\n",
      "  test:python\n",
      "    itk-wasm pnpm-script test:python\n",
      "  test:wasi\n",
      "    itk-wasm pnpm-script test:wasi\n"
     ]
    }
   ],
   "source": [
    "pnpm run"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "tags": []
   },
   "source": [
    "To run the CLI help test, run `pnpm test:wasi`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "> median-build@0.1.0 test:wasi /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script test:wasi\n",
      "\n",
      ">> pnpm -c exec pnpm test:data:download && itk-wasm test -- --output-on-failure\n",
      "\n",
      "> median-build@0.1.0 test:data:download /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> dam download test/data test/data.tar.gz bafkreigpkk3pqcoqzjzcauogw6dml52yig3ksmcrobau5pkoictymizzri https://github.com/InsightSoftwareConsortium/itk-wasm/releases/download/itk-wasm-v1.0.0-b.163/create-itk-wasm-test-data.tar.gz https://bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca.ipfs.w3s.link/ipfs/bafybeiczuxeuma5cjuli5mtapqnjqypeaum5ikd45zcmfhtt2emp365tca/create-itk-wasm-test-data.tar.gz https://ipfs.filebase.io/ipfs/QmcxyvUKnaoTTwUqEPXwp1sdcbrFh3XnnwckLKVRpctJx9\n",
      "\n",
      "Internal ctest changing into directory: /work/wasi-build\n",
      "Test project /work/wasi-build\n",
      "    Start 1: median-image-filter-help\n",
      "1/1 Test #1: median-image-filter-help .........   Passed    0.00 sec\n",
      "\n",
      "\u001b[0;32m100% tests passed\u001b[0;0m, 0 tests failed\u001b[0;0m out of 1\n",
      "\n",
      "Total Test time (real) =   0.00 sec\n"
     ]
    }
   ],
   "source": [
    "pnpm test:wasi"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This runs the equivalent of:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "warning: this CLI invocation of Wasmtime will be parsed differently in future\n",
      "         Wasmtime versions -- see this online issue for more information:\n",
      "         https://github.com/bytecodealliance/wasmtime/issues/7384\n",
      "\n",
      "         Wasmtime will now execute with the old (<= Wasmtime 13) CLI parsing,\n",
      "         however this behavior can also be temporarily configured with an\n",
      "         environment variable:\n",
      "\n",
      "         - WASMTIME_NEW_CLI=0 to indicate old semantics are desired and silence this warning, or\n",
      "         - WASMTIME_NEW_CLI=1 to indicate new semantics are desired and use the latest behavior\n",
      "\u001b[39m\u001b[94m\u001b[3m\u001b[2m       Welcome to\u001b[39m\u001b[1m\n",
      "  __\u001b[39m\u001b[93m/\\\\\\\\\\\\\\\\\\\\\\\u001b[39m\u001b[94m__\u001b[39m\u001b[93m/\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\u001b[39m\u001b[94m__\u001b[39m\u001b[93m/\\\\\\\u001b[39m\u001b[94m________\u001b[39m\u001b[93m/\\\\\\\u001b[39m\u001b[94m_\n",
      "  _\u001b[39m\u001b[93m\\/////\\\\\\///\u001b[39m\u001b[94m__\u001b[39m\u001b[93m\\///////\\\\\\/////\u001b[39m\u001b[94m__\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_____\u001b[39m\u001b[93m/\\\\\\//\u001b[39m\u001b[94m__\n",
      "  _____\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m___________\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m__\u001b[39m\u001b[93m/\\\\\\//\u001b[39m\u001b[94m_____\n",
      "    _____\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m___________\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\\\\\\\//\\\\\\\u001b[39m\u001b[94m_____\n",
      "    _____\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m___________\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\//\u001b[39m\u001b[94m_\u001b[39m\u001b[93m\\//\\\\\\\u001b[39m\u001b[94m____\n",
      "      _____\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m___________\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m____\u001b[39m\u001b[93m\\//\\\\\\\u001b[39m\u001b[94m___\n",
      "      _____\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m___________\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_____\u001b[39m\u001b[93m\\//\\\\\\\u001b[39m\u001b[94m__\n",
      "        __\u001b[39m\u001b[93m/\\\\\\\\\\\\\\\\\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m_______\u001b[39m\u001b[93m\\/\\\\\\\u001b[39m\u001b[94m______\u001b[39m\u001b[93m\\//\\\\\\\u001b[39m\u001b[94m_\n",
      "        _\u001b[39m\u001b[93m\\///////////\u001b[39m\u001b[94m________\u001b[39m\u001b[93m\\///\u001b[39m\u001b[94m________\u001b[39m\u001b[93m\\///\u001b[39m\u001b[94m________\u001b[39m\u001b[93m\\///\u001b[39m\u001b[94m__\n",
      "  \u001b[0m\u001b[49m\u001b[39m\n",
      "\u001b[95m\u001b[1mComputes an image where a given pixel is the median value of the the pixels in a neighborhood about the corresponding input pixel.\n",
      "\u001b[39m\u001b[0m\u001b[33mUsage:\u001b[39m\u001b[35m median-image-filter\u001b[1m\u001b[36m input-image output-image\u001b[32m [OPTIONS]\n",
      "\u001b[39m\u001b[0m\n",
      "\u001b[33mPositionals:\n",
      "\u001b[39m\u001b[36m  input-image\u001b[39m INPUT_IMAGE REQUIRED\n",
      "\u001b[36m   \u001b[39m                           The input image\n",
      "\u001b[36m  output-image\u001b[39m OUTPUT_IMAGE REQUIRED\n",
      "\u001b[36m   \u001b[39m                           The output image\n",
      "\n",
      "\u001b[33mOptions:\n",
      "\u001b[39m\u001b[32m  --version\u001b[39m                   Display program version information and exit\n",
      "\u001b[32m  -h,--help\u001b[39m                   Print this help message and exit\n",
      "\u001b[32m  -r,--radius\u001b[39m UINT            Kernel radius in pixels\n",
      "\n",
      "\u001b[34m\u001b[3mEnjoy ITK!\n",
      "\u001b[39m\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "wasmtime run --dir=./ wasi-build/median-image-filter/median-image-filter.wasi.wasm -- --help"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Add the following C++ code to *median-image-filter.cxx* to provide the logic and implementation of the processing pipeline.\n",
    "\n",
    "```cpp\n",
    "  #include \"itkMedianImageFilter.h\"\n",
    "\n",
    "  // [...]\n",
    "\n",
    "  using SmoothingFilterType = itk::MedianImageFilter<ImageType, ImageType>;\n",
    "  auto smoother = SmoothingFilterType::New();\n",
    "  smoother->SetInput(inputImage);\n",
    "  smoother->SetRadius(radius);\n",
    "\n",
    "  smoother->UpdateLargestPossibleRegion();\n",
    "  outputImage.Set(smoother->GetOutput());\n",
    "```\n",
    "\n",
    "and `ITKSmoothing` to the `ITK` package components in the top level *CMakeLists.txt*.\n",
    "\n",
    "Re-build."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "> median-build@0.1.0 build /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> pnpm build:gen:typescript && pnpm build:gen:python\n",
      "\n",
      "\n",
      "> median-build@0.1.0 build:gen:typescript /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:gen:typescript\n",
      "\n",
      ">> pnpm -c exec pnpm build:emscripten && pnpm bindgen:typescript && pnpm install && pnpm -r build\n",
      "\n",
      "> median-build@0.1.0 build:emscripten /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:emscripten\n",
      "\n",
      ">> pnpm -c exec itk-wasm build -i itkwasm/emscripten:20231217-40780708\n",
      "Not searching for unused variables given on the command line.\n",
      "-- Configuring done\n",
      "-- Generating done\n",
      "-- Build files have been written to: /work/emscripten-build\n",
      "ninja: Entering directory `emscripten-build'\n",
      "[2/2] Linking CXX executable median-image-filter/median-image-filter.js\u001b[Kcxx.o\u001b[K\n",
      "cache:INFO: generating system asset: symbol_lists/c824dc42a311ced7c4de2a6267617f2f158d990a.json... (this will be cached in \"/emsdk/upstream/emscripten/cache/symbol_lists/c824dc42a311ced7c4de2a6267617f2f158d990a.json\" for subsequent builds)\n",
      "cache:INFO:  - ok\n",
      "/work/emscripten-build/median-image-filter/median-image-filter.wasm : 31.64%   (   683 KiB =>    216 KiB, /work/emscripten-build/median-image-filter/median-image-filter.wasm.zst) \n",
      "\n",
      "> median-build@0.1.0 bindgen:typescript /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script bindgen:typescript\n",
      "\n",
      ">> pnpm -c exec itk-wasm -b emscripten-build bindgen --interface typescript --output-dir typescript --package-name @itk-wasm/median --package-description Apply a median filter to a 2D or 3D spatial image. --repository https://github.com/InsightSoftwareConsortium/itk-wasm\n",
      "Scope: all 2 workspace projects\n",
      "Lockfile is up to date, resolution step is skipped\n",
      "Already up to date\n",
      "Done in 403ms\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> pnpm build:tsc && pnpm build:browser:workerEmbedded && pnpm build:browser:workerEmbeddedMin && pnpm build:demo\n",
      "\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:tsc /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> tsc --pretty\n",
      "\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:browser:workerEmbedded /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> esbuild --loader:.worker.js=dataurl --bundle --format=esm --outfile=./dist/bundle/index-worker-embedded.js ./src/index-worker-embedded.ts\n",
      "\n",
      "\n",
      "  \u001b[37mdist/bundle/\u001b[0m\u001b[1mindex-worker-embedded.js\u001b[0m  \u001b[36m263.7kb\u001b[0m\n",
      "\n",
      "⚡ \u001b[32mDone in 8ms\u001b[0m\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:browser:workerEmbeddedMin /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> esbuild --minify --loader:.worker.js=dataurl --bundle --format=esm --outfile=./dist/bundle/index-worker-embedded.min.js ./src/index-worker-embedded.min.ts\n",
      "\n",
      "\n",
      "  \u001b[37mdist/bundle/\u001b[0m\u001b[1mindex-worker-embedded.min.js\u001b[0m  \u001b[36m134.7kb\u001b[0m\n",
      "\n",
      "⚡ \u001b[32mDone in 8ms\u001b[0m\n",
      "\n",
      "> @itk-wasm/median@0.1.0 build:demo /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> pnpm copyShoelaceAssets && vite build\n",
      "\n",
      "\n",
      "> @itk-wasm/median@0.1.0 copyShoelaceAssets /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/typescript\n",
      "> shx mkdir -p test/browser/demo-app/public && shx cp -r node_modules/@shoelace-style/shoelace/dist/assets test/browser/demo-app/public/\n",
      "\n",
      "\u001b[36mvite v4.5.2 \u001b[32mbuilding for production...\u001b[36m\u001b[39m\n",
      "\u001b[2K\u001b[1Gtransforming (1) \u001b[2mindex.html\u001b[22m\u001b[2K\u001b[1Gtransforming (60) \u001b[2m../../../../node_modules/.pnpm/@shoelace-style+shoelace@2\u001b[2K\u001b[1Gtransforming (160) \u001b[2m../../../../node_modules/.pnpm/@floating-ui+core@1.6.0/n\u001b[2K\u001b[1Gtransforming (237) \u001b[2m../../../../node_modules/.pnpm/@itk-wasm+image-io@1.1.0/\u001b[2K\u001b[1Gtransforming (296) \u001b[2m../../../../node_modules/.pnpm/itk-wasm@1.0.0-b.166/node\u001b[2K\u001b[1Gtransforming (349) \u001b[2m../../../../node_modules/.pnpm/@shoelace-style+shoelace@\u001b[2K\u001b[1G\u001b[32m✓\u001b[39m 352 modules transformed.\n",
      "\u001b[2K\u001b[1Grendering chunks (1)...\u001b[2K\u001b[1G\u001b[2K\u001b[1Gcomputing gzip size (0)...\u001b[2K\u001b[1Gcomputing gzip size (1)...\u001b[2K\u001b[1Gcomputing gzip size (2)...\u001b[2K\u001b[1Gcomputing gzip size (3)...\u001b[2K\u001b[1Gcomputing gzip size (4)...\u001b[2K\u001b[1Gcomputing gzip size (5)...\u001b[2K\u001b[1Gcomputing gzip size (6)...\u001b[2K\u001b[1G\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mtypescript-logo-336a54a4.svg          \u001b[39m\u001b[1m\u001b[2m  0.91 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  0.53 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mjavascript-logo-35328c60.svg          \u001b[39m\u001b[1m\u001b[2m  1.07 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  0.60 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mlogo-964238ba.svg                     \u001b[39m\u001b[1m\u001b[2m  2.95 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  1.38 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[32mindex.html                                   \u001b[39m\u001b[1m\u001b[2m  5.24 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  2.14 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[32mitk-wasm-pipeline.worker-21bb29ff.js  \u001b[39m\u001b[1m\u001b[2m 89.96 kB\u001b[22m\u001b[1m\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[35mindex-1a3477e4.css                    \u001b[39m\u001b[1m\u001b[2m 36.99 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip:  6.85 kB\u001b[22m\n",
      "\u001b[2m../../../demo-app/\u001b[22m\u001b[2massets/\u001b[22m\u001b[36mindex-0df74da5.js                     \u001b[39m\u001b[1m\u001b[2m326.52 kB\u001b[22m\u001b[1m\u001b[22m\u001b[2m │ gzip: 75.83 kB\u001b[22m\n",
      "\u001b[36m[vite-plugin-static-copy]\u001b[39m \u001b[32mCopied 201 items.\u001b[39m\n",
      "\u001b[32m✓ built in 1.17s\u001b[39m\n",
      "\n",
      "> median-build@0.1.0 build:gen:python /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:gen:python\n",
      "\n",
      ">> pnpm -c exec pnpm build:wasi && pnpm bindgen:python && pnpm build:micromamba && pnpm build:python:wasi\n",
      "\n",
      "> median-build@0.1.0 build:wasi /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:wasi\n",
      "\n",
      ">> pnpm -c exec itk-wasm build -i itkwasm/wasi:20231217-40780708\n",
      "Not searching for unused variables given on the command line.\n",
      "-- Configuring done\n",
      "-- Generating done\n",
      "-- Build files have been written to: /work/wasi-build\n",
      "ninja: Entering directory `wasi-build'\n",
      "[6/6] Linking CXX executable median-image-filter/median-image-filter.wasi.wasm\u001b[KK\n",
      "\n",
      "> median-build@0.1.0 bindgen:python /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script bindgen:python\n",
      "\n",
      ">> pnpm -c exec itk-wasm -b wasi-build bindgen --interface python --output-dir python --package-name itkwasm-median --package-description Apply a median filter to a 2D or 3D spatial image. --repository https://github.com/InsightSoftwareConsortium/itk-wasm\n",
      "\n",
      "> median-build@0.1.0 build:micromamba /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:micromamba\n",
      "\n",
      ">> pnpm -c exec setup-micromamba --micromamba-binary-path ./micromamba/micromamba --micromamba-root-path micromamba --init-shell none --create-environment true --environment-file environment.yml --log-level info --run-command clean -fya\n",
      "\u001b[44m\u001b[37m I \u001b[39m\u001b[49m Running micromamba command: clean\n",
      "Nothing to do.\n",
      "\n",
      "\n",
      "> median-build@0.1.0 build:python:wasi /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median\n",
      "> itk-wasm pnpm-script build:python:wasi\n",
      "\n",
      ">> pnpm -c exec /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/micromamba -r /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba -n median run --cwd python/itkwasm-median-wasi python -m pip install -e .\n",
      "Obtaining file:///home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/python/itkwasm-median-wasi\n",
      "  Installing build dependencies ... \u001b[?25ldone\n",
      "\u001b[?25h  Checking if build backend supports build_editable ... \u001b[?25ldone\n",
      "\u001b[?25h  Getting requirements to build editable ... \u001b[?25ldone\n",
      "\u001b[?25h  Preparing editable metadata (pyproject.toml) ... \u001b[?25ldone\n",
      "\u001b[?25hRequirement already satisfied: importlib-resources in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm-median-wasi==0.1.0) (6.1.1)\n",
      "Requirement already satisfied: itkwasm>=1.0.b145 in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm-median-wasi==0.1.0) (1.0b167)\n",
      "Requirement already satisfied: numpy in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0) (1.26.4)\n",
      "Requirement already satisfied: platformdirs in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0) (4.2.0)\n",
      "Requirement already satisfied: typing-extensions in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0) (4.9.0)\n",
      "Requirement already satisfied: wasmtime>=13.0.2 in /home/matt/src/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse/wasm-median/micromamba/envs/median/lib/python3.11/site-packages (from itkwasm>=1.0.b145->itkwasm-median-wasi==0.1.0) (17.0.1)\n",
      "Building wheels for collected packages: itkwasm-median-wasi\n",
      "  Building editable for itkwasm-median-wasi (pyproject.toml) ... \u001b[?25ldone\n",
      "\u001b[?25h  Created wheel for itkwasm-median-wasi: filename=itkwasm_median_wasi-0.1.0-py3-none-any.whl size=1677 sha256=acef4c0f039e84d85f3ba0713b81e75b4dee2e1626d67562a093fdf98bb76f79\n",
      "  Stored in directory: /tmp/pip-ephem-wheel-cache-giw4c285/wheels/3f/55/34/ab9538a13bc5102bb09c5da30883cb9c71026e0334149bff2d\n",
      "Successfully built itkwasm-median-wasi\n",
      "Installing collected packages: itkwasm-median-wasi\n",
      "  Attempting uninstall: itkwasm-median-wasi\n",
      "    Found existing installation: itkwasm-median-wasi 0.1.0\n",
      "    Uninstalling itkwasm-median-wasi-0.1.0:\n",
      "      Successfully uninstalled itkwasm-median-wasi-0.1.0\n",
      "Successfully installed itkwasm-median-wasi-0.1.0\n"
     ]
    }
   ],
   "source": [
    "pnpm build"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Congratulations!**. You created a WebAssembly module that con median-filter a 2D or 3D scientific image."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "jp-MarkdownHeadingCollapsed": true,
    "tags": []
   },
   "source": [
    "## Exercises\n",
    "\n",
    "### 1. Run the web demo-application\n",
    "\n",
    "A demo JavaScript application. Build and run it:\n",
    "\n",
    "```sh\n",
    "cd typescript\n",
    "pnpm install\n",
    "pnpm build\n",
    "pnpm start\n",
    "```\n",
    "\n",
    "### 2. Add a CTest test\n",
    "\n",
    "Add a CTest test in *median-image-filter/CMakeLists.txt* that runs on the *data/visible-male.nrrd* image.\n",
    "\n",
    "### 3. Create a Node.js test\n",
    "\n",
    "Create a Node.js test with the `ava` test runner.\n",
    "\n",
    "```sh\n",
    "cd typescript\n",
    "pnpm install -D ava\n",
    "# Add the tests in test/node/visible-male.js\n",
    "```\n",
    "\n",
    "*Hint:* See the itk-wasm packages for example code.\n",
    "\n",
    "### 4. Create a Python wasi test with pytest\n",
    "\n",
    "Create a pytest test in *python/itkwasm-median-wasi/test/*."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Enjoy ITK!"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Bash",
   "language": "bash",
   "name": "bash"
  },
  "language_info": {
   "codemirror_mode": "shell",
   "file_extension": ".sh",
   "mimetype": "text/x-sh",
   "name": "bash"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}