From 8768c83ed9bcbeac1f98927ad4aa2dad16828994 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Tue, 21 Nov 2023 13:42:50 +0100 Subject: [PATCH 01/31] added metadata to pyproject.toml --- pyproject.toml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..daac105f5 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,29 @@ +[project] +name = "elephant" +dynamic = ["version"] +description = "Elephant is a package for analysis of electrophysiology data in Python" +license = {file = "LICENSE.txt"} +classifiers = ["Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Natural Language :: English", "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3 :: Only", + "Topic :: Scientific/Engineering"] +authors = [{[name = "Elephant authors and contributors", email = "contact@python-elephant.org"]}] +readme = {file = "README.md", content-type = "text/markdown"} +requires-python = ">= 3.8" + +[project.urls] +Homepage = "http://python-elephant.org" +Documentation = "https://elephant.readthedocs.io/en/latest/" +Repository = "https://github.com/NeuralEnsemble/elephant" +Issues = "https://github.com/NeuralEnsemble/elephant/issues" +Changelog = "https://github.com/NeuralEnsemble/elephant/releases" + +# This file was created follwing this guide: +# https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml \ No newline at end of file From 80d8d8f1e3e72a26c8f98b598c9ab5650292dc04 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Tue, 21 Nov 2023 14:07:27 +0100 Subject: [PATCH 02/31] added dependencies --- pyproject.toml | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index daac105f5..d920f3925 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,9 +14,41 @@ classifiers = ["Development Status :: 5 - Production/Stable", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering"] -authors = [{[name = "Elephant authors and contributors", email = "contact@python-elephant.org"]}] +authors = [{name = "Elephant authors and contributors", email = "contact@python-elephant.org"}] readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" +dependencies = [ + "neo>=0.10.0", + "numpy>=1.19.5", + "quantities>=0.14.1", + "scipy>=1.5.4", + "six>=1.10.0", + "tqdm", + ] + +[project.optional-dependencies] +docs = ["numpydoc>=1.1.0", + "jupyter>=1.0.0", + "sphinx>=3.3.0", + "nbsphinx>=0.8.0", + "sphinxcontrib-bibtex>1.0.0", + "sphinx-tabs>=1.3.0", + "matplotlib>=3.3.2", + ] +extras = ["scikit-learn>=0.23.2", + "statsmodels>=0.12.1", + "jinja2>=2.11.2", + ] +opencl = ["pyopencl>=2020.2.2"] +cuda = ["pycuda>=2020.1"] +tests = ["pytest", + "nixio>=1.5.0", + ] +tutorials = ["matplotlib>=3.3.2", + "h5py>=3.1.0", + "nixio>=1.5.0", + ] + [project.urls] Homepage = "http://python-elephant.org" From 3ea8531233cfbdb08987ddf4ebc66ad9824a7627 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Tue, 21 Nov 2023 14:11:46 +0100 Subject: [PATCH 03/31] added build-system --- pyproject.toml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d920f3925..bfab98903 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,7 @@ +[build-system] +requires = ["setuptools >= 61.0"] +build-backend = "setuptools.build_meta" + [project] name = "elephant" dynamic = ["version"] @@ -49,7 +53,6 @@ tutorials = ["matplotlib>=3.3.2", "nixio>=1.5.0", ] - [project.urls] Homepage = "http://python-elephant.org" Documentation = "https://elephant.readthedocs.io/en/latest/" From f9199d1a9b3ee37607c71b20f78f2c5746713c42 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Tue, 21 Nov 2023 14:50:18 +0100 Subject: [PATCH 04/31] fix formatting --- pyproject.toml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index bfab98903..4114874a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,8 +21,7 @@ classifiers = ["Development Status :: 5 - Production/Stable", authors = [{name = "Elephant authors and contributors", email = "contact@python-elephant.org"}] readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" -dependencies = [ - "neo>=0.10.0", +dependencies = ["neo>=0.10.0", "numpy>=1.19.5", "quantities>=0.14.1", "scipy>=1.5.4", @@ -60,5 +59,5 @@ Repository = "https://github.com/NeuralEnsemble/elephant" Issues = "https://github.com/NeuralEnsemble/elephant/issues" Changelog = "https://github.com/NeuralEnsemble/elephant/releases" -# This file was created follwing this guide: +# This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml \ No newline at end of file From 444a7c37d34ddab07732b6567316f7991712809e Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Tue, 21 Nov 2023 15:35:51 +0100 Subject: [PATCH 05/31] build fim module using setup.py --- pyproject.toml | 3 +++ setup.py | 50 +------------------------------------------------- 2 files changed, 4 insertions(+), 49 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4114874a6..7cd5aaa01 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -59,5 +59,8 @@ Repository = "https://github.com/NeuralEnsemble/elephant" Issues = "https://github.com/NeuralEnsemble/elephant/issues" Changelog = "https://github.com/NeuralEnsemble/elephant/releases" +[tool.setuptools.dynamic] +version = {file = "elephant/VERSION"} + # This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml \ No newline at end of file diff --git a/setup.py b/setup.py index a5abae0ed..f4e3a50fa 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,3 @@ -# -*- coding: utf-8 -*- -import os.path import platform import sys @@ -7,19 +5,6 @@ from setuptools.command.install import install from setuptools.command.develop import develop -with open(os.path.join(os.path.dirname(__file__), - "elephant", "VERSION")) as version_file: - version = version_file.read().strip() - -with open("README.md") as f: - long_description = f.read() -with open('requirements/requirements.txt') as fp: - install_requires = fp.read().splitlines() -extras_require = {} -for extra in ['extras', 'docs', 'tests', 'tutorials', 'cuda', 'opencl']: - with open('requirements/requirements-{0}.txt'.format(extra)) as fp: - extras_require[extra] = fp.read() - if platform.system() == "Windows": fim_module = Extension( name='elephant.spade_src.fim', @@ -62,40 +47,7 @@ optional=True ) -setup_kwargs = { - "name": "elephant", - "version": version, - "packages": ['elephant', 'elephant.test'], - "include_package_data": True, - "install_requires": install_requires, - "extras_require": extras_require, - "author": "Elephant authors and contributors", - "author_email": "contact@python-elephant.org", - "description": "Elephant is a package for analysis of electrophysiology data in Python", # noqa - "long_description": long_description, - "long_description_content_type": "text/markdown", - "license": "BSD", - "url": 'http://python-elephant.org', - "project_urls": { - "Bug Tracker": "https://github.com/NeuralEnsemble/elephant/issues", - "Documentation": "https://elephant.readthedocs.io/en/latest/", - "Source Code": "https://github.com/NeuralEnsemble/elephant", - }, - "python_requires": ">=3.8", - "classifiers": [ - 'Development Status :: 5 - Production/Stable', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Natural Language :: English', - 'Operating System :: OS Independent', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Programming Language :: Python :: 3.10', - 'Programming Language :: Python :: 3.11', - 'Programming Language :: Python :: 3 :: Only', - 'Topic :: Scientific/Engineering'] -} +setup_kwargs = {} # no compile options and corresponding extensions options = {"--no-compile": None, "--no-compile-spade": fim_module} From 9952f5cbb9810f8030eb116d10d7c5a2e043f045 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 11:24:07 +0100 Subject: [PATCH 06/31] remove description from CITATION.txt, leave reference to docs --- CITATION.txt | 3 --- 1 file changed, 3 deletions(-) diff --git a/CITATION.txt b/CITATION.txt index c3423bb41..5a029b43b 100644 --- a/CITATION.txt +++ b/CITATION.txt @@ -1,4 +1 @@ -To refer to the Elephant software package in publications, please use - Elephant (RRID:SCR_003833) - To cite Elephant, please see doc/citation.rst. From 2053676c25fcb12fffaa835143623b93c9ae3bc8 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 11:24:27 +0100 Subject: [PATCH 07/31] fix formatting of pyproject.toml --- pyproject.toml | 83 ++++++++++++++++++++++++++------------------------ 1 file changed, 44 insertions(+), 39 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7cd5aaa01..88a3c39ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,50 +7,55 @@ name = "elephant" dynamic = ["version"] description = "Elephant is a package for analysis of electrophysiology data in Python" license = {file = "LICENSE.txt"} -classifiers = ["Development Status :: 5 - Production/Stable", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: BSD License", - "Natural Language :: English", "Operating System :: OS Independent", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3 :: Only", - "Topic :: Scientific/Engineering"] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Natural Language :: English", "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3 :: Only", + "Topic :: Scientific/Engineering"] authors = [{name = "Elephant authors and contributors", email = "contact@python-elephant.org"}] readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" -dependencies = ["neo>=0.10.0", - "numpy>=1.19.5", - "quantities>=0.14.1", - "scipy>=1.5.4", - "six>=1.10.0", - "tqdm", - ] +dependencies = [ + "neo>=0.10.0", + "numpy>=1.19.5", + "quantities>=0.14.1", + "scipy>=1.5.4", + "six>=1.10.0", + "tqdm"] [project.optional-dependencies] -docs = ["numpydoc>=1.1.0", - "jupyter>=1.0.0", - "sphinx>=3.3.0", - "nbsphinx>=0.8.0", - "sphinxcontrib-bibtex>1.0.0", - "sphinx-tabs>=1.3.0", - "matplotlib>=3.3.2", - ] -extras = ["scikit-learn>=0.23.2", - "statsmodels>=0.12.1", - "jinja2>=2.11.2", - ] -opencl = ["pyopencl>=2020.2.2"] -cuda = ["pycuda>=2020.1"] -tests = ["pytest", - "nixio>=1.5.0", - ] -tutorials = ["matplotlib>=3.3.2", - "h5py>=3.1.0", - "nixio>=1.5.0", - ] +docs = [ + "numpydoc>=1.1.0", + "jupyter>=1.0.0", + "sphinx>=3.3.0", + "nbsphinx>=0.8.0", + "sphinxcontrib-bibtex>1.0.0", + "sphinx-tabs>=1.3.0", + "matplotlib>=3.3.2"] + +extras = [ + "scikit-learn>=0.23.2", + "statsmodels>=0.12.1", + "jinja2>=2.11.2"] + +opencl = [ + "pyopencl>=2020.2.2"] +cuda = [ + "pycuda>=2020.1"] +tests = [ + "pytest", + "nixio>=1.5.0"] +tutorials = [ + "matplotlib>=3.3.2", + "h5py>=3.1.0", + "nixio>=1.5.0"] [project.urls] Homepage = "http://python-elephant.org" From 51fe31e3144062edd72a822787013347fb1a87a6 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 11:48:12 +0100 Subject: [PATCH 08/31] use requirement files for dependencies --- pyproject.toml | 46 +++++++++++++--------------------------------- 1 file changed, 13 insertions(+), 33 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 88a3c39ab..de8a54895 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,10 @@ build-backend = "setuptools.build_meta" [project] name = "elephant" -dynamic = ["version"] +dynamic = [ + "version", + "dependencies", + "optional-dependencies"] description = "Elephant is a package for analysis of electrophysiology data in Python" license = {file = "LICENSE.txt"} classifiers = [ @@ -22,40 +25,15 @@ classifiers = [ authors = [{name = "Elephant authors and contributors", email = "contact@python-elephant.org"}] readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" -dependencies = [ - "neo>=0.10.0", - "numpy>=1.19.5", - "quantities>=0.14.1", - "scipy>=1.5.4", - "six>=1.10.0", - "tqdm"] -[project.optional-dependencies] -docs = [ - "numpydoc>=1.1.0", - "jupyter>=1.0.0", - "sphinx>=3.3.0", - "nbsphinx>=0.8.0", - "sphinxcontrib-bibtex>1.0.0", - "sphinx-tabs>=1.3.0", - "matplotlib>=3.3.2"] +[tool.setuptools.dynamic.optional-dependencies] -extras = [ - "scikit-learn>=0.23.2", - "statsmodels>=0.12.1", - "jinja2>=2.11.2"] - -opencl = [ - "pyopencl>=2020.2.2"] -cuda = [ - "pycuda>=2020.1"] -tests = [ - "pytest", - "nixio>=1.5.0"] -tutorials = [ - "matplotlib>=3.3.2", - "h5py>=3.1.0", - "nixio>=1.5.0"] +docs = {file = ["requirements/requirements-docs.txt"]} +extras = {file = ["requirements/requirements-extras.txt"]} +opencl = {file = ["requirements/requirements-opencl.txt"]} +cuda = {file = ["requirements/requirements-cuda.txt"]} +tests = {file = ["requirements/requirements-tests.txt"]} +tutorials = {file = ["requirements/requirements-tutorials.txt"]} [project.urls] Homepage = "http://python-elephant.org" @@ -66,6 +44,8 @@ Changelog = "https://github.com/NeuralEnsemble/elephant/releases" [tool.setuptools.dynamic] version = {file = "elephant/VERSION"} +dependencies = {file = ["requirements/requirements.txt"]} + # This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml \ No newline at end of file From 60933ee61da9be013c0d68f789cd1df489fc74c0 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 12:16:03 +0100 Subject: [PATCH 09/31] add somesy config --- pyproject.toml | 62 ++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 45 insertions(+), 17 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index de8a54895..69205c7cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,29 +5,28 @@ build-backend = "setuptools.build_meta" [project] name = "elephant" dynamic = [ - "version", - "dependencies", - "optional-dependencies"] + "version", + "dependencies", + "optional-dependencies"] description = "Elephant is a package for analysis of electrophysiology data in Python" license = {file = "LICENSE.txt"} classifiers = [ - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: BSD License", - "Natural Language :: English", "Operating System :: OS Independent", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3 :: Only", - "Topic :: Scientific/Engineering"] + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Natural Language :: English", "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3 :: Only", + "Topic :: Scientific/Engineering"] authors = [{name = "Elephant authors and contributors", email = "contact@python-elephant.org"}] readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" [tool.setuptools.dynamic.optional-dependencies] - docs = {file = ["requirements/requirements-docs.txt"]} extras = {file = ["requirements/requirements-extras.txt"]} opencl = {file = ["requirements/requirements-opencl.txt"]} @@ -46,6 +45,35 @@ Changelog = "https://github.com/NeuralEnsemble/elephant/releases" version = {file = "elephant/VERSION"} dependencies = {file = ["requirements/requirements.txt"]} - # This file was created following this guide: -# https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml \ No newline at end of file +# https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml + +[tool.somesy.project] +name = "Elephant" +version = "1.0.0" +description = "Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as the local field potentials (LFP) or intracellular voltages.In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework that is built on a modular foundation. \nElephant is the direct successor to Neurotools and maintains ties to complementary projects such as OpenElectrophy and spykeviewer." +license = "BSD" +keywords = [ + "neuroscience", + "neurophysiology", + "electrophysiology", + "statistics", + "data-analysis"] + +[[tool.somesy.project.people]] +given-names = "Michael" +family-names = "Denker" +orcid = "https://orcid.org/0000-0003-1255-7300" +author = true # is a full author of the project (i.e. appears in citations) +maintainer = true # currently maintains the project (i.e. is a contact person) + + +[[tool.somesy.project.people]] +given-names = "Moritz" +family-names = "Kern" +orcid = "https://orcid.org/0000-0001-7292-1982" +author = true # is a full author of the project (i.e. appears in citations) +maintainer = true # currently maintains the project (i.e. is a contact person) + +[tool.somesy.config] +verbose = true # show detailed information about what somesy is doing \ No newline at end of file From 210a994c88023928a81c9db7396a07fc5eb57324 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 15:18:03 +0100 Subject: [PATCH 10/31] update somesy config --- pyproject.toml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 69205c7cf..ba4760d9b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,13 +3,13 @@ requires = ["setuptools >= 61.0"] build-backend = "setuptools.build_meta" [project] -name = "elephant" +name = "Elephant" dynamic = [ "version", "dependencies", "optional-dependencies"] -description = "Elephant is a package for analysis of electrophysiology data in Python" -license = {file = "LICENSE.txt"} +description = "Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as the local field potentials (LFP) or intracellular voltages.In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework that is built on a modular foundation. \nElephant is the direct successor to Neurotools and maintains ties to complementary projects such as OpenElectrophy and spykeviewer." +license = "BSD-3-Clause" classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", @@ -22,7 +22,7 @@ classifiers = [ "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering"] -authors = [{name = "Elephant authors and contributors", email = "contact@python-elephant.org"}] +keywords = ["neuroscience", "neurophysiology", "electrophysiology", "statistics", "data-analysis"] readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" @@ -52,7 +52,7 @@ dependencies = {file = ["requirements/requirements.txt"]} name = "Elephant" version = "1.0.0" description = "Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as the local field potentials (LFP) or intracellular voltages.In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework that is built on a modular foundation. \nElephant is the direct successor to Neurotools and maintains ties to complementary projects such as OpenElectrophy and spykeviewer." -license = "BSD" +license = "BSD-3-Clause" keywords = [ "neuroscience", "neurophysiology", @@ -64,16 +64,14 @@ keywords = [ given-names = "Michael" family-names = "Denker" orcid = "https://orcid.org/0000-0003-1255-7300" -author = true # is a full author of the project (i.e. appears in citations) -maintainer = true # currently maintains the project (i.e. is a contact person) + [[tool.somesy.project.people]] given-names = "Moritz" family-names = "Kern" orcid = "https://orcid.org/0000-0001-7292-1982" -author = true # is a full author of the project (i.e. appears in citations) -maintainer = true # currently maintains the project (i.e. is a contact person) + [tool.somesy.config] verbose = true # show detailed information about what somesy is doing \ No newline at end of file From c7bfe259c871810b8c0d5cc1b478c4fa606adc0e Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 15:20:16 +0100 Subject: [PATCH 11/31] remove somesy config --- pyproject.toml | 30 +----------------------------- 1 file changed, 1 insertion(+), 29 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ba4760d9b..ed23246b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ requires = ["setuptools >= 61.0"] build-backend = "setuptools.build_meta" [project] -name = "Elephant" +name = "elephant" dynamic = [ "version", "dependencies", @@ -47,31 +47,3 @@ dependencies = {file = ["requirements/requirements.txt"]} # This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml - -[tool.somesy.project] -name = "Elephant" -version = "1.0.0" -description = "Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as the local field potentials (LFP) or intracellular voltages.In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework that is built on a modular foundation. \nElephant is the direct successor to Neurotools and maintains ties to complementary projects such as OpenElectrophy and spykeviewer." -license = "BSD-3-Clause" -keywords = [ - "neuroscience", - "neurophysiology", - "electrophysiology", - "statistics", - "data-analysis"] - -[[tool.somesy.project.people]] -given-names = "Michael" -family-names = "Denker" -orcid = "https://orcid.org/0000-0003-1255-7300" - - - -[[tool.somesy.project.people]] -given-names = "Moritz" -family-names = "Kern" -orcid = "https://orcid.org/0000-0001-7292-1982" - - -[tool.somesy.config] -verbose = true # show detailed information about what somesy is doing \ No newline at end of file From b8a9f80b2b635c64594e0a463288ce9208d2be42 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 15:29:29 +0100 Subject: [PATCH 12/31] update license field --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ed23246b5..559309ec4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ dynamic = [ "dependencies", "optional-dependencies"] description = "Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as the local field potentials (LFP) or intracellular voltages.In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework that is built on a modular foundation. \nElephant is the direct successor to Neurotools and maintains ties to complementary projects such as OpenElectrophy and spykeviewer." -license = "BSD-3-Clause" +license = {file = "LICENSE.txt"} classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", From f60257aa50cb82b8b969d9e3b3c8b2de12ff178e Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 15:48:10 +0100 Subject: [PATCH 13/31] add wheel to build dependencies --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 559309ec4..7f858a96f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools >= 61.0"] +requires = ["setuptools >= 61.0", "wheel"] build-backend = "setuptools.build_meta" [project] From 0db66d482c10e072b0a949c12f0be0f98bec343b Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern Date: Wed, 22 Nov 2023 15:54:39 +0100 Subject: [PATCH 14/31] define packages for setuptools --- pyproject.toml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7f858a96f..b336a5cb2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,13 @@ keywords = ["neuroscience", "neurophysiology", "electrophysiology", "statistics" readme = {file = "README.md", content-type = "text/markdown"} requires-python = ">= 3.8" +[project.urls] +Homepage = "http://python-elephant.org" +Documentation = "https://elephant.readthedocs.io/en/latest/" +Repository = "https://github.com/NeuralEnsemble/elephant" +Issues = "https://github.com/NeuralEnsemble/elephant/issues" +Changelog = "https://github.com/NeuralEnsemble/elephant/releases" + [tool.setuptools.dynamic.optional-dependencies] docs = {file = ["requirements/requirements-docs.txt"]} extras = {file = ["requirements/requirements-extras.txt"]} @@ -34,16 +41,13 @@ cuda = {file = ["requirements/requirements-cuda.txt"]} tests = {file = ["requirements/requirements-tests.txt"]} tutorials = {file = ["requirements/requirements-tutorials.txt"]} -[project.urls] -Homepage = "http://python-elephant.org" -Documentation = "https://elephant.readthedocs.io/en/latest/" -Repository = "https://github.com/NeuralEnsemble/elephant" -Issues = "https://github.com/NeuralEnsemble/elephant/issues" -Changelog = "https://github.com/NeuralEnsemble/elephant/releases" - [tool.setuptools.dynamic] version = {file = "elephant/VERSION"} dependencies = {file = ["requirements/requirements.txt"]} +[tool.setuptools] +packages = ["elephant", "elephant.test"] + + # This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml From f89e1cf3d2bfd968f057ae976b18fdb944df7382 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 15:41:34 +0200 Subject: [PATCH 15/31] remove setup.py --- pyproject.toml | 4 +++- setup.py => setup_old.py | 0 2 files changed, 3 insertions(+), 1 deletion(-) rename setup.py => setup_old.py (100%) diff --git a/pyproject.toml b/pyproject.toml index b336a5cb2..e7fdbca51 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,9 @@ dependencies = {file = ["requirements/requirements.txt"]} [tool.setuptools] packages = ["elephant", "elephant.test"] - +ext-modules = [ + {name = "elephant.spade_src.fim", sources = ["elephant/spade_src/src/fim.cpp"],include-dirs=["elephant/spade_src/include"],language="c++", extra-compile-args=["-DMODULE_NAME=fim", "-DUSE_OPENMP", "-DWITH_SIG_TERM","-Dfim_EXPORTS", "-fopenmp", "/std:c++17"], optional=true} +] # This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml diff --git a/setup.py b/setup_old.py similarity index 100% rename from setup.py rename to setup_old.py From db354a216659d6cbf077eb2558e2f51924682684 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 15:50:49 +0200 Subject: [PATCH 16/31] update ci build wheel action --- .github/workflows/build_wheels.yml | 4 ++-- .gitignore | 4 +++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index b5dbea1f9..59fd62613 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -37,8 +37,8 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp*" - CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8" + CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* cp38-* pp*" + CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9" CIBW_ARCHS: "auto64" - uses: actions/upload-artifact@v3 diff --git a/.gitignore b/.gitignore index 6f6651146..f201f8a60 100644 --- a/.gitignore +++ b/.gitignore @@ -21,7 +21,9 @@ env/ .pytest_cache/ **/*/__pycache__ *.vscode - +.mypy_cache +.ruff_cache +.venv # Compiled source # ################### *.a From d47ba190f939d0de305ce4bad2418f17710b5318 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 15:53:02 +0200 Subject: [PATCH 17/31] update build wheel action --- .github/workflows/build_wheels.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 59fd62613..151fd066f 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -37,8 +37,8 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* cp38-* pp*" - CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9" + CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* cp38-* cp39-* pp*" + CIBW_PROJECT_REQUIRES_PYTHON: ">=3.10" CIBW_ARCHS: "auto64" - uses: actions/upload-artifact@v3 From beab2e4e4359b8038964d6d800eebc54a6179860 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 15:55:02 +0200 Subject: [PATCH 18/31] update ci build wheel action --- .github/workflows/build_wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 151fd066f..203699aa4 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -28,7 +28,7 @@ jobs: - name: Install cibuildwheel run: | python -m pip install --upgrade pip - python -m pip install cibuildwheel==2.16.2 + python -m pip install cibuildwheel - name: Install libomp if: runner.os == 'macOS' From b7e4fa097c9d921a3567d83d4cf9076153c06fb2 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 15:57:18 +0200 Subject: [PATCH 19/31] update cibuildwheel action --- .github/workflows/build_wheels.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 203699aa4..004c5c9dd 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -37,8 +37,8 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* cp38-* cp39-* pp*" - CIBW_PROJECT_REQUIRES_PYTHON: ">=3.10" + CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* cp38-* cp39-* cp310-* pp*" + CIBW_PROJECT_REQUIRES_PYTHON: ">=3.11" CIBW_ARCHS: "auto64" - uses: actions/upload-artifact@v3 From f6a043fb5e48f8b843006c3cfaf92231a670eaa2 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 15:58:36 +0200 Subject: [PATCH 20/31] update os for building wheels --- .github/workflows/build_wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 004c5c9dd..37e7d313c 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -15,7 +15,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-20.04, windows-2019] + os: [ubuntu-latest, windows-2019] steps: - uses: actions/checkout@v4 From 24e225a1cd2a455b328d31e7be70d5b6142efab2 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 16:15:26 +0200 Subject: [PATCH 21/31] change compile args for linux --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e7fdbca51..0b35ca909 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,9 +46,9 @@ version = {file = "elephant/VERSION"} dependencies = {file = ["requirements/requirements.txt"]} [tool.setuptools] -packages = ["elephant", "elephant.test"] +packages = ["elephant", "elephant.test", "elephant.spade_src.src"] ext-modules = [ - {name = "elephant.spade_src.fim", sources = ["elephant/spade_src/src/fim.cpp"],include-dirs=["elephant/spade_src/include"],language="c++", extra-compile-args=["-DMODULE_NAME=fim", "-DUSE_OPENMP", "-DWITH_SIG_TERM","-Dfim_EXPORTS", "-fopenmp", "/std:c++17"], optional=true} + {name = "elephant.spade_src.fim", sources = ["elephant/spade_src/src/fim.cpp"],include-dirs=["elephant/spade_src/include"],language="c++",libraries=["pthread", "gomp"], extra-compile-args=['-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM','-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra','-Weffc++', '-Wunused-result', '-Werror','-fopenmp', '-std=gnu++17']} ] # This file was created following this guide: From 158aa29889f7038443a5aa66f326dda059fc38d8 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 16:17:36 +0200 Subject: [PATCH 22/31] update python version for cibuildwheels --- .github/workflows/build_wheels.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 37e7d313c..60ca08edc 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -37,8 +37,8 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* cp38-* cp39-* cp310-* pp*" - CIBW_PROJECT_REQUIRES_PYTHON: ">=3.11" + CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp*" + CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8" CIBW_ARCHS: "auto64" - uses: actions/upload-artifact@v3 From 3533692bc02302731435869009230a531a8f0aaa Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 16:20:38 +0200 Subject: [PATCH 23/31] update ci buildwheel action --- .github/workflows/build_wheels.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 60ca08edc..d4a8127ac 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -15,7 +15,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-latest, windows-2019] + os: [ubuntu-22.04, windows-2019] steps: - uses: actions/checkout@v4 @@ -37,7 +37,7 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp*" + CIBW_SKIP: cp36-* cp37-* pp*" CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8" CIBW_ARCHS: "auto64" From d5b929f87689f651fef4ce26bba6c892467fe015 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 16:50:25 +0200 Subject: [PATCH 24/31] update compile args --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0b35ca909..ec53cfd0c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,9 +46,9 @@ version = {file = "elephant/VERSION"} dependencies = {file = ["requirements/requirements.txt"]} [tool.setuptools] -packages = ["elephant", "elephant.test", "elephant.spade_src.src"] +packages = ["elephant", "elephant.test"] ext-modules = [ - {name = "elephant.spade_src.fim", sources = ["elephant/spade_src/src/fim.cpp"],include-dirs=["elephant/spade_src/include"],language="c++",libraries=["pthread", "gomp"], extra-compile-args=['-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM','-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra','-Weffc++', '-Wunused-result', '-Werror','-fopenmp', '-std=gnu++17']} + {name = "elephant.spade_src.fim", sources = ["elephant/spade_src/src/fim.cpp"],include-dirs=["elephant/spade_src/include"],language="c++", extra-compile-args=['-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM','-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra','-Weffc++', '-Wunused-result', '-Werror','-fopenmp', '-std=gnu++17']} ] # This file was created following this guide: From 77069b8d2f21883e203cc8744dc7be05898f62ec Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 17:07:48 +0200 Subject: [PATCH 25/31] re add setup.py --- pyproject.toml | 3 --- setup_old.py => setup.py | 0 2 files changed, 3 deletions(-) rename setup_old.py => setup.py (100%) diff --git a/pyproject.toml b/pyproject.toml index ec53cfd0c..bfc880eda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,9 +47,6 @@ dependencies = {file = ["requirements/requirements.txt"]} [tool.setuptools] packages = ["elephant", "elephant.test"] -ext-modules = [ - {name = "elephant.spade_src.fim", sources = ["elephant/spade_src/src/fim.cpp"],include-dirs=["elephant/spade_src/include"],language="c++", extra-compile-args=['-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM','-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra','-Weffc++', '-Wunused-result', '-Werror','-fopenmp', '-std=gnu++17']} -] # This file was created following this guide: # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#writing-pyproject-toml diff --git a/setup_old.py b/setup.py similarity index 100% rename from setup_old.py rename to setup.py From 83de7f282a8a1366e4834a87b0cca9a9caa6ea70 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 17:09:39 +0200 Subject: [PATCH 26/31] update cibuildwheel version --- .github/workflows/build_wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index d4a8127ac..744eadb83 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -28,7 +28,7 @@ jobs: - name: Install cibuildwheel run: | python -m pip install --upgrade pip - python -m pip install cibuildwheel + python -m pip install cibuildwheel==2.20.0 - name: Install libomp if: runner.os == 'macOS' From c0b4899d072f647ec57f7ac559ab8c87b8f8f137 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 17:10:24 +0200 Subject: [PATCH 27/31] typo --- CITATION.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CITATION.txt b/CITATION.txt index 5a029b43b..3f12dc344 100644 --- a/CITATION.txt +++ b/CITATION.txt @@ -1 +1,4 @@ -To cite Elephant, please see doc/citation.rst. +To refer to the Elephant software package in publications, please use + Elephant (RRID:SCR_003833) + +To cite Elephant, please see doc/citation.rst. \ No newline at end of file From 571605d1644e1abf6e33e5074d1b25e710dcef87 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Wed, 4 Sep 2024 17:11:40 +0200 Subject: [PATCH 28/31] typo --- CITATION.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.txt b/CITATION.txt index 3f12dc344..c3423bb41 100644 --- a/CITATION.txt +++ b/CITATION.txt @@ -1,4 +1,4 @@ To refer to the Elephant software package in publications, please use Elephant (RRID:SCR_003833) -To cite Elephant, please see doc/citation.rst. \ No newline at end of file +To cite Elephant, please see doc/citation.rst. From 8140864da285074df3c8fa57549b1721fc5acdcc Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Mon, 16 Sep 2024 10:20:06 +0200 Subject: [PATCH 29/31] build wheels --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index f4e3a50fa..9fc62c74b 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ extra_compile_args=[ '-DMODULE_NAME=fim', '-DUSE_OPENMP', '-DWITH_SIG_TERM', '-Dfim_EXPORTS', '-fopenmp', '/std:c++17'], - optional=True + #optional=True ) elif platform.system() == "Darwin": fim_module = Extension( @@ -30,7 +30,7 @@ '-Weffc++', '-Wunused-result', '-Werror', '-Werror=return-type', '-Xpreprocessor', '-fopenmp', '-std=gnu++17'], - optional=True + #optional=True ) elif platform.system() == "Linux": fim_module = Extension( @@ -44,7 +44,7 @@ '-Dfim_EXPORTS', '-O3', '-pedantic', '-Wextra', '-Weffc++', '-Wunused-result', '-Werror', '-fopenmp', '-std=gnu++17'], - optional=True + #optional=True ) setup_kwargs = {} From eebdb06687b17f44d990bd16dfb35e61505273a6 Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Mon, 16 Sep 2024 10:24:40 +0200 Subject: [PATCH 30/31] update python version --- .github/workflows/build_wheels.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 744eadb83..1a28f2d2c 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -37,8 +37,8 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: cp36-* cp37-* pp*" - CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8" + CIBW_SKIP: cp36-* cp37-* cp38-* pp*" + CIBW_PROJECT_REQUIRES_PYTHON: ">3.8" CIBW_ARCHS: "auto64" - uses: actions/upload-artifact@v3 From 5c3fb6e2dcb898dadbf1f2b50e87812f6720e64c Mon Sep 17 00:00:00 2001 From: Moritz-Alexander-Kern <92092328+Moritz-Alexander-Kern@users.noreply.github.com> Date: Mon, 16 Sep 2024 10:30:36 +0200 Subject: [PATCH 31/31] update cibuildwheel --- .github/workflows/build_wheels.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 1a28f2d2c..deaead7cb 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -28,7 +28,7 @@ jobs: - name: Install cibuildwheel run: | python -m pip install --upgrade pip - python -m pip install cibuildwheel==2.20.0 + python -m pip install cibuildwheel==2.21.0 - name: Install libomp if: runner.os == 'macOS' @@ -37,8 +37,8 @@ jobs: - name: Build wheels run: python -m cibuildwheel --output-dir wheelhouse env: - CIBW_SKIP: cp36-* cp37-* cp38-* pp*" - CIBW_PROJECT_REQUIRES_PYTHON: ">3.8" + CIBW_SKIP: cp36-* cp37-* pp*" + CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8" CIBW_ARCHS: "auto64" - uses: actions/upload-artifact@v3