Bump recipes (#38)

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

.github/workflows/build.yml

@@ -191,14 +191,18 @@ jobs:
           path: ./repodata/
           retention-days: 15
 
+      - name: Compress build artifacts
+        run: |
+          tar -czvf packages.tar.gz repodata
+
       - name: Release
         uses: softprops/action-gh-release@v1
         if: startsWith(github.ref, 'refs/tags/')
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           files: |
-            ./repodata/*.whl
+            ./packages.tar.gz
 
   test:
     runs-on: ubuntu-latest

conftest.py

@@ -78,3 +78,8 @@ def pytest_collection_modifyitems(config, items):
 
 def package_is_built(package_name):
     return _package_is_built(package_name, pytest.pyodide_dist_dir)
+
+
+requires_jspi = pytest.mark.xfail_browsers(
+    firefox="requires jspi", safari="requires jspi"
+)

packages/awkward-cpp/meta.yaml

@@ -1,16 +1,14 @@
 package:
   name: awkward-cpp
-  version: "32"
+  version: "33"
   top-level:
     - awkward_cpp
 
 source:
-  url: https://files.pythonhosted.org/packages/e4/64/f95efa6441d08284e760a394545d6ac3ede2811011d24f0797d786cb2570/awkward-cpp-32.tar.gz
-  sha256: ad8c5af86206fb0f434b16749cc5cca69a15a88e16ca43e91e56c5cca77421f0
+  url: https://files.pythonhosted.org/packages/7e/4f/058f320b0952d7a59fdaa5dbd96ec7c4485271178b2404f644a79ef8b095/awkward-cpp-33.tar.gz
+  sha256: 550adebccd329d18d02e95226d0b89698188fd33e44f07450942c692881927d8
 
 build:
-  script: |
-    export CMAKE_ARGS="${CMAKE_ARGS} -DEMSCRIPTEN=1"
   exports: requested
 
 requirements:

packages/biopython/meta.yaml

@@ -4,12 +4,14 @@ package:
   top-level:
     - Bio
     - BioSQL
-requirements:
-  run:
-    - numpy
 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"
+requirements:
+  run:
+    - numpy
 about:
   home: https://biopython.org/
   PyPI: https://pypi.org/project/biopython

packages/biopython/patches/0001-Remove-error-message-if-wheel-is-not-installed.patch

@@ -0,0 +1,37 @@
+From 434770dc707c5192159249d098e6dbc660fa6556 Mon Sep 17 00:00:00 2001
+From: Hood Chatham <[email protected]>
+Date: Thu, 20 Jun 2024 12:31:15 -0700
+Subject: [PATCH] Remove error message if wheel is not installed
+
+Since pypa/setuptools#4369 was merged, wheel is vendored into setuptools and no
+longer needs to be installed for `bdist_wheel` to work.
+
+Upstream PR:
+https://github.com/biopython/biopython/pull/4749
+---
+ setup.py | 9 ---------
+ 1 file changed, 9 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 530b413a9..6cfc48de5 100644
+--- a/setup.py
++++ b/setup.py
+@@ -37,15 +37,6 @@ except ImportError:
+         "Try running: python -m ensurepip"
+     )
+
+-if "bdist_wheel" in sys.argv:
+-    try:
+-        import wheel  # noqa: F401
+-    except ImportError:
+-        sys.exit(
+-            "We need both setuptools AND wheel packages installed "
+-            "for bdist_wheel to work. Try running: pip install wheel"
+-        )
+-
+
+ # Make sure we have the right Python version.
+ MIN_PY_VER = (3, 9)
+-- 
+2.34.1
+

packages/cpp-exceptions-test2/meta.yaml

@@ -0,0 +1,11 @@
+package:
+  name: cpp-exceptions-test2
+  version: "1.0"
+  tag:
+    - core
+    - pyodide.test
+source:
+  path: src
+build:
+  cxxflags: -fexceptions
+  ldflags: -fexceptions

packages/cpp-exceptions-test2/src/cpp_exceptions_test2.cpp

@@ -0,0 +1,13 @@
+#include "Python.h"
+#include <stdexcept>
+
+extern "C" __attribute__((visibility("default"))) PyObject*
+PyInit_cpp_exceptions_test2()
+{
+  try {
+    throw std::runtime_error("something bad?");
+  } catch (const std::exception& e) {
+    PyErr_SetString(PyExc_ImportError, "oops");
+  }
+  return nullptr;
+}

packages/cpp-exceptions-test2/src/setup.py

@@ -0,0 +1,16 @@
+from setuptools import Extension, setup
+
+setup(
+    name="cpp-exceptions-test2",
+    version="1.0",
+    ext_modules=[
+        Extension(
+            name="cpp_exceptions_test2",  # as it would be imported
+            # may include packages/namespaces separated by `.`
+            language="c++",
+            sources=[
+                "cpp_exceptions_test2.cpp"
+            ],  # all sources are compiled into a single binary file
+        ),
+    ],
+)

packages/crc32c/meta.yaml

@@ -0,0 +1,16 @@
+package:
+  name: crc32c
+  version: "2.4"
+  top-level:
+    - crc32c
+source:
+  url: https://files.pythonhosted.org/packages/6f/19/47ac8d1d5b81a83272fe56d4cf425274437fd619ed0af9a5f9805484748c/crc32c-2.4.tar.gz
+  sha256: d985c4d9b1a1fd16c593d83f8735a8e4e156790a95338a1e0b199aac51ca1e5e
+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
+extra:
+  recipe-maintainers:
+    - agriyakhetarpal

packages/crc32c/test_crc32c.py

@@ -0,0 +1,60 @@
+# Test suite for the crc32c Pyodide package, based on the original test suite:
+# https://github.com/ICRAR/crc32c/blob/master/test/test_crc32c.py
+
+import pytest
+from pytest_pyodide import run_in_pyodide
+
+
+@run_in_pyodide(packages=["crc32c"])
+def test_zero(selenium):
+    import crc32c
+
+    assert crc32c.crc32c(b"") == 0
+
+
+TEST_DATA = [
+    ("Numbers1", b"123456789", 0xE3069283),
+    ("Numbers2", b"23456789", 0xBFE92A83),
+    ("Numbers3", b"1234567890", 0xF3DBD4FE),
+    ("Phrase", b"The quick brown fox jumps over the lazy dog", 0x22620404),
+    (
+        "LongPhrase",
+        (
+            b"Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc omni virtuti vitium contrario nomine opponitur. "
+            b"Conferam tecum, quam cuique verso rem subicias; Te ipsum, dignissimum maioribus tuis, voluptasne induxit, ut adolescentulus eriperes "
+            b"P. Conclusum est enim contra Cyrenaicos satis acute, nihil ad Epicurum. Duo Reges: constructio interrete. Tum Torquatus: Prorsus, inquit, assentior;\n"
+            b"Quando enim Socrates, qui parens philosophiae iure dici potest, quicquam tale fecit? Sed quid sentiat, non videtis. Haec quo modo conveniant, non "
+            b"sane intellego. Sed ille, ut dixi, vitiose. Dic in quovis conventu te omnia facere, ne doleas. Quod si ita se habeat, non possit beatam praestare "
+            b"vitam sapientia. Quis suae urbis conservatorem Codrum, quis Erechthei filias non maxime laudat? Primum divisit ineleganter; Huic mori optimum esse "
+            b"propter desperationem sapientiae, illi propter spem vivere."
+        ),
+        0xFCB7575A,
+    ),
+]
+
+
+@run_in_pyodide(packages=["crc32c"])
+@pytest.mark.parametrize("name, val, checksum", TEST_DATA)
+def test_all(selenium, name, val, checksum):
+    import crc32c
+
+    assert crc32c.crc32c(val) == checksum
+
+
+@run_in_pyodide(packages=["crc32c"])
+@pytest.mark.parametrize("name, val, checksum", TEST_DATA)
+def test_piece_by_piece(selenium, name, val, checksum):
+    # The initial CRC value
+    c = 0
+
+    # A generator that yields each byte of the input value
+    # as a separate byte
+    def as_individual_bytes(val):
+        for byte in val:
+            yield bytes([byte])
+
+    for x in as_individual_bytes(val):
+        import crc32c
+
+        c = crc32c.crc32c(x, c)
+    assert c == checksum

packages/cryptography/meta.yaml

@@ -10,15 +10,9 @@ source:
     - patches/0001-Tell-rust-lang-libc-that-time_t-is-64-bits.patch
 build:
   script: |
-    export OPENSSL_INCLUDE_PATH=$(pkg-config --cflags-only-I --dont-define-prefix openssl)
-    export OPENSSL_LIBRARY_PATH=$(pkg-config --libs-only-L --dont-define-prefix openssl)
     export OPENSSL_DIR=$WASM_LIBRARY_DIR
-  cflags: |
-    -Wno-implicit-function-declaration
-    $(OPENSSL_INCLUDE_PATH)
-  ldflags: |
-    $(OPENSSL_LIBRARY_PATH)
-    -Wl,--no-entry
+    # Allow linking to native libraries, otherwise libssl and libcrypto will be not linked to the final binary
+    export RUSTFLAGS="-Z link-native-libraries=yes"
 requirements:
   run:
     - openssl

packages/cvxpy-base/meta.yaml

@@ -1,12 +1,11 @@
 package:
   name: cvxpy-base
-  version: 1.5.0
+  version: 1.5.1
   top-level:
     - cvxpy
 source:
-  # TODO: replace with cvxpy-base from PyPI after 1.5 release
-  url: https://github.com/cvxpy/cvxpy/archive/23f1eaa.zip
-  sha256: 4b2a0d982a810d0fdb9f189ab5faa4dbef39679921335e54d737e1b57c555673
+  url: https://files.pythonhosted.org/packages/f8/9b/27b36409e5bfba14bee4de65af0735ea3ce2db5b81d825f33cbfb51873fc/cvxpy_base-1.5.1.tar.gz
+  sha256: ba4c7cb018c6afac7b779f355b13a61aa5c8dccaad91fa805b98c68ae1b99325
 requirements:
   run:
     # Dependencies that are needed to run the package

packages/ffmpeg/meta.yaml

@@ -18,7 +18,7 @@ build:
       --disable-stripping \
       --disable-programs \
       --disable-pthreads \
-      --nm=emnm \
+      --nm="$PYODIDE_ROOT/emsdk/emsdk/upstream/bin/llvm-nm -g" \
       --ar=emar --cc=emcc --cxx=em++ --objcc=emcc --dep-cc=emcc --ranlib=emranlib \
       --enable-cross-compile \
       --prefix=${WASM_LIBRARY_DIR}

packages/lakers-python/meta.yaml

@@ -0,0 +1,16 @@
+package:
+  name: lakers-python
+  version: 0.3.0
+  top-level:
+    - lakers
+source:
+  url: https://files.pythonhosted.org/packages/29/93/5d70b035f987a48dd854c1afc21025fb8446aae4d43c685b68691175623c/lakers_python-0.3.0.tar.gz
+  sha256: 009fc5e31b5a9a276216ff43ffd097004396a2a9131359a1da35d464e599cd1c
+requirements:
+  executable:
+    - rustup
+about:
+  home: https://github.com/openwsn-berkeley/lakers/
+  PyPI: https://pypi.org/project/lakers-python/
+  summary: An implementation of EDHOC (RFC 9528)
+  license: BSD-3-Clause

packages/lakers-python/test_lakers_python.py

@@ -0,0 +1,25 @@
+from pytest_pyodide import run_in_pyodide
+
+
+@run_in_pyodide(packages=["lakers-python"])
+def test_lakers_python(selenium_standalone):
+    import lakers
+
+    # Running an exchange needs some keys and credentials; those are from the EDHOC test vectors.
+    R = bytes.fromhex(
+        "72cc4761dbd4c78f758931aa589d348d1ef874a7e303ede2f140dcf3e6aa4aac"
+    )
+    CRED_R = bytes.fromhex(
+        "A2026008A101A5010202410A2001215820BBC34960526EA4D32E940CAD2A234148DDC21791A12AFBCBAC93622046DD44F02258204519E257236B2A0CE2023F0931F1F386CA7AFDA64FCDE0108C224C51EABF6072"
+    )
+
+    initiator = lakers.EdhocInitiator()
+    responder = lakers.EdhocResponder(R, CRED_R)
+
+    message_1 = initiator.prepare_message_1()
+    responder.process_message_1(message_1)
+    _message_2 = responder.prepare_message_2(
+        lakers.CredentialTransfer.ByReference, None, None
+    )
+
+    # There's a lot more that can be tested, but if this runs through, we've covered the most critical kinds of operations.

packages/libcst/meta.yaml

@@ -1,23 +1,23 @@
 package:
   name: libcst
-  version: 1.3.1
+  version: 1.4.0
   top-level:
     - libcst
 source:
-  url: https://files.pythonhosted.org/packages/f5/7e/11e25b1fc11bcad6b3f3a90fe515406387fe02e6b1ad36dea00ec125ca98/libcst-1.3.1.tar.gz
-  sha256: 03b1df1ae02456f1d465fcd5ead1d0d454bb483caefd8c8e6bde515ffdb53d1b
+  url: https://files.pythonhosted.org/packages/e4/bd/ff41d7a8efc4f60a61d903c3f9823565006f44f2b8b11c99701f552b0851/libcst-1.4.0.tar.gz
+  sha256: 449e0b16604f054fa7f27c3ffe86ea7ef6c409836fe68fe4e752a1894175db00
 about:
   home: ""
   PyPI: https://pypi.org/project/libcst
   summary:
     A concrete syntax tree with AST-like properties for Python 3.0 through
     3.12 programs.
   license:
-    "All contributions towards LibCST are MIT licensed.  Some Python files
-    have been derived from the standard library and are therefore PSF licensed. Modifications
+    All contributions towards LibCST are MIT licensed.  Some Python files have
+    been derived from the standard library and are therefore PSF licensed. Modifications
     on these files are dual licensed (both MIT and PSF). Some Python files have been
     taken from dataclasses and are therefore Apache licensed. Modifications on these
-    files are licensed under Apache 2.0 license."
+    files are licensed under Apache 2.0 license.
 extra:
   recipe-maintainers:
     - zsol

packages/libnetcdf/meta.yaml

@@ -16,7 +16,7 @@ requirements:
     - libxml
 
 build:
-  type: shared_library
+  type: static_library
   script: |
     export PATH=${WASM_LIBRARY_DIR}/bin:${PATH}
 
@@ -25,15 +25,18 @@ build:
     # dap + byterange: no libcurl
 
     emconfigure ./configure \
+      --host=none \
       --prefix=${WASM_LIBRARY_DIR} \
       --disable-doxygen \
       --enable-netcdf-4 \
       --disable-dap \
+      --disable-nczarr \
       --disable-byterange \
       --disable-dap-remote-tests \
       --disable-examples \
       --disable-utilities \
       --disable-testsets \
+      --disable-shared \
       CFLAGS="-fPIC -I${WASM_LIBRARY_DIR}/include -s USE_ZLIB=1" \
       CXXFLAGS="-fPIC -I${WASM_LIBRARY_DIR}/include -s USE_ZLIB=1" \
       LDFLAGS="-fPIC -s USE_ZLIB=1"

packages/libwebp/meta.yaml

@@ -22,6 +22,7 @@ build:
       -DWEBP_BUILD_WEBPINFO=OFF \
       -DWEBP_BUILD_WEBPMUX=OFF \
       -DWEBP_BUILD_EXTRAS=OFF \
+      -DWEBP_BUILD_ANIM_UTILS=OFF \
       ../
     emmake make -j ${PYODIDE_JOBS:-3}
     emmake make install

packages/lightgbm/test_lightgbm.py

@@ -2,6 +2,7 @@
 from pytest_pyodide import run_in_pyodide
 
 
+@pytest.mark.skip_pyproxy_check
 @pytest.mark.driver_timeout(60)
 @run_in_pyodide(packages=["lightgbm", "numpy"])
 def test_train_predict(selenium):

packages/netcdf4/meta.yaml

@@ -25,6 +25,10 @@ build:
     export PATH=${WASM_LIBRARY_DIR}/bin:${PATH}
     export HDF5_DIR=${WASM_LIBRARY_DIR}
     echo ${HDF5_DIR}
+  ldflags: |
+    -L$(WASM_LIBRARY_DIR)/lib
+    -lhdf5
+    -lhdf5_hl
 about:
   home: https://github.com/Unidata/netcdf4-python
   PyPI: https://pypi.org/project/netcdf4