Bump python and package versions in conda env (#34)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/build.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
+  schedule:
+  # Twice per week, on Monday and Thursday
+  - cron: "0 0 * * 1,4"
 
 permissions:
   contents: write
@@ -81,7 +84,7 @@ jobs:
         run : |
           which python
           python -m pip install git+https://github.com/pyodide/pyodide.git@main#subdirectory=pyodide-build
-          pyodide xbuildenv install --download --url http://pyodide-cache.s3-website-us-east-1.amazonaws.com/xbuildenv/dev/xbuildenv.tar.bz2
+          pyodide xbuildenv install --url http://pyodide-cache.s3-website-us-east-1.amazonaws.com/xbuildenv/dev/xbuildenv.tar.bz2
 
       - name: Check emscripten version
         shell: bash -l {0}

.gitignore

@@ -129,7 +129,8 @@ dmypy.json
 .pyre/
 
 .vscode/
-.pyodide-xbuildenv/
+.pyodide-xbuildenv*
 emsdk/
 ccache/
 pyodide
+packages/.libs/

environment.yml

@@ -2,8 +2,8 @@ name: pyodide-env
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
-  - nodejs
+  - python=3.12
+  - nodejs=20
   - ccache
   - f2c
   - swig
@@ -18,5 +18,5 @@ dependencies:
   - gfortran
   - pip:
     - pytest
-    - pytest-pyodide==0.53.1
+    - pytest-pyodide==0.56.2
     - pytest-httpserver

packages/Cartopy/meta.yaml

@@ -1,13 +1,11 @@
 package:
   name: Cartopy
-  version: 0.21.1
+  version: 0.23.0
   top-level:
     - cartopy
 source:
-  url: https://files.pythonhosted.org/packages/e8/11/ed3e364b3910f0951821e6b5a03a03ce425464b72aa3da08d47b78ae17bd/Cartopy-0.21.1.tar.gz
-  sha256: 89d5649712c8582231c6e11825a04c85f6f0cee94dbb89e4db23eabca1cc250a
-  patches:
-    - patches/0001-setup-geos-config.patch
+  url: https://files.pythonhosted.org/packages/a5/00/fed048eeb80129908f8bd5f5762e230864abc8a8fbbc493740bafcb696bd/Cartopy-0.23.0.tar.gz
+  sha256: 231f37b35701f2ba31d94959cca75e6da04c2eea3a7f14ce1c75ee3b0eae7676
 test:
   imports:
     - cartopy
@@ -29,8 +27,8 @@ requirements:
 build:
   vendor-sharedlib: true
   script: |
-    export GEOS_CONFIG=${WASM_LIBRARY_DIR}/bin/geos-config
-    echo ${GEOS_CONFIG}
+    # Put geos-config on the path
+    export PATH=$PATH:${WASM_LIBRARY_DIR}/bin/
 
 about:
   home: http://scitools.org.uk/cartopy

packages/Cartopy/test_cartopy.py

@@ -42,5 +42,5 @@ def test_matplotlib(selenium):
     plt.savefig(fd, format="svg")
 
     content = fd.getvalue().decode("utf8")
-    assert len(content) == 128402
+    assert len(content) > 100000
     assert content.startswith("<?xml")

packages/Jinja2/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: Jinja2
-  version: 3.1.2
+  version: 3.1.3
   tag:
     - core
     - min-scipy-stack
@@ -10,8 +10,8 @@ requirements:
   run:
     - MarkupSafe
 source:
-  sha256: 6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61
-  url: https://files.pythonhosted.org/packages/bc/c3/f068337a370801f372f2f8f6bad74a5c140f6fda3d9de154052708dd3c65/Jinja2-3.1.2-py3-none-any.whl
+  sha256: 7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa
+  url: https://files.pythonhosted.org/packages/30/6d/6de6be2d02603ab56e72997708809e8a5b0fbfee080735109b40a3564843/Jinja2-3.1.3-py3-none-any.whl
 about:
   home: https://palletsprojects.com/p/jinja/
   PyPI: https://pypi.org/project/Jinja2

packages/MarkupSafe/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: MarkupSafe
-  version: 2.1.3
+  version: 2.1.5
   top-level:
     - markupsafe
 source:
-  sha256: af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad
-  url: https://files.pythonhosted.org/packages/6d/7c/59a3248f411813f8ccba92a55feaac4bf360d29e2ff05ee7d8e1ef2d7dbf/MarkupSafe-2.1.3.tar.gz
+  sha256: d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b
+  url: https://files.pythonhosted.org/packages/87/5b/aae44c6655f3801e81aa3eef09dbbf012431987ba564d7231722f68df02d/MarkupSafe-2.1.5.tar.gz
 about:
   home: https://palletsprojects.com/p/markupsafe/
   PyPI: https://pypi.org/project/MarkupSafe

packages/Pillow/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: Pillow
-  version: 10.0.0
+  version: 10.2.0
   top-level:
     - PIL
 source:
-  sha256: 9c82b5b3e043c7af0d95792d0d20ccf68f61a1fec6b3530e718b688422727396
-  url: https://files.pythonhosted.org/packages/0f/8b/2ebaf9adcf4260c00f842154865f8730cf745906aa5dd499141fb6063e26/Pillow-10.0.0.tar.gz
+  sha256: e87f0b2c78157e12d7686b27d63c070fd65d994e8ddae6f328e0dcf4a0cd007e
+  url: https://files.pythonhosted.org/packages/f8/3e/32cbd0129a28686621434cbf17bb64bf1458bfb838f1f668262fefce145c/pillow-10.2.0.tar.gz
   patches:
     - patches/0001-Enable-image-formats.patch
 build:

packages/Pygments/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: Pygments
-  version: 2.16.1
+  version: 2.17.2
   top-level:
     - pygments
 source:
-  sha256: 13fc09fa63bc8d8671a6d247e1eb303c4b343eaee81d861f3404db2935653692
-  url: https://files.pythonhosted.org/packages/43/88/29adf0b44ba6ac85045e63734ae0997d3c58d8b1a91c914d240828d0d73d/Pygments-2.16.1-py3-none-any.whl
+  sha256: b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c
+  url: https://files.pythonhosted.org/packages/97/9c/372fef8377a6e340b1704768d20daaded98bf13282b5327beb2e2fe2c7ef/pygments-2.17.2-py3-none-any.whl
 about:
   home: https://pygments.org/
   PyPI: https://pypi.org/project/Pygments

packages/RobotRaconteur/meta.yaml

@@ -1,10 +1,10 @@
 package:
   name: RobotRaconteur
-  version: 0.15.1
+  version: 1.2.0
 
 source:
-  url: https://github.com/robotraconteur/robotraconteur_pyodide/releases/download/v0.15.1-pyodide/RobotRaconteur-pyodide-0.15.1-post1-Source.tar.gz
-  sha256: 224427d0922dcb34d17221c1f3b8b5e94ebddc109f24f8e9a3f7f5d090386dc6
+  url: https://github.com/robotraconteur/robotraconteur/releases/download/v1.2.0/RobotRaconteur-1.2.0-Source.tar.gz
+  sha256: "305cc0dc1f0e51181999247c14ac8b93d53aca755d9e7bccb78a5a3ef87ed86f"
 
 requirements:
   run:
@@ -20,36 +20,37 @@ build:
     export INSTALL_DIR=${WASM_LIBRARY_DIR}
 
     echo "set_property(GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS FALSE)" > ForceStaticLib.cmake
-    emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} -DBUILD_PYTHON=ON \
+    emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} -DBUILD_GEN=OFF -DBUILD_TESTING=OFF -DBUILD_PYTHON3=ON \
     -DCMAKE_PROJECT_INCLUDE=ForceStaticLib.cmake \
     -DNUMPY_INCLUDE_DIR=$HOSTINSTALLDIR/lib/python$PYMAJOR.$PYMINOR/site-packages/numpy/core/include/ \
-    -DPYTHON_INCLUDE_DIR=$PYTHONINCLUDE -DPYTHON_EXECUTABLE=python$PYMAJOR.$PYMINOR \
+    -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_DATE_TIME_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_date_time.bc \
-    -DBoost_DATE_TIME_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_date_time.bc \
-    -DBoost_FILESYSTEM_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_filesystem.bc \
-    -DBoost_FILESYSTEM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_filesystem.bc \
-    -DBoost_SYSTEM_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_system.bc \
-    -DBoost_SYSTEM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_system.bc \
-    -DBoost_REGEX_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_regex.bc \
-    -DBoost_SYSTEM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_regex.bc \
-    -DBoost_CHRONO_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_chrono.bc \
-    -DBoost_CHRONO_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_crono.bc \
-    -DBoost_RANDOM_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_random.bc \
-    -DBoost_RANDOM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_random.bc \
-    -DBoost_PROGRAM_OPTIONS_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_program_options.bc \
-    -DBoost_PROGRAM_OPTIONS_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_program_options.bc \
+    -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=$WASM_LIBRARY_DIR/lib/libboost_filesystem.a \
+    -DBoost_FILESYSTEM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_filesystem.a \
+    -DBoost_SYSTEM_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_system.a \
+    -DBoost_SYSTEM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_system.a \
+    -DBoost_REGEX_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_regex.a \
+    -DBoost_SYSTEM_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_regex.a \
+    -DBoost_CHRONO_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_chrono.a \
+    -DBoost_CHRONO_LIBRARY_DEBUG=$WASM_LIBRARY_DIR/lib/libboost_crono.a \
+    -DBoost_RANDOM_LIBRARY_RELEASE=$WASM_LIBRARY_DIR/lib/libboost_random.a \
+    -DBoost_RANDOM_LIBRARY_DEBUG=$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 \
     -DUSE_PREGENERATED_SOURCE=ON \
      .
     emmake make -j ${PYODIDE_JOBS:-3}
     emcc ${SIDE_MODULE_LDFLAGS} -fexceptions out/lib/libRobotRaconteurCore.a \
-      out/Python/RobotRaconteur/_RobotRaconteurPython.a \
-      $WASM_LIBRARY_DIR/lib/libboost_chrono.bc \
-      $WASM_LIBRARY_DIR/lib/libboost_date_time.bc \
-      $WASM_LIBRARY_DIR/lib/libboost_filesystem.bc \
-      $WASM_LIBRARY_DIR/lib/libboost_program_options.bc \
-      $WASM_LIBRARY_DIR/lib/libboost_random.bc \
-      $WASM_LIBRARY_DIR/lib/libboost_regex.bc \
-      $WASM_LIBRARY_DIR/lib/libboost_system.bc \
-      -o out/Python/RobotRaconteur/_RobotRaconteurPython.so
+      out/Python3/RobotRaconteur/_RobotRaconteurPython.a \
+      $WASM_LIBRARY_DIR/lib/libboost_chrono.a \
+      $WASM_LIBRARY_DIR/lib/libboost_date_time.a \
+      $WASM_LIBRARY_DIR/lib/libboost_filesystem.a \
+      $WASM_LIBRARY_DIR/lib/libboost_program_options.a \
+      $WASM_LIBRARY_DIR/lib/libboost_random.a \
+      $WASM_LIBRARY_DIR/lib/libboost_regex.a \
+      $WASM_LIBRARY_DIR/lib/libboost_system.a \
+      -o out/Python3/RobotRaconteur/_RobotRaconteurPython.so

packages/RobotRaconteur/test_robotraconteur_pyodide.py

@@ -16,5 +16,5 @@ def test_robotraconteur_exceptions(selenium):
     RRN = RR.RobotRaconteurNode.s
     RRN.SetNodeName("test_node")
     assert RRN.NodeName == "test_node"
-    with pytest.raises(Exception):
+    with pytest.raises(Exception):  # noqa: B017
         RRN.SetNodeName("test_node")

packages/aiohttp/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: aiohttp
-  version: 3.8.6
+  version: 3.9.5
   top-level:
     - aiohttp
 source:
-  url: https://files.pythonhosted.org/packages/fd/01/f180d31923751fd20185c96938994823f00918ee5ac7b058edc005382406/aiohttp-3.8.6.tar.gz
-  sha256: b0cf2a4501bff9330a8a5248b4ce951851e415bdcce9dc158e76cfd55e15085c
+  url: https://files.pythonhosted.org/packages/04/a4/e3679773ea7eb5b37a2c998e25b017cc5349edf6ba2739d1f32855cfb11b/aiohttp-3.9.5.tar.gz
+  sha256: edea7d15772ceeb29db4aff55e482d4bcfb6ae160ce144f2682de02f6d693551
 
 requirements:
   run:

packages/aiohttp/test_aiohttp.py

@@ -24,6 +24,6 @@ async def aiohttp_test_helper(selenium, patch, base_url, lock_data):
 
 def test_aiohttp(selenium):
     patch = (Path(__file__).parent / "aiohttp_patch.py").read_text()
-    dist_dir = cast(str, pytest.pyodide_dist_dir)
+    dist_dir = cast(str, pytest.pyodide_dist_dir)  # type:ignore[attr-defined]
     lock_data = (Path(dist_dir) / "pyodide-lock.json").read_text()
     aiohttp_test_helper(selenium, patch, selenium.base_url, lock_data)

packages/altair/meta.yaml

@@ -0,0 +1,25 @@
+package:
+  name: altair
+  version: 5.3.0
+  top-level:
+    - altair
+source:
+  url: https://files.pythonhosted.org/packages/46/30/2118537233fa72c1d91a81f5908a7e843a6601ccc68b76838ebc4951505f/altair-5.3.0-py3-none-any.whl
+  sha256: 7084a1dab4d83c5e7e5246b92dc1b4451a6c68fd057f3716ee9d315c8980e59a
+about:
+  home:
+  PyPI: https://pypi.org/project/altair
+  summary: "Vega-Altair: A declarative statistical visualization library for Python."
+  license:
+extra:
+  recipe-maintainers:
+    - joelostblom
+requirements:
+  run:
+    - typing-extensions
+    - Jinja2
+    - jsonschema
+    - numpy
+    - pandas
+    - toolz
+    - packaging

packages/altair/test_altair.py

@@ -0,0 +1,22 @@
+import pytest
+from pytest_pyodide import run_in_pyodide
+
+
+@pytest.mark.xfail_browsers(firefox="slow")
+@run_in_pyodide(packages=["altair"])
+def test_altair(selenium):
+    import altair as alt
+    import pandas as pd
+
+    data = pd.DataFrame(
+        {
+            "a": ["A", "B", "C", "D", "E", "F", "G", "H", "I"],
+            "b": [28, 55, 43, 91, 81, 53, 19, 87, 52],
+        }
+    )
+    c = alt.Chart(data).mark_bar().encode(x="a", y="b").to_dict()
+
+    assert c["mark"]["type"] == "bar"
+    assert c["encoding"]["x"]["field"] == "a"
+    assert c["encoding"]["y"]["type"] == "quantitative"
+    assert "name" in c["data"]

packages/annotated-types/meta.yaml

@@ -0,0 +1,13 @@
+package:
+  name: annotated-types
+  version: 0.6.0
+  top-level:
+    - annotated_types
+source:
+  url: https://files.pythonhosted.org/packages/28/78/d31230046e58c207284c6b2c4e8d96e6d3cb4e52354721b944d3e1ee4aa5/annotated_types-0.6.0-py3-none-any.whl
+  sha256: 0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43
+about:
+  home: ""
+  PyPI: https://pypi.org/project/annotated-types
+  summary: Reusable constraint types to use with typing.Annotated
+  license: ""

packages/astropy/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: astropy
-  version: 5.3.2
+  version: 6.0.1
   top-level:
     - astropy
 source:
-  url: https://files.pythonhosted.org/packages/5d/2a/0bb1e43f5643e47208e53882414f088f13d52b890b9349fa2c1c108d0e31/astropy-5.3.2.tar.gz
-  sha256: 222003dedd4d1ad00cf3b3a02747fd59c4fc93a97ddbe6328952916ad5f1558f
+  url: https://files.pythonhosted.org/packages/48/08/f205a24d75ad1f329586bb685b53574c5303c56acf80924166a6c8df8a09/astropy-6.0.1.tar.gz
+  sha256: 89a975de356d0608e74f1f493442fb3acbbb7a85b739e074460bb0340014b39c
 build:
   # The test module is imported from the top level `__init__.py`
   # so it cannot be unvendored
@@ -18,11 +18,11 @@ requirements:
     - packaging
     - numpy
   run:
-    - distutils
     - packaging
     - numpy
     - pyerfa
     - pyyaml
+    - astropy_iers_data
 test:
   imports:
     - astropy
@@ -50,3 +50,6 @@ about:
   PyPI: https://pypi.org/project/astropy
   summary: Astronomy and astrophysics core library
   license: BSD 3-Clause License
+extra:
+  recipe-maintainers:
+    - jobovy