add python 3.12 to the build and drop python 3.8 (gwastro#4716)

* drop python3.7, 3.8, 3.9 * add missing quotes * banish distutils * banish p39 in more places * tox needs some things early * move here * maybe? * try el9 * must use 311 for el9 * this might be the right name * updates * try this * more stuff * update * do not use imp module * more places where imp was used * bring back 39 * more reverts * update * update * fixes * this should be here * cc * fix web url * add back 3.9 to basic tests * centralize python12 backwards compatibility function * cc * simplify setup.py, ensure math is linked * cc
prayush · Nov 21, 2024 · 6bdd31d · 6bdd31d
1 parent 758afae
commit 6bdd31d
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Showing 17 changed files with 62 additions and 113 deletions.
diff --git a/.github/workflows/basic-tests.yml b/.github/workflows/basic-tests.yml
@@ -13,7 +13,7 @@ jobs:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         test-type: [unittest, search, docs]
     steps:
     - uses: actions/checkout@v3

diff --git a/.github/workflows/distribution.yml b/.github/workflows/distribution.yml
@@ -20,13 +20,13 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
+          CIBW_BUILD: cp39-* cp310-* cp311-* cp312-*
           CIBW_SKIP: "*musllinux*"
           CIBW_ARCHS_MACOS: x86_64 arm64
       - uses: actions/upload-artifact@v2
@@ -40,10 +40,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - uses: actions/download-artifact@v2
       with:
         path: ./

diff --git a/.github/workflows/inference-workflow.yml b/.github/workflows/inference-workflow.yml
@@ -10,7 +10,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

diff --git a/.github/workflows/mac-test.yml b/.github/workflows/mac-test.yml
@@ -13,7 +13,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [macos-12]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -25,5 +25,4 @@ jobs:
         pip install --upgrade pip setuptools "tox<4.0.0"
     - name: run basic pycbc test suite
       run: |
-        sudo chmod -R 777 /usr/local/miniconda/
         tox -e py-unittest
diff --git a/.github/workflows/search-workflow.yml b/.github/workflows/search-workflow.yml
@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

diff --git a/.github/workflows/tmpltbank-workflow.yml b/.github/workflows/tmpltbank-workflow.yml
@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

diff --git a/.github/workflows/tut-test.yml b/.github/workflows/tut-test.yml
@@ -13,7 +13,7 @@ jobs:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/workflow-tests.yml b/.github/workflows/workflow-tests.yml
@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

diff --git a/bin/all_sky_search/pycbc_cut_merge_triggers_to_tmpltbank b/bin/all_sky_search/pycbc_cut_merge_triggers_to_tmpltbank
@@ -21,12 +21,12 @@ Reduce a MERGE triggers file to a reduced template bank
 """
 
 import logging
-import imp
 import argparse
 import numpy
 import h5py
 import pycbc
 from pycbc.io import HFile
+from pycbc import load_source
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
@@ -50,7 +50,7 @@ pycbc.init_logging(opt.verbose)
 
 bank_fd = HFile(opt.full_template_bank, 'r')
 
-modl = imp.load_source('filter_func', opt.filter_func_file)
+modl = load_source('filter_func', opt.filter_func_file)
 func = modl.filter_tmpltbank
 bool_arr = func(bank_fd)
 

diff --git a/bin/all_sky_search/pycbc_reduce_template_bank b/bin/all_sky_search/pycbc_reduce_template_bank
@@ -23,10 +23,10 @@ Reduce a template bank using some input parameter cuts
 
 import numpy
 import logging
-import imp
 import argparse
 import pycbc
 from pycbc.io import HFile
+from pycbc import load_source
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
@@ -48,7 +48,7 @@ pycbc.init_logging(opt.verbose)
 
 bank_fd = HFile(opt.input_bank, 'r')
 
-modl = imp.load_source('filter_func', opt.filter_func_file)
+modl = load_source('filter_func', opt.filter_func_file)
 func = modl.filter_tmpltbank
 bool_arr = func(bank_fd)
 

diff --git a/bin/pycbc_banksim_match_combine b/bin/pycbc_banksim_match_combine
@@ -22,7 +22,6 @@ a set of injection files. The *order* of the injection files *must* match the
 bank files, and the number of injections in each must correspond one-to-one.
 """
 
-import imp
 import argparse
 import numpy as np
 
@@ -33,7 +32,7 @@ from pycbc import pnutils
 from pycbc.waveform import TemplateBank
 from pycbc.io.ligolw import LIGOLWContentHandler
 from pycbc.io.hdf import HFile
-
+from pycbc import load_source
 
 __author__  = "Ian Harry <[email protected]>"
 __version__ = pycbc.version.git_verbose_msg
@@ -137,7 +136,7 @@ for val in trig_par_list:
     f['trig_params/{}'.format(val)] = trig_params[val]
 
 if options.filter_func_file:
-    modl = imp.load_source('filter_func', options.filter_func_file)
+    modl = load_source('filter_func', options.filter_func_file)
     func = modl.filter_injections
     bool_arr = func(inj_params['mass1'], inj_params['mass2'],
                     inj_params['spin1z'], inj_params['spin2z'])

diff --git a/pycbc/__init__.py b/pycbc/__init__.py
@@ -32,6 +32,8 @@
 import logging
 import random
 import string
+import importlib.util
+import importlib.machinery
 from datetime import datetime as dt
 
 try:
@@ -227,3 +229,16 @@ def gps_now():
     from astropy.time import Time
 
     return float(Time.now().gps)
+
+# This is needed as a backwards compatibility. The function was removed in
+# python 3.12.
+def load_source(modname, filename):
+    loader = importlib.machinery.SourceFileLoader(modname, filename)
+    spec = importlib.util.spec_from_file_location(modname, filename,
+                                                  loader=loader)
+    module = importlib.util.module_from_spec(spec)
+    # The module is always executed and not cached in sys.modules.
+    # Uncomment the following line to cache the module.
+    # sys.modules[module.__name__] = module
+    loader.exec_module(module)
+    return module
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,16 +1,6 @@
 [build-system]
 requires = ["setuptools",
             "wheel",
-            "cython>=3.0.0",
-            "numpy==1.16.0; python_version <= '3.7'",
-            "numpy==1.17.3; python_version == '3.8'",
-            "numpy==1.19.3; python_version == '3.9'",
-            "numpy==1.21.4; python_version =='3.10'",
-            "numpy==1.23.4; python_version=='3.11'",
-            "numpy; python_version >= '3.12'",
+            "cython>=0.29.21",
+            "numpy>=2.0.0",
             ]
-
-# To ensure the best compatibility, try to match the numpy reqs
-# where possible to the following used by scipy and the minimum
-# of our normal numpy requirements in setup.py
-# https://github.com/scipy/oldest-supported-numpy/blob/master/setup.cfg
diff --git a/requirements-igwn.txt b/requirements-igwn.txt
@@ -1,4 +1,5 @@
 # For LDG service access
+ligo-proxy-utils
 ciecplib[kerberos] >= 0.7.0
 dqsegdb2 >= 1.1.4
 amqplib

diff --git a/setup.py b/setup.py
@@ -20,11 +20,9 @@
 """
 
 import sys
-import os, subprocess, shutil
+import os, subprocess
 import platform
 
-from distutils.command.clean import clean as _clean
-
 from setuptools import Extension, setup, Command
 from setuptools.command.build_ext import build_ext as _build_ext
 from setuptools import find_packages
@@ -83,27 +81,6 @@ def run(self):
 
         _build_ext.run(self)
 
-
-# Add swig-generated files to the list of things to clean, so they
-# get regenerated each time.
-class clean(_clean):
-    def finalize_options (self):
-        _clean.finalize_options(self)
-        self.clean_files = []
-        self.clean_folders = ['docs/_build']
-    def run(self):
-        _clean.run(self)
-        for f in self.clean_files:
-            try:
-                os.unlink(f)
-                print('removed ' + f)
-            except:
-                pass
-
-        for fol in self.clean_folders:
-            shutil.rmtree(fol, ignore_errors=True)
-            print('removed ' + fol)
-
 def get_version_info():
     """Get VCS info and write version info to version.py.
     """
@@ -192,7 +169,6 @@ def run(self):
 cmdclass = {
     'build_docs': build_docs,
     'build_gh_pages': build_gh_pages,
-    'clean': clean,
     'build_ext': cbuild_ext
 }
 
@@ -209,12 +185,21 @@ def run(self):
 # do the actual work of building the package
 VERSION = get_version_info()
 
-cythonext = ['waveform.spa_tmplt',
-             'waveform.utils',
-             'types.array',
-             'filter.matchedfilter',
-             'vetoes.chisq']
+cythonext = ['pycbc.waveform.spa_tmplt_cpu',
+             'pycbc.waveform.utils_cpu',
+             'pycbc.types.array_cpu',
+             'pycbc.filter.matchedfilter_cpu',
+             'pycbc.vetoes.chisq_cpu',
+             "pycbc.fft.fftw_pruned_cython",
+             "pycbc.events.eventmgr_cython",
+             "pycbc.events.simd_threshold_cython",
+             "pycbc.filter.simd_correlate_cython",
+             "pycbc.waveform.decompress_cpu_cython",
+             "pycbc.inference.models.relbin_cpu",
+             ]
 ext = []
+
+libraries = ['m']  # Some platforms / toolchains don't implicitly link this
 cython_compile_args = ['-O3', '-w', '-ffast-math',
                        '-ffinite-math-only']
 
@@ -233,57 +218,18 @@ def run(self):
     cython_compile_args += ["-stdlib=libc++"]
     cython_link_args += ["-stdlib=libc++"]
 
+
 for name in cythonext:
-    e = Extension("pycbc.%s_cpu" % name,
-                  ["pycbc/%s_cpu.pyx" % name.replace('.', '/')],
+    fname = name.replace('.', '/')
+    e = Extension(name,
+                  [f"{fname}.pyx"],
+                  language='c++',
                   extra_compile_args=cython_compile_args,
                   extra_link_args=cython_link_args,
+                  libraries=libraries,
                   compiler_directives={'embedsignature': True})
     ext.append(e)
 
-# Not all modules work like this:
-e = Extension("pycbc.fft.fftw_pruned_cython",
-              ["pycbc/fft/fftw_pruned_cython.pyx"],
-              extra_compile_args=cython_compile_args,
-              extra_link_args=cython_link_args,
-              compiler_directives={'embedsignature': True})
-ext.append(e)
-e = Extension("pycbc.events.eventmgr_cython",
-              ["pycbc/events/eventmgr_cython.pyx"],
-              extra_compile_args=cython_compile_args,
-              extra_link_args=cython_link_args,
-              compiler_directives={'embedsignature': True})
-ext.append(e)
-e = Extension("pycbc.events.simd_threshold_cython",
-              ["pycbc/events/simd_threshold_cython.pyx"],
-              language='c++',
-              extra_compile_args=cython_compile_args,
-              extra_link_args=cython_link_args,
-              compiler_directives={'embedsignature': True})
-ext.append(e)
-e = Extension("pycbc.filter.simd_correlate_cython",
-              ["pycbc/filter/simd_correlate_cython.pyx"],
-              language='c++',
-              extra_compile_args=cython_compile_args,
-              extra_link_args=cython_link_args,
-              compiler_directives={'embedsignature': True})
-ext.append(e)
-e = Extension("pycbc.waveform.decompress_cpu_cython",
-              ["pycbc/waveform/decompress_cpu_cython.pyx"],
-              language='c++',
-              extra_compile_args=cython_compile_args,
-              extra_link_args=cython_link_args,
-              compiler_directives={'embedsignature': True})
-ext.append(e)
-e = Extension("pycbc.inference.models.relbin_cpu",
-              ["pycbc/inference/models/relbin_cpu.pyx"],
-              language='c++',
-              extra_compile_args=cython_compile_args,
-              extra_link_args=cython_link_args,
-              compiler_directives={'embedsignature': True})
-ext.append(e)
-
-
 setup(
     name = 'PyCBC',
     version = VERSION,
@@ -292,7 +238,7 @@ def run(self):
     long_description_content_type='text/markdown',
     author = 'The PyCBC team',
     author_email = '[email protected]',
-    url = 'http://www.pycbc.org/',
+    url = 'http://pycbc.org/',
     download_url = f'https://github.com/gwastro/pycbc/tarball/v{VERSION}',
     keywords = [
         'ligo',
@@ -313,14 +259,13 @@ def run(self):
         'pycbc.neutron_stars': find_files('pycbc/neutron_stars')
     },
     ext_modules = ext,
-    python_requires='>=3.7',
+    python_requires='>=3.9',
     classifiers=[
         'Programming Language :: Python',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
         'Intended Audience :: Science/Research',
         'Natural Language :: English',
         'Topic :: Scientific/Engineering',

diff --git a/tools/docker_build_dist.sh b/tools/docker_build_dist.sh
@@ -43,7 +43,6 @@ if [ "x${PYCBC_CONTAINER}" == "xpycbc_rhel_virtualenv" ]; then
   yum clean all
   yum makecache
   yum -y install openssl-devel
-  yum -y install ligo-proxy-utils
   yum -y install python3-virtualenv
   yum -y install hdf5-static libxml2-static zlib-static libstdc++-static cfitsio-static glibc-static swig fftw-static gsl-static --skip-broken