Add out-of-tree Pyodide builds in CI for scikit-image

.github/workflows/emscripten.yml

@@ -0,0 +1,88 @@
+# Copied from NumPy https://github.com/numpy/numpy/pull/25894
+# https://github.com/numpy/numpy/blob/d2d2c25fa81b47810f5cbd85ea6485eb3a3ffec3/.github/workflows/emscripten.yml
+#
+
+name: Test Emscripten/Pyodide build
+
+on:
+  pull_request:
+    branches:
+      - main
+      - maintenance/**
+  # TODO: refine after this is ready to merge
+  push:
+    # branches:
+    #   - main
+    #   - maintenance/**
+  workflow_dispatch:
+
+env:
+  FORCE_COLOR: 3
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+jobs:
+  build-wasm-emscripten:
+    name: Build scikit-image distribution for Pyodide
+    runs-on: ubuntu-22.04
+    # To enable this workflow on a fork, comment out:
+    # if: github.repository == 'scikit-image/scikit-image'
+    env:
+      PYODIDE_VERSION: 0.25.0
+      # PYTHON_VERSION and EMSCRIPTEN_VERSION are determined by PYODIDE_VERSION.
+      # The appropriate versions can be found in the Pyodide repodata.json
+      # "info" field, or in Makefile.envs:
+      # https://github.com/pyodide/pyodide/blob/main/Makefile.envs#L2
+      PYTHON_VERSION: 3.11.3
+      EMSCRIPTEN_VERSION: 3.1.46
+      NODE_VERSION: 18
+    steps:
+      - name: Checkout scikit-image
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+
+      - name: Set up Python ${{ env.PYTHON_VERSION }}
+        id: setup-python
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Set up Emscripten toolchain
+        uses: mymindstorm/setup-emsdk@6ab9eb1bda2574c4ddb79809fc9247783eaf9021 # v14
+        with:
+          version: ${{ env.EMSCRIPTEN_VERSION }}
+          actions-cache-folder: emsdk-cache
+
+      # We need to apply a patch to the Emscripten SDK to work around a bug in
+      # the file system API. This patch is already applied in the Emscripten SDK
+      # upstream, but we need to apply it here because we are using an older
+      # version of the Emscripten SDK with Pyodide.
+      - name: Apply necessary patch(es)
+        run: |
+          patch -d $EMSDK/upstream/emscripten/ -p1 < tools/emscripten/patches/0001-fix-npy-file-access.patch
+
+      - name: Install pyodide-build
+        run: pip install "pydantic<2" pyodide-build==${{ env.PYODIDE_VERSION }}
+
+      - name: Build scikit-image for Pyodide
+        run: |
+          pyodide build
+
+      - name: Set up Node.js
+        uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4.0.2
+        with:
+          node-version: ${{ env.NODE_VERSION }}
+
+      - name: Set up Pyodide virtual environment and test scikit-image for Pyodide
+        env:
+          # Avoid using the default TkAgg backend, which requires GUI support
+          MPLBACKEND: "Agg"
+        run: |
+          pyodide venv .venv-pyodide
+          source .venv-pyodide/bin/activate
+          npm install pyodide@${{ env.PYODIDE_VERSION }}
+          node tools/emscripten/pytest_scikit_image_pyodide.js --pyargs skimage

skimage/__init__.py

@@ -163,6 +163,8 @@ def _raise_build_error(e):
         )
     except FileNotFoundError:
         pass
+    except OSError:
+        pass  # If skimage is built with emscripten which does not support processes
     else:
         out, err = p.communicate()
         if p.returncode == 0:

skimage/_shared/_dependency_checks.py

@@ -1,3 +1,7 @@
 from .version_requirements import is_installed
+import sys
+import platform
 
 has_mpl = is_installed("matplotlib", ">=3.3")
+
+is_wasm = (sys.platform == "emscripten") or (platform.machine() in ["wasm32", "wasm64"])

skimage/_shared/testing.py

@@ -3,9 +3,10 @@
 """
 
 import os
+import platform
 import re
 import struct
-import threading
+import sys
 import functools
 import inspect
 from tempfile import NamedTemporaryFile
@@ -32,6 +33,7 @@
 from ..data._fetchers import _fetch
 from ..util import img_as_uint, img_as_float, img_as_int, img_as_ubyte
 from ._warnings import expected_warnings
+from ._dependency_checks import is_wasm
 
 import pytest
 
@@ -44,7 +46,6 @@
 
 SKIP_RE = re.compile(r"(\s*>>>.*?)(\s*)#\s*skip\s+if\s+(.*)$")
 
-
 # true if python is running in 32bit mode
 # Calculate the size of a void * pointer in bits
 # https://docs.python.org/3/library/struct.html
@@ -322,12 +323,17 @@ def fetch(data_filename):
         pytest.skip(f'Unable to download {data_filename}', allow_module_level=True)
 
 
+# Ref: about the lack of threading support in WASM, please see
+# https://github.com/pyodide/pyodide/issues/237
 def run_in_parallel(num_threads=2, warnings_matching=None):
     """Decorator to run the same function multiple times in parallel.
 
     This decorator is useful to ensure that separate threads execute
     concurrently and correctly while releasing the GIL.
 
+    It is currently skipped when running on WASM-based platforms, as
+    the threading module is not supported.
+
     Parameters
     ----------
     num_threads : int, optional
@@ -346,19 +352,24 @@ def run_in_parallel(num_threads=2, warnings_matching=None):
     def wrapper(func):
         @functools.wraps(func)
         def inner(*args, **kwargs):
-            with expected_warnings(warnings_matching):
-                threads = []
-                for i in range(num_threads - 1):
-                    thread = threading.Thread(target=func, args=args, kwargs=kwargs)
-                    threads.append(thread)
-                for thread in threads:
-                    thread.start()
-
+            if not is_wasm:
+                with expected_warnings(warnings_matching):
+                    threads = []
+                    for i in range(num_threads - 1):
+                        import threading
+
+                        thread = threading.Thread(target=func, args=args, kwargs=kwargs)
+                        threads.append(thread)
+                    for thread in threads:
+                        thread.start()
+
+                    func(*args, **kwargs)
+
+                    for thread in threads:
+                        thread.join()
+            else:
                 func(*args, **kwargs)
 
-                for thread in threads:
-                    thread.join()
-
         return inner
 
     return wrapper

skimage/_shared/tests/test_testing.py

@@ -12,6 +12,7 @@
     assert_stacklevel,
 )
 from skimage._shared import testing
+from skimage._shared._dependency_checks import is_wasm
 
 from skimage._shared._warnings import expected_warnings
 from warnings import warn
@@ -81,6 +82,7 @@ def __init__(self):
         doctest_skip_parser(c)
 
 
+@pytest.mark.skipif(is_wasm, reason="Cannot start threads in WASM")
 def test_run_in_parallel():
     state = []
 

skimage/feature/_basic_features.py

@@ -1,9 +1,10 @@
 from itertools import combinations_with_replacement
 import itertools
+import sys
+import platform
 import numpy as np
 from skimage import filters, feature
 from skimage.util.dtype import img_as_float32
-from concurrent.futures import ThreadPoolExecutor
 
 
 def _texture_filter(gaussian_filtered):
@@ -72,6 +73,13 @@ def _mutiscale_basic_features_singlechannel(
     features : list
         List of features, each element of the list is an array of shape as img.
     """
+    # Guard threading import for Emscripten
+    threading_available = True
+    if (sys.platform == "emscripten") or (platform.machine() in ["wasm32", "wasm64"]):
+        threading_available = False
+    else:
+        from concurrent.futures import ThreadPoolExecutor
+
     # computations are faster as float32
     img = np.ascontiguousarray(img_as_float32(img))
     if num_sigma is None:
@@ -83,16 +91,26 @@ def _mutiscale_basic_features_singlechannel(
         base=2,
         endpoint=True,
     )
-    with ThreadPoolExecutor(max_workers=num_workers) as ex:
-        out_sigmas = list(
-            ex.map(
-                lambda s: _singlescale_basic_features_singlechannel(
-                    img, s, intensity=intensity, edges=edges, texture=texture
-                ),
-                sigmas,
+    if threading_available:
+        with ThreadPoolExecutor(max_workers=num_workers) as ex:
+            out_sigmas = list(
+                ex.map(
+                    lambda s: _singlescale_basic_features_singlechannel(
+                        img, s, intensity=intensity, edges=edges, texture=texture
+                    ),
+                    sigmas,
+                )
             )
-        )
-    features = itertools.chain.from_iterable(out_sigmas)
+        features = itertools.chain.from_iterable(out_sigmas)
+    # assumed threading is not available, so we use a serial version
+    else:
+        out_sigmas = [
+            _singlescale_basic_features_singlechannel(
+                img, s, intensity=intensity, edges=edges, texture=texture
+            )
+            for s in sigmas
+        ]
+        features = itertools.chain.from_iterable(out_sigmas)
     return features
 
 

skimage/feature/tests/test_util.py

@@ -68,6 +68,9 @@ def test_mask_border_keypoints():
 )
 def test_plot_matches(shapes):
     from matplotlib import pyplot as plt
+    from matplotlib import use
+
+    use('Agg')
 
     fig, ax = plt.subplots(nrows=1, ncols=1)
 
@@ -112,6 +115,9 @@ def test_plot_matches(shapes):
 )
 def test_plot_matched_features(shapes):
     from matplotlib import pyplot as plt
+    from matplotlib import use
+
+    use('Agg')
 
     fig, ax = plt.subplots()
 

skimage/io/tests/test_io.py

@@ -7,6 +7,7 @@
 
 from skimage import io
 from skimage._shared.testing import assert_array_equal, fetch
+from skimage._shared._dependency_checks import is_wasm
 from skimage.data import data_dir
 
 
@@ -47,6 +48,7 @@ def test_imread_file_url():
     assert image.shape == (512, 512)
 
 
+@pytest.mark.skipif(is_wasm, reason="no access to pytest-localserver")
 def test_imread_http_url(httpserver):
     # httpserver is a fixture provided by pytest-localserver
     # https://bitbucket.org/pytest-dev/pytest-localserver/

skimage/io/tests/test_mpl_imshow.py

@@ -6,6 +6,9 @@
 
 plt = pytest.importorskip("matplotlib.pyplot")
 
+if plt:
+    plt.switch_backend("Agg")
+
 
 def setup():
     io.reset_plugins()