Release pyodide-lock.json separately (#52)

.github/workflows/build.yml

@@ -198,6 +198,7 @@ jobs:
         with:
           files: |
             ./packages.tar.gz
+            ./repodata/pyodide-lock.json
 
   test:
     runs-on: ubuntu-latest

packages/pyarrow/test_pyarrow.py

@@ -1,6 +1,8 @@
+import pytest
 from pytest_pyodide import run_in_pyodide
 
 
+@pytest.mark.driver_timeout(120)
 @run_in_pyodide(packages=["pyarrow", "numpy", "pandas"])
 def test_read_write_parquet(selenium):
     import numpy as np

packages/scikit-learn/meta.yaml

@@ -1,13 +1,13 @@
 package:
   name: scikit-learn
-  version: 1.5.0
+  version: 1.5.1
   tag:
     - min-scipy-stack
   top-level:
     - sklearn
 source:
-  url: https://files.pythonhosted.org/packages/bf/8a/06e499bca463905000f50e461c9445e949aafdd33ea3b62024aa2238b83d/scikit_learn-1.5.0.tar.gz
-  sha256: 789e3db01c750ed6d496fa2db7d50637857b451e57bcae863bff707c1247bef7
+  url: https://files.pythonhosted.org/packages/92/72/2961b9874a9ddf2b0f95f329d4e67f67c3301c1d88ba5e239ff25661bb85/scikit_learn-1.5.1.tar.gz
+  sha256: 0ea5d40c0e3951df445721927448755d3fe1d80833b0b7308ebff5d2a45e6414
 
 build:
   cflags: -Wno-implicit-function-declaration

packages/scipy/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: scipy
-  version: 1.13.1
+  version: 1.14.0
   tag:
     - min-scipy-stack
   top-level:
@@ -17,25 +17,27 @@ package:
 # subroutine. Try deleting it.
 
 source:
-  url: https://files.pythonhosted.org/packages/ae/00/48c2f661e2816ccf2ecd77982f6605b2950afe60f60a52b4cbbc2504aa8f/scipy-1.13.1.tar.gz
-  sha256: 095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c
+  url: https://files.pythonhosted.org/packages/4e/e5/0230da034a2e1b1feb32621d7cd57c59484091d6dccc9e6b855b0d309fc9/scipy-1.14.0.tar.gz
+  sha256: b5923f48cb840380f9854339176ef21763118a7300a88203ccd0bdd26e58527b
 
   patches:
     - patches/0001-Fix-dstevr-in-special-lapack_defs.h.patch
     - patches/0002-int-to-string.patch
     - patches/0003-gemm_-no-const.patch
     - patches/0004-make-int-return-values.patch
-    - patches/0005-Remove-test-modules-that-fails-to-build.patch
-    - patches/0006-Fix-fitpack.patch
-    - patches/0007-Fix-gees-calls.patch
-    - patches/0008-MAINT-linalg-Remove-id_dist-Fortran-files.patch
-    - patches/0009-Mark-mvndst-functions-recursive.patch
-    - patches/0010-Make-sreorth-recursive.patch
-    - patches/0011-Link-openblas-with-modules-that-require-f2c.patch
-    - patches/0012-Remove-fpchec-inline-if-else-constructs.patch
-    - patches/0013-Remove-chla_transtype.patch
-    - patches/0014-Set-wrapper-return-type-to-int.patch
-    - patches/0015-Skip-svd_gesdd-test.patch
+    - patches/0005-Fix-fitpack.patch
+    - patches/0006-Fix-gees-calls.patch
+    - patches/0007-MAINT-linalg-Remove-id_dist-Fortran-files.patch
+    - patches/0008-Mark-mvndst-functions-recursive.patch
+    - patches/0009-Make-sreorth-recursive.patch
+    - patches/0010-Link-openblas-with-modules-that-require-f2c.patch
+    - patches/0011-Remove-fpchec-inline-if-then-endif-constructs.patch # remove with SciPy v1.15.0
+    - patches/0012-Remove-chla_transtype.patch
+    - patches/0013-Set-wrapper-return-type-to-int.patch
+    - patches/0014-Skip-svd_gesdd-test.patch # remove with SciPy v1.15.0
+    - patches/0015-Remove-f2py-generator.patch
+    - patches/0016-Make-sf_error_state_lib-a-static-library.patch
+    - patches/0017-Remove-test-modules-that-fail-to-build.patch
 
 build:
   cflags: |
@@ -50,8 +52,14 @@ build:
     -L$(NUMPY_LIB)/core/lib/
     -L$(NUMPY_LIB)/random/lib/
     -fexceptions
+
+  # Exclude tests via Meson's install tags functionality.
+  unvendor-tests: true
+  # install-args=--tags=runtime,python-runtime,devel
+  # Disable when running tests, enable when a PR is ready, i.e., building for distribution.
   backend-flags: |
     build-dir=build
+
   # IMPORTANT: Other locations important in scipy build process:
   # There are two files built in the "capture" pass that need patching:
   #    _blas_subroutines.h, and _cython

packages/scipy/patches/0001-Fix-dstevr-in-special-lapack_defs.h.patch

@@ -1,7 +1,7 @@
 From 45a31145679c83f2719b6420f234d484b9459697 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Fri, 18 Mar 2022 16:25:39 -0700
-Subject: [PATCH 1/15] Fix dstevr in special/lapack_defs.h
+Subject: [PATCH 1/17] Fix dstevr in special/lapack_defs.h
 
 ---
  scipy/special/lapack_defs.h | 5 ++---

packages/scipy/patches/0002-int-to-string.patch

@@ -1,7 +1,7 @@
 From d53ade3f03ba3557fd50fb38990d605f4ae7f8f1 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Sat, 25 Dec 2021 18:04:18 -0800
-Subject: [PATCH 2/15] int to string
+Subject: [PATCH 2/17] int to string
 
 f2c does not handle implicit casts of function arguments correctly. The msg
 argument of `xerrwv` is defined to be an `int *`, and then implicitly cast

packages/scipy/patches/0003-gemm_-no-const.patch

@@ -1,7 +1,7 @@
 From e528227dd37c8b0512381992c222789a114e3169 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Sat, 18 Dec 2021 11:41:15 -0800
-Subject: [PATCH 3/15] gemm_ no const
+Subject: [PATCH 3/17] gemm_ no const
 
 cgemm, dgemm, sgemm, and zgemm are declared with `const` in slu_cdefs.h, but
 other places don't have the cosnt causing compile errors.

packages/scipy/patches/0004-make-int-return-values.patch

@@ -1,7 +1,7 @@
 From a86a2304fd925f815bbb0e0753e46a7b863e2de2 Mon Sep 17 00:00:00 2001
 From: Joe Marshall <[email protected]>
 Date: Wed, 6 Apr 2022 21:25:13 -0700
-Subject: [PATCH 4/15] make int return values
+Subject: [PATCH 4/17] make int return values
 
 The return values of f2c functions are insignificant in most cases, so often it
 is treated as returning void, when it really should return int (values are

packages/scipy/patches/0006-Fix-fitpack.patch → packages/scipy/patches/0005-Fix-fitpack.patch

@@ -1,7 +1,7 @@
 From c784d3a1ee38da88943364de4ea847a3b9cd155f Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Tue, 30 Aug 2022 11:51:53 -0700
-Subject: [PATCH 6/15] Fix fitpack
+Subject: [PATCH 5/17] Fix fitpack
 
 ---
  scipy/interpolate/fitpack/dblint.f | 9 ++++-----

packages/scipy/patches/0007-Fix-gees-calls.patch → packages/scipy/patches/0006-Fix-gees-calls.patch

@@ -1,7 +1,7 @@
 From 8addc1da35bc63df651946ef14c723797a431e0c Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Mon, 26 Jun 2023 20:12:25 -0700
-Subject: [PATCH 7/15] Fix gees calls
+Subject: [PATCH 6/17] Fix gees calls
 
 ---
  scipy/linalg/flapack_gen.pyf.src | 8 ++++----

packages/scipy/patches/0008-MAINT-linalg-Remove-id_dist-Fortran-files.patch → packages/scipy/patches/0007-MAINT-linalg-Remove-id_dist-Fortran-files.patch

@@ -1,7 +1,7 @@
 From 12ba8a395ce04194074a24d362143c22e7ac54bd Mon Sep 17 00:00:00 2001
 From: Ilhan Polat <[email protected]>
 Date: Tue, 23 Apr 2024 09:26:38 +0200
-Subject: [PATCH 8/15] MAINT:linalg:Remove id_dist Fortran files
+Subject: [PATCH 7/17] MAINT:linalg:Remove id_dist Fortran files
 
 [skip ci]
 
@@ -41,7 +41,7 @@ DOC:linalg: Fix grammar and typos
  scipy/linalg/_decomp_interpolative.pyx        | 1992 +++++++++++
  scipy/linalg/_interpolative_backend.py        | 1681 ---------
  scipy/linalg/interpolative.py                 |  316 +-
- scipy/linalg/meson.build                      |   56 +-
+ scipy/linalg/meson.build                      |   55 +-
  scipy/linalg/src/id_dist/README.txt           |    6 -
  scipy/linalg/src/id_dist/doc/doc.bib          |   19 -
  scipy/linalg/src/id_dist/doc/doc.tex          |  977 ------
@@ -83,7 +83,7 @@ DOC:linalg: Fix grammar and typos
  scipy/linalg/src/id_dist/src/idzr_rsvd.f      |  159 -
  scipy/linalg/src/id_dist/src/prini.f          |  113 -
  scipy/linalg/tests/test_interpolative.py      |   78 +-
- 46 files changed, 2159 insertions(+), 18884 deletions(-)
+ 46 files changed, 2159 insertions(+), 18883 deletions(-)
  create mode 100644 scipy/linalg/_decomp_interpolative.pyx
  delete mode 100644 scipy/linalg/_interpolative_backend.py
  delete mode 100644 scipy/linalg/src/id_dist/README.txt
@@ -128,10 +128,10 @@ DOC:linalg: Fix grammar and typos
  delete mode 100644 scipy/linalg/src/id_dist/src/prini.f
 
 diff --git a/mypy.ini b/mypy.ini
-index 7613a464c..9c06dcb6c 100644
+index 4417af39dc..4bdbdf9750 100644
 --- a/mypy.ini
 +++ b/mypy.ini
-@@ -131,7 +131,7 @@ ignore_missing_imports = True
+@@ -140,7 +140,7 @@ ignore_missing_imports = True
  [mypy-scipy.linalg._solve_toeplitz]
  ignore_missing_imports = True
 
@@ -4441,11 +4441,10 @@ diff --git a/scipy/linalg/meson.build b/scipy/linalg/meson.build
 index cc208092e..777edd008 100644
 --- a/scipy/linalg/meson.build
 +++ b/scipy/linalg/meson.build
-@@ -103,58 +103,15 @@ interpolative_module = custom_target('interpolative_module',
-   input: 'interpolative.pyf',
-   command: [py3, generate_f2pymod, '@INPUT@', '-o', '@OUTDIR@']
- )
--
+@@ -111,57 +111,15 @@ py3.extension_module('_flapack',
+
+ # TODO: cblas/clapack are built *only* for ATLAS. Why? Is it still needed?
+
 -# id_dist contains a copy of FFTPACK, which has type mismatch warnings
 -# that are hard to fix. This code is terrible and noisy during the build,
 -# silence it completely.
@@ -4489,7 +4488,7 @@ index cc208092e..777edd008 100644
 -    'src/id_dist/src/idzr_rid.f',
 -    'src/id_dist/src/idzr_rsvd.f',
 -    'src/id_dist/src/prini.f',
--    interpolative_module,
+-    f2py_gen.process('interpolative.pyf'),
 -  ],
 -  fortran_args: [fortran_ignore_warnings, _suppress_all_warnings],
 +# _decomp_interpolative
@@ -4499,14 +4498,14 @@ index cc208092e..777edd008 100644
 +  dependencies: np_dep,
 +  c_args: numpy_nodepr_api,
    link_args: version_link_args,
--  dependencies: [lapack, fortranobject_dep],
+-  dependencies: [lapack_dep, fortranobject_dep],
    override_options: ['b_lto=false'],
    install: true,
 -  link_language: 'fortran',
    subdir: 'scipy/linalg'
  )
 
-@@ -273,7 +230,6 @@ python_sources = [
+@@ -278,7 +236,6 @@ python_sources = [
    '_decomp_schur.py',
    '_decomp_svd.py',
    '_expm_frechet.py',

packages/scipy/patches/0009-Mark-mvndst-functions-recursive.patch → packages/scipy/patches/0008-Mark-mvndst-functions-recursive.patch

@@ -1,7 +1,7 @@
 From c11745d763407d9a2bb195a21e2a8afaf7635248 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Sat, 6 Jul 2024 22:38:55 +0200
-Subject: [PATCH 9/15] Mark mvndst functions recursive
+Subject: [PATCH 8/17] Mark mvndst functions recursive
 
 ---
  scipy/stats/mvndst.f | 8 ++++----

packages/scipy/patches/0010-Make-sreorth-recursive.patch → packages/scipy/patches/0009-Make-sreorth-recursive.patch

@@ -1,7 +1,7 @@
 From e4d1a570fa8bd4c710e10400822f60232e6408eb Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Sat, 6 Jul 2024 22:33:51 +0200
-Subject: [PATCH 10/15] Make sreorth recursive
+Subject: [PATCH 9/17] Make sreorth recursive
 
 ---
  complex16/zreorth.F | 6 +++---

packages/scipy/patches/0011-Link-openblas-with-modules-that-require-f2c.patch → packages/scipy/patches/0010-Link-openblas-with-modules-that-require-f2c.patch

@@ -1,24 +1,26 @@
 From ccbb0fa0884d567c6139eeed7dc2dc9f8db4db3a Mon Sep 17 00:00:00 2001
 From: ryanking13 <[email protected]>
 Date: Sun, 28 Jul 2024 18:15:17 +0900
-Subject: [PATCH 11/15] Link openblas with modules that require f2c
+Subject: [PATCH 10/17] Link openblas with modules that require f2c
 
 Some fortran modules require symbols from f2c, which is provided by
 openblas.
 This patch adds openblas as a dependency to the modules that require f2c
 symbols.
+
+Co-Developed-by: Agriya Khetarpal <[email protected]>
 ---
  scipy/integrate/meson.build | 2 +-
  scipy/optimize/meson.build  | 6 +++---
  scipy/stats/meson.build     | 2 +-
  3 files changed, 5 insertions(+), 5 deletions(-)
 
 diff --git a/scipy/integrate/meson.build b/scipy/integrate/meson.build
-index edee2ca0ba..6f482db5fc 100644
+index 23a715dd58..e5cd9ad4c8 100644
 --- a/scipy/integrate/meson.build
 +++ b/scipy/integrate/meson.build
-@@ -167,7 +167,7 @@ py3.extension_module('_dop',
-   _dop_module,
+@@ -154,7 +154,7 @@ py3.extension_module('_dop',
+   f2py_gen.process('dop.pyf'),
    link_with: [dop_lib],
    c_args: [Wno_unused_variable],
 -  dependencies: [fortranobject_dep],
@@ -27,10 +29,10 @@ index edee2ca0ba..6f482db5fc 100644
    install: true,
    link_language: 'fortran',
 diff --git a/scipy/optimize/meson.build b/scipy/optimize/meson.build
-index 3dfe128749..45c23f43bc 100644
+index d6c20d3d53..d7f0284b5b 100644
 --- a/scipy/optimize/meson.build
 +++ b/scipy/optimize/meson.build
-@@ -134,7 +134,7 @@ py3.extension_module('_cobyla',
+@@ -125,7 +125,7 @@ py3.extension_module('_cobyla',
    c_args: [Wno_unused_variable],
    fortran_args: fortran_ignore_warnings,
    link_args: version_link_args,
@@ -39,17 +41,17 @@ index 3dfe128749..45c23f43bc 100644
    install: true,
    link_language: 'fortran',
    subdir: 'scipy/optimize'
-@@ -150,7 +150,7 @@ py3.extension_module('_minpack2',
-   [minpack2_module, 'minpack2/dcsrch.f', 'minpack2/dcstep.f'],
+@@ -135,7 +135,7 @@ py3.extension_module('_minpack2',
+   [f2py_gen.process('minpack2/minpack2.pyf'), 'minpack2/dcsrch.f', 'minpack2/dcstep.f'],
    fortran_args: fortran_ignore_warnings,
    link_args: version_link_args,
 -  dependencies: [fortranobject_dep],
 +  dependencies: [lapack, fortranobject_dep],
    override_options: ['b_lto=false'],
    install: true,
    link_language: 'fortran',
-@@ -167,7 +167,7 @@ py3.extension_module('_slsqp',
-   [slsqp_module, 'slsqp/slsqp_optmz.f'],
+@@ -146,7 +146,7 @@ py3.extension_module('_slsqp',
+   [f2py_gen.process('slsqp/slsqp.pyf'), 'slsqp/slsqp_optmz.f'],
    fortran_args: fortran_ignore_warnings,
    link_args: version_link_args,
 -  dependencies: [fortranobject_dep],
@@ -58,10 +60,10 @@ index 3dfe128749..45c23f43bc 100644
    link_language: 'fortran',
    subdir: 'scipy/optimize'
 diff --git a/scipy/stats/meson.build b/scipy/stats/meson.build
-index 33b12574a8..d97168ab49 100644
+index bb43e3b2e9..358279a93b 100644
 --- a/scipy/stats/meson.build
 +++ b/scipy/stats/meson.build
-@@ -43,7 +43,7 @@ py3.extension_module('_mvn',
+@@ -36,7 +36,7 @@ py3.extension_module('_mvn',
    # Wno-surprising is to suppress a pointless warning with GCC 10-12
    # (see GCC bug 98411: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=98411)
    fortran_args: [fortran_ignore_warnings, _fflag_Wno_surprising],

packages/scipy/patches/0012-Remove-fpchec-inline-if-else-constructs.patch → packages/scipy/patches/0011-Remove-fpchec-inline-if-then-endif-constructs.patch

@@ -1,7 +1,16 @@
 From b43a231f8326d6953929030131c3fb6b2cb163bd Mon Sep 17 00:00:00 2001
 From: Agriya Khetarpal <[email protected]>
 Date: Wed, 15 May 2024 21:29:02 +0530
-Subject: [PATCH 12/15] Remove fpchec inline if-else constructs
+Subject: [PATCH 11/17] Remove fpchec inline if-then-endif constructs
+
+This PR removes the single-line if-then-endif constructs in fpchec.f
+that were causing syntactical errors when compiling with f2c, possibly
+because fpchec uses some dated, punch-card FORTRAN syntax. It converts
+them to statements split over multiple lines.
+
+This patch has been upstreamed via https://github.com/scipy/scipy/pull/21365
+and it can be safely removed once SciPy v1.15.0 is released and is being
+integrated in Pyodide.
 
 ---
  scipy/interpolate/fitpack/fpchec.f | 42 +++++++++++++++++++++++-------

packages/scipy/patches/0013-Remove-chla_transtype.patch → packages/scipy/patches/0012-Remove-chla_transtype.patch

@@ -1,7 +1,7 @@
 From 848c94e218e89d866978fbc883cbb2d919f56ce9 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Wed, 31 Jul 2024 10:29:47 +0200
-Subject: [PATCH 13/15] Remove chla_transtype
+Subject: [PATCH 12/17] Remove chla_transtype
 
 The signature should probably be `int chla_transtype(char* res, int *trans)`.
 This just deletes it entirely due to laziness.

packages/scipy/patches/0014-Set-wrapper-return-type-to-int.patch → packages/scipy/patches/0013-Set-wrapper-return-type-to-int.patch

@@ -1,25 +1,25 @@
 From b5d05197de084ab3cab52241f163bae7519b6027 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <[email protected]>
 Date: Wed, 31 Jul 2024 11:48:12 +0200
-Subject: [PATCH 14/15] Set wrapper return type to int
+Subject: [PATCH 13/17] Set wrapper return type to int
 
 ---
  scipy/linalg/_generate_pyx.py | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 
 diff --git a/scipy/linalg/_generate_pyx.py b/scipy/linalg/_generate_pyx.py
-index a8078f7ab..1bc2dcc7c 100644
+index 8a00f5d279..aeb86e8926 100644
 --- a/scipy/linalg/_generate_pyx.py
 +++ b/scipy/linalg/_generate_pyx.py
-@@ -483,7 +483,7 @@ def generate_decl_c(name, return_type, argnames, argtypes):
+@@ -520,7 +520,7 @@ def generate_decl_c(name, return_type, argnames, argtypes, accelerate):
      if name in WRAPPED_FUNCS:
          argnames = ['out'] + argnames
          c_argtypes = [c_return_type] + c_argtypes
 -        c_return_type = 'void'
 +        c_return_type = 'int'
-     blas_macro, blas_name = get_blas_macro_and_name(name)
+     blas_macro, blas_name = get_blas_macro_and_name(name, accelerate)
      c_args = ', '.join(f'{t} *{n}' for t, n in zip(c_argtypes, argnames))
      return f"{c_return_type} {blas_macro}({blas_name})({c_args});\n"
 -- 
-2.34.1
+2.39.3 (Apple Git-146)