Merge branch 'main' into cleanup-test-lists

.circleci/config.yml

@@ -8,14 +8,14 @@ defaults: &defaults
     #       (e.g. `rg -F --hidden <old_tag>`)
     - image: pyodide/pyodide-env:20241106-chrome130-firefox132
   environment:
-    - EMSDK_NUM_CORES: 3
-      EMCC_CORES: 3
-      PYODIDE_JOBS: 3
-      # Make sure the ccache dir is consistent between core and package builds
-      # (it's not the case otherwise)
-      CCACHE_DIR: /root/.ccache/
-      # Disable the compression of wheels, so they are better compressed by the CDN
-      PYODIDE_ZIP_COMPRESSION_LEVEL: 0
+    EMSDK_NUM_CORES: 3
+    EMCC_CORES: 3
+    PYODIDE_JOBS: 3
+    # Make sure the ccache dir is consistent between core and package builds
+    # (it's not the case otherwise)
+    CCACHE_DIR: /root/.ccache/
+    # Disable the compression of wheels, so they are better compressed by the CDN
+    PYODIDE_ZIP_COMPRESSION_LEVEL: 0
 
 jobs:
   build-core:
@@ -574,7 +574,6 @@ jobs:
               --access-key-env "AWS_ACCESS_KEY_ID_CACHE" --secret-key-env "AWS_SECRET_ACCESS_KEY_CACHE"
 
 workflows:
-  version: 2
   build-and-deploy:
     jobs:
       - build-core:

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.0"
+    rev: "v0.8.1"
     hooks:
       - id: ruff
         args: [--fix]
@@ -53,7 +53,7 @@ repos:
             "--ignore-words-list",
             "ags,aray,asend,ba,crate,falsy,feld,inflight,lits,nd,slowy,te,oint,conveniant,atmost",
           ]
-        exclude: ^(benchmark/benchmarks/pystone_benchmarks/pystone\.py|src/js/package-lock\.json)$
+        exclude: ^(benchmark/benchmarks/pystone_benchmarks/pystone\.py|src/js/package-lock\.json|packages/matplotlib/extras/fontlist\.json)$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v1.11.0"

benchmark/benchmark.py

@@ -20,8 +20,8 @@
 def print_entry(name, res):
     print(" - ", name)
     print(" " * 4, end="")
-    for name, dt in res.items():
-        print(f"{name}: {dt:.6f}  ", end="")
+    for res_name, dt in res.items():
+        print(f"{res_name}: {dt:.6f}  ", end="")
     print("")
 
 

benchmark/benchmarks/matplotlib_benchmarks/canvas_image.py

@@ -8,7 +8,7 @@
 
 matplotlib.use("module://matplotlib_pyodide.html5_canvas_backend")
 
-import matplotlib.cm as cm  # noqa: E402
+from matplotlib import cm  # noqa: E402
 from matplotlib import pyplot as plt  # noqa: E402
 
 

benchmark/benchmarks/matplotlib_benchmarks/wasm_image.py

@@ -8,7 +8,7 @@
 
 matplotlib.use("module://matplotlib_pyodide.wasm_backend")
 
-import matplotlib.cm as cm  # noqa: E402
+from matplotlib import cm  # noqa: E402
 from matplotlib import pyplot as plt  # noqa: E402
 
 

conftest.py

@@ -181,7 +181,7 @@ def pytest_configure(config):
     it to reduce the verbosity of the test names in the table.  This leaves
     enough room to see the information about the test failure in the summary.
     """
-    global CONFIG
+    global CONFIG  # noqa: PLW0602
 
     old_cwd_relative_nodeid = config.cwd_relative_nodeid
 

docs/conf.py

@@ -21,19 +21,19 @@
 copyright = "2019-2024, Pyodide contributors and Mozilla"
 
 nitpicky = True
-nitpick_ignore = []
+nitpick_ignore: list[tuple[str, str]] = []
 
 
 def ignore_typevars():
     """These are all intentionally broken. Disable the warnings about it."""
-    PY_TYPEVARS_TO_IGNORE = ["T", "T_co", "T_contra", "V_co", "KT", "VT", "VT_co"]
-    JS_TYPEVARS_TO_IGNORE = ["TResult", "TResult1", "TResult2", "U"]
+    PY_TYPEVARS_TO_IGNORE = ("T", "T_co", "T_contra", "V_co", "KT", "VT", "VT_co")
+    JS_TYPEVARS_TO_IGNORE = ("TResult", "TResult1", "TResult2", "U")
 
-    for typevar in PY_TYPEVARS_TO_IGNORE:
-        nitpick_ignore.append(("py:obj", f"_pyodide._core_docs.{typevar}"))
-
-    for typevar in JS_TYPEVARS_TO_IGNORE:
-        nitpick_ignore.append(("js:func", typevar))
+    nitpick_ignore.extend(
+        ("py:obj", f"_pyodide._core_docs.{typevar}")
+        for typevar in PY_TYPEVARS_TO_IGNORE
+    )
+    nitpick_ignore.extend(("js:func", typevar) for typevar in JS_TYPEVARS_TO_IGNORE)
 
 
 ignore_typevars()
@@ -292,7 +292,7 @@ def ensure_typedoc_on_path():
     if shutil.which("typedoc"):
         return
     if IN_READTHEDOCS:
-        subprocess.run(["npm", "ci"], cwd="../src/js")
+        subprocess.run(["npm", "ci"], cwd="../src/js", check=True)
         Path("../node_modules").symlink_to("../src/js/node_modules")
     if shutil.which("typedoc"):
         return

docs/development/building-from-sources.md

@@ -24,6 +24,23 @@ Pyodide can be built from sources on different platforms,
 
 ## Build instructions
 
+The Pyodide repository has a git submodule called `pyodide-build`. Make sure to
+do a recursive clone:
+
+```bash
+git clone --recursive https://github.com/pyodide/pyodide
+```
+
+or if you have already cloned the Pyodide repository without the `--recursive`
+flag, you may initialize the submodule with:
+
+```bash
+git submodule update --init
+```
+
+If you change git branches, make sure you update `pyodide-build` with
+`git submodule update`.
+
 ### Using Docker
 
 We provide a Debian-based x86_64 Docker image

docs/project/changelog.md

@@ -66,8 +66,49 @@ myst:
   for more information.
   {pr}`5100`
 
+- {{ Breaking }} The WASM backend is now the default backend for `matplotlib-pyodide` and
+  the HTML5 backend has been disabled, temporarily redirecting to it. Power users
+  might see minor incompatibilities and subtle differences. Please see
+  https://github.com/pyodide/matplotlib-pyodide/issues/64 and
+  https://github.com/pyodide/matplotlib-pyodide/issues/65
+  for more information and if you wish to contribute to the discussion.
+  {pr}`4510`
+
 ### Packages
 
+- Upgraded `numpy` to 2.0.2 {pr}`4925`
+- Upgraded `RobotRaconteur` to 1.2.2 {pr}`4925`
+- Upgraded `gsw` to 3.6.19 {pr}`4925`
+- Upgraded `opencv-python` to 4.10.0.84 {pr}`4925`
+- Upgraded `yt` to 4.3.1 {pr}`4925`
+- Upgraded `xgboost` to 2.1.2 {pr}`4925`
+- Upgraded `autograd` to 1.7.0 {pr}`4925`
+- Upgraded `sisl` to 0.15.1 {pr}`4925`
+- Upgraded `cartopy` to 0.24.1 {pr}`4925`
+- Upgraded `astropy` to 7.0.0 {pr}`4925`
+- Upgraded `biopython` to 1.84 {pr}`4925`
+- Upgraded `fastparquet` to 2024.5.0 {pr}`4925`
+- Upgraded `geopandas` to 1.0.1 {pr}`4925`
+- Upgraded `imageio` to 2.36.0 {pr}`4925`
+- Upgraded `lightgbm` to 4.5.0 {pr}`4925`
+- Upgraded `netcdf4` to 1.7.2 {pr}`4925`
+- Upgraded `networkx` to 3.4.2 {pr}`4925`
+- Upgraded `numcodecs` to 0.13.1 {pr}`4925`
+- Upgraded `pandas` to 2.2.3 {pr}`4893`, {pr}`4925`
+- Upgraded `pywavelets` to 1.7.0 {pr}`4925`
+- Upgraded `shapely` to 2.0.6 {pr}`4925`
+- Upgraded `threadpoolctl` to 3.5.0 {pr}`4925`
+- Upgraded `unyt` to 3.0.3 {pr}`4925`
+- Upgraded `xarray` to 2024.10.0 {pr}`4925`
+- Upgraded `zarr` to 2.18.3 {pr}`4925`
+- Upgraded `h5py` to 3.12.1 {pr}`4925`
+- Upgraded `cftime` to 1.6.4.post1 {pr}`4925`
+- Upgraded `clarabel` to 0.9.0 {pr}`4925`
+- Upgraded `ewah_bool_utils` to 1.2.2 {pr}`4925`
+- Upgraded `galpy` to 1.10.1 {pr}`4925`
+- Upgraded `mne-python` to 1.8.0 {pr}`4925`
+- Upgraded `pyxirr` to 0.10.6 {pr}`4925`
+- Upgraded `regex` to 2024.9.11 {pr}`4925`
 - Upgraded `crc32c` to 2.7.1 {pr}`5169`
 - Upgraded `rebound` to 4.4.3 {pr}`5163`
 - Upgraded `reboundx` to 4.3.0 {pr}`5163`
@@ -80,11 +121,11 @@ myst:
 - Upgraded `scikit-learn` to 1.5.2 {pr}`4823`, {pr}`5016`, {pr}`5072`
 - Upgraded `libcst` to 1.4.0 {pr}`4856`
 - Upgraded `lakers` to 0.3.3 {pr}`4885`
-- Upgraded `certifi` to 2024.7.4 {pr}`5035`
+- Upgraded `certifi` to 2024.12.14 {pr}`5257`
 - Upgraded `bokeh` to 3.6.0 {pr}`4888`, {pr}`5047`, {pr}`5118`
-- Upgraded `pandas` to 2.2.2 {pr}`4893`
+- Upgraded `awkward-cpp` to 43 {pr}`5214`, {pr}`5247`
 - Upgraded `zengl` to 2.5.0 {pr}`4894`
-- Upgraded `protobuf` to 5.27.3 {pr}`4601`
+- Upgraded `protobuf` to 5.29.1 {pr}`5257`
 - Upgraded `sourmash` to 4.8.11 {pr}`4980`
 - Upgraded `scipy` to 1.14.1 {pr}`4719`, {pr}`5011`, {pr}`5012`, {pr}`5031`
 - Upgraded `scikit-image` to 0.24.0 {pr}`5003`
@@ -97,12 +138,15 @@ myst:
 - Upgraded `altair` to 5.4.1 {pr}`5124`
 - Upgraded `PyYAML` to 6.0.2 {pr}`5137`
 - Upgraded `duckdb` to 1.1.2 {pr}`5142`
+- Upgraded `matplotlib` to 3.8.4 {pr}`4510`
+- Upgraded `matplotlib-pyodide` to 0.2.3 {pr}`4510`
+- Upgraded `cysignals` to 1.12.2 {pr}`5267`
 - Added `soxr` 0.5.0.post1 {pr}`5150`
 - Added `tiktoken` v0.8.0 in {pr}`5147`
-- Added `casadi` 3.6.6 {pr}`4936`, {pr}`5057`
+- Added `casadi` 3.6.7 {pr}`4936`, {pr}`5057`, {pr}`4925`
 - Added `pyarrow` 17.0.0 {pr}`4950`
-- Added `rasterio` 1.13.10, `affine` 2.4.0 {pr}`4983`
-- Added `iminuit` 2.29.1 {pr}`4767`, {pr}`5072`
+- Added `rasterio` 1.4.2, `affine` 2.4.0 {pr}`4983`, {pr}`4925`
+- Added `iminuit` 2.30.1 {pr}`4767`, {pr}`5072`, {pr}`4925`
 - Added `arro3-core`, `arro3-io`, and `arro3-compute` 0.3.0, 0.4.0, 0.4.1 {pr}`5020`, {pr}`5095`, {pr}`5104`
 - Added `tree-sitter` 0.23.0 {pr}`5099`
 - Added `tree-sitter-go` 0.23.1 {pr}`5102`
@@ -116,6 +160,10 @@ myst:
 - Upgraded `tree-sitter-go` to 0.23.3 {pr}`5185`
 - Upgraded `tree-sitter-java` to 0.23.4 {pr}`5185`
 - Upgraded `tree-sitter-python` to 0.23.4 {pr}`5185`
+- Upgraded `xarray` to 2024.11.0 {pr}`5224`
+- Upgraded `lakers-python` to 0.4.1 {pr}`5225`
+- Upgraded `pure-eval` to 0.2.3 {pr}`5086`, {pr}`5244`
+- Upgraded `cffi` to 1.17.1 {pr}`5261`
 
 ## Version 0.26.4
 

packages/Cartopy/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: Cartopy
-  version: 0.23.0
+  version: 0.24.1
   top-level:
     - cartopy
 source:
-  url: https://files.pythonhosted.org/packages/a5/00/fed048eeb80129908f8bd5f5762e230864abc8a8fbbc493740bafcb696bd/Cartopy-0.23.0.tar.gz
-  sha256: 231f37b35701f2ba31d94959cca75e6da04c2eea3a7f14ce1c75ee3b0eae7676
+  url: https://files.pythonhosted.org/packages/e0/75/94aff4fef338887641aa780d13795609861e6e9f9593bd66d4917ab7954b/cartopy-0.24.1.tar.gz
+  sha256: 01c910d5634c69a7efdec46e0a17d473d2328767f001d4dc0b5c4b48e585c8bd
 test:
   imports:
     - cartopy

packages/RobotRaconteur/meta.yaml

@@ -1,16 +1,17 @@
 package:
   name: RobotRaconteur
-  version: 1.2.0
+  version: 1.2.2
 
 source:
-  url: https://github.com/robotraconteur/robotraconteur/releases/download/v1.2.0/RobotRaconteur-1.2.0-Source.tar.gz
-  sha256: "305cc0dc1f0e51181999247c14ac8b93d53aca755d9e7bccb78a5a3ef87ed86f"
+  url: https://github.com/robotraconteur/robotraconteur/releases/download/v1.2.2/RobotRaconteur-1.2.2-Source.tar.gz
+  sha256: "837710102b5ee6ad81a22e14b313b1dd09995c3da3e7846355866553b3c52715"
 
 requirements:
   run:
     - numpy
   host:
     - boost-cpp
+    - openssl
     - numpy
 
 build:
@@ -22,11 +23,11 @@ build:
     echo "set_property(GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS FALSE)" > ForceStaticLib.cmake
     emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} -DBUILD_GEN=OFF -DBUILD_TESTING=OFF -DBUILD_PYTHON3=ON \
     -DCMAKE_PROJECT_INCLUDE=ForceStaticLib.cmake \
-    -DNUMPY_INCLUDE_DIR=$HOSTINSTALLDIR/lib/python$PYMAJOR.$PYMINOR/site-packages/numpy/core/include/ \
+    -DNUMPY_INCLUDE_DIR=$HOSTINSTALLDIR/lib/python$PYMAJOR.$PYMINOR/site-packages/numpy/_core/include/ \
     -DPYTHON3_INCLUDE_DIR=$PYTHONINCLUDE -DPYTHON3_EXECUTABLE=python$PYMAJOR.$PYMINOR \
     -DPYTHON3_LIBRARY=$HOSTINSTALLDIR/lib/python$PYMAJOR.$PYMINOR.a \
     -DCMAKE_CXX_FLAGS="-fPIC -fexceptions -DBOOST_AP_DISABLE_THREADS=1 -O2 -DBOOST_BIND_GLOBAL_PLACEHOLDERS=1 -Wno-enum-constexpr-conversion" \
-    -DBOOST_INCLUDEDIR=$WASM_LIBRARY_DIR/include -DBOOST_LIBRARYDIR=$WASM_LIBRARY_DIR/lib \
+    -DBoost_INCLUDE_DIR=$WASM_LIBRARY_DIR/include -DBoost_LIBRARY_DIR=$WASM_LIBRARY_DIR/lib \
     -DBoost_DATE_TIME_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_date_time.a \
     -DBoost_DATE_TIME_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_date_time.a \
     -DBoost_FILESYSTEM_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_filesystem.a \
@@ -41,6 +42,9 @@ build:
     -DBoost_RANDOM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_random.a \
     -DBoost_PROGRAM_OPTIONS_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_program_options.a \
     -DBoost_PROGRAM_OPTIONS_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_program_options.a \
+    -DOpenSSL_CRYPTO_LIBRARY=$WASM_LIBRARY_DIR/lib/libcrypto.a \
+    -DOpenSSL_INCLUDE_DIR=$WASM_LIBRARY_DIR/include \
+    -DOpenSSL_USE_STATIC_LIBS=ON \
     -DUSE_PREGENERATED_SOURCE=ON \
      .
     emmake make -j ${PYODIDE_JOBS:-3}
@@ -57,3 +61,6 @@ build:
 about:
   home: https://github.com/robotraconteur/robotraconteur
   license: Apache-2.0
+extra:
+  recipe-maintainers:
+    - johnwason

packages/astropy/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: astropy
-  version: 6.0.1
+  version: 7.0.0
   top-level:
     - astropy
 source:
-  url: https://files.pythonhosted.org/packages/48/08/f205a24d75ad1f329586bb685b53574c5303c56acf80924166a6c8df8a09/astropy-6.0.1.tar.gz
-  sha256: 89a975de356d0608e74f1f493442fb3acbbb7a85b739e074460bb0340014b39c
+  url: https://files.pythonhosted.org/packages/6a/12/d6ad68d5acd751e3827d54a64333e0dd789bcc747fe9528f5758b35421f8/astropy-7.0.0.tar.gz
+  sha256: e92d7c9fee86eb3df8714e5dd41bbf9f163d343e1a183d95bf6bd09e4313c940
 build:
   # The test module is imported from the top level `__init__.py`
   # so it cannot be unvendored

packages/astropy/test_astropy.py

@@ -18,7 +18,9 @@
         ("coordinates", "test_erfa_astrom.py"),
         ("coordinates", "test_frames_with_velocity.py"),
         ("coordinates", "test_icrs_observed_transformations.py"),
-        ("coordinates", "test_matching.py"),
+        # Needs SciPy but optional dependency not declared, can be re-enabled
+        # later when we unvendor recipes
+        # ("coordinates", "test_matching.py"),
         ("coordinates", "test_representation.py and not test_unitphysics"),
         ("coordinates", "test_sky_coord.py"),
         ("coordinates", "test_sky_coord_velocities.py"),

packages/autograd/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: autograd
-  version: 1.6.2
+  version: 1.7.0
   top-level:
     - autograd
 source:
-  sha256: 8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb
-  url: https://files.pythonhosted.org/packages/42/03/9d00fbea21fd702970f157a6b79caa1a947b08c1c518296fe94cb7d549f0/autograd-1.6.2.tar.gz
+  sha256: de743fd368d6df523cd37305dcd171861a9752a144493677d2c9f5a56983ff2f
+  url: https://files.pythonhosted.org/packages/28/ed/67975d75c0fe71220c8df2370c6c1390805790a641359b502f39c042c0c1/autograd-1.7.0.tar.gz
 requirements:
   host:
     - numpy

packages/awkward-cpp/meta.yaml

@@ -1,12 +1,12 @@
 package:
   name: awkward-cpp
-  version: "39"
+  version: "43"
   top-level:
     - awkward_cpp
 
 source:
-  url: https://files.pythonhosted.org/packages/6e/57/972e2a808c197d9331a129d0e749b3d6d5c39b5d175a047dbf6254a9b1a5/awkward_cpp-39.tar.gz
-  sha256: 61da001199ea2094484e28ca074591d2ec660f117e9a97ab89e60da405272385
+  url: https://files.pythonhosted.org/packages/c4/6b/b1ddc01206296322544247dfef8e1958292154b785a6d545bb12fb703d51/awkward_cpp-43.tar.gz
+  sha256: c1ed75596ec82af666da084b5bf805d9b72c83532d035d2b65e0795905d25ead
 
 build:
   exports: requested

packages/biopython/meta.yaml

@@ -1,14 +1,12 @@
 package:
   name: biopython
-  version: "1.83"
+  version: "1.84"
   top-level:
     - Bio
     - BioSQL
 source:
-  sha256: 78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7
-  url: https://files.pythonhosted.org/packages/cc/d4/3d8848191a7a37187704c382e6dfda4d6a47d05a14cd64f004c55a3cd5a1/biopython-1.83.tar.gz
-  patches:
-    - "patches/0001-Remove-error-message-if-wheel-is-not-installed.patch"
+  sha256: 60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4
+  url: https://files.pythonhosted.org/packages/9e/7f/eaca4de03f0ee06c9d578d2730fd55858a57cee3620c62d3bc17b5da5447/biopython-1.84.tar.gz
 requirements:
   run:
     - numpy