feat(bindgen): Add python WASI support

.github/workflows/python-wasm.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -30,3 +30,26 @@ jobs:
         uses: mikepenz/action-junit-report@v2
         with:
           report_paths: 'src/python/itkwasm/junit/test-results*.xml'
+
+  test-pythonpackages:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 3
+      matrix:
+        os: [ubuntu-22.04, windows-2022, macos-12]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install hatch
+      - name: Test compress-stringify wasi
+        working-directory: ./packages/compress-stringify/python/compress-stringify-wasi
+        run: |
+          hatch run test

package.json

@@ -35,12 +35,13 @@
     "build:emscripten": "node ./src/build-emscripten.js",
     "build:emscripten:compress-stringify": "node ./src/itk-wasm-cli.js -s packages/compress-stringify -b emscripten-build build ",
     "build:bindgen:typescript:compress-stringify": "./src/itk-wasm-cli.js -s packages/compress-stringify -b emscripten-build bindgen --package-name @itk-wasm/compress-stringify --package-description \"Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:python:compress-stringify": "./src/itk-wasm-cli.js -s packages/compress-stringify -b wasi-build bindgen --language python --package-name compress-stringify --package-description \"Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:emscripten:dicom": "node ./src/itk-wasm-cli.js -s packages/dicom -b emscripten-build build ",
     "build:bindgen:typescript:dicom": "./src/itk-wasm-cli.js -s packages/dicom -b emscripten-build bindgen --package-name @itk-wasm/dicom --package-description \"Read files and images related to DICOM file format.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:emscripten:packages": "npm run build:emscripten:compress-stringify && npm run build:bindgen:typescript:compress-stringify && npm run build:emscripten:dicom && npm run build:bindgen:typescript:dicom",
     "build:wasi": "node ./src/build-wasi.js && npm run build:wasi:packages",
     "build:wasi:compress-stringify": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/compress-stringify -b wasi-build build",
-    "build:wasi:packages": "npm run build:wasi:compress-stringify",
+    "build:wasi:packages": "npm run build:wasi:compress-stringify && npm run build:bindgen:python:compress-stringify",
     "cypress:open": "npx cypress open",
     "cypress:run": "npx cypress run --config defaultCommandTimeout=8000",
     "cypress:install": "npx cypress install",

packages/compress-stringify/python/compress-stringify-wasi/README.md

@@ -0,0 +1,11 @@
+# compress-stringify-wasi
+
+[![PyPI version](https://badge.fury.io/py/compress-stringify-wasi.svg)](https://badge.fury.io/py/compress-stringify-wasi)
+
+Zstandard compression and decompression and base64 encoding and decoding in WebAssembly. WASI implementation.
+
+## Installation
+
+```sh
+pip install compress-stringify-wasi
+```

packages/compress-stringify/python/compress-stringify-wasi/compress_stringify_wasi/__init__.py

@@ -0,0 +1,6 @@
+"""compress-stringify-wasi: Zstandard compression and decompression and base64 encoding and decoding in WebAssembly. WASI implementation."""
+
+from .compress_stringify import compress_stringify
+from .parse_string_decompress import parse_string_decompress
+
+from ._version import __version__

packages/compress-stringify/python/compress-stringify-wasi/compress_stringify_wasi/_version.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

packages/compress-stringify/python/compress-stringify-wasi/compress_stringify_wasi/compress_stringify.py

@@ -0,0 +1,83 @@
+# Generated file. Do not edit.
+
+from pathlib import Path
+import os
+from typing import Dict, Tuple
+
+from importlib_resources import files as file_resources
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    BinaryStream,
+)
+
+def compress_stringify(
+    input: bytes,
+    stringify: bool = False,
+    compression_level: int = 3,
+    data_url_prefix: str = "data:base64,",
+) -> bytes:
+    """Given a binary, compress and optionally base64 encode.
+
+    Parameters
+    ----------
+
+    input: bytes
+        Input binary
+
+    stringify: bool, optional
+        Stringify the output
+
+    compression_level: int, optional
+        Compression level, typically 1-9
+
+    data_url_prefix: str, optional
+        dataURL prefix
+
+
+    Returns
+    -------
+
+    bytes
+        Output compressed binary
+
+    """
+    pipeline = Pipeline(file_resources('compress_stringify_wasi').joinpath(Path('wasm_modules') / Path('compress-stringify.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.BinaryStream),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.BinaryStream, BinaryStream(input)),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    args.append('0')
+    # Outputs
+    args.append('0')
+    # Options
+    if stringify is not None:
+        args.append('--stringify')
+
+    if compression_level is not None:
+        args.append('--compression-level')
+        args.append(str(compression_level))
+
+    if data_url_prefix is not None:
+        args.append('--data-url-prefix')
+        args.append(str(data_url_prefix))
+
+
+
+    outputs = pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = outputs[0].data.data
+    return result
+
+
+    del pipeline

packages/compress-stringify/python/compress-stringify-wasi/compress_stringify_wasi/parse_string_decompress.py

@@ -0,0 +1,67 @@
+# Generated file. Do not edit.
+
+from pathlib import Path
+import os
+from typing import Dict, Tuple
+
+from importlib_resources import files as file_resources
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    BinaryStream,
+)
+
+def parse_string_decompress(
+    input: bytes,
+    parse_string: bool = False,
+) -> bytes:
+    """Given a binary or string produced with compress-stringify, decompress and optionally base64 decode.
+
+    Parameters
+    ----------
+
+    input: bytes
+        Compressed input
+
+    parse_string: bool, optional
+        Parse the input string before decompression
+
+
+    Returns
+    -------
+
+    bytes
+        Output decompressed binary
+
+    """
+    pipeline = Pipeline(file_resources('compress_stringify_wasi').joinpath(Path('wasm_modules') / Path('parse-string-decompress.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.BinaryStream),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.BinaryStream, BinaryStream(input)),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    args.append('0')
+    # Outputs
+    args.append('0')
+    # Options
+    if parse_string is not None:
+        args.append('--parse-string')
+
+
+
+    outputs = pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = outputs[0].data.data
+    return result
+
+
+    del pipeline

packages/compress-stringify/python/compress-stringify-wasi/pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "compress-stringify-wasi"
+readme = "README.md"
+license = "Apache-2.0"
+dynamic = ["version", "description"]
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python",
+    "Programming Language :: C++",
+    "Environment :: WebAssembly",
+    "Environment :: WebAssembly :: Emscripten",
+    "Environment :: WebAssembly :: WASI",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+keywords = [
+    "itkwasm",
+    "webassembly",
+    "emscripten",
+    "wasi",
+]
+
+requires-python = ">=3.7"
+dependencies = [
+    "itkwasm >= 1.0b.82",
+    "importlib_resources",
+]
+
+[tool.hatch.version]
+path = "compress_stringify_wasi/_version.py"
+
+[tool.hatch.envs.default]
+dependencies = [
+  "pytest",
+]
+
+[tool.hatch.envs.default.scripts]
+test = "pytest"
+
+[tool.hatch.build]
+exclude = [
+  "/examples",
+]

packages/compress-stringify/python/compress-stringify-wasi/test/test_compress_stringify.py

@@ -0,0 +1,33 @@
+from compress_stringify_wasi import compress_stringify, parse_string_decompress
+
+def test_decompress_returns_what_was_compressed():
+    data = bytes([222, 173, 190, 239])
+    compressed_data = compress_stringify(data, compression_level=8)
+    decompressed_data = parse_string_decompress(compressed_data)
+
+    assert decompressed_data[0] == 222
+    assert decompressed_data[1] == 173
+    assert decompressed_data[2] == 190
+    assert decompressed_data[3] == 239
+
+def test_we_can_stringify_during_compression():
+    data = bytes([222, 173, 190, 239])
+    compressed_data = compress_stringify(data, compression_level=8, stringify=True)
+    assert compressed_data.decode() == 'data:base64,KLUv/SAEIQAA3q2+7w=='
+    decompressed_data = parse_string_decompress(compressed_data, parse_string=True)
+
+    assert decompressed_data[0] == 222
+    assert decompressed_data[1] == 173
+    assert decompressed_data[2] == 190
+    assert decompressed_data[3] == 239
+
+def test_we_can_use_a_custom_data_url_prefix():
+    data = bytes([222, 173, 190, 239])
+    compressed_data = compress_stringify(data, compression_level=8, stringify=True, data_url_prefix='custom,')
+    assert compressed_data.decode() == 'custom,KLUv/SAEIQAA3q2+7w=='
+    decompressed_data = parse_string_decompress(compressed_data, parse_string=True)
+
+    assert decompressed_data[0] == 222
+    assert decompressed_data[1] == 173
+    assert decompressed_data[2] == 190
+    assert decompressed_data[3] == 239

packages/compress-stringify/typescript/test/node/compressStringifyTest.js

@@ -28,9 +28,9 @@ test('We can stringify during compression', async t => {
 
 test('We can use a custom dataUrlPrefix', async t => {
   const data = new Uint8Array([222, 173, 190, 239])
-  const { output: compressedData } = await compressStringifyNode(data, { compressionLevel: 8, stringify: true, dataUrlPrefix: 'data:base64,' })
+  const { output: compressedData } = await compressStringifyNode(data, { compressionLevel: 8, stringify: true, dataUrlPrefix: 'custom,' })
   const decoder = new TextDecoder()
-  t.is(decoder.decode(compressedData.buffer), 'data:base64,KLUv/SAEIQAA3q2+7w==')
+  t.is(decoder.decode(compressedData.buffer), 'custom,KLUv/SAEIQAA3q2+7w==')
   const { output: decompressedData } = await parseStringDecompressNode(compressedData, { parseString: true })
 
   t.is(decompressedData[0], 222)

packages/dicom/typescript/src/apply-presentation-state-to-image-options.ts

@@ -1,6 +1,6 @@
 interface ApplyPresentationStateToImageOptions {
   /** filename: string. Process using presentation state file */
-  presentationStateFile?: Uint8Array
+  presentationStateFile: Uint8Array
 
   /** filename: string. Process using settings from configuration file */
   configFile?: string

src/bindgen/interfaceJsonNodeWasi.js

@@ -0,0 +1,20 @@
+import { readFile } from 'node:fs/promises';
+import { WASI } from 'wasi';
+import { argv, env } from 'node:process';
+
+const wasi = new WASI({
+  args: ['--interface-json'],
+  env,
+  preopens: {
+  },
+});
+
+const importObject = { wasi_snapshot_preview1: wasi.wasiImport };
+
+const wasm = await WebAssembly.compile(
+  await readFile(new URL(process.argv[2], import.meta.url)),
+);
+const instance = await WebAssembly.instantiate(wasm, importObject);
+
+wasi.initialize(instance);
+instance.exports['']()

src/bindgen/interfaceJsonTypeToInterfaceType.js

@@ -0,0 +1,19 @@
+const interfaceJsonTypeToInterfaceType = new Map([
+  ['INPUT_TEXT_FILE:FILE', 'TextFile'],
+  ['OUTPUT_TEXT_FILE:FILE', 'TextFile'],
+  ['INPUT_BINARY_FILE:FILE', 'BinaryFile'],
+  ['OUTPUT_BINARY_FILE:FILE', 'BinaryFile'],
+  ['INPUT_TEXT_STREAM', 'TextStream'],
+  ['OUTPUT_TEXT_STREAM', 'TextStream'],
+  ['INPUT_BINARY_STREAM', 'BinaryStream'],
+  ['OUTPUT_BINARY_STREAM', 'BinaryStream'],
+  ['INPUT_IMAGE', 'Image'],
+  ['OUTPUT_IMAGE', 'Image'],
+  ['INPUT_MESH', 'Mesh'],
+  ['OUTPUT_MESH', 'Mesh'],
+  ['INPUT_POLYDATA', 'PolyData'],
+  ['OUTPUT_POLYDATA', 'PolyData'],
+  ['OUTPUT_JSON', 'JsonObject'],
+])
+
+export default interfaceJsonTypeToInterfaceType