From 5a87919f6d4571a669acb5d96c102d9d2d09daab Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Fri, 28 Jun 2024 11:20:06 -0400
Subject: [PATCH 01/44] Added meson build system files

---
 meson.build        | 110 +++++++++++++++++++++++++++++++++++++++++++++
 pixell/meson.build |  36 +++++++++++++++
 pyproject.toml     |  60 +++++++++++++++++++++++++
 3 files changed, 206 insertions(+)
 create mode 100644 meson.build
 create mode 100644 pixell/meson.build
 create mode 100644 pyproject.toml

diff --git a/meson.build b/meson.build
new file mode 100644
index 0000000..18d64d3
--- /dev/null
+++ b/meson.build
@@ -0,0 +1,110 @@
+# Main build file for pixell, helping with building the fortran,
+# c, and cython extensions.
+
+project('pixell', ['c', 'fortran', 'cython'])
+
+py = import('python').find_installation(pure: false)
+
+# Dependencies
+py_dep = py.dependency()
+omp_dep = dependency('openmp')
+
+# Directories
+library_install_dir = py.get_install_dir() / 'pixell'
+
+# Includes
+incdir_numpy = run_command(
+    py,
+    ['-c', 'import numpy; print(numpy.get_include())'],
+    check: true
+).stdout().strip()
+
+incdir_f2py = run_command(
+    py,
+    ['-c', 'import numpy.f2py; print(numpy.f2py.get_include())'],
+    check: true
+).stdout().strip()
+
+# Build fortran extensions
+
+# Pixell oddity - need to run the makefile (make -C fortran)
+# to generate specific fortran files before we can build them.
+# TODO: put those commands in this meson file instead.
+run_command('make', '-C', 'fortran', check: true)
+
+fortran_include = include_directories(incdir_numpy, incdir_f2py)
+
+fortran_sources = {
+    'fortran/interpol_32.f90': '_interpol_32',
+    'fortran/interpol_64.f90': '_interpol_64',
+    'fortran/colorize.f90': '_colorize',
+    'fortran/array_ops_32.f90': '_array_ops_32',
+    'fortran/array_ops_64.f90': '_array_ops_64',
+}
+
+foreach source_name, module_name : fortran_sources
+    f2py_output = custom_target(
+        input: source_name,
+        output: [module_name + '-f2pywrappers2.f90', module_name + 'module.c'],
+        command: [py, '-m', 'numpy.f2py', '@INPUT@', '-m', module_name, '--lower'],
+    )
+
+    py.extension_module(
+        module_name,
+        [source_name, f2py_output],
+        incdir_f2py / 'fortranobject.c',
+        include_directories: fortran_include,
+        dependencies: [py_dep, omp_dep],
+        install: true,
+        install_dir: library_install_dir
+    )
+endforeach
+
+
+# Build c(ython) extensions.
+
+# Before building cython, we must build shared libraries for all of
+# the underlying c code that those cython extensions rely on.
+
+helper_sources = {
+    'cython/cmisc_core.c': '_cmisc_shared',
+    'cython/distances_core.c': '_distances_shared',
+    'cython/srcsim_core.c': '_srcsim_shared',
+}
+
+linkables = []
+
+foreach source_name, module_name : helper_sources
+    linkables += shared_library(
+        module_name,
+        source_name,
+        install: true,
+        install_dir: library_install_dir,
+        include_directories: [incdir_numpy],
+        dependencies: [omp_dep],
+    )
+endforeach
+
+# Now we can build cython and link our shared libraries to them.
+
+cython_sources = {
+    'cython/cmisc.pyx': 'cmisc',
+    'cython/distances.pyx': 'distances',
+    'cython/srcsim.pyx': 'srcsim',
+}
+
+foreach source_name, module_name : cython_sources
+    cython_module = py.extension_module(
+        module_name,
+        source_name,
+        include_directories: ['cython', incdir_numpy],
+        dependencies: [py_dep, omp_dep],
+        link_with: linkables,
+        install: true,
+        install_dir: library_install_dir
+    )
+endforeach
+
+# The actual python install itself is left up to a helper build
+# script deifned in pixell/
+subdir('pixell')
\ No newline at end of file
diff --git a/pixell/meson.build b/pixell/meson.build
new file mode 100644
index 0000000..458a5ca
--- /dev/null
+++ b/pixell/meson.build
@@ -0,0 +1,36 @@
+python_sources = [
+    '__init__.py',
+    '_version.py',
+    'aberration.py',
+    'analysis.py',
+    'array_ops.py',
+    'bunch.py',
+    'cgrid.py',
+    'colorize.py',
+    'colors.py',
+    'coordinates.py',
+    'curvedsky.py',
+    'enmap.py',
+    'enplot.py',
+    'fft.py',
+    'interpol.py',
+    'lensing.py',
+    'memory.py',
+    'mpi.py',
+    'multimap.py',
+    'old_aberration.py',
+    'pointsrcs.py',
+    'powspec.py',
+    'reproject.py',
+    'resample.py',
+    'tilemap.py',
+    'uharm.py',
+    'utils.py',
+    'wavelets.py',
+    'wcsutils.py',
+]
+
+py.install_sources(
+    python_sources,
+    subdir: 'pixell'
+)
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..01f4853
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,60 @@
+[build-system]
+build-backend = 'mesonpy'
+requires = ['meson-python', 'numpy', 'cython', 'versioneer[toml]']
+
+[project]
+name = 'mytestlib'
+# TODO: Versioneer
+version = '1.0.0'
+description = "A rectangular pixel map manipulation and harmonic analysis library derived from Sigurd Naess' enlib."
+readme = 'README.rst'
+requires-python = '>=3.8'
+license = {file = 'LICENSE'}
+authors = [
+    {name = "Simons Observatory Collaboration Analysis Library Task Force"},
+]
+maintainers = [
+    {name = "Mathew Madhavacheril", email = "mathewsyriac@gmail.com"}
+]
+dependencies = [
+    'numpy>=1.20.0',
+    'astropy>=2.0',
+    'setuptools>=39',
+    'h5py>=2.7',
+    'scipy>=1.0',
+    'python_dateutil>=2.7',
+    'cython<3.0.4',
+    'healpy>=1.13',
+    'matplotlib>=2.0',
+    'pyyaml>=5.0',
+    'Pillow>=5.3.0',
+    'pytest-cov>=2.6',
+    'coveralls>=1.5',
+    'pytest>=4.6',
+    'ducc0>=0.34.0',
+    'numba>=0.54.0'
+]
+
+[project.optional-dependencies]
+test = [
+    'pip>=9.0',
+    'bumpversion>=0.5',
+    'wheel>=0.30',
+    'watchdog>=0.8',
+    'flake8>=3.5',
+    'coverage>=4.5',
+    'Sphinx>=1.7',
+    'twine>=1.10',
+    'numpy>=1.20',
+    'astropy>=2.0',
+    'setuptools>=39.2',
+    'h5py>=2.7,<=2.10',
+    'scipy>=1.0',
+    'python_dateutil>=2.7',
+    'cython<3.0.4',
+    'matplotlib>=2.0',
+    'pyyaml>=5.0',
+    'pytest-cov>=2.6',
+    'coveralls>=1.5',
+    'pytest>=4.6'
+]
\ No newline at end of file

From 009864f05407d5fe2e8880f3d0a4509c192e3cb4 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Fri, 28 Jun 2024 14:01:08 -0400
Subject: [PATCH 02/44] Massage paths into relative

---
 meson.build | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/meson.build b/meson.build
index 18d64d3..946302f 100644
--- a/meson.build
+++ b/meson.build
@@ -13,15 +13,18 @@ omp_dep = dependency('openmp')
 library_install_dir = py.get_install_dir() / 'pixell'
 
 # Includes
+
+# Need to massage these into relative paths to keep meson happy.
+# It does not allow for absolute paths.
 incdir_numpy = run_command(
     py,
-    ['-c', 'import numpy; print(numpy.get_include())'],
+    ['-c', 'import numpy; import os; print(os.path.relpath(numpy.get_include()))'],
     check: true
 ).stdout().strip()
 
 incdir_f2py = run_command(
     py,
-    ['-c', 'import numpy.f2py; print(numpy.f2py.get_include())'],
+    ['-c', 'import numpy.f2py; import os; print(os.path.relpath(numpy.f2py.get_include()))'],
     check: true
 ).stdout().strip()
 

From d09aa96ca574ef51d4ab5c0cf1cb9c8d109547ce Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Fri, 28 Jun 2024 14:06:27 -0400
Subject: [PATCH 03/44] Add libmath as a dependency?

---
 meson.build | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/meson.build b/meson.build
index 946302f..361acae 100644
--- a/meson.build
+++ b/meson.build
@@ -9,6 +9,13 @@ py = import('python').find_installation(pure: false)
 py_dep = py.dependency()
 omp_dep = dependency('openmp')
 
+# Libraries
+cc = meson.get_compiler('c')
+c_m_dep = cc.find_library('m', required: true)
+
+fc = meson.get_compiler('fortran')
+fortran_m_dep = fc.find_library('m', required: true)
+
 # Directories
 library_install_dir = py.get_install_dir() / 'pixell'
 
@@ -57,7 +64,7 @@ foreach source_name, module_name : fortran_sources
         [source_name, f2py_output],
         incdir_f2py / 'fortranobject.c',
         include_directories: fortran_include,
-        dependencies: [py_dep, omp_dep],
+        dependencies: [py_dep, omp_dep, c_m_dep, fortran_m_dep],
         install: true,
         install_dir: library_install_dir
     )
@@ -84,7 +91,7 @@ foreach source_name, module_name : helper_sources
         install: true,
         install_dir: library_install_dir,
         include_directories: [incdir_numpy],
-        dependencies: [omp_dep],
+        dependencies: [omp_dep, c_m_dep],
     )
 endforeach
 
@@ -101,7 +108,7 @@ foreach source_name, module_name : cython_sources
         module_name,
         source_name,
         include_directories: ['cython', incdir_numpy],
-        dependencies: [py_dep, omp_dep],
+        dependencies: [py_dep, omp_dep, c_m_dep],
         link_with: linkables,
         install: true,
         install_dir: library_install_dir

From f440061d6d89ded4187880e11ffe7fabe227b5f0 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 09:22:05 -0400
Subject: [PATCH 04/44] See what happens without 38

---
 .github/workflows/build.yml | 18 ++++++++----------
 pyproject.toml              |  6 +++---
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index a0e3b05..961a996 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python: ["3.11", "3.10", "3.9", "3.8"]
+        python: ["3.12", "3.11", "3.10", "3.9"]
 
     steps:
       - uses: actions/checkout@v1
@@ -44,7 +44,7 @@ jobs:
       - uses: actions/checkout@v1
       - uses: actions/setup-python@v1
         with:
-          python-version: "3.9"
+          python-version: "3.10"
 
       - name: Install Dependencies (MacOS)
         run: |
@@ -74,10 +74,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04]
-        cp: [cp38, cp39, cp310, cp311]
+        cp: [cp39, cp310, cp311]
         include:
-          - cp: cp38
-            numpyver: "1.20"
           - cp: cp39
             numpyver: "1.20"
           - cp: cp310
@@ -137,16 +135,16 @@ jobs:
       matrix:
         os: [macos-12]
         # We don't build 3.7 wheels for MacOS because that's x86 only.
-        cp: [cp38, cp39, cp310, cp311]
+        cp: [cp39, cp310, cp311, cp312]
         include:
-          - cp: cp38
-            numpyver: "1.20"
           - cp: cp39
             numpyver: "1.20"
           - cp: cp310
             numpyver: "1.22"
           - cp: cp311
             numpyver: "1.22"
+          - cp: cp312
+            numpyver: "2.0"
 
     steps:
       - uses: actions/checkout@v2
@@ -154,7 +152,7 @@ jobs:
       - uses: actions/setup-python@v2
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install cibuildwheel and other dependencies
         run: |
@@ -203,7 +201,7 @@ jobs:
       - uses: actions/setup-python@v2
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.10'
 
       - name: Build sdist
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index 01f4853..e36d92b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ name = 'mytestlib'
 version = '1.0.0'
 description = "A rectangular pixel map manipulation and harmonic analysis library derived from Sigurd Naess' enlib."
 readme = 'README.rst'
-requires-python = '>=3.8'
+requires-python = '>=3.9'
 license = {file = 'LICENSE'}
 authors = [
     {name = "Simons Observatory Collaboration Analysis Library Task Force"},
@@ -23,7 +23,7 @@ dependencies = [
     'h5py>=2.7',
     'scipy>=1.0',
     'python_dateutil>=2.7',
-    'cython<3.0.4',
+    'cython',
     'healpy>=1.13',
     'matplotlib>=2.0',
     'pyyaml>=5.0',
@@ -51,7 +51,7 @@ test = [
     'h5py>=2.7,<=2.10',
     'scipy>=1.0',
     'python_dateutil>=2.7',
-    'cython<3.0.4',
+    'cython',
     'matplotlib>=2.0',
     'pyyaml>=5.0',
     'pytest-cov>=2.6',

From 13f752918ca498aaa8d4a5fa4efbb05bd59d51bd Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 09:23:39 -0400
Subject: [PATCH 05/44] Remove setup.py

---
 setup.py | 284 -------------------------------------------------------
 1 file changed, 284 deletions(-)
 delete mode 100644 setup.py

diff --git a/setup.py b/setup.py
deleted file mode 100644
index c8c0b42..0000000
--- a/setup.py
+++ /dev/null
@@ -1,284 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""The setup script."""
-from __future__ import print_function
-import setuptools
-from setuptools import find_packages
-from distutils.errors import DistutilsError
-from numpy.distutils.core import setup, Extension, build_ext, build_src
-import versioneer
-import os, sys
-import subprocess as sp
-import numpy as np
-
-build_ext = build_ext.build_ext
-build_src = build_src.build_src
-
-CYTHON_NOT_FOUND_MSG = """Cython not found.
-Please run either one of the following commands to install Cython first
-    mamba install cython
-    conda install cython
-    pip install cython
-"""
-
-
-compile_opts = {
-    #'extra_compile_args': ['-std=c99','-fopenmp', '-Wno-strict-aliasing', '-g', '-O0', '-fPIC', '-fsanitize=address', '-fsanitize=undefined'],
-    'extra_compile_args': ['-std=c99','-fopenmp', '-Wno-strict-aliasing', '-g', '-Ofast', '-fPIC'],
-    'extra_f90_compile_args': ['-fopenmp', '-Wno-conversion', '-Wno-tabs', '-fPIC'],
-    'f2py_options': ['skip:', 'map_border', 'calc_weights', ':'],
-    'extra_link_args': ['-fopenmp', '-g', '-fPIC', '-fno-lto']
-    }
-
-# Set compiler options
-# Windows
-if sys.platform == 'win32':
-    raise DistutilsError('Windows is not supported.')
-elif sys.platform == 'darwin' or sys.platform == 'linux':
-    environment = os.environ
-
-    if not 'CC' in environment:
-        environment["CC"] = "gcc"
-    
-    if not "CXX" in environment:
-        environment["CXX"] = "g++"
-    
-    if not "FC" in environment:
-        environment["FC"] = "gfortran"
-
-    # Now, try out our environment!
-    c_return = sp.call([environment["CC"], *compile_opts["extra_compile_args"], "scripts/omp_hello.c", "-o", "/tmp/pixell-cc-test"], env=environment)
-    
-    try:
-        os.remove("/tmp/pixell-cc-test")
-    except OSError:
-        pass
-
-    if c_return != 0:
-        raise EnvironmentError(
-            "Your C compiler does not support the following flags, required by pixell: "
-            f"{' '.join(compile_opts['extra_compile_args'])}"
-            ". Consider setting the value of environment variable CC to a known good gcc install. "
-            "The built-in Apple clang does not support OpenMP. Use Homebrew to install either gcc or llvm. "
-            f"Current value of $CC is {environment['CC']}.",
-        )
-    else:
-        print(f"C compiler found ({environment['CC']}) and supports OpenMP.")
-    
-    cxx_return = sp.call([environment["CXX"], *compile_opts["extra_compile_args"], "scripts/omp_hello.c", "-o", "/tmp/pixell-cxx-test"], env=environment)
-
-    try:
-        os.remove("/tmp/pixell-cxx-test")
-    except OSError:
-        pass
-
-    if cxx_return != 0:
-        raise EnvironmentError(
-            "Your CXX compiler does not support the following flags, required by pixell: "
-            f"{' '.join(compile_opts['extra_compile_args'])}"
-            ". Consider setting the value of environment variable CXX to a known good gcc install. "
-             "The built-in Apple clang does not support OpenMP. Use Homebrew to install either gcc or llvm. "
-            f"Current value of $CXX is {environment['CXX']}.",
-        )
-    else:
-        print(f"CXX compiler found ({environment['CXX']}) and supports OpenMP.")
-    
-    fc_return = sp.call([environment["FC"], *compile_opts["extra_f90_compile_args"], "scripts/omp_hello.f90", "-o", "/tmp/pixell-fc-test"], env=environment)
-    
-    try:
-        os.remove("/tmp/pixell-fc-test")
-    except OSError:
-        pass
-    
-    if fc_return != 0:
-        raise EnvironmentError(
-            "Your Fortran compiler does not support the following flags, required by pixell: "
-            f"{' '.join(compile_opts['extra_f90_compile_args'])}"
-            ". Consider setting the value of environment variable FC to a known good gfortran install."
-            f"Current value of $FC is {environment['FC']}.",
-        )
-    else:
-        print(f"Fortran compiler found ({environment['FC']}) and supports OpenMP.")
-
-    # Why do we remove -fPIC here?
-    compile_opts['extra_link_args'] = ['-fopenmp']
-else:
-    raise EnvironmentError("Unknown platform. Please file an issue on GitHub.")
-
-with open('README.rst') as readme_file:
-    readme = readme_file.read()
-
-with open('HISTORY.rst') as history_file:
-    history = history_file.read()
-
-requirements =  ['numpy>=1.20.0',
-                 'astropy>=2.0',
-                 'setuptools>=39',
-                 'h5py>=2.7',
-                 'scipy>=1.0',
-                 'python_dateutil>=2.7',
-                 'cython<3.0.4',
-                 'healpy>=1.13',
-                 'matplotlib>=2.0',
-                 'pyyaml>=5.0',
-                 'Pillow>=5.3.0',
-                 'pytest-cov>=2.6',
-                 'coveralls>=1.5',
-                 'pytest>=4.6',
-                 'ducc0>=0.34.0',
-                 'numba>=0.54.0']
-
-
-test_requirements = ['pip>=9.0',
-                     'bumpversion>=0.5',
-                     'wheel>=0.30',
-                     'watchdog>=0.8',
-                     'flake8>=3.5',
-                     'coverage>=4.5',
-                     'Sphinx>=1.7',
-                     'twine>=1.10',
-                     'numpy>=1.20',
-                     'astropy>=2.0',
-                     'setuptools>=39.2',
-                     'h5py>=2.7,<=2.10',
-                     'scipy>=1.0',
-                     'python_dateutil>=2.7',
-                     'cython<3.0.4',
-                     'matplotlib>=2.0',
-                     'pyyaml>=5.0',
-                     'pytest-cov>=2.6',
-                     'coveralls>=1.5',
-                     'pytest>=4.6']
-
-# Why are we doing this instead of allowing the environment to do this? We should just use -O3 and -fPIC.
-fcflags = os.getenv('FCFLAGS')
-if fcflags is None or fcflags.strip() == '':
-    fcflags = ['-O3','-fPIC']
-    #fcflags = ['-O0','-fPIC', '-fsanitize=address', '-fsanitize=undefined']
-else:
-    print('User supplied fortran flags: ', fcflags)
-    print('These will supersede other optimization flags.')
-    fcflags = fcflags.split()
-    
-compile_opts['extra_f90_compile_args'].extend(fcflags)
-compile_opts['extra_f77_compile_args'] = compile_opts['extra_f90_compile_args']
-
-def presrc():
-    # Create f90 files for f2py.
-    if sp.call('make -C fortran', shell=True) != 0:
-        raise DistutilsError('Failure in the fortran source-prep step.')
-    
-def prebuild():
-    # Handle cythonization
-    no_cython = sp.call('cython --version',shell=True)
-    if no_cython:
-        raise DistutilsError(CYTHON_NOT_FOUND_MSG)
-
-    if sp.call('make -C cython',  shell=True) != 0:
-        raise DistutilsError('Failure in the cython pre-build step.')
-
-
-class CustomBuild(build_ext):
-    def run(self):
-        print("Running build...")
-        prebuild()
-        # Then let setuptools do its thing.
-        return build_ext.run(self)
-
-class CustomSrc(build_src):
-    def run(self):
-        print("Running src...")
-        presrc()
-        # Then let setuptools do its thing.
-        return build_src.run(self)
-
-class CustomEggInfo(setuptools.command.egg_info.egg_info):
-    def run(self):
-        print("Running EggInfo...")
-        presrc()
-        prebuild()
-        return setuptools.command.egg_info.egg_info.run(self)   
-
-# Cascade your overrides here.
-cmdclass = {
-    'build_ext': CustomBuild,
-    'build_src': CustomSrc,
-    'egg_info': CustomEggInfo,
-}
-cmdclass = versioneer.get_cmdclass(cmdclass)
-
-
-setup(
-    author="Simons Observatory Collaboration Analysis Library Task Force",
-    author_email='mathewsyriac@gmail.com',
-    classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers',
-        'License :: OSI Approved :: BSD License',
-        'Natural Language :: English',
-        "Programming Language :: Python :: 2",
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-    ],
-    description="pixell",
-    package_dir={"pixell": "pixell"},
-    entry_points={
-    },
-    ext_modules=[
-        Extension('pixell.cmisc',
-            sources=['cython/cmisc.c','cython/cmisc_core.c'],
-            libraries=['m'],
-            include_dirs=[np.get_include()],
-            **compile_opts),
-        Extension('pixell.distances',
-            sources=['cython/distances.c','cython/distances_core.c'],
-            libraries=['m'],
-            include_dirs=[np.get_include()],
-            **compile_opts),
-        Extension('pixell.srcsim',
-            sources=['cython/srcsim.c','cython/srcsim_core.c'],
-            libraries=['m'],
-            include_dirs=[np.get_include()],
-            **compile_opts),
-        Extension('pixell._interpol_32',
-            sources=['fortran/interpol_32.f90'],
-            **compile_opts),
-        Extension('pixell._interpol_64',
-            sources=['fortran/interpol_64.f90'],
-            **compile_opts),
-        Extension('pixell._colorize',
-            sources=['fortran/colorize.f90'],
-            **compile_opts),
-        Extension('pixell._array_ops_32',
-            sources=['fortran/array_ops_32.f90'],
-            **compile_opts),
-        Extension('pixell._array_ops_64',
-            sources=['fortran/array_ops_64.f90'],
-            **compile_opts),
-    ],
-    include_dirs = [],
-    library_dirs = [],
-    install_requires=requirements,
-    extras_require = {'fftw':['pyFFTW>=0.10'],'mpi':['mpi4py>=2.0']},
-    license="BSD license",
-    long_description=readme + '\n\n' + history,
-    package_data={'pixell': ['pixell/tests/data/*.fits','pixell/tests/data/*.dat','pixell/tests/data/*.pkl']},
-    include_package_data=True,    
-    data_files=[('pixell', ['pixell/arial.ttf'])],
-    keywords='pixell',
-    name='pixell',
-    packages=find_packages(),
-    test_suite='pixell.tests',
-    tests_require=test_requirements,
-    url='https://github.com/simonsobs/pixell',
-    version=versioneer.get_version(),
-    zip_safe=False,
-    cmdclass=cmdclass,
-    scripts=['scripts/test-pixell']
-)
-
-print('\n[setup.py request was successful.]')

From 4f1f27b17f165b39ad19e45c76f7c43c2bb60113 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 09:28:00 -0400
Subject: [PATCH 06/44] Remove references to setup.py

---
 .github/workflows/build.yml | 5 ++---
 pyproject.toml              | 4 ++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 961a996..745b73b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -21,7 +21,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install pytest-cov numpy "Cython<3.0.4"
-          python setup.py build_ext -i
           python -m pip install .
           pytest --cov-report html --cov-report xml --cov-report annotate --cov=pixell pixell/tests/ -s
           
@@ -58,7 +57,6 @@ jobs:
         run: |
           ln -s $FC $(dirname $(which $FC))/gfortran
           echo "Using FC=$FC CXX=$CXX CC=$CC"
-          python setup.py build_ext -i 
           python -m pip install .
 
       - name: Run Tests (MacOS)
@@ -210,7 +208,8 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install "Cython<3.0.4"
           python -m pip install numpy
-          python setup.py sdist
+          python -m pip install build
+          python -m build . --sdist
 
       - uses: actions/upload-artifact@v2
         with:
diff --git a/pyproject.toml b/pyproject.toml
index e36d92b..c2bd5e7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [build-system]
 build-backend = 'mesonpy'
-requires = ['meson-python', 'numpy', 'cython', 'versioneer[toml]']
+requires = ['meson-python', 'numpy', 'cython', 'versioneer[toml]', 'build']
 
 [project]
 name = 'mytestlib'
@@ -57,4 +57,4 @@ test = [
     'pytest-cov>=2.6',
     'coveralls>=1.5',
     'pytest>=4.6'
-]
\ No newline at end of file
+]

From cf2e571d0721403748eb35b2bce850a75d207e7d Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 09:31:56 -0400
Subject: [PATCH 07/44] Use build tool not setup.py in wheel builder

---
 scripts/build_wheels.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/scripts/build_wheels.sh b/scripts/build_wheels.sh
index a19b71a..9bcea15 100755
--- a/scripts/build_wheels.sh
+++ b/scripts/build_wheels.sh
@@ -12,9 +12,8 @@ set -x
 # in the pyproject.toml file, while the tests are run
 # against the most recent version of the dependencies
 
-python -m pip install --upgrade pip setuptools wheel
-python -m pip install cibuildwheel
-python setup.py build_ext -i
+python -m pip install --upgrade pip setuptools wheel build
+python -m pip build
 python -m pip install .
 py.test --cov=pixell pixell/tests/ -s
 find . -type f -iname '*.so' -print -delete

From 3f8cfa9e503d73d1d49d5e0b148e460d49efaafa Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 09:33:00 -0400
Subject: [PATCH 08/44] Remedy typo in build_wheelsh.sh

---
 scripts/build_wheels.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/build_wheels.sh b/scripts/build_wheels.sh
index 9bcea15..05672cc 100755
--- a/scripts/build_wheels.sh
+++ b/scripts/build_wheels.sh
@@ -13,7 +13,7 @@ set -x
 # against the most recent version of the dependencies
 
 python -m pip install --upgrade pip setuptools wheel build
-python -m pip build
+python -m build
 python -m pip install .
 py.test --cov=pixell pixell/tests/ -s
 find . -type f -iname '*.so' -print -delete

From 1873f84287fb68fa1c7cde8923e57213e5af64db Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 11:38:23 -0400
Subject: [PATCH 09/44] Refactor tests

---
 meson.build                                   |   4 +-
 pixell/curvedsky.py                           |   4 +-
 pixell/enmap.py                               |   4 +-
 pixell/meson.build                            |   2 +
 pixell/tests/__init__.py                      |   3 -
 pixell/tests/pixel_tests.py                   | 182 -----------------
 pyproject.toml                                |   7 +-
 {pixell/tests => tests}/data/MM_041121.pkl    | Bin
 .../data/MM_lensed_071123.fits                | Bin
 .../data/MM_offset_grad_071123.fits           | Bin
 .../data/MM_offset_obs_pos_071123.fits        |   0
 .../data/MM_offset_raw_pos_071123.fits        | Bin
 .../data/MM_unlensed_071123.fits              | Bin
 {pixell/tests => tests}/data/annot.txt        |   0
 .../data/cosmo2017_10K_acc3_lensedCls.dat     |   0
 ...0x_9.4_arcminute_pixel_shape_wcs_tuple.pkl | Bin
 {pixell/tests => tests}/data/test_scalCls.dat |   0
 {pixell/tests => tests}/test_geom.py          |   0
 {pixell/tests => tests}/test_io.py            |   0
 {pixell/tests => tests}/test_pixell.py        | 184 +++++++++++++++++-
 {pixell/tests => tests}/tests.yml             |   0
 21 files changed, 190 insertions(+), 200 deletions(-)
 delete mode 100644 pixell/tests/__init__.py
 delete mode 100644 pixell/tests/pixel_tests.py
 rename {pixell/tests => tests}/data/MM_041121.pkl (100%)
 rename {pixell/tests => tests}/data/MM_lensed_071123.fits (100%)
 rename {pixell/tests => tests}/data/MM_offset_grad_071123.fits (100%)
 rename {pixell/tests => tests}/data/MM_offset_obs_pos_071123.fits (100%)
 rename {pixell/tests => tests}/data/MM_offset_raw_pos_071123.fits (100%)
 rename {pixell/tests => tests}/data/MM_unlensed_071123.fits (100%)
 rename {pixell/tests => tests}/data/annot.txt (100%)
 rename {pixell/tests => tests}/data/cosmo2017_10K_acc3_lensedCls.dat (100%)
 rename {pixell/tests => tests}/data/cutsky_geometry_scaled_20x_9.4_arcminute_pixel_shape_wcs_tuple.pkl (100%)
 rename {pixell/tests => tests}/data/test_scalCls.dat (100%)
 rename {pixell/tests => tests}/test_geom.py (100%)
 rename {pixell/tests => tests}/test_io.py (100%)
 rename {pixell/tests => tests}/test_pixell.py (87%)
 rename {pixell/tests => tests}/tests.yml (100%)

diff --git a/meson.build b/meson.build
index 361acae..d1dbf56 100644
--- a/meson.build
+++ b/meson.build
@@ -66,7 +66,7 @@ foreach source_name, module_name : fortran_sources
         include_directories: fortran_include,
         dependencies: [py_dep, omp_dep, c_m_dep, fortran_m_dep],
         install: true,
-        install_dir: library_install_dir
+        subdir: 'pixell'
     )
 endforeach
 
@@ -111,7 +111,7 @@ foreach source_name, module_name : cython_sources
         dependencies: [py_dep, omp_dep, c_m_dep],
         link_with: linkables,
         install: true,
-        install_dir: library_install_dir
+        subdir: 'pixell',
     )
 endforeach
 
diff --git a/pixell/curvedsky.py b/pixell/curvedsky.py
index 155f2bb..4d3d074 100644
--- a/pixell/curvedsky.py
+++ b/pixell/curvedsky.py
@@ -2,7 +2,9 @@
 full sky."""
 from __future__ import print_function, division
 import numpy as np, os, warnings
-from . import enmap, powspec, wcsutils, utils, bunch, cmisc
+from . import enmap, powspec, wcsutils, utils, bunch
+
+from . import cmisc
 # Initialize DUCC's thread num variable from OMP's if it's not already set.
 # This must be done before importing ducc0 for the first time. Doing this
 # limits wasted memory from ducc allocating too big a thread pool. For computes
diff --git a/pixell/enmap.py b/pixell/enmap.py
index 1575545..76c8306 100644
--- a/pixell/enmap.py
+++ b/pixell/enmap.py
@@ -2729,7 +2729,9 @@ def fix_endian(map):
 	"""Make endianness of array map match the current machine.
 	Returns the result."""
 	if map.dtype.byteorder not in ['=','<' if sys.byteorder == 'little' else '>']:
-		map = map.byteswap(True).newbyteorder()
+		# Compatibility to numpy 2.0
+		map = map.byteswap(True)
+		map = map.view(map.dtype.newbyteorder())
 	map.dtype = utils.fix_dtype_mpi4py(map.dtype)
 	return map
 
diff --git a/pixell/meson.build b/pixell/meson.build
index 458a5ca..c77a724 100644
--- a/pixell/meson.build
+++ b/pixell/meson.build
@@ -28,6 +28,8 @@ python_sources = [
     'utils.py',
     'wavelets.py',
     'wcsutils.py',
+    # Not technically a python source file, but is required for pixell
+    'arial.ttf',
 ]
 
 py.install_sources(
diff --git a/pixell/tests/__init__.py b/pixell/tests/__init__.py
deleted file mode 100644
index 8ce6130..0000000
--- a/pixell/tests/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from .test_geom import *
-from .test_io import *
-from .test_pixell import *
diff --git a/pixell/tests/pixel_tests.py b/pixell/tests/pixel_tests.py
deleted file mode 100644
index de561ef..0000000
--- a/pixell/tests/pixel_tests.py
+++ /dev/null
@@ -1,182 +0,0 @@
-from __future__ import print_function
-import matplotlib
-matplotlib.use('Agg')
-from pixell import enmap,curvedsky,wcsutils,reproject
-import numpy as np
-import itertools,yaml,pickle,os,sys
-import matplotlib.pyplot as plt
-
-TEST_DIR = os.path.dirname(__file__)
-DATA_PREFIX = os.path.join(TEST_DIR, 'data/')
-
-"""
-This script generates a set of reference values against which
-pixell tests will be done.
-
-"""
-
-
-def get_reference_pixels(shape):
-    """For a given 2D array, return a list of pixel indices
-    corresponding to locations of a pre-determined and fixed
-    pattern of reference pixels.
-
-    e.g even x even
-    1100110011
-    1100110011
-    0000000000
-    0000000000
-    1100110011
-    1100110011
-    0000000000
-    0000000000
-    1100110011
-    1100110011
-
-    e,g. odd x odd
-    110010011
-    110010011
-    000000000
-    000000000
-    110010011
-    000000000
-    000000000
-    110010011
-    110010011
-
-    e.g even x odd
-    110010011
-    110010011
-    000000000
-    000000000
-    110010011
-    110010011
-    000000000
-    000000000
-    110010011
-    110010011
-
-    requires N>=5 in each axis
-    """
-    Ny,Nx = shape[-2:]
-    assert (Ny>=5) and (Nx>=5), "Tests are not implemented for arrays with a dimension<5."
-    """Given N, return 0,1,{x},N-2,N-1, where {x} is N//2-1,N//2 if N is even
-    and {x} is N//2 if N is odd.
-    """
-    midextremes = lambda N: [0,1,N//2-1,N//2,N-2,N-1] if N%2==0 else [0,1,N//2,N-2,N-1]
-    ys = midextremes(Ny)
-    xs = midextremes(Nx)
-    pixels = np.array(list(itertools.product(ys,xs)))
-    return pixels
-
-def mask(arr,pixels,val=0):
-    """Mask an array arr based on array pixels of (y,x) pixel coordinates of (Npix,2)"""
-    arr[...,pixels[:,0],pixels[:,1]] = val
-    return arr
-
-def get_pixel_values(arr,pixels):
-    """Get values of arr at pixels specified in pixels (Npix,2)"""
-    return arr[...,pixels[:,0],pixels[:,1]]
-
-def get_meansquare(arr):
-    return np.mean(arr*2.)
-
-def save_mask_image(filename,shape):
-    """Save a minimal plot of an array masked by the currently implemented reference
-    pixel geometry
-
-    e.g.
-    > shape = (11,12)
-    > save_mask_image("test_mask.png",shape)
-    """
-    arr = np.zeros(shape)
-    pixels = get_reference_pixels(shape)
-    masked = mask(arr,pixels,val=1)
-    fig = plt.figure()
-    im = plt.imshow(masked,cmap='rainbow')
-    ax = plt.gca()
-    ax.set_xticks(np.arange(0,shape[1])+0.5);
-    ax.set_yticks(np.arange(0,shape[0])+0.5);
-    ax.grid(which='major',color='w', linestyle='-', linewidth=5)
-    ax.tick_params(axis='x', colors=(0,0,0,0))
-    ax.tick_params(axis='y', colors=(0,0,0,0))
-    for spine in im.axes.spines.values():
-        spine.set_edgecolor((0,0,0,0))
-    plt.savefig(filename, bbox_inches='tight')
-
-def get_spectrum(ntype,noise,lmax,lmax_pad):
-    ells = np.arange(0,lmax+lmax_pad)
-    if ntype=="white": return np.ones(shape=(ells.size,))*(noise**2.)*((np.pi/180./60.)**2.)
-    if ntype=="white_dl":
-        spec = np.zeros(shape=(ells.size,))
-        spec[2:] = (noise**2.)*((np.pi/180./60.)**2.)*2.*np.pi/ells[2:]/(ells+1.)[2:]
-        return spec
-    raise NotImplementedError
-
-def get_spectra(yml_section,lmax,lmax_pad):
-    spectra = {}
-    for s in yml_section:
-        spectra[s['name']] = get_spectrum(s['type'],s['noise'],lmax,lmax_pad)
-    return spectra
-
-def get_geometries(yml_section):
-    geos = {}
-    for g in yml_section:
-        if g['type']=='fullsky':
-            geos[g['name']] = enmap.fullsky_geometry(res=np.deg2rad(g['res_arcmin']/60.),proj=g['proj'])
-        elif g['type']=='pickle':
-            geos[g['name']] = pickle.load(open(DATA_PREFIX+"%s"%g['filename'],'rb'))
-        else:
-            raise NotImplementedError
-    return geos
-
-def generate_map(shape,wcs,powspec,lmax,seed):
-    return curvedsky.rand_map(shape, wcs, powspec, lmax=lmax, dtype=np.float64, seed=seed, spin=[0,2], method="auto", verbose=False)
-
-def check_equality(imap1,imap2):
-    assert np.all(imap1.shape==imap2.shape)
-    assert wcsutils.equal(imap1.wcs,imap2.wcs)
-    try:
-        assert np.all(np.isclose(imap1,imap2))
-    except:
-        from orphics import io
-        io.plot_img(imap1,"i1.png",lim=[-1.5,2])
-        io.plot_img(imap2,"i2.png",lim=[-1.5,2])
-        io.plot_img((imap1-imap2)/imap1,"ip.png",lim=[-0.1,0.1])
-        assert 1==0
-
-    
-def get_extraction_test_results(yaml_file):
-    print("Starting tests from ",yaml_file)
-    with open(yaml_file) as f:
-        config = yaml.safe_load(f)
-    geos = get_geometries(config['geometries'])
-    lmax = config['lmax'] ; lmax_pad = config['lmax_pad']
-    spectra = get_spectra(config['spectra'],lmax,lmax_pad)
-    seed = config['seed']
-
-    results = {}
-    for g in geos.keys():
-        results[g] = {}
-        for s in spectra.keys():
-            results[g][s] = {}
-            imap = generate_map(geos[g][0][-2:],geos[g][1],spectra[s],lmax,seed)
-
-            # Do write and read test
-            filename = "temporary_map.fits" # NOT THREAD SAFE
-            enmap.write_map(filename,imap)
-            imap_in = enmap.read_map(filename)
-            check_equality(imap,imap_in)
-            for e in config['extracts']:
-                print("Doing test for extract ",e['name']," with geometry ",g," and spectrum ",s,"...")
-                if e['type']=='slice':
-                    box = np.deg2rad(np.array(e['box_deg']))
-                    cutout = enmap.read_map(filename,box=box)
-                    cutout_internal = imap.submap(box=box)
-                check_equality(cutout,cutout_internal)
-                pixels = get_reference_pixels(cutout.shape)
-                results[g][s]['refpixels'] = get_pixel_values(cutout,pixels)
-                results[g][s]['meansquare'] = get_meansquare(cutout)
-
-    os.remove(filename)
-    return results,config['result_name']
diff --git a/pyproject.toml b/pyproject.toml
index c2bd5e7..3a0b59e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ build-backend = 'mesonpy'
 requires = ['meson-python', 'numpy', 'cython', 'versioneer[toml]', 'build']
 
 [project]
-name = 'mytestlib'
+name = 'pixell'
 # TODO: Versioneer
 version = '1.0.0'
 description = "A rectangular pixel map manipulation and harmonic analysis library derived from Sigurd Naess' enlib."
@@ -58,3 +58,8 @@ test = [
     'coveralls>=1.5',
     'pytest>=4.6'
 ]
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests",
+]
diff --git a/pixell/tests/data/MM_041121.pkl b/tests/data/MM_041121.pkl
similarity index 100%
rename from pixell/tests/data/MM_041121.pkl
rename to tests/data/MM_041121.pkl
diff --git a/pixell/tests/data/MM_lensed_071123.fits b/tests/data/MM_lensed_071123.fits
similarity index 100%
rename from pixell/tests/data/MM_lensed_071123.fits
rename to tests/data/MM_lensed_071123.fits
diff --git a/pixell/tests/data/MM_offset_grad_071123.fits b/tests/data/MM_offset_grad_071123.fits
similarity index 100%
rename from pixell/tests/data/MM_offset_grad_071123.fits
rename to tests/data/MM_offset_grad_071123.fits
diff --git a/pixell/tests/data/MM_offset_obs_pos_071123.fits b/tests/data/MM_offset_obs_pos_071123.fits
similarity index 100%
rename from pixell/tests/data/MM_offset_obs_pos_071123.fits
rename to tests/data/MM_offset_obs_pos_071123.fits
diff --git a/pixell/tests/data/MM_offset_raw_pos_071123.fits b/tests/data/MM_offset_raw_pos_071123.fits
similarity index 100%
rename from pixell/tests/data/MM_offset_raw_pos_071123.fits
rename to tests/data/MM_offset_raw_pos_071123.fits
diff --git a/pixell/tests/data/MM_unlensed_071123.fits b/tests/data/MM_unlensed_071123.fits
similarity index 100%
rename from pixell/tests/data/MM_unlensed_071123.fits
rename to tests/data/MM_unlensed_071123.fits
diff --git a/pixell/tests/data/annot.txt b/tests/data/annot.txt
similarity index 100%
rename from pixell/tests/data/annot.txt
rename to tests/data/annot.txt
diff --git a/pixell/tests/data/cosmo2017_10K_acc3_lensedCls.dat b/tests/data/cosmo2017_10K_acc3_lensedCls.dat
similarity index 100%
rename from pixell/tests/data/cosmo2017_10K_acc3_lensedCls.dat
rename to tests/data/cosmo2017_10K_acc3_lensedCls.dat
diff --git a/pixell/tests/data/cutsky_geometry_scaled_20x_9.4_arcminute_pixel_shape_wcs_tuple.pkl b/tests/data/cutsky_geometry_scaled_20x_9.4_arcminute_pixel_shape_wcs_tuple.pkl
similarity index 100%
rename from pixell/tests/data/cutsky_geometry_scaled_20x_9.4_arcminute_pixel_shape_wcs_tuple.pkl
rename to tests/data/cutsky_geometry_scaled_20x_9.4_arcminute_pixel_shape_wcs_tuple.pkl
diff --git a/pixell/tests/data/test_scalCls.dat b/tests/data/test_scalCls.dat
similarity index 100%
rename from pixell/tests/data/test_scalCls.dat
rename to tests/data/test_scalCls.dat
diff --git a/pixell/tests/test_geom.py b/tests/test_geom.py
similarity index 100%
rename from pixell/tests/test_geom.py
rename to tests/test_geom.py
diff --git a/pixell/tests/test_io.py b/tests/test_io.py
similarity index 100%
rename from pixell/tests/test_io.py
rename to tests/test_io.py
diff --git a/pixell/tests/test_pixell.py b/tests/test_pixell.py
similarity index 87%
rename from pixell/tests/test_pixell.py
rename to tests/test_pixell.py
index aaf191a..a21caf0 100644
--- a/pixell/tests/test_pixell.py
+++ b/tests/test_pixell.py
@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
 """Tests for `pixell` package."""
 
 import unittest
@@ -24,13 +21,180 @@
 import pickle
 import os,sys
 
-try:                              # when invoked directly...
-    import pixel_tests as ptests
-except ImportError:               # when imported through py.test
-    from . import pixel_tests as ptests
+import matplotlib
+matplotlib.use('Agg')
+import numpy as np
+import itertools,yaml,pickle,os,sys
+import matplotlib.pyplot as plt
+
+TEST_DIR = os.path.dirname(__file__)
+DATA_PREFIX = os.path.join(TEST_DIR, 'data/')
+
+def get_reference_pixels(shape):
+    """For a given 2D array, return a list of pixel indices
+    corresponding to locations of a pre-determined and fixed
+    pattern of reference pixels.
+
+    e.g even x even
+    1100110011
+    1100110011
+    0000000000
+    0000000000
+    1100110011
+    1100110011
+    0000000000
+    0000000000
+    1100110011
+    1100110011
+
+    e,g. odd x odd
+    110010011
+    110010011
+    000000000
+    000000000
+    110010011
+    000000000
+    000000000
+    110010011
+    110010011
+
+    e.g even x odd
+    110010011
+    110010011
+    000000000
+    000000000
+    110010011
+    110010011
+    000000000
+    000000000
+    110010011
+    110010011
+
+    requires N>=5 in each axis
+    """
+    Ny,Nx = shape[-2:]
+    assert (Ny>=5) and (Nx>=5), "Tests are not implemented for arrays with a dimension<5."
+    """Given N, return 0,1,{x},N-2,N-1, where {x} is N//2-1,N//2 if N is even
+    and {x} is N//2 if N is odd.
+    """
+    midextremes = lambda N: [0,1,N//2-1,N//2,N-2,N-1] if N%2==0 else [0,1,N//2,N-2,N-1]
+    ys = midextremes(Ny)
+    xs = midextremes(Nx)
+    pixels = np.array(list(itertools.product(ys,xs)))
+    return pixels
+
+def mask(arr,pixels,val=0):
+    """Mask an array arr based on array pixels of (y,x) pixel coordinates of (Npix,2)"""
+    arr[...,pixels[:,0],pixels[:,1]] = val
+    return arr
+
+def get_pixel_values(arr,pixels):
+    """Get values of arr at pixels specified in pixels (Npix,2)"""
+    return arr[...,pixels[:,0],pixels[:,1]]
+
+def get_meansquare(arr):
+    return np.mean(arr*2.)
+
+def save_mask_image(filename,shape):
+    """Save a minimal plot of an array masked by the currently implemented reference
+    pixel geometry
+
+    e.g.
+    > shape = (11,12)
+    > save_mask_image("test_mask.png",shape)
+    """
+    arr = np.zeros(shape)
+    pixels = get_reference_pixels(shape)
+    masked = mask(arr,pixels,val=1)
+    fig = plt.figure()
+    im = plt.imshow(masked,cmap='rainbow')
+    ax = plt.gca()
+    ax.set_xticks(np.arange(0,shape[1])+0.5);
+    ax.set_yticks(np.arange(0,shape[0])+0.5);
+    ax.grid(which='major',color='w', linestyle='-', linewidth=5)
+    ax.tick_params(axis='x', colors=(0,0,0,0))
+    ax.tick_params(axis='y', colors=(0,0,0,0))
+    for spine in im.axes.spines.values():
+        spine.set_edgecolor((0,0,0,0))
+    plt.savefig(filename, bbox_inches='tight')
+
+def get_spectrum(ntype,noise,lmax,lmax_pad):
+    ells = np.arange(0,lmax+lmax_pad)
+    if ntype=="white": return np.ones(shape=(ells.size,))*(noise**2.)*((np.pi/180./60.)**2.)
+    if ntype=="white_dl":
+        spec = np.zeros(shape=(ells.size,))
+        spec[2:] = (noise**2.)*((np.pi/180./60.)**2.)*2.*np.pi/ells[2:]/(ells+1.)[2:]
+        return spec
+    raise NotImplementedError
+
+def get_spectra(yml_section,lmax,lmax_pad):
+    spectra = {}
+    for s in yml_section:
+        spectra[s['name']] = get_spectrum(s['type'],s['noise'],lmax,lmax_pad)
+    return spectra
+
+def get_geometries(yml_section):
+    geos = {}
+    for g in yml_section:
+        if g['type']=='fullsky':
+            geos[g['name']] = enmap.fullsky_geometry(res=np.deg2rad(g['res_arcmin']/60.),proj=g['proj'])
+        elif g['type']=='pickle':
+            geos[g['name']] = pickle.load(open(DATA_PREFIX+"%s"%g['filename'],'rb'))
+        else:
+            raise NotImplementedError
+    return geos
+
+def generate_map(shape,wcs,powspec,lmax,seed):
+    return curvedsky.rand_map(shape, wcs, powspec, lmax=lmax, dtype=np.float64, seed=seed, spin=[0,2], method="auto", verbose=False)
+
+def check_equality(imap1,imap2):
+    assert np.all(imap1.shape==imap2.shape)
+    assert wcsutils.equal(imap1.wcs,imap2.wcs)
+    try:
+        assert np.all(np.isclose(imap1,imap2))
+    except:
+        from orphics import io
+        io.plot_img(imap1,"i1.png",lim=[-1.5,2])
+        io.plot_img(imap2,"i2.png",lim=[-1.5,2])
+        io.plot_img((imap1-imap2)/imap1,"ip.png",lim=[-0.1,0.1])
+        assert 1==0
+
+    
+def get_extraction_test_results(yaml_file):
+    print("Starting tests from ",yaml_file)
+    with open(yaml_file) as f:
+        config = yaml.safe_load(f)
+    geos = get_geometries(config['geometries'])
+    lmax = config['lmax'] ; lmax_pad = config['lmax_pad']
+    spectra = get_spectra(config['spectra'],lmax,lmax_pad)
+    seed = config['seed']
+
+    results = {}
+    for g in geos.keys():
+        results[g] = {}
+        for s in spectra.keys():
+            results[g][s] = {}
+            imap = generate_map(geos[g][0][-2:],geos[g][1],spectra[s],lmax,seed)
+
+            # Do write and read test
+            filename = "temporary_map.fits" # NOT THREAD SAFE
+            enmap.write_map(filename,imap)
+            imap_in = enmap.read_map(filename)
+            check_equality(imap,imap_in)
+            for e in config['extracts']:
+                print("Doing test for extract ",e['name']," with geometry ",g," and spectrum ",s,"...")
+                if e['type']=='slice':
+                    box = np.deg2rad(np.array(e['box_deg']))
+                    cutout = enmap.read_map(filename,box=box)
+                    cutout_internal = imap.submap(box=box)
+                check_equality(cutout,cutout_internal)
+                pixels = get_reference_pixels(cutout.shape)
+                results[g][s]['refpixels'] = get_pixel_values(cutout,pixels)
+                results[g][s]['meansquare'] = get_meansquare(cutout)
+
+    os.remove(filename)
+    return results,config['result_name']
 
-TEST_DIR = ptests.TEST_DIR
-DATA_PREFIX = ptests.DATA_PREFIX
 lens_version = '071123'
 
 def get_offset_result(res=1.,dtype=np.float64,seed=1):
@@ -328,7 +492,7 @@ def test_pixels(self):
         """Runs reference pixel and mean-square comparisons on extracts from randomly generated
         maps"""
         print("Testing reference pixels...")
-        results,rname = ptests.get_extraction_test_results(TEST_DIR+"/tests.yml")
+        results,rname = get_extraction_test_results(TEST_DIR+"/tests.yml")
         cresults = pickle.load(open(DATA_PREFIX+"%s.pkl" % rname,'rb'))
         assert sorted(results.keys())==sorted(cresults.keys())
         for g in results.keys():
diff --git a/pixell/tests/tests.yml b/tests/tests.yml
similarity index 100%
rename from pixell/tests/tests.yml
rename to tests/tests.yml

From 12c48c5bdf8d59a1c0da6bef805fb5c4ca5612c7 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 11:41:00 -0400
Subject: [PATCH 10/44] Fix test pathing

---
 .github/workflows/build.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 745b73b..9ae4f87 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -22,7 +22,7 @@ jobs:
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install pytest-cov numpy "Cython<3.0.4"
           python -m pip install .
-          pytest --cov-report html --cov-report xml --cov-report annotate --cov=pixell pixell/tests/ -s
+          pytest --cov-report html --cov-report xml --cov-report annotate --cov=pixell -s
           
       - uses: codecov/codecov-action@v2
         with:
@@ -61,7 +61,7 @@ jobs:
 
       - name: Run Tests (MacOS)
         run: |
-          pytest pixell/tests/ -s
+          pytest -s
 
 
   build_wheels_linux:
@@ -111,7 +111,7 @@ jobs:
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: >
             cd /
-            pytest {project}/pixell/tests -s
+            pytest {project}/tests -s
           PYTHON: "python"
           PIP: "pip"
 
@@ -179,7 +179,7 @@ jobs:
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: >
             cd /
-            pytest {project}/pixell/tests -s
+            pytest {project}/tests -s
           # Cannot test arm64 on non-native runner
           CIBW_TEST_SKIP: "*_arm64"
           PYTHON: "python"

From 3a168de926516d5ebe95c87c251362adcd6f918d Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:03:37 -0400
Subject: [PATCH 11/44] Remove pixell in test path

---
 scripts/build_wheels.sh                        | 2 +-
 scripts/generate_tests/pixel_test_generator.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/build_wheels.sh b/scripts/build_wheels.sh
index 05672cc..ef75bfc 100755
--- a/scripts/build_wheels.sh
+++ b/scripts/build_wheels.sh
@@ -15,7 +15,7 @@ set -x
 python -m pip install --upgrade pip setuptools wheel build
 python -m build
 python -m pip install .
-py.test --cov=pixell pixell/tests/ -s
+py.test --cov=pixell -s
 find . -type f -iname '*.so' -print -delete
 rm -rf _deps/
 python -m cibuildwheel --output-dir wheelhouse
diff --git a/scripts/generate_tests/pixel_test_generator.py b/scripts/generate_tests/pixel_test_generator.py
index 53364be..33f4af2 100644
--- a/scripts/generate_tests/pixel_test_generator.py
+++ b/scripts/generate_tests/pixel_test_generator.py
@@ -1,6 +1,6 @@
 from pixell import sharp
 import sys
-sys.path.append('../../pixell/tests')
+sys.path.append('../../tests')
 import pixel_tests as ptests
 import pickle
 import os

From 9187d4815df87df19a08c6578951aa8cf5ba3ed3 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:09:41 -0400
Subject: [PATCH 12/44] Potential bug in pillow causing test failures?

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3a0b59e..4c01135 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     'healpy>=1.13',
     'matplotlib>=2.0',
     'pyyaml>=5.0',
-    'Pillow>=5.3.0',
+    '5.3.0<=Pillow<10.4.0',
     'pytest-cov>=2.6',
     'coveralls>=1.5',
     'pytest>=4.6',

From a676fe92a873a9ad052a77d4986a5ac98fe2ae4b Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:12:47 -0400
Subject: [PATCH 13/44] Attempt to use correct pyproject.toml dependency
 specification syntax

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4c01135..da4ce01 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     'healpy>=1.13',
     'matplotlib>=2.0',
     'pyyaml>=5.0',
-    '5.3.0<=Pillow<10.4.0',
+    'Pillow>=5.3.0, != 10.4.0',
     'pytest-cov>=2.6',
     'coveralls>=1.5',
     'pytest>=4.6',

From ad7987c83bbad77b76f0e356a4d07a3f8625c1d8 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:17:44 -0400
Subject: [PATCH 14/44] Use build library to build wheels

---
 .github/workflows/build.yml | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 9ae4f87..ac4d4f4 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -93,14 +93,12 @@ jobs:
         run: |
           python -m pip install -U pip
           python -m pip install -U setuptools
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install pytest-cov numpy "Cython<3.0.4"
-          python -m pip install cibuildwheel
+          python -m pip install --upgrade pip setuptools wheel build meson
 
       - name: Test and build wheels
         run: |
           ln -s $FC $(dirname $(which $FC))/gfortran
-          bash scripts/build_wheels.sh
+          python3 -m build
         env:
           CIBW_ENVIRONMENT: OMP_NUM_THREADS=2
                             OPENBLAS_NUM_THREADS=2
@@ -156,14 +154,11 @@ jobs:
         run: |
           python -m pip install -U pip
           python -m pip install -U setuptools
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install pytest-cov numpy "Cython<3.0.4"
-          python -m pip install cibuildwheel
-
+          python -m pip install --upgrade pip setuptools wheel build
       - name: Test and build wheels
         run: |
           ln -s $FC $(dirname $(which $FC))/gfortran
-          bash scripts/build_wheels.sh
+          python3 -m build
         env:
           CIBW_ENVIRONMENT: OMP_NUM_THREADS=2
                             OPENBLAS_NUM_THREADS=2

From 7d81f1de244dcde2f95b67c831a8432afc6a340e Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:40:47 -0400
Subject: [PATCH 15/44] Use cibuildwheel runner

---
 .github/workflows/build.yml | 22 +++++++++++++++++++---
 pyproject.toml              |  6 ++++++
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index ac4d4f4..0eafdca 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -64,6 +64,24 @@ jobs:
           pytest -s
 
 
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.19.1
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
   build_wheels_linux:
     name: Build wheels on Linux
     runs-on: ubuntu-latest
@@ -158,11 +176,10 @@ jobs:
       - name: Test and build wheels
         run: |
           ln -s $FC $(dirname $(which $FC))/gfortran
-          python3 -m build
+          python -m build
         env:
           CIBW_ENVIRONMENT: OMP_NUM_THREADS=2
                             OPENBLAS_NUM_THREADS=2
-          CIBW_BEFORE_BUILD: "python -m pip install numpy==${{ matrix.numpyver }} scipy 'cython<3.0.4'"
           CIBW_BUILD_VERBOSITY: 3
           # To build for both x86_64 and arm64, uncomment the following lines.
           # That would require a fortran compiler that can cross-comile from
@@ -183,7 +200,6 @@ jobs:
       - uses: actions/upload-artifact@v2
         with:
           path: ./wheelhouse/*.whl
-      
 
   build_sdist:
     name: Build source distribution
diff --git a/pyproject.toml b/pyproject.toml
index da4ce01..9324403 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,3 +63,9 @@ test = [
 testpaths = [
     "tests",
 ]
+
+
+[tool.cibuildwheel]
+test-requires = "pytest"
+test-command = "pytest"
+build = "cp39-* cp310-* cp311-* cp312-*"
\ No newline at end of file

From e5358a4c3edcd9f1baa92a48b2d5d4a6bf21f003 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:41:42 -0400
Subject: [PATCH 16/44] Remove old wheel builders

---
 .github/workflows/build.yml | 120 +-----------------------------------
 1 file changed, 1 insertion(+), 119 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 0eafdca..dd063b2 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -82,125 +82,7 @@ jobs:
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
-  build_wheels_linux:
-    name: Build wheels on Linux
-    runs-on: ubuntu-latest
-    strategy:
-      # Ensure that a wheel builder finishes even if another fails
-      fail-fast: false
-      matrix:
-        os: [ubuntu-20.04]
-        cp: [cp39, cp310, cp311]
-        include:
-          - cp: cp39
-            numpyver: "1.20"
-          - cp: cp310
-            numpyver: "1.22"
-          - cp: cp311
-            numpyver: "1.22"
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: actions/setup-python@v2
-        name: Install Python
-        with:
-          python-version: '3.8'
-
-      - name: Install cibuildwheel and other dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install -U setuptools
-          python -m pip install --upgrade pip setuptools wheel build meson
-
-      - name: Test and build wheels
-        run: |
-          ln -s $FC $(dirname $(which $FC))/gfortran
-          python3 -m build
-        env:
-          CIBW_ENVIRONMENT: OMP_NUM_THREADS=2
-                            OPENBLAS_NUM_THREADS=2
-          CIBW_BEFORE_BUILD: "python -m pip install numpy==${{ matrix.numpyver }} scipy 'cython<3.0.4'"
-          CIBW_BUILD_VERBOSITY: 3
-          # If users are still on 32 bit systems or PPC they should build from source.
-          CIBW_BUILD: "${{ matrix.cp }}-manylinux_{x86_64,aarch64}"
-          CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: >
-            cd /
-            pytest {project}/tests -s
-          PYTHON: "python"
-          PIP: "pip"
-
-      - uses: actions/upload-artifact@v2
-        with:
-          path: ./wheelhouse/*.whl
-
-  build_wheels_macos:
-    name: Build wheels on MacOS
-    runs-on: macos-12
-    env:
-      CC: gcc-12
-      CXX: gcc-12
-      FC: gfortran-12
-      DUCC0_NUM_THREADS: 2
-    strategy:
-      # Ensure that a wheel builder finishes even if another fails
-      fail-fast: false
-      matrix:
-        os: [macos-12]
-        # We don't build 3.7 wheels for MacOS because that's x86 only.
-        cp: [cp39, cp310, cp311, cp312]
-        include:
-          - cp: cp39
-            numpyver: "1.20"
-          - cp: cp310
-            numpyver: "1.22"
-          - cp: cp311
-            numpyver: "1.22"
-          - cp: cp312
-            numpyver: "2.0"
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: actions/setup-python@v2
-        name: Install Python
-        with:
-          python-version: '3.10'
-
-      - name: Install cibuildwheel and other dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install -U setuptools
-          python -m pip install --upgrade pip setuptools wheel build
-      - name: Test and build wheels
-        run: |
-          ln -s $FC $(dirname $(which $FC))/gfortran
-          python -m build
-        env:
-          CIBW_ENVIRONMENT: OMP_NUM_THREADS=2
-                            OPENBLAS_NUM_THREADS=2
-          CIBW_BUILD_VERBOSITY: 3
-          # To build for both x86_64 and arm64, uncomment the following lines.
-          # That would require a fortran compiler that can cross-comile from
-          # x86_64 to arm64, as well as an OMP library that's cross-compiled.
-          # CIBW_BUILD: "${{ matrix.cp }}-macosx_{x86_64,arm64}"
-          CIBW_BUILD: "${{ matrix.cp }}-macosx_x86_64"
-          #CIBW_ARCHS_MACOS: "x86_64 arm64"
-          CIBW_ARCHS_MACOS: "x86_64"
-          CIBW_TEST_REQUIRES: pytest
-          CIBW_TEST_COMMAND: >
-            cd /
-            pytest {project}/tests -s
-          # Cannot test arm64 on non-native runner
-          CIBW_TEST_SKIP: "*_arm64"
-          PYTHON: "python"
-          PIP: "pip"
-
-      - uses: actions/upload-artifact@v2
-        with:
-          path: ./wheelhouse/*.whl
-
+ 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest

From acd12d937f65481650b17be30489c4709eaaa7e7 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:44:54 -0400
Subject: [PATCH 17/44] Correctly link build targets

---
 .github/workflows/build.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index dd063b2..d459bcc 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -63,14 +63,13 @@ jobs:
         run: |
           pytest -s
 
-
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        os: [ubuntu-latest, macos-13, macos-14]
 
     steps:
       - uses: actions/checkout@v4
@@ -109,7 +108,7 @@ jobs:
           path: dist/*.tar.gz
 
   upload_pypi:
-    needs: [build_wheels_linux, build_wheels_macos, build_sdist]
+    needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     # upload to PyPI on every tag starting with 'v'
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')

From 147aca3a3aea605bf5b69daa514dae930ed1317b Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:49:05 -0400
Subject: [PATCH 18/44] explicitly set fortran compiler

---
 .github/workflows/build.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index d459bcc..97370ad 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -78,6 +78,8 @@ jobs:
         uses: pypa/cibuildwheel@v2.19.1
 
       - uses: actions/upload-artifact@v4
+        env:
+          FC: gfortran-12
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl

From 7117ce257ab244246a1e834143dea6952bf391b7 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:52:07 -0400
Subject: [PATCH 19/44] Give gforaran-12 to correct step

---
 .github/workflows/build.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 97370ad..39241de 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -76,13 +76,14 @@ jobs:
 
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.19.1
-
-      - uses: actions/upload-artifact@v4
         env:
           FC: gfortran-12
+
+      - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
+
  
   build_sdist:
     name: Build source distribution

From eb9db50ae7f5ae99fecb3c01809cd71b3b16e7f8 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:53:21 -0400
Subject: [PATCH 20/44] Force gcc-12 as compiler

---
 .github/workflows/build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 39241de..d36c175 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -78,6 +78,7 @@ jobs:
         uses: pypa/cibuildwheel@v2.19.1
         env:
           FC: gfortran-12
+          CC: gcc-12
 
       - uses: actions/upload-artifact@v4
         with:

From 5996b80a8d1aebea1351b229cbfa8cab2721fee7 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 15:55:24 -0400
Subject: [PATCH 21/44] Try without arm macs (for now)

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index d36c175..7cd065b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -69,7 +69,7 @@ jobs:
     strategy:
       matrix:
         # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-latest, macos-13, macos-14]
+        os: [ubuntu-latest, macos-13]
 
     steps:
       - uses: actions/checkout@v4

From 536b230f4914245b66c96d42485577cf4e4ff408 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:27:21 -0400
Subject: [PATCH 22/44] Add macos arm wheels and change min deployment

---
 .github/workflows/build.yml | 28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 7cd065b..6eeae47 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -79,13 +79,37 @@ jobs:
         env:
           FC: gfortran-12
           CC: gcc-12
+          MACOSX_DEPLOYMENT_TARGET: 13.0
 
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
- 
+  build_wheels_macos_arm:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [macos-14]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.19.1
+        env:
+          FC: gfortran-12
+          CC: gcc-12
+          MACOSX_DEPLOYMENT_TARGET: 14.0
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
@@ -112,7 +136,7 @@ jobs:
           path: dist/*.tar.gz
 
   upload_pypi:
-    needs: [build_wheels, build_sdist]
+    needs: [build_wheels, build_sdist, build_wheels_macos_arm]
     runs-on: ubuntu-latest
     # upload to PyPI on every tag starting with 'v'
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')

From 43d7554f2d885c1b683c3a382666c6950dffc303 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:32:28 -0400
Subject: [PATCH 23/44] Set MACOSX_DEPLOYMENT_TARGET to be string

---
 .github/workflows/build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6eeae47..251d038 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -79,7 +79,7 @@ jobs:
         env:
           FC: gfortran-12
           CC: gcc-12
-          MACOSX_DEPLOYMENT_TARGET: 13.0
+          MACOSX_DEPLOYMENT_TARGET: "13.0"
 
       - uses: actions/upload-artifact@v4
         with:
@@ -102,7 +102,7 @@ jobs:
         env:
           FC: gfortran-12
           CC: gcc-12
-          MACOSX_DEPLOYMENT_TARGET: 14.0
+          MACOSX_DEPLOYMENT_TARGET: "14.0"
 
       - uses: actions/upload-artifact@v4
         with:

From 8179282b1c78c5407b0164a4ede6c7686b00c9af Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:35:35 -0400
Subject: [PATCH 24/44] Add correct test command for cibuildwheel

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9324403..9aa5ed4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,5 +67,5 @@ testpaths = [
 
 [tool.cibuildwheel]
 test-requires = "pytest"
-test-command = "pytest"
+test-command = "pytest {project}/tests"
 build = "cp39-* cp310-* cp311-* cp312-*"
\ No newline at end of file

From 53d9b74267783436ff6d465901c5156eac0293c2 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:39:50 -0400
Subject: [PATCH 25/44] Simplify build instruction

---
 README.rst | 59 +++++++++++++++---------------------------------------
 1 file changed, 16 insertions(+), 43 deletions(-)

diff --git a/README.rst b/README.rst
index 193e56d..e08fe9f 100644
--- a/README.rst
+++ b/README.rst
@@ -25,14 +25,13 @@ pixell
 Dependencies
 ------------
 
-* Python>=3.7 but Python 3.12 is not currently supported
+* Python>=3.9.
 * gcc/gfortran or Intel compilers (clang might not work out of the box), if compiling from source
 * ducc0_, healpy, Cython, astropy, numpy, scipy, matplotlib, pyyaml, h5py, Pillow (Python Image Library)
 
 On MacOS, and other systems with non-traditional environments, you should specify the following standard environment variables:
 
 * ``CC``: C compiler (example: ``gcc``)
-* ``CXX``: C++ compiler (example: ``g++``)
 * ``FC``: Fortran compiler (example: ``gfortran``)
 
 We recommend using ``gcc`` installed from Homebrew to access these compilers on
@@ -64,59 +63,33 @@ Make sure your ``pip`` tool is up-to-date. To install ``pixell``, run:
 .. code-block:: console
 		
    $ pip install pixell --user
-   $ test-pixell
 
-This will install a pre-compiled binary suitable for your system (only Linux and Mac OS X with Python>=3.7 are supported). Note that you need ``~/.local/bin`` to be in your ``PATH`` for the latter ``test-pixell`` to work.
+This will install a pre-compiled binary suitable for your system (only Linux and Mac OS X with Python>=3.9 are supported). 
 
-If you require more control over your installation, e.g. using Intel compilers, please see the section below on compiling from source.  The ``test-pixell`` command will run a suite of unit tests.
+If you require more control over your installation, e.g. using Intel compilers, please see the section below on compiling from source.
 
 Compiling from source (advanced / development workflow)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 For compilation instructions specific to NERSC/cori, see NERSC_.
 
-For all other, below are general instructions.
+The easiest way to install from source is to use the ``pip`` tool,
+with the ``--no-binary`` flag. This will download the source distribution
+and compile it for you. Don't forget to make sure you have CC and FC set
+if you have any problems.
 
-First, download the source distribution or ``git clone`` this repository. You can work from ``master`` or checkout one of the released version tags (see the Releases section on Github). Then change into the cloned/source directory.
+For all other cases, below are general instructions.
 
+First, download the source distribution or ``git clone`` this repository. You
+can work from ``master`` or checkout one of the released version tags (see the
+Releases section on Github). Then change into the cloned/source directory.
 
-Run ``setup.py``
-~~~~~~~~~~~~~~~~
-
-If not using Intel compilers (see below), build the package using 
-
-.. code-block:: console
-		
-   $ python setup.py build_ext -i
-
-You may now test the installation:
-
-.. code-block:: console
-		
-   $ py.test pixell/tests/
-   
-If the tests pass, you can install the package (optionally with ``-e`` if you would like to edit the files after installation)
-   
-.. code-block:: console
-
-   $ python setup.py install --user
-
-   
-Intel compilers
-~~~~~~~~~~~~~~~
-
-Intel compilers require you to modify the build step above as follows
-
-.. code-block:: console
-		
-   $ python setup.py build_ext -i --fcompiler=intelem --compiler=intelem
-
-On some systems, further specification might be required (make sure to get a fresh copy of the repository before trying out a new install method), e.g.:
-
-.. code-block:: console
-
-   $ LDSHARED="icc -shared" LD=icc LINKCC=icc CC=icc python setup.py build_ext -i --fcompiler=intelem --compiler=intelem
+Once downloaded, you can install using ``pip install .`` inside the project
+directory. We use the ``meson`` build system, which should be understood by
+``pip`` (it will build in an isolated environment).
 
+We suggest you then test the installation by running the unit tests. You
+can do this by running ``pytest``.
 
 
 Contributions

From 3a7afbc6d8a26ac5def206f5cdef4cc974607ef4 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:46:59 -0400
Subject: [PATCH 26/44] MUST use editable install for coverage to work

---
 .github/workflows/build.yml |  4 ++--
 pyproject.toml              | 12 ++++++++++--
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 251d038..3cf09ba 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -21,8 +21,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install pytest-cov numpy "Cython<3.0.4"
-          python -m pip install .
-          pytest --cov-report html --cov-report xml --cov-report annotate --cov=pixell -s
+          python -m pip install -e .
+          pytest --cov-report html --cov-report xml --cov-report annotate -s
           
       - uses: codecov/codecov-action@v2
         with:
diff --git a/pyproject.toml b/pyproject.toml
index 9aa5ed4..744648e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -64,8 +64,16 @@ testpaths = [
     "tests",
 ]
 
-
 [tool.cibuildwheel]
 test-requires = "pytest"
 test-command = "pytest {project}/tests"
-build = "cp39-* cp310-* cp311-* cp312-*"
\ No newline at end of file
+build = "cp39-* cp310-* cp311-* cp312-*"
+
+[tool.coverage.run]
+source = [
+    "pixell"
+]
+
+[tool.coverage.report]
+exclude_lines = ["pragma: no cover"]
+exclude_also = ["if TYPE_CHECKING:"]
\ No newline at end of file

From 0f1c60d491bb87479c21281c9726ac8089a17016 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:50:19 -0400
Subject: [PATCH 27/44] Attempt to remedy issue with editable install

---
 .github/workflows/build.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 3cf09ba..dae2bb7 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -19,9 +19,7 @@ jobs:
       
       - name: Run Tests (Linux)
         run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install pytest-cov numpy "Cython<3.0.4"
-          python -m pip install -e .
+          python -m pip install -e '.[test]'
           pytest --cov-report html --cov-report xml --cov-report annotate -s
           
       - uses: codecov/codecov-action@v2

From d7b0e4369343a0e57680b37784aae5c07a75c7f4 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:52:53 -0400
Subject: [PATCH 28/44] try upgrading pip

---
 .github/workflows/build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index dae2bb7..99a1809 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -19,6 +19,7 @@ jobs:
       
       - name: Run Tests (Linux)
         run: |
+          python -m pip install --upgrade pip setuptools wheel
           python -m pip install -e '.[test]'
           pytest --cov-report html --cov-report xml --cov-report annotate -s
           

From c33c94d22b6153d9a99551d53a1b5f47fc78dbd7 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 16:55:46 -0400
Subject: [PATCH 29/44] Remove upper limit on h5py

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 744648e..4df1b23 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,7 +48,7 @@ test = [
     'numpy>=1.20',
     'astropy>=2.0',
     'setuptools>=39.2',
-    'h5py>=2.7,<=2.10',
+    'h5py>=2.7',
     'scipy>=1.0',
     'python_dateutil>=2.7',
     'cython',

From 06f18bead532d80852c8c705ffec2b543a95db94 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 17:10:12 -0400
Subject: [PATCH 30/44] Add meson no build isolation to editable installs

---
 .github/workflows/build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 99a1809..1d44133 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -19,8 +19,8 @@ jobs:
       
       - name: Run Tests (Linux)
         run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install -e '.[test]'
+          python -m pip install --upgrade pip setuptools wheel meson ninja meson-python
+          python -m pip install --no-build-isolation --editable '.[test]'
           pytest --cov-report html --cov-report xml --cov-report annotate -s
           
       - uses: codecov/codecov-action@v2

From 70b3514728c9b721147dc37e349e88d99842f836 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 17:10:57 -0400
Subject: [PATCH 31/44] Pre-install cythona nd numpy

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 1d44133..7cde067 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -19,7 +19,7 @@ jobs:
       
       - name: Run Tests (Linux)
         run: |
-          python -m pip install --upgrade pip setuptools wheel meson ninja meson-python
+          python -m pip install --upgrade pip setuptools wheel meson ninja meson-python cython numpy
           python -m pip install --no-build-isolation --editable '.[test]'
           pytest --cov-report html --cov-report xml --cov-report annotate -s
           

From 29dd8e55b5d8b6ad53f068afd58ddb17560b3009 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Mon, 1 Jul 2024 17:18:12 -0400
Subject: [PATCH 32/44] Actually run coverage... That would help

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 7cde067..09f7344 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -21,7 +21,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools wheel meson ninja meson-python cython numpy
           python -m pip install --no-build-isolation --editable '.[test]'
-          pytest --cov-report html --cov-report xml --cov-report annotate -s
+          pytest --cov --cov-report html --cov-report xml --cov-report annotate -s
           
       - uses: codecov/codecov-action@v2
         with:

From 1caf1adf99ef0f322a8bc3be1851582c85c562c3 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Tue, 2 Jul 2024 09:01:19 -0400
Subject: [PATCH 33/44] Remove some unused source files and make benchmark
 easier to use

---
 README.rst                         |  7 ++++
 meson.build                        |  3 +-
 pyproject.toml                     |  5 +++
 scripts/benchmark_pixell.py        | 21 ++++++++++
 scripts/benchmark_pixell_runner.py | 31 +++++++++++++++
 scripts/build_wheels.sh            | 22 -----------
 scripts/meson.build                | 11 ++++++
 scripts/omp_hello.c                | 38 ------------------
 scripts/omp_hello.f90              | 15 -------
 scripts/test-pixell                | 63 ------------------------------
 10 files changed, 77 insertions(+), 139 deletions(-)
 create mode 100644 scripts/benchmark_pixell.py
 create mode 100644 scripts/benchmark_pixell_runner.py
 delete mode 100755 scripts/build_wheels.sh
 create mode 100644 scripts/meson.build
 delete mode 100644 scripts/omp_hello.c
 delete mode 100644 scripts/omp_hello.f90
 delete mode 100755 scripts/test-pixell

diff --git a/README.rst b/README.rst
index e08fe9f..6c7e5c8 100644
--- a/README.rst
+++ b/README.rst
@@ -55,6 +55,13 @@ have both efficiency and performance cores, you may wish to set ``OMP_NUM_THREAD
 the number of performance cores in your system. This will ensure that the efficiency cores
 are not used for the parallelized parts of ``pixell`` and ``ducc0``.
 
+You can check the threading behaviour (and the installation of ``pixell``) by running
+the benchmark script:
+
+.. code-block:: console
+
+   $ benchmark-pixell-runner
+
 Installing
 ----------
 
diff --git a/meson.build b/meson.build
index d1dbf56..7290da9 100644
--- a/meson.build
+++ b/meson.build
@@ -117,4 +117,5 @@ endforeach
 
 # The actual python install itself is left up to a helper build
 # script deifned in pixell/
-subdir('pixell')
\ No newline at end of file
+subdir('pixell')
+subdir('scripts')
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 4df1b23..da6a23d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,6 +35,11 @@ dependencies = [
     'numba>=0.54.0'
 ]
 
+[project.scripts]
+# See scripts/meson.build for installation
+benchmark-pixell-runner = "pixell.scripts.benchmark_pixell_runner:main"
+benchmark-pixell = "pixell.scripts.benchmark_pixell:main"
+
 [project.optional-dependencies]
 test = [
     'pip>=9.0',
diff --git a/scripts/benchmark_pixell.py b/scripts/benchmark_pixell.py
new file mode 100644
index 0000000..7e31416
--- /dev/null
+++ b/scripts/benchmark_pixell.py
@@ -0,0 +1,21 @@
+import subprocess
+import multiprocessing
+import sys
+from pathlib import Path
+
+
+def main():
+    max_threads = multiprocessing.cpu_count()
+    assert max_threads >= 1
+
+    def run_benchmark(nthreads):
+        subprocess.call(
+            [sys.executable, Path(__file__).parent / "benchmark_pixell_runner.py"],
+            env={"OMP_NUM_THREADS": str(nthreads)},
+        )
+
+    print("Single threaded alm test:")
+    run_benchmark(1)
+
+    print(f"Multi-threaded alm test with {max_threads} threads:")
+    run_benchmark(max_threads)
diff --git a/scripts/benchmark_pixell_runner.py b/scripts/benchmark_pixell_runner.py
new file mode 100644
index 0000000..cbed72c
--- /dev/null
+++ b/scripts/benchmark_pixell_runner.py
@@ -0,0 +1,31 @@
+"""
+Core benchmark script to be evaluated with various threading
+configurations. See benchmark_pixell.py for the actual benchmark
+that varies the number of threads.
+"""
+
+from pixell import curvedsky, enmap, utils
+import time
+import numpy as np
+
+
+def main():
+    np.random.seed(100)
+    shape, wcs = enmap.fullsky_geometry(res=12.0 * utils.arcmin)
+    imap = enmap.enmap(np.random.random(shape), wcs)
+
+    nsims = 40
+    lmax = int(6000 * (2.0 / 16.0))
+
+    t0 = time.time()
+    for i in range(nsims):
+        alm = curvedsky.map2alm(imap, lmax=lmax)
+        curvedsky.alm2map(alm, enmap.empty(shape, wcs))
+    t1 = time.time()
+
+    total = t1 - t0
+    print(f"{total:.4f} seconds.")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/scripts/build_wheels.sh b/scripts/build_wheels.sh
deleted file mode 100755
index ef75bfc..0000000
--- a/scripts/build_wheels.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/bash
-# Adapted from scikit-learn
-# https://raw.githubusercontent.com/scikit-learn/scikit-learn/21312644df0a6b4c6f3c27a74ac9d26cf49c2304/build_tools/wheels/build_wheels.sh
-
-
-#!/bin/bash
-
-set -e
-set -x
-
-# The version of the built dependencies are specified
-# in the pyproject.toml file, while the tests are run
-# against the most recent version of the dependencies
-
-python -m pip install --upgrade pip setuptools wheel build
-python -m build
-python -m pip install .
-py.test --cov=pixell -s
-find . -type f -iname '*.so' -print -delete
-rm -rf _deps/
-python -m cibuildwheel --output-dir wheelhouse
-ls wheelhouse
diff --git a/scripts/meson.build b/scripts/meson.build
new file mode 100644
index 0000000..301363f
--- /dev/null
+++ b/scripts/meson.build
@@ -0,0 +1,11 @@
+# Install the script in a new directory, pixell/scripts.
+
+python_scripts = [
+    'benchmark_pixell_runner.py',
+    'benchmark_pixell.py',
+]
+
+py.install_sources(
+    python_scripts,
+    subdir: 'pixell/scripts'
+)
\ No newline at end of file
diff --git a/scripts/omp_hello.c b/scripts/omp_hello.c
deleted file mode 100644
index fb471f5..0000000
--- a/scripts/omp_hello.c
+++ /dev/null
@@ -1,38 +0,0 @@
-/******************************************************************************
-* FILE: omp_hello.c
-* DESCRIPTION:
-*   OpenMP Example - Hello World - C/C++ Version
-*   In this simple example, the master thread forks a parallel region.
-*   All threads in the team obtain their unique thread number and print it.
-*   The master thread only prints the total number of threads.  Two OpenMP
-*   library routines are used to obtain the number of threads and each
-*   thread's number.
-* AUTHOR: Blaise Barney  5/99
-* LAST REVISED: 04/06/05
-******************************************************************************/
-#include <omp.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-int main (int argc, char *argv[]) 
-{
-  int nthreads, tid;
-  
-  /* Fork a team of threads giving them their own copies of variables */
-  #pragma omp parallel private(nthreads, tid)
-  {
-  
-  /* Obtain thread number */
-  tid = omp_get_thread_num();
-  printf("Hello World from thread = %d\n", tid);
-  
-  /* Only master thread does this */
-  if (tid == 0) 
-   {
-   nthreads = omp_get_num_threads();
-   printf("Number of threads = %d\n", nthreads);
-   }
-  
-  }  /* All threads join master thread and disband */
-
-}
diff --git a/scripts/omp_hello.f90 b/scripts/omp_hello.f90
deleted file mode 100644
index bd560cf..0000000
--- a/scripts/omp_hello.f90
+++ /dev/null
@@ -1,15 +0,0 @@
-! Hello world test program for fortran.
-
-program example
-    use :: omp_lib
-    implicit none
-
-    ! Set number of threads to use.
-    call omp_set_num_threads(2)
-
-    !$omp parallel
-
-        print '("Thread: ", i0)', omp_get_thread_num()
-
-    !$omp end parallel
-end program example
diff --git a/scripts/test-pixell b/scripts/test-pixell
deleted file mode 100755
index c34bb52..0000000
--- a/scripts/test-pixell
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-
-import os,sys
-import unittest
-
-# Must do the thread setup before we import pixell tests, otherwise those
-# dependent on the threadpool will fail.
-
-import multiprocessing
-max_threads = multiprocessing.cpu_count()
-assert max_threads>=1
-
-# On MacOS default values of `DUCC0_NUM_THREADS` (used for run-time thread number selection
-# as ducc0 uses pthreads not OMP) are not correctly handled, we must set it to a valid 
-# integer value.
-if sys.platform == "darwin":
-    if "DUCC0_NUM_THREADS" not in os.environ:
-        os.environ["DUCC0_NUM_THREADS"] = str(max_threads)
-        print(f"Setting DUCC0_NUM_THREADS (not present) to {max_threads}.")
-
-    try:
-        ducc0_num_threads = int(os.environ["DUCC0_NUM_THREADS"])
-    except ValueError:
-        # We have a non-integer value for this environment variable.
-        # Ducc0 does not currently (2023-10-16) have error handling for this
-        # (at least on MacOS 13), so we need to set it to a valid value.
-        os.environ["DUCC0_NUM_THREADS"] = str(max_threads)
-
-from pixell.tests import *
-
-unittest.main(exit=False)
-
-def run_alm_benchmark(nthreads):
-    os.system(f"""OMP_NUM_THREADS={nthreads} python -c 'from pixell import curvedsky,enmap,utils ;
-import time ;
-import numpy as np ;
-
-np.random.seed(100) ;
-shape,wcs = enmap.fullsky_geometry(res=12.*utils.arcmin) ;
-imap = enmap.enmap(np.random.random(shape),wcs) ;
-
-nsims = 40 ; 
-lmax = int(6000 * (2./16.)); 
-
-t0 = time.time() ;
-for i in range(nsims): alm = curvedsky.map2alm(imap,lmax=lmax) ; omap = curvedsky.alm2map(alm,enmap.empty(shape,wcs)) ;
-t1 = time.time();
-
-total = t1-t0;
-print(f"{{total:.4f}} seconds.");
-'
-    """)
-
-print("Single threaded alm test:")
-run_alm_benchmark(1)
-
-if max_threads==1:
-    print("Multi-threading not detected.")
-else:
-    print(f"Multi-threaded alm test with {max_threads} threads:")
-    run_alm_benchmark(max_threads)
-    
-

From 2a2830898d8655c94349bf7c3d663329de9bf8a2 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Tue, 2 Jul 2024 09:33:15 -0400
Subject: [PATCH 34/44] Allow for dynamic versioning with versioneer

---
 docs/conf.py       |  2 +-
 meson.build        | 16 ++++++++++++++--
 pixell/__init__.py | 10 +++++++---
 pixell/_version.py |  4 ++++
 pyproject.toml     | 13 ++++++++++---
 setup.cfg          | 20 --------------------
 6 files changed, 36 insertions(+), 29 deletions(-)
 delete mode 100644 setup.cfg

diff --git a/docs/conf.py b/docs/conf.py
index 4b20cc7..4de6094 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -60,7 +60,7 @@
 # the built documents.
 #
 # The short X.Y version.
-version = pixell.__version__
+version = ".".join(pixell.__version__.split(".")[:2])
 # The full version, including alpha/beta/rc tags.
 release = pixell.__version__
 
diff --git a/meson.build b/meson.build
index 7290da9..b8d2833 100644
--- a/meson.build
+++ b/meson.build
@@ -1,7 +1,19 @@
 # Main build file for pixell, helping with building the fortran,
 # c, and cython extensions.
-
-project('pixell', ['c', 'fortran', 'cython'])
+project(
+    'pixell',
+    ['c', 'fortran', 'cython'],
+    version: run_command(
+        [
+            # Note that _version.py doesn't actually 'dynamically' set the
+            # version number. We call it at build time and set it as a meson
+            # property.
+            'python',
+            'pixell/_version.py'
+        ],
+        check: true,
+    ).stdout().strip()
+)
 
 py = import('python').find_installation(pure: false)
 
diff --git a/pixell/__init__.py b/pixell/__init__.py
index a5ba748..8b0bf87 100644
--- a/pixell/__init__.py
+++ b/pixell/__init__.py
@@ -2,8 +2,12 @@
 
 """Top-level package for pixell."""
 
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("pixell")
+except PackageNotFoundError:
+    __version__ = "unknown"
+    
 __author__ = """Simons Observatory Collaboration Analysis Library Task Force"""
 __email__ = ''
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
diff --git a/pixell/_version.py b/pixell/_version.py
index 4553e96..b383259 100644
--- a/pixell/_version.py
+++ b/pixell/_version.py
@@ -518,3 +518,7 @@ def get_versions():
     return {"version": "0+unknown", "full-revisionid": None,
             "dirty": None,
             "error": "unable to compute version", "date": None}
+
+
+if __name__ == "__main__":
+    print(get_versions()["version"])
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index da6a23d..32dd1c4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,9 +3,8 @@ build-backend = 'mesonpy'
 requires = ['meson-python', 'numpy', 'cython', 'versioneer[toml]', 'build']
 
 [project]
+dynamic = ["version"]
 name = 'pixell'
-# TODO: Versioneer
-version = '1.0.0'
 description = "A rectangular pixel map manipulation and harmonic analysis library derived from Sigurd Naess' enlib."
 readme = 'README.rst'
 requires-python = '>=3.9'
@@ -81,4 +80,12 @@ source = [
 
 [tool.coverage.report]
 exclude_lines = ["pragma: no cover"]
-exclude_also = ["if TYPE_CHECKING:"]
\ No newline at end of file
+exclude_also = ["if TYPE_CHECKING:"]
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "pixell/_version.py"
+versionfile_build = "pixell/_version.py"
+tag_prefix = "v"
+parentdir_prefix = "pixell-"
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 1cdee40..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,20 +0,0 @@
-[bumpversion]
-current_version = 0.24.0
-commit = True
-tag = True
-
-[bdist_wheel]
-universal = 1
-
-[flake8]
-exclude = docs
-
-[aliases]
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = pixell/_version.py
-versionfile_build = pixell/_version.py
-tag_prefix = v
-parentdir_prefix = pixell-

From 64eef4e622d700ca589c1864a5acfae3f7ed8671 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Tue, 2 Jul 2024 09:43:11 -0400
Subject: [PATCH 35/44] Main Makefile compatible with new build system

---
 MANIFEST.in | 24 ------------------------
 Makefile    | 15 +++++----------
 2 files changed, 5 insertions(+), 34 deletions(-)
 delete mode 100644 MANIFEST.in

diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 97a6b68..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,24 +0,0 @@
-include AUTHORS.rst
-include CONTRIBUTING.rst
-include HISTORY.rst
-include LICENSE
-include README.rst
-include requirements.txt
-include optional-requirements.txt
-include requirements_dev.txt
-
-recursive-include cython *
-recursive-include fortran *
-recursive-include pixell/tests *
-recursive-include pixell/tests/data *
-recursive-include scripts *
-recursive-include * *.ttf
-recursive-exclude cython sharp.c
-recursive-exclude fortran interpol_*.f90
-recursive-exclude * temporary_map.fits
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
-include versioneer.py
-include pixell/_version.py
diff --git a/Makefile b/Makefile
index 9da19b1..ed243fb 100644
--- a/Makefile
+++ b/Makefile
@@ -27,12 +27,10 @@ export PRINT_HELP_PYSCRIPT
 BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
 python = python
--include options.mk
 
 # Main targets:
-
 develop:
-	OPT="" $(python) setup.py build_ext --inplace $(build_opts)
+	OPT="" $(python) -m pip install --no-build-isolation -e .
 
 help:
 	@$(python) -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
@@ -52,12 +50,10 @@ lint: ## check style with flake8
 	flake8 pixell tests
 
 test: ## run tests quickly with the default Python
-	$(python) setup.py test $(build_opts)
+	pytest
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source pixell setup.py test
-	coverage report -m
-	coverage html
+	pytest --cov --cov-report=html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
@@ -75,9 +71,8 @@ release: dist ## package and upload a release
 	twine upload dist/*
 
 dist: clean ## builds source and wheel package
-	$(python) setup.py sdist $(build_opts)
-	$(python) setup.py bdist_wheel $(build_opts)
+	$(python) build
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	$(python) setup.py install $(build_opts)
+	pip install .

From 0d0536072d7dee16674418867eedf898d5e99572 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Tue, 2 Jul 2024 09:44:38 -0400
Subject: [PATCH 36/44] Docs update

---
 .readthedocs.yaml | 2 +-
 docs/nersc.rst    | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 87eebf0..3e0822d 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -7,7 +7,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.7"
+    python: "3.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
diff --git a/docs/nersc.rst b/docs/nersc.rst
index e90dc47..5205ee3 100644
--- a/docs/nersc.rst
+++ b/docs/nersc.rst
@@ -2,6 +2,9 @@
 NERSC Installation
 ==================
 
+NOTE: This documentation is severely out of date. Pixell requires python 3.9.
+If you are using pixell on NERSC for SO, you should use one of the pre-prepared envs.
+
 If you have not set a Python environment already, we recommend using this module:
 
 .. code:: shell

From 08aa7b330ad31ea5925da8f52f277fd148e8a4bf Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 10:11:56 -0400
Subject: [PATCH 37/44] Don't build i686 wheelsrem

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 32dd1c4..2b19543 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,6 +72,7 @@ testpaths = [
 test-requires = "pytest"
 test-command = "pytest {project}/tests"
 build = "cp39-* cp310-* cp311-* cp312-*"
+skip = "*i686*"
 
 [tool.coverage.run]
 source = [

From 7c75b0c8f5a9a93f68f8f9d0c3c0d03e63c58fec Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 10:12:01 -0400
Subject: [PATCH 38/44] Remove NERSC section

---
 README.rst     |  2 --
 docs/nersc.rst | 54 --------------------------------------------------
 2 files changed, 56 deletions(-)
 delete mode 100644 docs/nersc.rst

diff --git a/README.rst b/README.rst
index 6c7e5c8..1e9edc6 100644
--- a/README.rst
+++ b/README.rst
@@ -78,8 +78,6 @@ If you require more control over your installation, e.g. using Intel compilers,
 Compiling from source (advanced / development workflow)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-For compilation instructions specific to NERSC/cori, see NERSC_.
-
 The easiest way to install from source is to use the ``pip`` tool,
 with the ``--no-binary`` flag. This will download the source distribution
 and compile it for you. Don't forget to make sure you have CC and FC set
diff --git a/docs/nersc.rst b/docs/nersc.rst
deleted file mode 100644
index 5205ee3..0000000
--- a/docs/nersc.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-==================
-NERSC Installation
-==================
-
-NOTE: This documentation is severely out of date. Pixell requires python 3.9.
-If you are using pixell on NERSC for SO, you should use one of the pre-prepared envs.
-
-If you have not set a Python environment already, we recommend using this module:
-
-.. code:: shell
-
-    module load python/3.7-anaconda-2019.07
-
-You can put this line in your .bashrc.ext in order to load it automatically when
-logging in.
-
-Then, clone pixell and install as follows,
-
-.. code:: shell
-
-    git clone https://github.com/simonsobs/pixell.git
-    cd pixell
-    python setup.py build_ext -i --fcompiler=intelem --compiler=intelem
-
-Make sure to test the installation
-
-.. code:: shell
-		  
-    py.test
-
-which should display no errors.
-
-
-and then finally symbolically link pixell into your Python path
-
-.. code:: shell
-
-    pip install -e . --user
-
-
-To update your installation,
-
-
-.. code:: shell
-
-    git pull origin master
-    python setup.py build_ext -i --fcompiler=intelem --compiler=intelem
-    py.test
-    pip install -e . --user
-
-	
-Note that all of this assumes you will be using the default Intel suite on
-NERSC. If for some reason you have set up your environment to use GNU, then you
-should not include `--fcompiler=intelem --compiler=intelem` in any of the above.

From b5e7f8c01335da65c4003128cf03a00cc44e6fbc Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 10:48:33 -0400
Subject: [PATCH 39/44] Fix numpy 2.0 errors

---
 pixell/enmap.py      | 5 ++++-
 pixell/enplot.py     | 8 ++++++++
 pixell/tilemap.py    | 5 ++++-
 tests/test_pixell.py | 4 ----
 4 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/pixell/enmap.py b/pixell/enmap.py
index 76c8306..837bff9 100644
--- a/pixell/enmap.py
+++ b/pixell/enmap.py
@@ -48,7 +48,10 @@ def __array_finalize__(self, obj):
 	def __repr__(self):
 		return "ndmap(%s,%s)" % (np.asarray(self), wcsutils.describe(self.wcs))
 	def __str__(self): return repr(self)
-	def __array_wrap__(self, arr, context=None):
+	def __array_wrap__(self, arr, context=None, return_scalar=False):
+		# In the future need to support `return_scalar`, but that is seemingly
+		# undocumented and not actually supported in numpy 2.0? So for now we
+		# just ignore it.
 		if arr.ndim < 2: return arr
 		return ndmap(arr, self.wcs)
 	def __reduce__(self):
diff --git a/pixell/enplot.py b/pixell/enplot.py
index 11a4b76..f1d5bae 100644
--- a/pixell/enplot.py
+++ b/pixell/enplot.py
@@ -542,6 +542,14 @@ def draw_colorbar(crange, width, args):
 	fmt  = "%g"
 	labels, boxes = [], []
 	for val in crange:
+		# Val could be a one-element array. In NumPy 1.25 this is not
+		# acceptable to string formatters.
+
+		try:
+			val = val[0]
+		except (TypeError, IndexError):
+			pass
+		
 		labels.append(fmt % val)
 		boxes.append(font.getbbox(labels[-1])[-2:])
 	boxes = np.array(boxes,int)
diff --git a/pixell/tilemap.py b/pixell/tilemap.py
index cab0054..22766ce 100644
--- a/pixell/tilemap.py
+++ b/pixell/tilemap.py
@@ -71,7 +71,10 @@ def __array_finalize__(self, obj):
 	def __repr__(self):
 		return "TileMap(%s,%s)" % (np.asarray(self), str(self.geometry))
 	def __str__(self): return repr(self)
-	def __array_wrap__(self, arr, context=None):
+	def __array_wrap__(self, arr, context=None, return_scalar=False):
+		# In the future need to support `return_scalar`, but that is seemingly
+		# undocumented and not actually supported in numpy 2.0? So for now we
+		# just ignore it.
 		return TileMap(arr, self.geometry)
 	def __getitem__(self, sel):
 		# Split sel into normal and wcs parts.
diff --git a/tests/test_pixell.py b/tests/test_pixell.py
index a21caf0..f55aa34 100644
--- a/tests/test_pixell.py
+++ b/tests/test_pixell.py
@@ -1121,7 +1121,3 @@ def test_tilemap(self):
         assert m1c.geometry.nactive == 2
         assert np.allclose(m1c, 1)
 
-
-if __name__ == '__main__':
-    unittest.main()
-    test_sim_slice()

From 778a8fc181819b26a6632f4b3e1feab1a75755ae Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 10:51:50 -0400
Subject: [PATCH 40/44] Don't build musllinux wheels

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b19543..496d5f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,7 +72,7 @@ testpaths = [
 test-requires = "pytest"
 test-command = "pytest {project}/tests"
 build = "cp39-* cp310-* cp311-* cp312-*"
-skip = "*i686*"
+skip = "*i686* *musllinux*"
 
 [tool.coverage.run]
 source = [

From 8298c05d50704259ba73ef052319d9ee8d4665a6 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 11:40:09 -0400
Subject: [PATCH 41/44] Add editable install info

---
 README.rst | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/README.rst b/README.rst
index 1e9edc6..2636f12 100644
--- a/README.rst
+++ b/README.rst
@@ -96,6 +96,14 @@ directory. We use the ``meson`` build system, which should be understood by
 We suggest you then test the installation by running the unit tests. You
 can do this by running ``pytest``.
 
+To run an editable install, you will need to do so in a way that does not
+have build isolation (as the backend build system, `meson` and `ninja`, actually
+perform micro-builds on usage in this case):
+
+.. code-block:: console
+   
+   $ pip install --editable --no-build-isolation .
+
 
 Contributions
 -------------

From 760b21b48dd39663c02bbed3f02e82b93f415273 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 12:15:10 -0400
Subject: [PATCH 42/44] Swap order of editable args

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 2636f12..5ac232b 100644
--- a/README.rst
+++ b/README.rst
@@ -102,7 +102,7 @@ perform micro-builds on usage in this case):
 
 .. code-block:: console
    
-   $ pip install --editable --no-build-isolation .
+   $ pip install  --no-build-isolation --editable.
 
 
 Contributions

From d4eddf61da42ce592346e6d4c89571082c0fe286 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 12:15:19 -0400
Subject: [PATCH 43/44] Add space in editable install

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 5ac232b..66e3d32 100644
--- a/README.rst
+++ b/README.rst
@@ -102,7 +102,7 @@ perform micro-builds on usage in this case):
 
 .. code-block:: console
    
-   $ pip install  --no-build-isolation --editable.
+   $ pip install  --no-build-isolation --editable .
 
 
 Contributions

From 6972ee7e530dafb025c1a2be53c51c265189b743 Mon Sep 17 00:00:00 2001
From: Josh Borrow <josh@joshborrow.com>
Date: Wed, 3 Jul 2024 12:28:15 -0400
Subject: [PATCH 44/44] Add note that you need to include build dependencies
 before no build isolation

---
 README.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.rst b/README.rst
index 66e3d32..0f76952 100644
--- a/README.rst
+++ b/README.rst
@@ -102,6 +102,7 @@ perform micro-builds on usage in this case):
 
 .. code-block:: console
    
+   $ pip install --upgrade pip meson ninja meson-python cython numpy
    $ pip install  --no-build-isolation --editable .