From be20c8fab041ac24c8e70b85a361ca33405dde15 Mon Sep 17 00:00:00 2001 From: Talon Chandler Date: Mon, 27 May 2024 19:37:06 -0400 Subject: [PATCH 1/2] Authorship and release updates (#165) * author and release updates * nits --------- Co-authored-by: Shalin Mehta <2934183+mattersoflight@users.noreply.github.com> --- CITATION.cff | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index bbd684fe..dc624506 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,30 +4,32 @@ cff-version: 1.2.0 title: waveorder message: >- - A generalist library of wave optical models and inverse - algorithms for label-free imaging of density & - orientation. + Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation. type: software authors: - - given-names: Li-Hao - family-names: Yeh - affiliation: CZ Biohub - orcid: 'https://orcid.org/0000-0003-2803-5996' - given-names: Talon family-names: Chandler - affiliation: CZ Biohub + affiliation: Chan Zuckerberg Biohub San Francisco orcid: 'https://orcid.org/0000-0002-3033-674X' + - given-names: Li-Hao + family-names: Yeh + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0003-2803-5996' - given-names: Ivan family-names: Ivanov - affiliation: CZ Biohub + affiliation: Chan Zuckerberg Biohub San Francisco orcid: 'https://orcid.org/0000-0002-4675-5287' - given-names: Cameron family-names: Foltz - affiliation: CZ Biohub + affiliation: Chan Zuckerberg Biohub San Francisco orcid: 'https://orcid.org/0000-0001-8933-2172' + - given-names: Ziwen + family-names: Liu + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0001-7482-1299' - given-names: Shalin family-names: Mehta - affiliation: CZ Biohub + affiliation: Chan Zuckerberg Biohub San Francisco orcid: 'https://orcid.org/0000-0002-2542-3582' identifiers: - type: doi @@ -67,6 +69,7 @@ keywords: - qlipp - mipolscope - simulation + - reconstruction license: BSD-3-Clause -version: 1.0.0rc1 -date-released: '2023-02-22' +version: 2.1.0 +date-released: '2024-03-12' From c691f2f0411ead4c5e6f1ed3fa44831d8763c3a4 Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Thu, 13 Jun 2024 13:51:28 -0700 Subject: [PATCH 2/2] Bump Python (#168) * migrate to pyproject.toml * bump python * remove inaccurate topics from pyproject.toml * Revert "remove inaccurate topics from pyproject.toml" This reverts commit 46a5e72500501b9bff3b8d5fb1fe467d44b3bd44. * remove inaccurate topic metadata --- .github/workflows/pytests.yml | 2 +- README.md | 2 +- pyproject.toml | 59 ++++++++++++++++++++++++++++++++++- setup.cfg | 52 ------------------------------ setup.py | 3 -- 5 files changed, 60 insertions(+), 58 deletions(-) delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.github/workflows/pytests.yml b/.github/workflows/pytests.yml index deb6faa6..8028c79d 100644 --- a/.github/workflows/pytests.yml +++ b/.github/workflows/pytests.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.8', '3.9', '3.10'] + python-version: ['3.10', '3.11', '3.12'] steps: - name: Checkout repo diff --git a/README.md b/README.md index 5bbb9530..07674395 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ Please cite this repository, along with the relevant preprint or paper, if you u (Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment: ```sh -conda create -y -n waveorder python=3.9 +conda create -y -n waveorder python=3.11 conda activate waveorder ``` diff --git a/pyproject.toml b/pyproject.toml index 7caead92..1a57bb79 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,9 +5,66 @@ build-backend = "setuptools.build_meta" [tool.setuptools_scm] write_to = "waveorder/_version.py" +[project] +name = "waveorder" +description = "Wave-optical simulations and deconvolution of optical properties" +readme = "README.md" +requires-python = ">=3.10" +license = { file = "LICENSE" } +authors = [{ name = "CZ Biohub SF", email = "compmicro@czbiohub.org" }] +maintainers = [ + { name = "Talon Chandler", email = "talon.chandler@czbiohub.org" }, + { name = "Shalin Mehta", email = "shalin.mehta@czbiohub.org" }, +] +keywords = [ + "simulation", + 'optics', + 'phase', + 'scattering', + 'polarization', + 'label-free', + 'permittivity', + "reconstruction-algorithm", + 'qlipp', + 'mipolscope', + 'permittivity-tensor-imaging', +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Image Processing", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Operating System :: POSIX :: Linux", + "Operating System :: Microsoft :: Windows", + "Operating System :: MacOS", +] +dependencies = [ + "numpy>=1.21", + "matplotlib>=3.1.1", + "scipy>=1.3.0", + "pywavelets>=1.1.1", + "ipywidgets>=7.5.1", + "torch>=2.2.1", +] +dynamic = ["version"] + +[project.optional-dependencies] +dev = ["pytest", "pytest-cov"] + +[project.urls] +Homepage = "https://github.com/mehta-lab/waveorder" +Repository = "https://github.com/mehta-lab/waveorder" +Issues = "https://github.com/mehta-lab/waveorder/issues" + [tool.black] line-length = 79 [tool.isort] profile = "black" -line_length = 79 \ No newline at end of file +line_length = 79 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 8c6a13ef..00000000 --- a/setup.cfg +++ /dev/null @@ -1,52 +0,0 @@ -[metadata] -name = waveorder -author = Computational Microscopy Platform, CZ Biohub -author_email = shalin.mehta@czbiohub.org -url = https://github.com/mehta-lab/waveorder -license = BSD 3-Clause License -description = Wave optical simulations and deconvolution of optical properties -long_description = file: README.md -long_description_content_type = text/markdown -classifiers = - Development Status :: 4 - Beta - Intended Audience :: Science/Research - License :: OSI Approved :: BSD License - Programming Language :: Python :: 3 :: Only - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.9 - Programming Language :: Python :: 3.10 - Topic :: Scientific/Engineering - Topic :: Scientific/Engineering :: Image Processing - Topic :: Scientific/Engineering :: Visualization - Topic :: Scientific/Engineering :: Information Analysis - Topic :: Scientific/Engineering :: Bio-Informatics - Operating System :: Microsoft :: Windows - Operating System :: POSIX - Operating System :: Unix - Operating System :: MacOS -project_urls = - Bug Tracker = https://github.com/mehta-lab/waveorder/issues - Documentation = https://github.com/mehta-lab/waveorder - Source Code = https://github.com/mehta-lab/waveorder - User Support = https://github.com/mehta-lab/waveorder/issues - -[options] -package = find: -include_package_data = True -python_requires = >=3.8 -setup_requires = setuptools_scm -# add your package requirements here -install_requires = - numpy>=1.21 - matplotlib>=3.1.1 - scipy>=1.3.0 - pywavelets>=1.1.1 - ipywidgets>=7.5.1 - torch>=2.0.0 - -[options.extras_require] -dev = - flake8 - pytest>=5.0.0 - pytest-cov - \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index 60684932..00000000 --- a/setup.py +++ /dev/null @@ -1,3 +0,0 @@ -from setuptools import setup - -setup()