d

.circleci/config.yml

@@ -119,16 +119,16 @@ jobs:
           no_output_timeout: 25m
           command: |
             export PYTHONPATH=$PWD/build-install/lib/python3.8/site-packages
-            python dev.py -n -j2 --doc html-scipyorg
+            python dev.py -n -j2 --doc html
 
       - store_artifacts:
-          path: doc/build/html-scipyorg
-          destination: html-scipyorg
+          path: doc/build/html
+          destination: html
 
       - persist_to_workspace:
           root: doc/build
           paths:
-            - html-scipyorg
+            - html
 
 # Run benchmarks
 
@@ -185,7 +185,7 @@ jobs:
             (git checkout --orphan tmp && git branch -D gh-pages || true);
             git checkout --orphan gh-pages;
             git reset --hard;
-            cp -R /tmp/build/html-scipyorg/. .;
+            cp -R /tmp/build/html/. .;
             touch .nojekyll;
             git config --global user.email "scipy-circleci-bot@nomail";
             git config --global user.name "scipy-circleci-bot";

.github/FUNDING.yml

@@ -1,3 +1,3 @@
 github: [numfocus]
 tidelift: pypi/scipy
-custom: https://scipy.org/donations
+custom: https://scipy.org/about/#donate

.github/workflows/circle_artifacts.yml

@@ -8,6 +8,6 @@ jobs:
         uses: larsoner/circleci-artifacts-redirector-action@master
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-          artifact-path: 0/html-scipyorg/index.html
+          artifact-path: 0/html/index.html
           circleci-jobs: build_docs
           job-title: Check the rendered docs here!

.github/workflows/linux.yml

@@ -61,7 +61,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11-dev"]
 
     steps:
     - uses: actions/checkout@v3
@@ -74,18 +74,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
         architecture: x64
 
-# Keeping this for later 3.11. Might not be needed as GH seems to provide
-# pre-released versions of 3.11
-#    - name: Install Python 3.11
-#      if: matrix.python-version == '3.11'
-#      run: |
-#        sudo add-apt-repository ppa:deadsnakes/ppa
-#        sudo apt-get update
-#        sudo apt install -y --no-install-recommends python3.11-dev python3.11-distutils python3.11-venv
-#        # GitHub doesn't provide a pip interface with py3.11 yet. Therefore, install it manually :
-#        curl -O https://bootstrap.pypa.io/get-pip.py && python3.11 get-pip.py && rm get-pip.py
-#        python3.11 -m pip install --upgrade pip setuptools
-
     - name: Install other build dependencies
       run: |
         sudo apt-get install libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev

.github/workflows/linux_meson.yml

@@ -57,7 +57,7 @@ jobs:
 
     - name: Install Python packages
       run: |
-        python -m pip install numpy setuptools wheel cython pytest pytest-xdist pybind11 mpmath gmpy2 pythran ninja meson==0.60.3
+        python -m pip install numpy setuptools wheel cython pytest pytest-xdist pybind11 mpmath gmpy2 pythran ninja meson
 
     - name:  Prepare compiler cache
       id:    prep-ccache
@@ -102,3 +102,42 @@ jobs:
       run: |
         export OMP_NUM_THREADS=2
         python dev.py -n -j 2
+
+  test_venv_install:
+    name: Pip install into venv
+    if: "github.repository == 'scipy/scipy' || github.repository == ''"
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - name: Setup Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+
+    - name: Install Ubuntu dependencies
+      run: |
+        # We're not running the full test suite here, only testing the install
+        # into a venv is working, so leave out optional dependencies. That's
+        # also why we can get away with an old version of OpenBLAS from Ubuntu
+        sudo apt-get update
+        sudo apt-get install -y libopenblas-dev pkg-config gfortran
+
+    - name: Create venv, install SciPy
+      run: |
+        python -m venv ../venvs/scipy-venv
+        source ../venvs/scipy-venv/bin/activate
+        # Note that this uses build isolation. That's why we don't need build
+        # dependencies to be installed in the venv itself.
+        python -m pip install . -vv
+
+    - name: Basic imports and tests
+      run: |
+        source ../venvs/scipy-venv/bin/activate
+        cd ..
+        python -c "import scipy"
+        python -c "import scipy.linalg"
+        python -m pip install pytest
+        python -c "from scipy import cluster; cluster.test()"

.gitignore

@@ -136,6 +136,7 @@ benchmarks/results
 benchmarks/scipy
 benchmarks/html
 benchmarks/scipy-benchmarks
+.mesonpy-native-file.ini
 scipy/__config__.py
 scipy/_lib/_ccallback_c.c
 scipy/_lib/messagestream.c

.mailmap

@@ -41,6 +41,7 @@
 ADmitri <[email protected]> ADmitri <[email protected]>
 Aditya Vijaykumar <[email protected]> adivijaykumar <[email protected]>
 Akash Goel <[email protected]> Goel <[email protected]>
+Albert Steppi <[email protected]> steppi <[email protected]>
 Aldrian Obaja <> ubuntu <>
 Alex Griffing <[email protected]> alex <[email protected]>
 Alex Griffing <[email protected]> argriffing <[email protected]>
@@ -77,6 +78,7 @@ Arthur Volant <[email protected]> Arthur <[email protected]
 Ashwin Pathak <[email protected]> ashwinpathak20 <[email protected]>
 Ashwin Pathak <[email protected]> ashwinpathak20nov1996 <[email protected]>
 Atsushi Sakai <[email protected]> Atsushi Sakai <[email protected]>
+Aviv Yaish <[email protected]> Aviv <[email protected]>
 Balint Pato <[email protected]> balopat <[email protected]>
 Behzad Nouri <[email protected]> behzad nouri <[email protected]>
 Benjamin Root <> weathergod <>
@@ -92,6 +94,7 @@ Brandon David <[email protected]> brandondavid <[email protected]>
 Brett R. Murphy <[email protected]> brettrmurphy <[email protected]>
 Brian Hawthorne <brian.hawthorne@localhost> brian.hawthorne <brian.hawthorne@localhost>
 Brian Newsom <[email protected]> Brian Newsom <[email protected]>
+Caio Agiani <[email protected]> caioagiani <[email protected]>
 Callum Jacob Hays <[email protected]> callumJHays <[email protected]>
 Carlos Ramos Carreño <[email protected]> vnmabus <[email protected]>
 Charles Jekel <[email protected]> cjekel <[email protected]>
@@ -126,6 +129,7 @@ Daniel B. Smith <[email protected]> Daniel Smith <smithd@daniel-laptop.(
 Daniel B. Smith <[email protected]> Daniel B. Smith <[email protected]>
 Daniel B. Smith <[email protected]> Daniel B. Smith <[email protected]>
 Daniel B. Smith <[email protected]> Daniel <[email protected]>
+Daniel Schmitz <[email protected]> dschmitz89 <[email protected]>
 Danilo Augusto <[email protected]> daniloagst <[email protected]>
 Danilo Horta <[email protected]> Horta <[email protected]>
 David Huard <dhuard@localhost> dhuard <dhuard@localhost>
@@ -301,6 +305,7 @@ Lars Buitinck <[email protected]> Lars Buitinck <[email protected]>
 Lars G <[email protected]> Lars G <[email protected]>
 Lars G <[email protected]> Lars Grueter <[email protected]>
 Lars G <[email protected]> Lars Grüter <[email protected]>
+Laurynas Mikšys <[email protected]> Laurynas <[email protected]>
 Lei Ma <[email protected]> OctoMiao <[email protected]>
 Levi John Wolf <[email protected]> ljwolf <[email protected]>
 Liam Damewood <[email protected]> ldamewood <[email protected]>
@@ -340,6 +345,9 @@ Max Argus <[email protected]> BlGene <[email protected]>
 Max Argus <[email protected]> max argus <[email protected]>
 Max Bolingbroke <[email protected]> DSG User <>
 Max Bolingbroke <[email protected]> Max Bolingbroke <[email protected]>
+Melissa Weber Mendonça <[email protected]> melissawm <[email protected]>
+Melissa Weber Mendonça <[email protected]> Melissa Weber Mendonça <[email protected]>
+Melissa Weber Mendonça <[email protected]> Melissa Weber <[email protected]>
 Michael Benfield <[email protected]> mikebenfield <[email protected]>
 Michael Droettboom <> mdroe <>
 Michael Dunphy <[email protected]> Michael Dunphy <[email protected]>
@@ -414,6 +422,7 @@ Robert Uhl <[email protected]> Robert Uhl <[email protected]
 Roman Mirochnik <[email protected]> mirochni <[email protected]>
 Rupak Das <[email protected]> Rupak <[email protected]>
 Ruslan Yevdokymov <[email protected]> Ruslan Yevdokymov <[email protected]>
+Ryan Gibson <[email protected]> ragibson <[email protected]>
 Sam Lewis <[email protected]> Sam Lewis <[email protected]>
 Sam McCormack <[email protected]> Sam McCormack <[email protected]>
 Sam Mason <[email protected]> Sam Mason <[email protected]>
@@ -430,6 +439,7 @@ Scott Sievert <[email protected]> <[email protected]>
 Sebastian Haase <> sebhaase <>
 Sebastian Pucilowski <[email protected]> Sebastian Pucilowski <[email protected]>
 Sebastian Skoupý <[email protected]> Sebascn <[email protected]>
+Shivnaren Srinivasan <[email protected]> srinivasan <[email protected]>
 Skipper Seabold <[email protected]> skip <skip@localhost>
 Shinya SUZUKI <[email protected]> Shinya SUZUKI <[email protected]>
 Smit Lunagariya <[email protected]> Smit-create <[email protected]>

CONTRIBUTING.rst

@@ -7,7 +7,7 @@ any help you give. Note that a code of conduct applies to all spaces
 managed by the SciPy project, including issues and pull requests:
 https://github.com/scipy/scipy/blob/main/doc/source/dev/conduct/code_of_conduct.rst.
 
-When submitting a pull request, we ask you check the following:
+When submitting a pull request, we ask you to check the following:
 
 1. **Unit tests**, **documentation**, and **code style** are in order.
    For details, please read
@@ -21,5 +21,5 @@ When submitting a pull request, we ask you check the following:
    https://github.com/scipy/scipy/blob/main/LICENSE.txt.
    If you did not write the code yourself, you ensure the existing
    license is compatible and include the license information in the
-   contributed files, or obtain a permission from the original
+   contributed files, or obtain permission from the original
    author to relicense the contributed code.

HACKING.rst.txt

@@ -31,7 +31,7 @@ this code belong?  That question is hard to answer here, so we start with a
 more specific one: *what code is suitable for putting into SciPy?*
 Almost all of the new code added to SciPy has in common that it's potentially
 useful in multiple scientific domains and it fits in the scope of existing
-SciPy subpackages (see :ref:`deciding-on-new-features`).  In principle new
+SciPy subpackages (see :ref:`deciding-on-new-features`).  In principle, new
 subpackages can be added too, but this is far less common.  For code that is
 specific to a single application, there may be an existing project that can
 use the code.  Some SciKits (`scikit-learn`_, `scikit-image`_, `statsmodels`_,
@@ -41,9 +41,9 @@ more domain-specific code than SciPy.
 Now if you have code that you would like to see included in SciPy, how do you
 go about it?  After checking that your code can be distributed in SciPy under a
 compatible license (see :ref:`license-considerations`), the first step is to
-discuss on the scipy-dev mailing list.  All new features, as well as changes to
-existing code, are discussed and decided on there.  You can, and probably
-should, already start this discussion before your code is finished. Remember
+discuss it on the scipy-dev mailing list.  All new features, as well as changes to
+existing code, are discussed and decided on there. You can, and probably
+should already start this discussion before your code is finished. Remember
 that in order to be added to SciPy your code will need to be reviewed by
 someone else, so try to find someone willing to review your work while you're
 at it.
@@ -54,7 +54,7 @@ Before code is added to SciPy, it at least has to have good documentation, unit
 tests, benchmarks, and correct code style.
 
 1. Unit tests
-    In principle you should aim to create unit tests that exercise all the code
+    In principle, you should aim to create unit tests that exercise all the code
     that you are adding.  This gives some degree of confidence that your code
     runs correctly, also on Python versions and hardware or OSes that you don't
     have available yourself.  An extensive description of how to write unit
@@ -74,7 +74,7 @@ tests, benchmarks, and correct code style.
     and classes -- which includes at least a basic description, type and
     meaning of all parameters and returns values, and usage examples in
     `doctest`_ format -- is put in docstrings.  Those docstrings can be read
-    within the interpreter, and are compiled into a reference guide in html and
+    within the interpreter, and are compiled into a reference guide in HTML and
     pdf format.  Higher-level documentation for key (areas of) functionality is
     provided in tutorial format and/or in module docstrings.  A guide on how to
     write documentation is given in :ref:`numpy:howto-document`, and
@@ -95,7 +95,7 @@ available at the end of the example :ref:`development-workflow`.
 
 Another question you may have is: *where exactly do I put my code*?  To answer
 this, it is useful to understand how the SciPy public API (application
-programming interface) is defined.  For most modules the API is two levels
+programming interface) is defined.  For most modules, the API is two levels
 deep, which means your new function should appear as
 ``scipy.subpackage.my_new_func``.  ``my_new_func`` can be put in an existing or
 new file under ``/scipy/<subpackage>/``, its name is added to the ``__all__``
@@ -113,7 +113,7 @@ feature, be sure to also mention this on the scipy-dev mailing list.  This can
 prompt interested people to help review your PR.  Assuming that you already got
 positive feedback before on the general idea of your code/feature, the purpose
 of the code review is to ensure that the code is correct, efficient and meets
-the requirements outlined above.  In many cases the code review happens
+the requirements outlined above.  In many cases, the code review happens
 relatively quickly, but it's possible that it stalls.  If you have addressed
 all feedback already given, it's perfectly fine to ask on the mailing list
 again for review (after a reasonable amount of time, say a couple of weeks, has
@@ -159,7 +159,7 @@ Maintaining existing code
 =========================
 
 The previous section talked specifically about adding new functionality to
-SciPy.  A large part of that discussion also applies to maintenance of existing
+SciPy.  A large part of that discussion also applies to the maintenance of existing
 code.  Maintenance means fixing bugs, improving code quality, documenting
 existing functionality better, adding missing unit tests, adding performance
 benchmarks, keeping build scripts up-to-date, etc.  The SciPy `issue list`_
@@ -207,7 +207,7 @@ themselves some or all of the following questions:
   literature; otherwise, closer look at correctness is valuable.
 - Is the intended behavior clear under all conditions (e.g. unexpected inputs
   like empty arrays or nan/inf values)?
-- Does the code meet the quality, test and documentation expectation outline
+- Does the code meet the quality, test and documentation expectations outlined
   under `Contributing new code`_?
 
 If we do not know you yet, consider introducing yourself.
@@ -220,7 +220,7 @@ There are many ways to contribute other than writing code.
 
 Triaging issues (investigating bug reports for validity and possible actions to
 take) is also a useful activity.  SciPy has many hundreds of open issues;
-closing invalid ones and correctly labeling valid ones (ideally with some first
+closing invalid ones and correctly labelling valid ones (ideally with some first
 thoughts in a comment) allows prioritizing maintenance work and finding related
 issues easily when working on an existing function or subpackage.
 

INSTALL.rst.txt

@@ -53,7 +53,7 @@ __ https://github.com/pybind/pybind11
 
 __ http://www.sphinx-doc.org/
 
-6) Cython__ >= 0.29.18
+6) Cython__ >= 0.29.21
 
 __ http://cython.org/
 

LICENSES_bundled.txt

@@ -245,4 +245,9 @@ License: Boost Software License - Version 1.0
 Name: Biasedurn
 Files: scipy/stats/biasedurn/*
 License 3-Clause BSD
-  For details, see scipy/stats/biasedurn/license.txt
+  For details, see scipy/stats/biasedurn/license.txt
+
+Name: UNU.RAN
+Files: scipy/_lib/unuran/*
+License 3-Clause BSD
+  For details, see scipy/_lib/unuran/license.txt

azure-pipelines.yml

@@ -169,6 +169,11 @@ stages:
         git submodule update --init
       displayName: 'Fetch submodules'
     - script: |
+            # For when updating this job to Meson: the `openblas` used here is
+            # missing pkg-config files. Ubunty Jammy (LTS 22.04) has openblas
+            # 3.20, so if that Docker image is available by then, just remove
+            # the unusual install method. For the bug report about missing .pc
+            # files: https://github.com/MacPython/openblas-libs/issues/74
             set -euo pipefail
             docker pull i386/ubuntu:bionic
             docker run -v $(pwd):/scipy i386/ubuntu:bionic /usr/bin/linux32 /bin/bash -c "cd scipy && \
@@ -177,15 +182,15 @@ stages:
             curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && \
             python3.8 get-pip.py && \
             pip3 --version && \
-            pip3 install setuptools==59.6.0 wheel numpy==1.18.5 cython==0.29.18 pybind11 pytest pytest-timeout pytest-xdist pytest-env pytest-cov Pillow mpmath pythran==0.10.0 --user && \
+            pip3 install setuptools==59.6.0 wheel numpy==1.18.5 cython==0.29.21 pybind11 pytest pytest-timeout pytest-xdist pytest-env pytest-cov Pillow mpmath pythran==0.10.0 && \
             apt-get -y install gcc-5 g++-5 gfortran-8 wget && \
             cd .. && \
             mkdir openblas && cd openblas && \
             target=\$(python3.8 ../scipy/tools/openblas_support.py) && \
             cp -r \$target/lib/* /usr/lib && \
             cp \$target/include/* /usr/include && \
             cd ../scipy && \
-            CC=gcc-5 CXX=g++-5 F77=gfortran-8 F90=gfortran-8 pip3 install . && \
+            CC=gcc-5 CXX=g++-5 F77=gfortran-8 F90=gfortran-8 python3.8 setup.py install && \
             python3.8 tools/openblas_support.py --check_version $(openblas_version) && \
             python3.8 runtests.py -n --mode=full -- -n auto -s --junitxml=junit/test-results.xml --cov-config=.coveragerc --cov-report=xml --cov-report=html"
       displayName: 'Run 32-bit Ubuntu Docker Build / Tests'
@@ -333,8 +338,9 @@ stages:
         }
         $env:PATH = "C:\\ProgramData\\chocolatey\\lib\\mingw\\tools\\install\\mingw$(BITS)\\bin;" + $env:PATH
 
-        mkdir dist
-        pip wheel --no-build-isolation -v -v -v --wheel-dir=dist .
+        # Still testing distutils here (`pip wheel --no-use-pep517` cannot be
+        # used, so back to `setup.py` it is ...)
+        python setup.py bdist_wheel
         ls dist -r | Foreach-Object {
             pip install $_.FullName
         }