Merge branch 'main' into buffer-fixes

hoodmane · Oct 9, 2024 · 5164ee3 · 5164ee3
2 parents c123133 + 92d6e22
commit 5164ee3
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,7 +6,7 @@ defaults: &defaults
     # Note: when updating the docker image version,
     #       make sure there are no extra old versions lying around.
     #       (e.g. `rg -F --hidden <old_tag>`)
-    - image: pyodide/pyodide-env:20240801-chrome127-firefox128
+    - image: pyodide/pyodide-env:20240928-chrome127-firefox128
   environment:
     - EMSDK_NUM_CORES: 3
       EMCC_CORES: 3

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,7 +1,7 @@
 {
   "name": "Docker",
   // keep in sync with "run_docker"
-  "image": "pyodide/pyodide-env:20240312-chrome122-firefox122",
+  "image": "pyodide/pyodide-env:20240928-chrome127-firefox128",
   "remoteUser": "root",
   "onCreateCommand": ".devcontainer/onCreate-docker.sh"
 }
diff --git a/docs/project/changelog.md b/docs/project/changelog.md
@@ -82,14 +82,17 @@ myst:
 - 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`
+- Upgraded `statsmodels` to 0.14.4 {pr}`5058`
 - Upgraded `contourpy` to 1.3.0 {pr}`5048`
 - Upgraded `boost-histogram` to 1.5.0 {pr}`5074`
 - Upgraded `duckdb` to 1.1.0 {pr}`5078`
+- Upgraded `sympy` to 1.13.3 {pr}`5098`
 - Added `casadi` 3.6.6 {pr}`4936`, {pr}`5057`
 - 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 `arro3-core`, `arro3-io`, and `arro3-compute` 0.3.0 {pr}`5020`
+- 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`
 
 ## Version 0.26.2
 

diff --git a/docs/usage/working-with-bundlers.md b/docs/usage/working-with-bundlers.md
@@ -27,7 +27,8 @@ using a Vite plugin:
 ```js
 import { defineConfig } from "vite";
 import { copyFile, mkdir } from "fs/promises";
-import { join } from "path";
+import { dirname, join } from "path";
+import { fileURLToPath } from "url";
 
 export default defineConfig({
   optimizeDeps: { exclude: ["pyodide"] },
@@ -43,9 +44,10 @@ export default defineConfig({
           "pyodide.asm.wasm",
           "python_stdlib.zip",
         ];
+        const modulePath = fileURLToPath(import.meta.resolve("pyodide"));
         for (const file of files) {
           await copyFile(
-            join("node_modules/pyodide", file),
+            join(dirname(modulePath), file),
             join(assetsDir, file),
           );
         }

diff --git a/packages/Cartopy/meta.yaml b/packages/Cartopy/meta.yaml
@@ -34,4 +34,4 @@ about:
   home: http://scitools.org.uk/cartopy
   PyPI: https://pypi.org/project/Cartopy/
   summary: A library providing cartographic tools for python
-  license: LGPL-3.0-or-later
+  license: LGPL-3.0+
diff --git a/packages/Pygments/meta.yaml b/packages/Pygments/meta.yaml
@@ -10,4 +10,4 @@ about:
   home: https://pygments.org/
   PyPI: https://pypi.org/project/Pygments
   summary: Pygments is a syntax highlighting package written in Python.
-  license: BSD License
+  license: BSD-2-Clause
diff --git a/packages/RobotRaconteur/meta.yaml b/packages/RobotRaconteur/meta.yaml
@@ -54,3 +54,6 @@ build:
       $WASM_LIBRARY_DIR/lib/libboost_regex.a \
       $WASM_LIBRARY_DIR/lib/libboost_system.a \
       -o out/Python3/RobotRaconteur/_RobotRaconteurPython.so
+about:
+  home: https://github.com/robotraconteur/robotraconteur
+  license: Apache-2.0
diff --git a/packages/affine/meta.yaml b/packages/affine/meta.yaml
@@ -7,10 +7,10 @@ source:
   url: https://files.pythonhosted.org/packages/0b/f7/85273299ab57117850cc0a936c64151171fac4da49bc6fba0dad984a7c5f/affine-2.4.0-py3-none-any.whl
   sha256: 8a3df80e2b2378aef598a83c1392efd47967afec4242021a0b06b4c7cbc61a92
 about:
-  home: ""
+  home: https://github.com/rasterio/affine
   PyPI: https://pypi.org/project/affine
   summary: Matrices describing affine transformation of the plane
-  license: ""
+  license: BSD-3-Clause
 extra:
   recipe-maintainers:
     - kjmalek
diff --git a/packages/aiohttp/meta.yaml b/packages/aiohttp/meta.yaml
@@ -21,4 +21,4 @@ about:
   home: https://github.com/aio-libs/aiohttp
   PyPI: https://pypi.org/project/aiohttp
   summary: Async http client/server framework (asyncio)
-  license: Apache 2
+  license: Apache-2.0
diff --git a/packages/aiosignal/meta.yaml b/packages/aiosignal/meta.yaml
@@ -15,4 +15,4 @@ about:
   home: https://github.com/aio-libs/aiosignal
   PyPI: https://pypi.org/project/aiosignal
   summary: "aiosignal: a list of registered asynchronous callbacks"
-  license: Apache 2.0
+  license: Apache-2.0
diff --git a/packages/altair/meta.yaml b/packages/altair/meta.yaml
@@ -7,10 +7,10 @@ source:
   url: https://files.pythonhosted.org/packages/46/30/2118537233fa72c1d91a81f5908a7e843a6601ccc68b76838ebc4951505f/altair-5.3.0-py3-none-any.whl
   sha256: 7084a1dab4d83c5e7e5246b92dc1b4451a6c68fd057f3716ee9d315c8980e59a
 about:
-  home:
+  home: https://altair-viz.github.io/
   PyPI: https://pypi.org/project/altair
   summary: "Vega-Altair: A declarative statistical visualization library for Python."
-  license:
+  license: BSD-3-Clause
 extra:
   recipe-maintainers:
     - joelostblom

diff --git a/packages/annotated-types/meta.yaml b/packages/annotated-types/meta.yaml
@@ -7,7 +7,7 @@ source:
   url: https://files.pythonhosted.org/packages/28/78/d31230046e58c207284c6b2c4e8d96e6d3cb4e52354721b944d3e1ee4aa5/annotated_types-0.6.0-py3-none-any.whl
   sha256: 0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43
 about:
-  home: ""
+  home: https://github.com/annotated-types/annotated-types
   PyPI: https://pypi.org/project/annotated-types
   summary: Reusable constraint types to use with typing.Annotated
-  license: ""
+  license: MIT
diff --git a/packages/arro3-compute/meta.yaml b/packages/arro3-compute/meta.yaml
@@ -1,11 +1,11 @@
 package:
   name: arro3-compute
-  version: 0.3.0
+  version: 0.4.1
   top-level:
     - "arro3.compute"
 source:
-  url: https://github.com/kylebarron/arro3/releases/download/py-v0.3.0/arro3_compute-0.3.0-cp312-cp312-emscripten_3_1_58_wasm32.whl
-  sha256: 0753b631c43c674dfa8651366c3e9f9a3221c13c1dab7c9da6606f45264a5f56
+  url: https://github.com/kylebarron/arro3/releases/download/py-v0.4.1/arro3_compute-0.4.1-cp312-cp312-emscripten_3_1_58_wasm32.whl
+  sha256: 4501c0e9814a03e06e66988aab3bdb25d46594b6693d907158b67311ab29d7df
 requirements:
   run:
     - arro3-core

diff --git a/packages/arro3-core/meta.yaml b/packages/arro3-core/meta.yaml
@@ -1,11 +1,11 @@
 package:
   name: arro3-core
-  version: 0.3.0
+  version: 0.4.1
   top-level:
     - "arro3.core"
 source:
-  url: https://github.com/kylebarron/arro3/releases/download/py-v0.3.0/arro3_core-0.3.0-cp312-cp312-emscripten_3_1_58_wasm32.whl
-  sha256: 3ddeb31980f94e72a882bcdafe65cf7eb0bd2dce7bf306c327ef7dec6a72ec87
+  url: https://github.com/kylebarron/arro3/releases/download/py-v0.4.1/arro3_core-0.4.1-cp312-cp312-emscripten_3_1_58_wasm32.whl
+  sha256: ea1ff02a0dd67129ba9dc81dde85415029cdc61c4172790857189328167c6be3
 extra:
   recipe-maintainers:
     - kylebarron

diff --git a/packages/arro3-io/meta.yaml b/packages/arro3-io/meta.yaml
@@ -1,11 +1,11 @@
 package:
   name: arro3-io
-  version: 0.3.0
+  version: 0.4.1
   top-level:
     - "arro3.io"
 source:
-  url: https://github.com/kylebarron/arro3/releases/download/py-v0.3.0/arro3_io-0.3.0-cp312-cp312-emscripten_3_1_58_wasm32.whl
-  sha256: ca5a05da31f1d72ac77ade6c5532b3d333317257eab768c61dc2cf46149e33e5
+  url: https://github.com/kylebarron/arro3/releases/download/py-v0.4.1/arro3_io-0.4.1-cp312-cp312-emscripten_3_1_58_wasm32.whl
+  sha256: bf290dd5950603ae45e66a4d85747c1c53c373d0c2c7b7fe4293d6e283dfb8f1
 requirements:
   run:
     - arro3-core

diff --git a/packages/astropy/meta.yaml b/packages/astropy/meta.yaml
@@ -49,7 +49,7 @@ about:
   home: http://astropy.org
   PyPI: https://pypi.org/project/astropy
   summary: Astronomy and astrophysics core library
-  license: BSD 3-Clause License
+  license: BSD-3-Clause
 extra:
   recipe-maintainers:
     - jobovy
diff --git a/packages/astropy_iers_data/meta.yaml b/packages/astropy_iers_data/meta.yaml
@@ -10,23 +10,4 @@ about:
   home: ""
   PyPI: https://pypi.org/project/astropy_iers_data
   summary: IERS Earth Rotation and Leap Second tables for the astropy core package
-  license:
-    'Copyright (c) 2023, Astropy Developers  All rights reserved.  Redistribution
-    and use in source and binary forms, with or without modification, are permitted
-    provided that the following conditions are met:  * Redistributions of source code
-    must retain the above copyright notice, this list of conditions and the following
-    disclaimer. * Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the documentation
-    and/or other materials provided with the distribution. * Neither the name of the
-    Astropy Team nor the names of its contributors may be used to endorse or promote
-    products derived from this software without specific prior written permission.  THIS
-    SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
-    EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-    OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
-    EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-    INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
-    TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-    OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-    IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
-    IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
-    OF SUCH DAMAGE. '
+  license: BSD-3-Clause
diff --git a/packages/asttokens/meta.yaml b/packages/asttokens/meta.yaml
@@ -13,4 +13,4 @@ about:
   home: https://github.com/gristlabs/asttokens
   PyPI: https://pypi.org/project/asttokens
   summary: Annotate AST trees with source code positions
-  license: Apache 2.0
+  license: Apache-2.0
diff --git a/packages/async-timeout/meta.yaml b/packages/async-timeout/meta.yaml
@@ -10,4 +10,4 @@ about:
   home: https://github.com/aio-libs/async-timeout
   PyPI: https://pypi.org/project/async-timeout
   summary: Timeout context manager for asyncio programs
-  license: Apache 2
+  license: Apache-2.0
diff --git a/packages/b2d/meta.yaml b/packages/b2d/meta.yaml
@@ -19,6 +19,9 @@ test:
   imports:
     - b2d
     - b2d.testbed
+about:
+  home: https://github.com/pyb2d/pyb2d
+  license: MIT
 extra:
   recipe-maintainers:
     - DerThorsten
diff --git a/packages/bcrypt/meta.yaml b/packages/bcrypt/meta.yaml
@@ -13,4 +13,4 @@ about:
   home: https://github.com/pyca/bcrypt/
   PyPI: https://pypi.org/project/bcrypt
   summary: Modern password hashing for your software and your servers
-  license: Apache License, Version 2.0
+  license: Apache-2.0
diff --git a/packages/biopython/meta.yaml b/packages/biopython/meta.yaml
@@ -16,3 +16,4 @@ about:
   home: https://biopython.org/
   PyPI: https://pypi.org/project/biopython
   summary: Freely available tools for computational molecular biology.
+  license: Biopython
diff --git a/packages/bitstring/meta.yaml b/packages/bitstring/meta.yaml
@@ -10,7 +10,7 @@ requirements:
   run:
     - bitarray
 about:
-  home: ""
+  home: https://github.com/scott-griffiths/bitstring
   PyPI: https://pypi.org/project/bitstring
   summary: Simple construction, analysis and modification of binary data.
-  license: ""
+  license: MIT
diff --git a/packages/bleach/meta.yaml b/packages/bleach/meta.yaml
@@ -15,4 +15,4 @@ about:
   home: https://github.com/mozilla/bleach
   PyPI: https://pypi.org/project/bleach
   summary: An easy safelist-based HTML-sanitizing tool.
-  license: Apache Software License
+  license: Apache-2.0
diff --git a/packages/boost-cpp/meta.yaml b/packages/boost-cpp/meta.yaml
@@ -30,6 +30,7 @@ build:
 about:
   home: https://www.boost.org/
   summary: Free peer-reviewed portable C++ source libraries.
+  license: Boost
 extra:
   recipe-maintainers:
     - johnwason
diff --git a/packages/casadi/meta.yaml b/packages/casadi/meta.yaml
@@ -21,7 +21,7 @@ about:
   home: http://casadi.org
   PyPI: https://pypi.org/project/casadi
   summary: CasADi -- framework for algorithmic differentiation and numeric optimization
-  license: GNU Lesser General Public License v3 or later (LGPLv3+)
+  license: LGPL-3.0+
 extra:
   recipe-maintainers:
     - agriyakhetarpal
diff --git a/packages/cbor-diag/meta.yaml b/packages/cbor-diag/meta.yaml
@@ -16,4 +16,4 @@ about:
   home: https://github.com/chrysn/cbor-diag-py
   PyPI: https://pypi.org/project/cbor-diag/
   summary: Conversion between CBOR and CBOR Diagnostic Notation
-  license: MIT OR Apache-2.0
+  license: Apache-2.0 OR MIT
diff --git a/packages/certifi/meta.yaml b/packages/certifi/meta.yaml
@@ -13,4 +13,4 @@ about:
     Certifi provides Mozilla’s carefully curated collection of Root Certificates
     for validating the trustworthiness of SSL certificates while verifying the identity
     of TLS hosts.
-  license: "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)"
+  license: MPL-2.0
diff --git a/packages/cffi_example/meta.yaml b/packages/cffi_example/meta.yaml
@@ -11,3 +11,6 @@ requirements:
 source:
   url: https://github.com/wolever/python-cffi-example/archive/ec14da61ee0de770750ff3781b412a3b25f020eb.zip
   sha256: 4d7844ff45e5e870dc7996b4cc61636eabd33c32cc8663cf2cd21e3f4f893abc
+about:
+  home: https://github.com/wolever/python-cffi-example
+  license: BSD-2-Clause
diff --git a/packages/cftime/meta.yaml b/packages/cftime/meta.yaml
@@ -17,4 +17,4 @@ about:
   home: https://github.com/Unidata/cftime
   PyPI: https://pypi.org/project/cftime
   summary: Time-handling functionality from netcdf4-python
-  license: "License :: OSI Approved :: MIT License"
+  license: MIT
diff --git a/packages/cligj/meta.yaml b/packages/cligj/meta.yaml
@@ -14,4 +14,4 @@ about:
   home: https://github.com/mapbox/cligj
   PyPI: https://pypi.org/project/cligj
   summary: Click params for command line interfaces to GeoJSON
-  license: BSD
+  license: BSD-3-Clause
diff --git a/packages/cloudpickle/meta.yaml b/packages/cloudpickle/meta.yaml
@@ -10,4 +10,4 @@ about:
   home: https://github.com/cloudpipe/cloudpickle
   PyPI: https://pypi.org/project/cloudpickle
   summary: Extended pickling support for Python objects
-  license: BSD 3-Clause License
+  license: BSD-3-Clause
diff --git a/packages/cmyt/meta.yaml b/packages/cmyt/meta.yaml
@@ -16,4 +16,4 @@ about:
   home: https://github.com/yt-project/yt
   PyPI: https://pypi.org/project/cmyt
   summary: A collection of Matplotlib colormaps from the yt project
-  license: BSD 3-Clause
+  license: BSD-3-Clause
diff --git a/packages/coverage/meta.yaml b/packages/coverage/meta.yaml
@@ -13,4 +13,4 @@ about:
   home: https://github.com/nedbat/coveragepy
   PyPI: https://pypi.org/project/coverage
   summary: Code coverage measurement for Python
-  license: Apache 2.0
+  license: Apache-2.0
diff --git a/packages/cpp-exceptions-test/meta.yaml b/packages/cpp-exceptions-test/meta.yaml
@@ -14,3 +14,5 @@ build:
     em++ ${SIDE_MODULE_CFLAGS} -fexceptions -I${PYTHONINCLUDE} -flto -fno-lto -std=c++20 -c catch.cpp -o catch.o -mreference-types
     em++ ${SIDE_MODULE_LDFLAGS} -fexceptions  -o ${DISTDIR}/cpp-exceptions-test-throw.so throw.o
     em++ ${SIDE_MODULE_LDFLAGS} -fexceptions  -o ${DISTDIR}/cpp-exceptions-test-catch.so catch.o
+about:
+  license: MPL-2.0
diff --git a/packages/cpp-exceptions-test2/meta.yaml b/packages/cpp-exceptions-test2/meta.yaml
@@ -9,3 +9,5 @@ source:
 build:
   cxxflags: -fexceptions
   ldflags: -fexceptions
+about:
+  license: MPL-2.0
diff --git a/packages/crc32c/meta.yaml b/packages/crc32c/meta.yaml
@@ -10,7 +10,7 @@ about:
   home: https://github.com/ICRAR/crc32c
   PyPI: https://pypi.org/project/crc32c
   summary: A python package implementing the crc32c algorithm in hardware and software
-  license: LGPL-2.1-or-later
+  license: LGPL-2.1+
 extra:
   recipe-maintainers:
     - agriyakhetarpal
diff --git a/packages/cssselect/meta.yaml b/packages/cssselect/meta.yaml
@@ -10,4 +10,4 @@ about:
   home: https://github.com/scrapy/cssselect
   PyPI: https://pypi.org/project/cssselect
   summary: cssselect parses CSS3 Selectors and translates them to XPath 1.0
-  license: BSD
+  license: BSD-3-Clause
diff --git a/packages/cvxpy-base/meta.yaml b/packages/cvxpy-base/meta.yaml
@@ -18,7 +18,7 @@ about:
   summary:
     A domain-specific language for modeling convex optimization problems in
     Python.
-  license: Apache License, Version 2.0
+  license: Apache-2.0
 extra:
   recipe-maintainers:
     - phschiele
diff --git a/packages/cycler/meta.yaml b/packages/cycler/meta.yaml
@@ -13,4 +13,4 @@ about:
   home: https://github.com/matplotlib/cycler
   PyPI: https://pypi.org/project/cycler
   summary: Composable style cycles
-  license: BSD
+  license: BSD-3-Clause
diff --git a/packages/cysignals/meta.yaml b/packages/cysignals/meta.yaml
@@ -13,7 +13,7 @@ about:
   home: https://github.com/sagemath/cysignals
   PyPI: https://pypi.org/project/cysignals
   summary: Interrupt and signal handling for Cython
-  license: LGPL v3
+  license: LGPL-3.0
 extra:
   recipe-maintainers:
     - mkoeppe
diff --git a/packages/cytoolz/meta.yaml b/packages/cytoolz/meta.yaml
@@ -13,4 +13,4 @@ about:
   home: https://github.com/pytoolz/cytoolz
   PyPI: https://pypi.org/project/cytoolz
   summary: "Cython implementation of Toolz: High performance functional utilities"
-  license: BSD
+  license: BSD-3-Clause
diff --git a/packages/decorator/meta.yaml b/packages/decorator/meta.yaml
@@ -10,4 +10,4 @@ about:
   home: https://github.com/micheles/decorator
   PyPI: https://pypi.org/project/decorator
   summary: Decorators for Humans
-  license: new BSD License
+  license: BSD-3-Clause
diff --git a/packages/deprecation/meta.yaml b/packages/deprecation/meta.yaml
@@ -13,4 +13,4 @@ about:
   home: http://deprecation.readthedocs.io/
   PyPI: https://pypi.org/project/deprecation
   summary: A library to handle automated deprecations
-  license: Apache 2
+  license: Apache-2.0
diff --git a/packages/docutils/meta.yaml b/packages/docutils/meta.yaml
@@ -10,4 +10,4 @@ about:
   home: https://docutils.sourceforge.io/
   PyPI: https://pypi.org/project/docutils
   summary: Docutils -- Python Documentation Utilities
-  license: public domain, Python, 2-Clause BSD, GPL 3 (see COPYING.txt)
+  license: Mixed public domain, Python, BSD-2-Clause, GPL-3.0 (see COPYING.txt)