SciPy v1.16.0

.github/workflows/build.yml

@@ -36,6 +36,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          submodules: recursive
+          persist-credentials: false
 
       - name: Install Emscripten ccache
         run: |
@@ -244,6 +246,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+          persist-credentials: false
 
       - name: Cache conda
         uses: actions/cache@v4
@@ -316,6 +322,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          submodules: recursive
+          persist-credentials: false
 
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v3

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "pyodide-build"]
+	path = pyodide-build
+	url = https://github.com/pyodide/pyodide-build
+	branch = updates-for-scipy

.gitpod.yml

@@ -1,13 +1,18 @@
 additionalRepositories:
   - url: https://github.com/emscripten-core/emsdk
+  - url: https://github.com/pyodide/pyodide-build
+    checkoutLocation: pyodide-build
 tasks:
+  - name: Sync submodule(s)
+    init: git submodule update --init --recursive
+    command: echo "Submodules initialized"
   - name: Setup
     init: |
       pyenv global system
       conda env create -f environment.yml
       conda activate pyodide-env
 
-      pip install git+https://github.com/pyodide/pyodide-build.git
+      pip install ./pyodide-build/
       pyodide xbuildenv install
 
       EMSCRIPTEN_VERSION=$(pyodide config get emscripten_version)

README.md

@@ -4,13 +4,22 @@ Collections of package recipes for Pyodide
 
 ## Adding a new package
 
-> Note: Use Python 3.12 or upper to run the following commands.
+> Note: Use Python 3.13 or upper to run the following commands.
 
 To add a new package, create a package recipe in the `packages` directory.
-You can start by creating a boilerplate recipe with the following command:
+
+It is required to clone the repository with the `--recurse-submodules` option to ensure
+that all submodules are initialized. If hyou have already cloned the repository without
+this option, you can run the following command to initialize the submodules:
+
+```bash
+$ git submodule update --init --recursive
+```
+
+You can then start by creating a boilerplate recipe with the following command:
 
 ```bash
-$ pip install pyodide-build
+$ pip install ./pyodide-build
 $ pyodide skeleton pypi <package-name>
 ```
 

docs/MAINTAINERS.md

@@ -30,7 +30,7 @@ by updating the `Makefile.envs` file in the pyodide/pyodide repository.
 To build and test packages locally, you need to prepare the necessary tools and dependencies.
 
 - compatible Python version
-- pyodide-build
+- pyodide-build, which is provided by the `pyodide-build` Git submodule in the repository root
 - emscripten
 - selenium (for testing)
 
@@ -71,9 +71,9 @@ The `pyodide-recipes` repository is used to build packages for both stable and n
 We use different branches for those versions:
 
 - `main`: the default branch, used for nightly versions of Pyodide
-  - It uses nightly xbuildenv and nightly pyodide-build to build packages.
+  - It uses nightly xbuildenv and the pyodide-build submodule to build packages.
 - `<version>`: a branch for stable versions of Pyodide
-  - It uses stable xbuildenv and nightly (or stable if there is any breaking change) pyodide-build to build packages.
+  - It uses stable xbuildenv and pyodide-build submodule (or a stable version, if there are any breaking changes) to build packages.
 
 Let's say we have a stable Pyodide version `0.27.0`, and we are developing a new version `0.28.0`.
 

packages/scipy/meta.yaml

@@ -1,7 +1,6 @@
 package:
   name: scipy
-  version: 1.14.1
-  pinned: true
+  version: 1.16.0
   tag:
     - min-scipy-stack
   top-level:
@@ -18,8 +17,8 @@ package:
 # subroutine. Try deleting it.
 
 source:
-  url: https://files.pythonhosted.org/packages/62/11/4d44a1f274e002784e4dbdb81e0ea96d2de2d1045b2132d5af62cc31fd28/scipy-1.14.1.tar.gz
-  sha256: 5a275584e726026a5699459aa72f828a610821006228e841b94275c4a7c08417
+  url: https://files.pythonhosted.org/packages/source/s/scipy/scipy-1.16.0.tar.gz
+  sha256: b5ef54021e832869c8cfb03bc3bf20366cbcd426e02a58e8a58d7584dfbb8f62
 
   patches:
     - patches/0001-Fix-dstevr-in-special-lapack_defs.h.patch
@@ -28,18 +27,14 @@ source:
     - patches/0004-make-int-return-values.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-generators.patch
-    - patches/0016-Make-sf_error_state_lib-a-static-library.patch
-    - patches/0017-Remove-test-modules-that-fail-to-build.patch
-    - patches/0018-Fix-lapack-larfg-function-signature.patch
+    - patches/0007-Make-sreorth-recursive.patch
+    - patches/0008-Link-openblas-with-modules-that-require-f2c.patch
+    - patches/0009-Remove-chla_transtype.patch
+    - patches/0010-Set-wrapper-return-type-to-int.patch
+    - patches/0011-Remove-test-modules-that-fail-to-build.patch
+    - patches/0012-Fix-lapack-larfg-function-signature.patch
+    - patches/0013-ENH-MAINT-sparse.linalg-rewrite-ARPACK-in-C-22748.patch
+    - patches/0014-Remove-f2py-generators.patch
 
 build:
   # NumPy 2.1 disabled visibility for symbols outside of extension modules
@@ -98,7 +93,12 @@ build:
     sed -i 's/extern void/extern int/g' scipy/optimize/__minpack.h
     sed -i 's/void/int/g' scipy/linalg/cython_blas_signatures.txt
     sed -i 's/void/int/g' scipy/linalg/cython_lapack_signatures.txt
+    sed -i 's/^void/int/g' scipy/linalg/_common_array_utils.h
+
     sed -i 's/^void/int/g' scipy/interpolate/src/_fitpackmodule.c
+    sed -i 's/^void/int/g' scipy/interpolate/src/__fitpack.h
+    sed -i 's/^void/int/g' scipy/interpolate/src/__fitpack.cc
+    sed -i 's/void BLAS_FUNC/int BLAS_FUNC/g' scipy/interpolate/src/__fitpack.h
 
     sed -i 's/extern void/extern int/g' scipy/sparse/linalg/_dsolve/SuperLU/SRC/*.{c,h}
     sed -i 's/PUBLIC void/PUBLIC int/g' scipy/sparse/linalg/_dsolve/SuperLU/SRC/*.{c,h}
@@ -107,16 +107,36 @@ build:
     sed -i 's/void \(.\)print/int \1/g' scipy/sparse/linalg/_dsolve/SuperLU/SRC/*.{c,h}
     sed -i 's/TYPE_GENERIC_FUNC(\(.*\), void)/TYPE_GENERIC_FUNC(\1, int)/g' scipy/sparse/linalg/_dsolve/_superluobject.h
 
+    sed -i 's/^void/int/g' scipy/optimize/__nnls.h
+    sed -i 's/^void/int/g' scipy/optimize/__nnls.c
+    sed -i 's/^void/int/g' scipy/optimize/__slsqp.h
+    sed -i 's/^void/int/g' scipy/optimize/__slsqp.c
+    sed -i 's/^static void/static int/g' scipy/optimize/__slsqp.c
+
     sed -i 's/^void/int/g' scipy/optimize/_trlib/trlib_private.h
     sed -i 's/^void/int/g' scipy/optimize/_trlib/trlib/trlib_private.h
     sed -i 's/^void/int/g' scipy/_build_utils/src/wrap_dummy_g77_abi.c
     sed -i 's/, int)/)/g' scipy/optimize/_trlib/trlib_private.h
     sed -i 's/, 1)/)/g' scipy/optimize/_trlib/trlib_private.h
 
+    sed -i 's/^void/int/g' scipy/linalg/_matfuncs_expm.h
+    sed -i 's/^void/int/g' scipy/linalg/_matfuncs_expm.c
+    sed -i 's/^void/int/g' scipy/linalg/_matfuncs_sqrtm.h
+    sed -i 's/^void/int/g' scipy/linalg/_matfuncs_sqrtm.c
+
+    sed -i 's/^void/int/g' scipy/sparse/linalg/_eigen/arpack/ARPACK/_arpack_n_double_complex.h
+    sed -i 's/^void/int/g' scipy/sparse/linalg/_eigen/arpack/ARPACK/_arpack_n_double.h
+    sed -i 's/^void/int/g' scipy/sparse/linalg/_eigen/arpack/ARPACK/_arpack_n_single_complex.h
+    sed -i 's/^void/int/g' scipy/sparse/linalg/_eigen/arpack/ARPACK/_arpack_n_single.h
+    sed -i 's/^void/int/g' scipy/sparse/linalg/_eigen/arpack/ARPACK/_arpack_s_double.h
+    sed -i 's/^void/int/g' scipy/sparse/linalg/_eigen/arpack/ARPACK/_arpack_s_single.h
+
     sed -i 's/^void/int/g' scipy/spatial/qhull_misc.h
     sed -i 's/, size_t)/)/g' scipy/spatial/qhull_misc.h
     sed -i 's/,1)/)/g' scipy/spatial/qhull_misc.h
 
+    sed -i 's/^void/int/g' scipy/optimize/__lbfgsb.h
+
     # Input error causes "duplicate symbol" linker errors. Empty out the file.
     echo "" > scipy/sparse/linalg/_dsolve/SuperLU/SRC/input_error.c
 

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 1/18] Fix dstevr in special/lapack_defs.h
+Subject: [PATCH 1/14] 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 2/18] int to string
+Subject: [PATCH 2/14] 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 3/18] gemm_ no const
+Subject: [PATCH 3/14] 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 4/18] make int return values
+Subject: [PATCH 4/14] 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
@@ -240,21 +240,20 @@ index 67e83bcc77..e5757d5c4d 100644
 
  /* Macro definitions */
 diff --git a/scipy/sparse/linalg/_dsolve/SuperLU/SRC/slu_scomplex.h b/scipy/sparse/linalg/_dsolve/SuperLU/SRC/slu_scomplex.h
-index 83be8c971f..047a07ce9c 100644
+index 1e53fbca5..b35313ccb 100644
 --- a/scipy/sparse/linalg/_dsolve/SuperLU/SRC/slu_scomplex.h
 +++ b/scipy/sparse/linalg/_dsolve/SuperLU/SRC/slu_scomplex.h
-@@ -27,8 +27,9 @@ at the top-level directory.
-
+@@ -28,7 +28,9 @@ at the top-level directory.
  #ifndef SCOMPLEX_INCLUDE
  #define SCOMPLEX_INCLUDE
--
+ 
 -typedef struct { float r, i; } singlecomplex;
-+#include"scipy_slu_config.h"
++#include "scipy_slu_config.h"
 +// defined in  CLAPACK
 +//typedef struct { float r, i; } singlecomplex;
 
-
- /* Macro definitions */
+ #if defined(SUPERLU_TYPEDEF_COMPLEX) || DOXYGEN
+ //! \brief backward compatibility with older versions of SuperLU
 diff --git a/scipy/sparse/linalg/_dsolve/_superlu_utils.c b/scipy/sparse/linalg/_dsolve/_superlu_utils.c
 index 49b928a431..0822687719 100644
 --- a/scipy/sparse/linalg/_dsolve/_superlu_utils.c

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 5/18] Fix fitpack
+Subject: [PATCH 5/14] Fix fitpack
 
 ---
  scipy/interpolate/fitpack/dblint.f | 9 ++++-----

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 6/18] Fix gees calls
+Subject: [PATCH 6/14] Fix gees calls
 
 ---
  scipy/linalg/flapack_gen.pyf.src | 8 ++++----