From a7e39b9d3c3c6a10eb65c578f5b8ed805c16ac74 Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Fri, 13 Dec 2024 13:07:51 +0100 Subject: [PATCH 01/10] allow python12 and higher PyQT versions --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 819fa459..0ddf6429 100755 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ URL = "https://gitlab.com/lanzara-group/python-arpes" EMAIL = "chstan@berkeley.edu" AUTHOR = "Conrad Stansbury" -REQUIRES_PYTHON = ">=3.8.0,<3.12" # we're being less permissive because of pyqtgraph +REQUIRES_PYTHON = ">=3.8.0,<3.13" # we're being less permissive because of pyqtgraph about = {} with open("./arpes/__init__.py") as fp: @@ -29,7 +29,7 @@ "xarray>=0.16.1", "h5py>=3.2.1", "pyqtgraph>=0.12.0,<0.13.0", - "PyQt5==5.15", + "PyQt5>5.15", "netCDF4>=1.5.0,<1.7.0", "colorcet", "pint", From 5130ed0187214f90f8566f4c799e363421587181 Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 00:46:35 +0100 Subject: [PATCH 02/10] add installation through pyproject.toml --- pyproject.toml | 90 +++++++++++++++++++++++- requirements.txt | 2 - setup.cfg | 5 -- setup.py | 178 ----------------------------------------------- 4 files changed, 89 insertions(+), 186 deletions(-) delete mode 100644 requirements.txt delete mode 100644 setup.cfg delete mode 100755 setup.py diff --git a/pyproject.toml b/pyproject.toml index a75e5ba0..3f4f67df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,92 @@ -[tool.black] +[build-system] +requires = ["setuptools >= 61.2"] + +[project] +name = "arpes" +dynamic = ["version"] +authors = [ + {name = "Conrad Stansbury", email = "chstan@berkeley.edu"}, +] +description = "Modular data analysis code for angle resolved photoemission spectroscopy (ARPES)" +readme = "README.rst" +license = { file = "LICENSE" } +requires-python = ">=3.8.0,<3.13" +classifiers = [ + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python", + "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 :: 3.12", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Physics", + "Topic :: Software Development :: Libraries :: Python Modules", +] +dependencies = [ + "PyQt5>5.15", + "ase>=3.17.0,<3.22.0", + "astropy", + "bokeh>=2.0.0,<3.0.0", + "colorama", + "colorcet", + "dill", + "h5py>=3.2.1", + "imageio", + "ipywidgets>8.0.0", + "lmfit>=1.0.0,<2.0.0", + "matplotlib>=3.0.3", + "netCDF4>=1.5.0,<1.7.0", + "numba>=0.53.0,<1.0.0", + "numpy>=1.20.0,<2.0.0", + "packaging", + "pandas", + "pint", + "pyqtgraph>=0.12.0,<0.13.0", + "rx", + "scipy>=1.6.0,<2.0.0", + "titlecase", + "tqdm", + "xarray>=0.16.1", +] + +[project.urls] +Homepage = "https://gitlab.com/lanzara-group/python-arpes" +[project.optional-dependencies] +igor = [ + "igor==0.3.1", +] +ml= [ + "scikit-learn>=0.24.0,<1.0.0", + "scikit-image", + "cvxpy", + "libgcc", +] +jupyter = [ + "jupyter", + "ipython", + "jupyter_contrib_nbextensions", + "notebook>=5.7.0", +] + +dev = [ + "markdown-include", + "attrs==17.4.0", + "pluggy==0.6.0", + "py==1.5.2", + "pytest==3.3.2", +] + +[tool.setuptools] +packages = ["arpes", "resources"] + +[tool.black] line-length = 100 [tool.pydocstyle] @@ -19,3 +106,4 @@ exclude_lines = [ "raise NotImplementedError", "pragma: no cover", ] + diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index e64fa34f..00000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -# Use dependencies from setup.py -. diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 4e666b49..00000000 --- a/setup.cfg +++ /dev/null @@ -1,5 +0,0 @@ -[bdist_wheel] -universal = 0 - -[aliases] -test = pytest diff --git a/setup.py b/setup.py deleted file mode 100755 index 0ddf6429..00000000 --- a/setup.py +++ /dev/null @@ -1,178 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -"""Specifies installation requirements and build steps.""" - -import io -import os - -from setuptools import find_packages, setup -from setuptools.command.install import install - -NAME = "arpes" -DESCRIPTION = ( - "Modular data analysis code for angle resolved photoemission spectroscopy (ARPES)" -) -URL = "https://gitlab.com/lanzara-group/python-arpes" -EMAIL = "chstan@berkeley.edu" -AUTHOR = "Conrad Stansbury" -REQUIRES_PYTHON = ">=3.8.0,<3.13" # we're being less permissive because of pyqtgraph - -about = {} -with open("./arpes/__init__.py") as fp: - exec(fp.read(), about) - -VERSION = about["VERSION"] - -DEPENDENCY_GROUPS = { - "core": [ - "astropy", - "xarray>=0.16.1", - "h5py>=3.2.1", - "pyqtgraph>=0.12.0,<0.13.0", - "PyQt5>5.15", - "netCDF4>=1.5.0,<1.7.0", - "colorcet", - "pint", - "pandas", - "numpy>=1.20.0,<2.0.0", - "scipy>=1.6.0,<2.0.0", - "lmfit>=1.0.0,<2.0.0", - "scikit-learn", - # plotting - "matplotlib>=3.0.3", - "bokeh>=2.0.0,<3.0.0", - "ipywidgets>=7.0.1,<8.0.0", - # Misc deps - "packaging", - "colorama", - "imageio", - "titlecase", - "tqdm", - "rx", - "dill", - "ase>=3.17.0,<3.22.0", - "numba>=0.53.0,<1.0.0", - ], - "igor": ["igor==0.3.1"], - "ml": [ - "scikit-learn>=0.24.0,<1.0.0", - "scikit-image", - "cvxpy", - "libgcc", - ], -} - -requirements = [ - y for k, v in DEPENDENCY_GROUPS.items() for y in v if k not in {"igor", "ml"} -] - -DEV_DEPENDENCIES = { - "jupyter": [ - "jupyter", - "ipython", - "jupyter_contrib_nbextensions", - "notebook>=5.7.0", - ], - "test": [ - "attrs==17.4.0", - "pluggy==0.6.0", - "py==1.5.2", - "pytest==3.3.2", - "setuptools==38.4.0", - ], -} - - -with open("./pypi-readme.rst", "r") as f_readme: - long_description = f_readme.read() - - -DOCUMENTATION_URL = "https://arpes.readthedocs.io/" - -POST_INSTALL_MESSAGE = """ -Documentation available at: {} - -You should follow standard best practices for working with IPython and Jupyter. - -To get the interactive volumetric data explorer `qt_tool` you will need to install -`PyQt5` and `pyqtgraph`. - -To use the Igor data loading libraries in PyARPES you will need to install the `igor` -module from 'https://github.com/chstan/igorpy/tarball/712a4c4#egg=igor-0.3.1'. - -Some functionality, including PCA/Factor Analysis decomposition tools, require -additional heavy dependencies such as `scikit-learn` and `scikit-image`. - -For Jupyter integration, please have a look at the documentation (link above). -For support issues, contact chstansbury@gmail.com or chstan@berkeley.edu. -""".format(DOCUMENTATION_URL) - -packages = find_packages( - exclude=( - "tests", - "source", - "info_session", - "scripts", - "docs", - "example_configuration", - "conda", - "figures", - "exp", - "datasets", - "resources", - ) -) - -here = os.path.abspath(os.path.dirname(__file__)) - -with io.open(os.path.join(here, "README.rst"), encoding="utf-8") as f: - LONG_DESCRIPTION = "\n" + f.read() - - -class PostInstallCommand(install): - """Provides some extra information and context after install.""" - - def run(self): - """Print the post-installation message after successful install.""" - install.run(self) - print(POST_INSTALL_MESSAGE) - - -# Where the magic happens: -setup( - name=NAME, - version=VERSION, - description=DESCRIPTION, - long_description=LONG_DESCRIPTION, - author=AUTHOR, - author_email=EMAIL, - python_requires=REQUIRES_PYTHON, - url=URL, - packages=packages, - dependency_links=[ - "https://github.com/chstan/igorpy/tarball/712a4c4#egg=igor-0.3.1", - ], - install_requires=requirements, - include_package_data=True, - license="GPLv3", - classifiers=[ - # Trove classifiers - # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: Implementation :: CPython", - "Natural Language :: English", - "Intended Audience :: Science/Research", - "Intended Audience :: Developers", - "Operating System :: OS Independent", - "Topic :: Scientific/Engineering :: Physics", - "Topic :: Scientific/Engineering", - "Topic :: Software Development :: Libraries :: Python Modules", - ], - # $ setup.py publish support. - cmdclass={ - "install": PostInstallCommand, - }, -) From fb25c66fc35cc74f704cf4b1634b291c70a86382 Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 00:54:44 +0100 Subject: [PATCH 03/10] move to src layout --- pyproject.toml | 9 +++++++-- {arpes => src/arpes}/__init__.py | 0 {arpes => src/arpes}/all.py | 0 {arpes => src/arpes}/analysis/__init__.py | 0 {arpes => src/arpes}/analysis/align.py | 0 {arpes => src/arpes}/analysis/all.py | 0 {arpes => src/arpes}/analysis/background.py | 0 {arpes => src/arpes}/analysis/band_analysis.py | 0 .../arpes}/analysis/band_analysis_utils.py | 0 {arpes => src/arpes}/analysis/decomposition.py | 0 {arpes => src/arpes}/analysis/deconvolution.py | 0 {arpes => src/arpes}/analysis/derivative.py | 0 {arpes => src/arpes}/analysis/filters.py | 0 {arpes => src/arpes}/analysis/gap.py | 0 {arpes => src/arpes}/analysis/general.py | 0 {arpes => src/arpes}/analysis/kfermi.py | 0 {arpes => src/arpes}/analysis/mask.py | 0 {arpes => src/arpes}/analysis/moire.py | 0 {arpes => src/arpes}/analysis/path.py | 0 {arpes => src/arpes}/analysis/pocket.py | 0 {arpes => src/arpes}/analysis/resolution.py | 0 {arpes => src/arpes}/analysis/sarpes.py | 0 {arpes => src/arpes}/analysis/savitzky_golay.py | 0 {arpes => src/arpes}/analysis/self_energy.py | 0 {arpes => src/arpes}/analysis/shirley.py | 0 {arpes => src/arpes}/analysis/statistics.py | 0 {arpes => src/arpes}/analysis/tarpes.py | 0 {arpes => src/arpes}/analysis/xps.py | 0 {arpes => src/arpes}/bootstrap.py | 0 {arpes => src/arpes}/config.py | 0 {arpes => src/arpes}/constants.py | 0 {arpes => src/arpes}/corrections/__init__.py | 0 {arpes => src/arpes}/corrections/background.py | 0 .../arpes}/corrections/fermi_edge_corrections.py | 0 {arpes => src/arpes}/deep_learning/__init__.py | 0 {arpes => src/arpes}/deep_learning/formatters.py | 0 {arpes => src/arpes}/deep_learning/interpret.py | 0 {arpes => src/arpes}/deep_learning/io.py | 0 .../arpes}/deep_learning/models/__init__.py | 0 .../arpes}/deep_learning/models/regression.py | 0 {arpes => src/arpes}/deep_learning/transforms.py | 0 {arpes => src/arpes}/endstations/__init__.py | 0 {arpes => src/arpes}/endstations/fits_utils.py | 0 {arpes => src/arpes}/endstations/igor_utils.py | 0 {arpes => src/arpes}/endstations/nexus_utils.py | 0 {arpes => src/arpes}/endstations/plugin/ALG_main.py | 0 .../arpes}/endstations/plugin/ALG_spin_ToF.py | 0 {arpes => src/arpes}/endstations/plugin/ANTARES.py | 0 .../arpes}/endstations/plugin/BL10_SARPES.py | 0 .../endstations/plugin/Elettra_spectromicroscopy.py | 0 {arpes => src/arpes}/endstations/plugin/HERS.py | 0 {arpes => src/arpes}/endstations/plugin/MAESTRO.py | 0 {arpes => src/arpes}/endstations/plugin/MBS.py | 0 .../arpes}/endstations/plugin/SSRF_NSRL.py | 0 {arpes => src/arpes}/endstations/plugin/SToF_DLD.py | 0 {arpes => src/arpes}/endstations/plugin/__init__.py | 0 .../arpes}/endstations/plugin/example_data.py | 0 {arpes => src/arpes}/endstations/plugin/fallback.py | 0 .../arpes}/endstations/plugin/igor_export.py | 0 .../arpes}/endstations/plugin/igor_plugin.py | 0 {arpes => src/arpes}/endstations/plugin/kaindl.py | 0 {arpes => src/arpes}/endstations/plugin/merlin.py | 0 {arpes => src/arpes}/endstations/plugin/nexus.py | 0 {arpes => src/arpes}/example_data/cut.fits | 0 {arpes => src/arpes}/example_data/fermi_surface.nc | Bin {arpes => src/arpes}/example_data/nano_xps.nc | Bin {arpes => src/arpes}/example_data/photon_energy.nc | Bin .../arpes}/example_data/temperature_dependence.nc | Bin {arpes => src/arpes}/exceptions.py | 0 {arpes => src/arpes}/experiment/__init__.py | 0 {arpes => src/arpes}/fits/__init__.py | 0 {arpes => src/arpes}/fits/broadcast_common.py | 0 {arpes => src/arpes}/fits/fit_models/__init__.py | 0 {arpes => src/arpes}/fits/fit_models/backgrounds.py | 0 {arpes => src/arpes}/fits/fit_models/decay.py | 0 {arpes => src/arpes}/fits/fit_models/dirac.py | 0 {arpes => src/arpes}/fits/fit_models/fermi_edge.py | 0 .../arpes}/fits/fit_models/functional_forms.py | 0 {arpes => src/arpes}/fits/fit_models/misc.py | 0 {arpes => src/arpes}/fits/fit_models/peaks.py | 0 .../arpes}/fits/fit_models/two_dimensional.py | 0 {arpes => src/arpes}/fits/fit_models/wrapped.py | 0 .../arpes}/fits/fit_models/x_model_mixin.py | 0 {arpes => src/arpes}/fits/hot_pool.py | 0 {arpes => src/arpes}/fits/lmfit_html_repr.py | 0 {arpes => src/arpes}/fits/lmfit_plot.py | 0 {arpes => src/arpes}/fits/mp_fits.py | 0 {arpes => src/arpes}/fits/utilities.py | 0 {arpes => src/arpes}/fits/zones.py | 0 {arpes => src/arpes}/io.py | 0 {arpes => src/arpes}/laser.py | 0 {arpes => src/arpes}/laue/__init__.py | 0 {arpes => src/arpes}/load_pxt.py | 0 {arpes => src/arpes}/models/__init__.py | 0 {arpes => src/arpes}/models/band.py | 0 {arpes => src/arpes}/optics.py | 0 {arpes => src/arpes}/plotting/__init__.py | 0 {arpes => src/arpes}/plotting/all.py | 0 {arpes => src/arpes}/plotting/annotations.py | 0 {arpes => src/arpes}/plotting/band_tool.py | 0 {arpes => src/arpes}/plotting/bands.py | 0 {arpes => src/arpes}/plotting/basic.py | 0 .../arpes}/plotting/basic_tools/__init__.py | 0 {arpes => src/arpes}/plotting/bz.py | 0 .../plotting/bz_tool/CoordinateOffsetWidget.py | 0 .../plotting/bz_tool/RangeOrSingleValueWidget.py | 0 {arpes => src/arpes}/plotting/bz_tool/__init__.py | 0 {arpes => src/arpes}/plotting/comparison_tool.py | 0 {arpes => src/arpes}/plotting/curvature_tool.py | 0 {arpes => src/arpes}/plotting/dispersion.py | 0 {arpes => src/arpes}/plotting/dos.py | 0 {arpes => src/arpes}/plotting/dyn_tool.py | 0 {arpes => src/arpes}/plotting/dynamic_tool.py | 0 {arpes => src/arpes}/plotting/false_color.py | 0 {arpes => src/arpes}/plotting/fermi_edge.py | 0 {arpes => src/arpes}/plotting/fermi_surface.py | 0 .../arpes}/plotting/fit_inspection_tool.py | 0 {arpes => src/arpes}/plotting/fit_tool/__init__.py | 0 .../arpes}/plotting/fit_tool/fit_inspection_plot.py | 0 {arpes => src/arpes}/plotting/fits.py | 0 {arpes => src/arpes}/plotting/interactive.py | 0 {arpes => src/arpes}/plotting/interactive_utils.py | 0 {arpes => src/arpes}/plotting/mask_tool.py | 0 {arpes => src/arpes}/plotting/movie.py | 0 {arpes => src/arpes}/plotting/parameter.py | 0 {arpes => src/arpes}/plotting/path_tool.py | 0 {arpes => src/arpes}/plotting/qt_ktool/__init__.py | 0 .../arpes}/plotting/qt_tool/AxisInfoWidget.py | 0 .../arpes}/plotting/qt_tool/BinningInfoWidget.py | 0 {arpes => src/arpes}/plotting/qt_tool/__init__.py | 0 {arpes => src/arpes}/plotting/spatial.py | 0 {arpes => src/arpes}/plotting/spin.py | 0 {arpes => src/arpes}/plotting/stack_plot.py | 0 {arpes => src/arpes}/plotting/tof.py | 0 {arpes => src/arpes}/plotting/utils.py | 0 {arpes => src/arpes}/preparation/__init__.py | 0 .../arpes}/preparation/axis_preparation.py | 0 .../arpes}/preparation/coord_preparation.py | 0 .../arpes}/preparation/hemisphere_preparation.py | 0 {arpes => src/arpes}/preparation/tof_preparation.py | 0 {arpes => src/arpes}/provenance.py | 0 {arpes => src/arpes}/repair.py | 0 {arpes => src/arpes}/simulation.py | 0 {arpes => src/arpes}/trace.py | 0 {arpes => src/arpes}/typing.py | 0 {arpes => src/arpes}/utilities/__init__.py | 0 {arpes => src/arpes}/utilities/attrs.py | 0 {arpes => src/arpes}/utilities/bz.py | 0 {arpes => src/arpes}/utilities/bz_spec.py | 0 {arpes => src/arpes}/utilities/collections.py | 0 .../arpes}/utilities/conversion/__init__.py | 0 {arpes => src/arpes}/utilities/conversion/base.py | 0 .../utilities/conversion/bounds_calculations.py | 0 .../arpes}/utilities/conversion/calibration.py | 0 {arpes => src/arpes}/utilities/conversion/core.py | 0 .../arpes}/utilities/conversion/fast_interp.py | 0 .../arpes}/utilities/conversion/forward.py | 0 {arpes => src/arpes}/utilities/conversion/grids.py | 0 .../arpes}/utilities/conversion/kx_ky_conversion.py | 0 .../arpes}/utilities/conversion/kz_conversion.py | 0 .../utilities/conversion/remap_manipulator.py | 0 .../arpes}/utilities/conversion/trapezoid.py | 0 {arpes => src/arpes}/utilities/dict.py | 0 {arpes => src/arpes}/utilities/excepthook.py | 0 {arpes => src/arpes}/utilities/funcutils.py | 0 {arpes => src/arpes}/utilities/geometry.py | 0 {arpes => src/arpes}/utilities/image.py | 0 {arpes => src/arpes}/utilities/jupyter.py | 0 {arpes => src/arpes}/utilities/math.py | 0 {arpes => src/arpes}/utilities/normalize.py | 0 {arpes => src/arpes}/utilities/qt/__init__.py | 0 {arpes => src/arpes}/utilities/qt/app.py | 0 .../arpes}/utilities/qt/data_array_image_view.py | 0 {arpes => src/arpes}/utilities/qt/help_dialogs.py | 0 {arpes => src/arpes}/utilities/qt/utils.py | 0 {arpes => src/arpes}/utilities/qt/windows.py | 0 {arpes => src/arpes}/utilities/region.py | 0 {arpes => src/arpes}/utilities/selections.py | 0 {arpes => src/arpes}/utilities/string.py | 0 {arpes => src/arpes}/utilities/transform.py | 0 {arpes => src/arpes}/utilities/ui.py | 0 {arpes => src/arpes}/utilities/widgets.py | 0 {arpes => src/arpes}/utilities/xarray.py | 0 {arpes => src/arpes}/widgets.py | 0 {arpes => src/arpes}/workflow.py | 0 {arpes => src/arpes}/xarray_extensions.py | 0 186 files changed, 7 insertions(+), 2 deletions(-) rename {arpes => src/arpes}/__init__.py (100%) rename {arpes => src/arpes}/all.py (100%) rename {arpes => src/arpes}/analysis/__init__.py (100%) rename {arpes => src/arpes}/analysis/align.py (100%) rename {arpes => src/arpes}/analysis/all.py (100%) rename {arpes => 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rename {arpes => src/arpes}/endstations/__init__.py (100%) rename {arpes => src/arpes}/endstations/fits_utils.py (100%) rename {arpes => src/arpes}/endstations/igor_utils.py (100%) rename {arpes => src/arpes}/endstations/nexus_utils.py (100%) rename {arpes => src/arpes}/endstations/plugin/ALG_main.py (100%) rename {arpes => src/arpes}/endstations/plugin/ALG_spin_ToF.py (100%) rename {arpes => src/arpes}/endstations/plugin/ANTARES.py (100%) rename {arpes => src/arpes}/endstations/plugin/BL10_SARPES.py (100%) rename {arpes => src/arpes}/endstations/plugin/Elettra_spectromicroscopy.py (100%) rename {arpes => src/arpes}/endstations/plugin/HERS.py (100%) rename {arpes => src/arpes}/endstations/plugin/MAESTRO.py (100%) rename {arpes => src/arpes}/endstations/plugin/MBS.py (100%) rename {arpes => src/arpes}/endstations/plugin/SSRF_NSRL.py (100%) rename {arpes => src/arpes}/endstations/plugin/SToF_DLD.py (100%) rename {arpes => src/arpes}/endstations/plugin/__init__.py (100%) rename {arpes => src/arpes}/endstations/plugin/example_data.py (100%) rename {arpes => src/arpes}/endstations/plugin/fallback.py (100%) rename {arpes => src/arpes}/endstations/plugin/igor_export.py (100%) rename {arpes => src/arpes}/endstations/plugin/igor_plugin.py (100%) rename {arpes => src/arpes}/endstations/plugin/kaindl.py (100%) rename {arpes => src/arpes}/endstations/plugin/merlin.py (100%) rename {arpes => src/arpes}/endstations/plugin/nexus.py (100%) rename {arpes => src/arpes}/example_data/cut.fits (100%) rename {arpes => src/arpes}/example_data/fermi_surface.nc (100%) rename {arpes => src/arpes}/example_data/nano_xps.nc (100%) rename {arpes => src/arpes}/example_data/photon_energy.nc (100%) rename {arpes => src/arpes}/example_data/temperature_dependence.nc (100%) rename {arpes => src/arpes}/exceptions.py (100%) rename {arpes => src/arpes}/experiment/__init__.py (100%) rename {arpes => src/arpes}/fits/__init__.py (100%) rename {arpes => src/arpes}/fits/broadcast_common.py (100%) rename {arpes => src/arpes}/fits/fit_models/__init__.py (100%) rename {arpes => src/arpes}/fits/fit_models/backgrounds.py (100%) rename {arpes => src/arpes}/fits/fit_models/decay.py (100%) rename {arpes => src/arpes}/fits/fit_models/dirac.py (100%) rename {arpes => src/arpes}/fits/fit_models/fermi_edge.py (100%) rename {arpes => src/arpes}/fits/fit_models/functional_forms.py (100%) rename {arpes => src/arpes}/fits/fit_models/misc.py (100%) rename {arpes => src/arpes}/fits/fit_models/peaks.py (100%) rename {arpes => src/arpes}/fits/fit_models/two_dimensional.py (100%) rename {arpes => src/arpes}/fits/fit_models/wrapped.py (100%) rename {arpes => src/arpes}/fits/fit_models/x_model_mixin.py (100%) rename {arpes => src/arpes}/fits/hot_pool.py (100%) rename {arpes => src/arpes}/fits/lmfit_html_repr.py (100%) rename {arpes => src/arpes}/fits/lmfit_plot.py (100%) rename {arpes => src/arpes}/fits/mp_fits.py (100%) rename {arpes => src/arpes}/fits/utilities.py (100%) rename {arpes => src/arpes}/fits/zones.py (100%) rename {arpes => src/arpes}/io.py (100%) rename {arpes => src/arpes}/laser.py (100%) rename {arpes => src/arpes}/laue/__init__.py (100%) rename {arpes => src/arpes}/load_pxt.py (100%) rename {arpes => src/arpes}/models/__init__.py (100%) rename {arpes => src/arpes}/models/band.py (100%) rename {arpes => src/arpes}/optics.py (100%) rename {arpes => src/arpes}/plotting/__init__.py (100%) rename {arpes => src/arpes}/plotting/all.py (100%) rename {arpes => src/arpes}/plotting/annotations.py (100%) rename {arpes => src/arpes}/plotting/band_tool.py (100%) rename {arpes => src/arpes}/plotting/bands.py (100%) rename {arpes => src/arpes}/plotting/basic.py (100%) rename {arpes => src/arpes}/plotting/basic_tools/__init__.py (100%) rename {arpes => src/arpes}/plotting/bz.py (100%) rename {arpes => src/arpes}/plotting/bz_tool/CoordinateOffsetWidget.py (100%) rename {arpes => src/arpes}/plotting/bz_tool/RangeOrSingleValueWidget.py (100%) rename {arpes => src/arpes}/plotting/bz_tool/__init__.py (100%) rename {arpes => src/arpes}/plotting/comparison_tool.py (100%) rename {arpes => src/arpes}/plotting/curvature_tool.py (100%) rename {arpes => src/arpes}/plotting/dispersion.py (100%) rename {arpes => src/arpes}/plotting/dos.py (100%) rename {arpes => src/arpes}/plotting/dyn_tool.py (100%) rename {arpes => src/arpes}/plotting/dynamic_tool.py (100%) rename {arpes => src/arpes}/plotting/false_color.py (100%) rename {arpes => src/arpes}/plotting/fermi_edge.py (100%) rename {arpes => src/arpes}/plotting/fermi_surface.py (100%) rename {arpes => src/arpes}/plotting/fit_inspection_tool.py (100%) rename {arpes => src/arpes}/plotting/fit_tool/__init__.py (100%) rename {arpes => src/arpes}/plotting/fit_tool/fit_inspection_plot.py (100%) rename {arpes => src/arpes}/plotting/fits.py (100%) rename {arpes => src/arpes}/plotting/interactive.py (100%) rename {arpes => src/arpes}/plotting/interactive_utils.py (100%) rename {arpes => src/arpes}/plotting/mask_tool.py (100%) rename {arpes => src/arpes}/plotting/movie.py (100%) rename {arpes => src/arpes}/plotting/parameter.py (100%) rename {arpes => src/arpes}/plotting/path_tool.py (100%) rename {arpes => src/arpes}/plotting/qt_ktool/__init__.py (100%) rename {arpes => src/arpes}/plotting/qt_tool/AxisInfoWidget.py (100%) rename {arpes => src/arpes}/plotting/qt_tool/BinningInfoWidget.py (100%) rename {arpes => src/arpes}/plotting/qt_tool/__init__.py (100%) rename {arpes => src/arpes}/plotting/spatial.py (100%) rename {arpes => src/arpes}/plotting/spin.py (100%) rename {arpes => src/arpes}/plotting/stack_plot.py (100%) rename {arpes => src/arpes}/plotting/tof.py (100%) rename {arpes => src/arpes}/plotting/utils.py (100%) rename {arpes => src/arpes}/preparation/__init__.py (100%) rename {arpes => src/arpes}/preparation/axis_preparation.py (100%) rename {arpes => src/arpes}/preparation/coord_preparation.py (100%) rename {arpes => src/arpes}/preparation/hemisphere_preparation.py (100%) rename {arpes => src/arpes}/preparation/tof_preparation.py (100%) rename {arpes => src/arpes}/provenance.py (100%) rename {arpes => src/arpes}/repair.py (100%) rename {arpes => src/arpes}/simulation.py (100%) rename {arpes => src/arpes}/trace.py (100%) rename {arpes => src/arpes}/typing.py (100%) rename {arpes => src/arpes}/utilities/__init__.py (100%) rename {arpes => src/arpes}/utilities/attrs.py (100%) rename {arpes => src/arpes}/utilities/bz.py (100%) rename {arpes => src/arpes}/utilities/bz_spec.py (100%) rename {arpes => src/arpes}/utilities/collections.py (100%) rename {arpes => src/arpes}/utilities/conversion/__init__.py (100%) rename {arpes => src/arpes}/utilities/conversion/base.py (100%) rename {arpes => src/arpes}/utilities/conversion/bounds_calculations.py (100%) rename {arpes => src/arpes}/utilities/conversion/calibration.py (100%) rename {arpes => src/arpes}/utilities/conversion/core.py (100%) rename {arpes => src/arpes}/utilities/conversion/fast_interp.py (100%) rename {arpes => src/arpes}/utilities/conversion/forward.py (100%) rename {arpes => src/arpes}/utilities/conversion/grids.py (100%) rename {arpes => src/arpes}/utilities/conversion/kx_ky_conversion.py (100%) rename {arpes => src/arpes}/utilities/conversion/kz_conversion.py (100%) rename {arpes => src/arpes}/utilities/conversion/remap_manipulator.py (100%) rename {arpes => src/arpes}/utilities/conversion/trapezoid.py (100%) rename {arpes => src/arpes}/utilities/dict.py (100%) rename {arpes => src/arpes}/utilities/excepthook.py (100%) rename {arpes => src/arpes}/utilities/funcutils.py (100%) rename {arpes => src/arpes}/utilities/geometry.py (100%) rename {arpes => src/arpes}/utilities/image.py (100%) rename {arpes => src/arpes}/utilities/jupyter.py (100%) rename {arpes => src/arpes}/utilities/math.py (100%) rename {arpes => src/arpes}/utilities/normalize.py (100%) rename {arpes => src/arpes}/utilities/qt/__init__.py (100%) rename {arpes => src/arpes}/utilities/qt/app.py (100%) rename {arpes => src/arpes}/utilities/qt/data_array_image_view.py (100%) rename {arpes => src/arpes}/utilities/qt/help_dialogs.py (100%) rename {arpes => src/arpes}/utilities/qt/utils.py (100%) rename {arpes => src/arpes}/utilities/qt/windows.py (100%) rename {arpes => src/arpes}/utilities/region.py (100%) rename {arpes => src/arpes}/utilities/selections.py (100%) rename {arpes => src/arpes}/utilities/string.py (100%) rename {arpes => src/arpes}/utilities/transform.py (100%) rename {arpes => src/arpes}/utilities/ui.py (100%) rename {arpes => src/arpes}/utilities/widgets.py (100%) rename {arpes => src/arpes}/utilities/xarray.py (100%) rename {arpes => src/arpes}/widgets.py (100%) rename {arpes => src/arpes}/workflow.py (100%) rename {arpes => src/arpes}/xarray_extensions.py (100%) diff --git a/pyproject.toml b/pyproject.toml index 3f4f67df..e65d3fdc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -83,8 +83,13 @@ dev = [ "pytest==3.3.2", ] -[tool.setuptools] -packages = ["arpes", "resources"] +[tool.setuptools.packages.find] +where = [ + "src", +] + +[tool.setuptools.package-data] +pynxtools = ["resources"] [tool.black] line-length = 100 diff --git a/arpes/__init__.py b/src/arpes/__init__.py similarity index 100% rename from arpes/__init__.py rename to src/arpes/__init__.py diff --git a/arpes/all.py b/src/arpes/all.py similarity index 100% rename from arpes/all.py rename to src/arpes/all.py diff --git a/arpes/analysis/__init__.py b/src/arpes/analysis/__init__.py similarity index 100% rename from arpes/analysis/__init__.py rename to src/arpes/analysis/__init__.py diff --git a/arpes/analysis/align.py b/src/arpes/analysis/align.py similarity index 100% rename from arpes/analysis/align.py rename to src/arpes/analysis/align.py diff --git a/arpes/analysis/all.py b/src/arpes/analysis/all.py similarity index 100% rename from arpes/analysis/all.py rename to src/arpes/analysis/all.py diff --git a/arpes/analysis/background.py b/src/arpes/analysis/background.py similarity index 100% rename from arpes/analysis/background.py rename to src/arpes/analysis/background.py diff --git a/arpes/analysis/band_analysis.py b/src/arpes/analysis/band_analysis.py similarity index 100% rename from arpes/analysis/band_analysis.py rename to src/arpes/analysis/band_analysis.py diff --git a/arpes/analysis/band_analysis_utils.py b/src/arpes/analysis/band_analysis_utils.py similarity index 100% rename from arpes/analysis/band_analysis_utils.py rename to src/arpes/analysis/band_analysis_utils.py diff --git a/arpes/analysis/decomposition.py b/src/arpes/analysis/decomposition.py similarity index 100% rename from arpes/analysis/decomposition.py rename to src/arpes/analysis/decomposition.py diff --git a/arpes/analysis/deconvolution.py b/src/arpes/analysis/deconvolution.py similarity index 100% rename from arpes/analysis/deconvolution.py rename to src/arpes/analysis/deconvolution.py diff --git a/arpes/analysis/derivative.py b/src/arpes/analysis/derivative.py similarity index 100% rename from arpes/analysis/derivative.py rename to src/arpes/analysis/derivative.py diff --git a/arpes/analysis/filters.py b/src/arpes/analysis/filters.py similarity index 100% rename from arpes/analysis/filters.py rename to src/arpes/analysis/filters.py diff --git a/arpes/analysis/gap.py b/src/arpes/analysis/gap.py similarity index 100% rename from arpes/analysis/gap.py rename to src/arpes/analysis/gap.py diff --git a/arpes/analysis/general.py b/src/arpes/analysis/general.py similarity index 100% rename from arpes/analysis/general.py rename to src/arpes/analysis/general.py diff --git a/arpes/analysis/kfermi.py b/src/arpes/analysis/kfermi.py similarity index 100% rename from arpes/analysis/kfermi.py rename to src/arpes/analysis/kfermi.py diff --git a/arpes/analysis/mask.py b/src/arpes/analysis/mask.py similarity index 100% rename from arpes/analysis/mask.py rename to src/arpes/analysis/mask.py diff --git a/arpes/analysis/moire.py b/src/arpes/analysis/moire.py similarity index 100% rename from arpes/analysis/moire.py rename to src/arpes/analysis/moire.py diff --git a/arpes/analysis/path.py b/src/arpes/analysis/path.py similarity index 100% rename from arpes/analysis/path.py rename to src/arpes/analysis/path.py diff --git a/arpes/analysis/pocket.py b/src/arpes/analysis/pocket.py similarity index 100% rename from arpes/analysis/pocket.py rename to src/arpes/analysis/pocket.py diff --git a/arpes/analysis/resolution.py b/src/arpes/analysis/resolution.py similarity index 100% rename from arpes/analysis/resolution.py rename to src/arpes/analysis/resolution.py diff --git a/arpes/analysis/sarpes.py b/src/arpes/analysis/sarpes.py similarity index 100% rename from arpes/analysis/sarpes.py rename to src/arpes/analysis/sarpes.py diff --git a/arpes/analysis/savitzky_golay.py b/src/arpes/analysis/savitzky_golay.py similarity index 100% rename from arpes/analysis/savitzky_golay.py rename to src/arpes/analysis/savitzky_golay.py diff --git a/arpes/analysis/self_energy.py b/src/arpes/analysis/self_energy.py similarity index 100% rename from arpes/analysis/self_energy.py rename to src/arpes/analysis/self_energy.py diff --git a/arpes/analysis/shirley.py b/src/arpes/analysis/shirley.py similarity index 100% rename from arpes/analysis/shirley.py rename to src/arpes/analysis/shirley.py diff --git a/arpes/analysis/statistics.py b/src/arpes/analysis/statistics.py similarity index 100% rename from arpes/analysis/statistics.py rename to src/arpes/analysis/statistics.py diff --git a/arpes/analysis/tarpes.py b/src/arpes/analysis/tarpes.py similarity index 100% rename from arpes/analysis/tarpes.py rename to src/arpes/analysis/tarpes.py diff --git a/arpes/analysis/xps.py b/src/arpes/analysis/xps.py similarity index 100% rename from arpes/analysis/xps.py rename to src/arpes/analysis/xps.py diff --git a/arpes/bootstrap.py b/src/arpes/bootstrap.py similarity index 100% rename from arpes/bootstrap.py rename to src/arpes/bootstrap.py diff --git a/arpes/config.py b/src/arpes/config.py similarity index 100% rename from arpes/config.py rename to src/arpes/config.py diff --git a/arpes/constants.py b/src/arpes/constants.py similarity index 100% rename from arpes/constants.py rename to src/arpes/constants.py diff --git a/arpes/corrections/__init__.py b/src/arpes/corrections/__init__.py similarity index 100% rename from arpes/corrections/__init__.py rename to src/arpes/corrections/__init__.py diff --git a/arpes/corrections/background.py b/src/arpes/corrections/background.py similarity index 100% rename from arpes/corrections/background.py rename to src/arpes/corrections/background.py diff --git a/arpes/corrections/fermi_edge_corrections.py b/src/arpes/corrections/fermi_edge_corrections.py similarity index 100% rename from arpes/corrections/fermi_edge_corrections.py rename to src/arpes/corrections/fermi_edge_corrections.py diff --git a/arpes/deep_learning/__init__.py b/src/arpes/deep_learning/__init__.py similarity index 100% rename from arpes/deep_learning/__init__.py rename to src/arpes/deep_learning/__init__.py diff --git a/arpes/deep_learning/formatters.py b/src/arpes/deep_learning/formatters.py similarity index 100% rename from arpes/deep_learning/formatters.py rename to src/arpes/deep_learning/formatters.py diff --git a/arpes/deep_learning/interpret.py b/src/arpes/deep_learning/interpret.py similarity index 100% rename from arpes/deep_learning/interpret.py rename to src/arpes/deep_learning/interpret.py diff --git a/arpes/deep_learning/io.py b/src/arpes/deep_learning/io.py similarity index 100% rename from arpes/deep_learning/io.py rename to src/arpes/deep_learning/io.py diff --git a/arpes/deep_learning/models/__init__.py b/src/arpes/deep_learning/models/__init__.py similarity index 100% rename from arpes/deep_learning/models/__init__.py rename to src/arpes/deep_learning/models/__init__.py diff --git a/arpes/deep_learning/models/regression.py b/src/arpes/deep_learning/models/regression.py similarity index 100% rename from arpes/deep_learning/models/regression.py rename to src/arpes/deep_learning/models/regression.py diff --git a/arpes/deep_learning/transforms.py b/src/arpes/deep_learning/transforms.py similarity index 100% rename from arpes/deep_learning/transforms.py rename to src/arpes/deep_learning/transforms.py diff --git a/arpes/endstations/__init__.py b/src/arpes/endstations/__init__.py similarity index 100% rename from arpes/endstations/__init__.py rename to src/arpes/endstations/__init__.py diff --git a/arpes/endstations/fits_utils.py b/src/arpes/endstations/fits_utils.py similarity index 100% rename from arpes/endstations/fits_utils.py rename to src/arpes/endstations/fits_utils.py diff --git a/arpes/endstations/igor_utils.py b/src/arpes/endstations/igor_utils.py similarity index 100% rename from arpes/endstations/igor_utils.py rename to src/arpes/endstations/igor_utils.py diff --git a/arpes/endstations/nexus_utils.py b/src/arpes/endstations/nexus_utils.py similarity index 100% rename from arpes/endstations/nexus_utils.py rename to src/arpes/endstations/nexus_utils.py diff --git a/arpes/endstations/plugin/ALG_main.py b/src/arpes/endstations/plugin/ALG_main.py similarity index 100% rename from arpes/endstations/plugin/ALG_main.py rename to src/arpes/endstations/plugin/ALG_main.py diff --git a/arpes/endstations/plugin/ALG_spin_ToF.py b/src/arpes/endstations/plugin/ALG_spin_ToF.py similarity index 100% rename from arpes/endstations/plugin/ALG_spin_ToF.py rename to src/arpes/endstations/plugin/ALG_spin_ToF.py diff --git a/arpes/endstations/plugin/ANTARES.py b/src/arpes/endstations/plugin/ANTARES.py similarity index 100% rename from arpes/endstations/plugin/ANTARES.py rename to src/arpes/endstations/plugin/ANTARES.py diff --git a/arpes/endstations/plugin/BL10_SARPES.py b/src/arpes/endstations/plugin/BL10_SARPES.py similarity index 100% rename from arpes/endstations/plugin/BL10_SARPES.py rename to src/arpes/endstations/plugin/BL10_SARPES.py diff --git a/arpes/endstations/plugin/Elettra_spectromicroscopy.py b/src/arpes/endstations/plugin/Elettra_spectromicroscopy.py similarity index 100% rename from arpes/endstations/plugin/Elettra_spectromicroscopy.py rename to src/arpes/endstations/plugin/Elettra_spectromicroscopy.py diff --git a/arpes/endstations/plugin/HERS.py b/src/arpes/endstations/plugin/HERS.py similarity index 100% rename from arpes/endstations/plugin/HERS.py rename to src/arpes/endstations/plugin/HERS.py diff --git a/arpes/endstations/plugin/MAESTRO.py b/src/arpes/endstations/plugin/MAESTRO.py similarity index 100% rename from arpes/endstations/plugin/MAESTRO.py rename to src/arpes/endstations/plugin/MAESTRO.py diff --git a/arpes/endstations/plugin/MBS.py b/src/arpes/endstations/plugin/MBS.py similarity index 100% rename from arpes/endstations/plugin/MBS.py rename to src/arpes/endstations/plugin/MBS.py diff --git a/arpes/endstations/plugin/SSRF_NSRL.py b/src/arpes/endstations/plugin/SSRF_NSRL.py similarity index 100% rename from arpes/endstations/plugin/SSRF_NSRL.py rename to src/arpes/endstations/plugin/SSRF_NSRL.py diff --git a/arpes/endstations/plugin/SToF_DLD.py b/src/arpes/endstations/plugin/SToF_DLD.py similarity index 100% rename from arpes/endstations/plugin/SToF_DLD.py rename to src/arpes/endstations/plugin/SToF_DLD.py diff --git a/arpes/endstations/plugin/__init__.py b/src/arpes/endstations/plugin/__init__.py similarity index 100% rename from arpes/endstations/plugin/__init__.py rename to src/arpes/endstations/plugin/__init__.py diff --git a/arpes/endstations/plugin/example_data.py b/src/arpes/endstations/plugin/example_data.py similarity index 100% rename from arpes/endstations/plugin/example_data.py rename to src/arpes/endstations/plugin/example_data.py diff --git a/arpes/endstations/plugin/fallback.py b/src/arpes/endstations/plugin/fallback.py similarity index 100% rename from arpes/endstations/plugin/fallback.py rename to src/arpes/endstations/plugin/fallback.py diff --git a/arpes/endstations/plugin/igor_export.py b/src/arpes/endstations/plugin/igor_export.py similarity index 100% rename from arpes/endstations/plugin/igor_export.py rename to src/arpes/endstations/plugin/igor_export.py diff --git a/arpes/endstations/plugin/igor_plugin.py b/src/arpes/endstations/plugin/igor_plugin.py similarity index 100% rename from arpes/endstations/plugin/igor_plugin.py rename to src/arpes/endstations/plugin/igor_plugin.py diff --git a/arpes/endstations/plugin/kaindl.py b/src/arpes/endstations/plugin/kaindl.py similarity index 100% rename from arpes/endstations/plugin/kaindl.py rename to src/arpes/endstations/plugin/kaindl.py diff --git a/arpes/endstations/plugin/merlin.py b/src/arpes/endstations/plugin/merlin.py similarity index 100% rename from arpes/endstations/plugin/merlin.py rename to src/arpes/endstations/plugin/merlin.py diff --git 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a/arpes/example_data/temperature_dependence.nc b/src/arpes/example_data/temperature_dependence.nc similarity index 100% rename from arpes/example_data/temperature_dependence.nc rename to src/arpes/example_data/temperature_dependence.nc diff --git a/arpes/exceptions.py b/src/arpes/exceptions.py similarity index 100% rename from arpes/exceptions.py rename to src/arpes/exceptions.py diff --git a/arpes/experiment/__init__.py b/src/arpes/experiment/__init__.py similarity index 100% rename from arpes/experiment/__init__.py rename to src/arpes/experiment/__init__.py diff --git a/arpes/fits/__init__.py b/src/arpes/fits/__init__.py similarity index 100% rename from arpes/fits/__init__.py rename to src/arpes/fits/__init__.py diff --git a/arpes/fits/broadcast_common.py b/src/arpes/fits/broadcast_common.py similarity index 100% rename from arpes/fits/broadcast_common.py rename to src/arpes/fits/broadcast_common.py diff --git a/arpes/fits/fit_models/__init__.py 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b/src/arpes/utilities/region.py similarity index 100% rename from arpes/utilities/region.py rename to src/arpes/utilities/region.py diff --git a/arpes/utilities/selections.py b/src/arpes/utilities/selections.py similarity index 100% rename from arpes/utilities/selections.py rename to src/arpes/utilities/selections.py diff --git a/arpes/utilities/string.py b/src/arpes/utilities/string.py similarity index 100% rename from arpes/utilities/string.py rename to src/arpes/utilities/string.py diff --git a/arpes/utilities/transform.py b/src/arpes/utilities/transform.py similarity index 100% rename from arpes/utilities/transform.py rename to src/arpes/utilities/transform.py diff --git a/arpes/utilities/ui.py b/src/arpes/utilities/ui.py similarity index 100% rename from arpes/utilities/ui.py rename to src/arpes/utilities/ui.py diff --git a/arpes/utilities/widgets.py b/src/arpes/utilities/widgets.py similarity index 100% rename from arpes/utilities/widgets.py rename to src/arpes/utilities/widgets.py diff --git a/arpes/utilities/xarray.py b/src/arpes/utilities/xarray.py similarity index 100% rename from arpes/utilities/xarray.py rename to src/arpes/utilities/xarray.py diff --git a/arpes/widgets.py b/src/arpes/widgets.py similarity index 100% rename from arpes/widgets.py rename to src/arpes/widgets.py diff --git a/arpes/workflow.py b/src/arpes/workflow.py similarity index 100% rename from arpes/workflow.py rename to src/arpes/workflow.py diff --git a/arpes/xarray_extensions.py b/src/arpes/xarray_extensions.py similarity index 100% rename from arpes/xarray_extensions.py rename to src/arpes/xarray_extensions.py From eaf1c35dc4a25e65372008fb028219e54872fc5a Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 22:24:51 +0100 Subject: [PATCH 04/10] fix windows numba problem, enable py3.12 in tests, update dev requirements --- .github/workflows/test.yml | 2 +- pyproject.toml | 11 ++++++----- src/arpes/__init__.py | 4 ++++ 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index b515fac0..e3e65bc2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python_version: ["3.8", "3.9", "3.10", "3.11"] + python_version: ["3.8", "3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 diff --git a/pyproject.toml b/pyproject.toml index e65d3fdc..cd8e93ef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,7 +60,7 @@ Homepage = "https://gitlab.com/lanzara-group/python-arpes" [project.optional-dependencies] igor = [ - "igor==0.3.1", + "igor @ git+https://github.com/chstan/igorpy.git", ] ml= [ "scikit-learn>=0.24.0,<1.0.0", @@ -77,10 +77,11 @@ jupyter = [ dev = [ "markdown-include", - "attrs==17.4.0", - "pluggy==0.6.0", - "py==1.5.2", - "pytest==3.3.2", + "attrs>=17.4.0", + "pluggy>=0.6.0", + "py>=1.5.2", + "pytest>=3.3.2", + "pytest-qt>=4.0.0", ] [tool.setuptools.packages.find] diff --git a/src/arpes/__init__.py b/src/arpes/__init__.py index ac688d01..4144a35b 100644 --- a/src/arpes/__init__.py +++ b/src/arpes/__init__.py @@ -5,6 +5,10 @@ from typing import Union +import os +# Set NUMBA_DISABLE_INTEL_SVML for windows +os.environ['NUMBA_DISABLE_INTEL_SVML'] = "1" + # Use both version conventions for people's sanity. VERSION = "3.0.1" __version__ = VERSION From de3d1ec3449f59840a32c5a983a5051a5737585c Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 22:26:33 +0100 Subject: [PATCH 05/10] use dev requirementes for tests --- .github/workflows/test.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e3e65bc2..26566ac6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -30,8 +30,7 @@ jobs: python -m pip install --upgrade pip - name: Install package run: | - pip install -e ".[core, test]" - pip install pytest pytest-qt + pip install -e ".[dev]" - name: Test with pytest run: | pytest -sv --show-capture=no tests \ No newline at end of file From 1da3f71e2a9efb24483174391b55d1f29229694e Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 22:37:38 +0100 Subject: [PATCH 06/10] fix ml dependencies --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index cd8e93ef..8d495761 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,10 +63,9 @@ igor = [ "igor @ git+https://github.com/chstan/igorpy.git", ] ml= [ - "scikit-learn>=0.24.0,<1.0.0", + "scikit-learn>=0.24.0", "scikit-image", "cvxpy", - "libgcc", ] jupyter = [ "jupyter", From 9635bcc44215f08e5b44df2c20c5a1de2043f773 Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 22:48:27 +0100 Subject: [PATCH 07/10] fix version --- pyproject.toml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 8d495761..3842ec0e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,9 @@ [build-system] -requires = ["setuptools >= 61.2"] +requires = ["setuptools>=64.0.1", "setuptools-scm[toml]>=6.2"] +build-backend = "setuptools.build_meta" + +[tool.setuptools.dynamic] +version = {attr = "arpes.__version__"} [project] name = "arpes" From decb1be844f3dad054b4608604f63b73748be9d5 Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 23:14:43 +0100 Subject: [PATCH 08/10] remove package limits --- pyproject.toml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3842ec0e..863243f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,26 +34,26 @@ classifiers = [ ] dependencies = [ "PyQt5>5.15", - "ase>=3.17.0,<3.22.0", + "ase>=3.17.0", "astropy", - "bokeh>=2.0.0,<3.0.0", + "bokeh>=2.0.0", "colorama", "colorcet", "dill", "h5py>=3.2.1", "imageio", "ipywidgets>8.0.0", - "lmfit>=1.0.0,<2.0.0", + "lmfit>=1.0.0", "matplotlib>=3.0.3", - "netCDF4>=1.5.0,<1.7.0", - "numba>=0.53.0,<1.0.0", + "netCDF4>=1.5.0", + "numba>=0.53.0", "numpy>=1.20.0,<2.0.0", "packaging", "pandas", "pint", - "pyqtgraph>=0.12.0,<0.13.0", + "pyqtgraph>=0.12.0", "rx", - "scipy>=1.6.0,<2.0.0", + "scipy>=1.6.0", "titlecase", "tqdm", "xarray>=0.16.1", From aedc76bef08d672202258c8559522276efc317a0 Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 23:29:34 +0100 Subject: [PATCH 09/10] limit netCDF for py3.8 --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 863243f4..c94a731f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,8 @@ dependencies = [ "ipywidgets>8.0.0", "lmfit>=1.0.0", "matplotlib>=3.0.3", - "netCDF4>=1.5.0", + "netCDF4>=1.5.0,<1.7.0; python_version<'3.9'", + "netCDF4>=1.5.0; python_version>='3.9'", "numba>=0.53.0", "numpy>=1.20.0,<2.0.0", "packaging", From 48f3ced2da5306bc35c9c1fa8c85a44f64835fef Mon Sep 17 00:00:00 2001 From: Laurenz Rettig Date: Sat, 14 Dec 2024 23:34:53 +0100 Subject: [PATCH 10/10] remove legacy files --- conda/meta.yaml | 85 ------------------------------------- environment-readthedocs.yml | 49 --------------------- environment-update-test.yml | 12 ------ environment.yml | 42 ------------------ lefthook.yml | 11 ----- package.json | 24 ----------- yarn.lock | 8 ---- 7 files changed, 231 deletions(-) delete mode 100644 conda/meta.yaml delete mode 100644 environment-readthedocs.yml delete mode 100644 environment-update-test.yml delete mode 100644 environment.yml delete mode 100644 lefthook.yml delete mode 100644 package.json delete mode 100644 yarn.lock diff --git a/conda/meta.yaml b/conda/meta.yaml deleted file mode 100644 index b1bfe542..00000000 --- a/conda/meta.yaml +++ /dev/null @@ -1,85 +0,0 @@ -# To see what comes out after this template is processed, run: -# conda-render ./conda/ - -{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %} - -package: - name: {{ data.name }} - version: "{{ data.version }}" - -source: - # Source from tarball - # note: must 'make dist-pypi' or `python setup.py sdist` before running conda-build as we now rely on MANIFEST.IN to - # only pick desired files and avoid copying data folders and alike - and its puts its clean tarball under /dist/: - url: ../dist/{{ data.name }}-{{ data.version }}.tar.gz - -build: - number: 2 - noarch: python - script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt" - -# PyQt5 and ase are not available on conda so they are installed via the script above -requirements: - build: - - conda-build - host: - - python =3.8 - - pip - run: - - python =3.8 - - - astropy - - xarray >=0.16.1 - - h5py >=3.2.1 - - pyqtgraph >=0.12.0,<0.13.0 - - pyqt - - - pint - - pandas - - numpy>=1.20.0,<2.0.0 - - scipy>=1.6.0,<2.0.0 - - netcdf4 >=1.5.0,<2.0.0 - - lmfit >=1.0.0,<2.0.0 - - - colorcet - - matplotlib >=3.0.3 - - bokeh >=2.0.0,<3.0.0 - - ipywidgets >=7.0.1,<8.0.0 - - - scikit-learn >=0.24.0,<1.0.0 - - - packaging - - numba >=0.53.0,<1.0.0 - - - colorama - - imageio - - titlecase - - - tqdm - - rx - - dill - - -test: - imports: - - arpes - requires: - - python - -about: - home: https://arpes.readthedocs.io/ - license: GPL-3.0 - license_family: GPL - license_file: LICENSE - summary: 'Modular data analysis code for angle resolved photoemission spectroscopy (ARPES)' - description: 'Modular data analysis code for angle resolved photoemission spectroscopy (ARPES)' - doc_url: https://arpes.readthedocs.io/ - dev_url: https://gitlab.com/lanzara-group/python-arpes - -extra: - recipe-maintainers: - - chstan - deploy: - - anaconda-client - - setuptools >=0.39 - - twine >=1.12 diff --git a/environment-readthedocs.yml b/environment-readthedocs.yml deleted file mode 100644 index 6a10f18d..00000000 --- a/environment-readthedocs.yml +++ /dev/null @@ -1,49 +0,0 @@ -name: arpes -channels: - - defaults - - conda-forge -dependencies: - - python=3.8 - - - astropy - - xarray>=0.16.1 - - h5py>=3.2.1 - - pyqtgraph>=0.12.0,<0.13.0 - - - pint - - pandas - - - numpy>=1.20.0,<2.0.0 - - scipy>=1.6.0,<2.0.0 - - lmfit>=1.0.0,<2.0.0 - - netCDF4>=1.5.0,<2.0.0 - - # plotting - - colorcet - - matplotlib>=3.0.3 - - bokeh>=2.0.0,<3.0.0 - - ipywidgets>=7.0.1,<8.0.0 - - # Misc deps - - pip - - # pip - - pip: - - PyQt5==5.15 - - packaging - - numba>=0.53.0,<1.0.0 - - colorama - - imageio - - titlecase - - tqdm - - rx - - dill - - ase>=3.20.0,<4.0.0 - - # documentation dependencies are basically only these - - sphinx - - sphinxcontrib-restbuilder - - sphinx_rtd_theme - - nbsphinx - - sphinx_copybutton - - -e . diff --git a/environment-update-test.yml b/environment-update-test.yml deleted file mode 100644 index 18b06845..00000000 --- a/environment-update-test.yml +++ /dev/null @@ -1,12 +0,0 @@ -channels: - - defaults -dependencies: - - pip - - pip: - - pytest - - pytest-cov - - pytest-mock - - pytest-qt - - pytest-env - - pytest-xvfb - - "https://github.com/chstan/igorpy/tarball/712a4c4#egg=igor" diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 4a307b02..00000000 --- a/environment.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: arpes -channels: - - defaults - - conda-forge -dependencies: - - python=3.8 - - - astropy - - xarray>=0.16.1 - - h5py>=3.2.1 - - pyqtgraph>=0.12.0,<0.13.0 - - - pint - - pandas - - numpy>=1.20.0,<2.0.0 - - scipy>=1.6.0,<2.0.0 - - lmfit>=1.0.0,<2.0.0 - - netCDF4>=1.5.0,<2.0.0 - - # plotting - - colorcet - - matplotlib>=3.0.3 - - bokeh>=2.0.0,<3.0.0 - - ipywidgets>=7.0.1,<8.0.0 - - # Misc deps - - scikit-learn>=0.24.0,<1.0.0 - - pip - - # pip - - pip: - - PyQt5==5.15 - - packaging - - numba>=0.53.0,<1.0.0 - - colorama - - imageio - - titlecase - - tqdm - - rx - - dill - - ase>=3.17.0,<3.22.0 - - -e . diff --git a/lefthook.yml b/lefthook.yml deleted file mode 100644 index a617767a..00000000 --- a/lefthook.yml +++ /dev/null @@ -1,11 +0,0 @@ -pre-commit: - parallel: true - commands: - black: - glob: "*.py" - run: yarn check-black {staged_files} - pytest: - run: yarn test - pydocstyle: - glob: "*.py" - run: yarn check-docstyle {staged_files} diff --git a/package.json b/package.json deleted file mode 100644 index 9938997b..00000000 --- a/package.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "name": "python3", - "version": "3.0.0", - "description": "Data analysis utilities for ARPES in Python", - "main": "index.js", - "repository": "git@gitlab.com:lanzara-group/python-arpes.git", - "author": "Conrad Stansbury ", - "license": "GPL-3.0", - "scripts": { - "test": "pytest -c pytest-config/pytest.ini", - "integration-test": "pytest -c pytest-config/pytest.ini tests/test_qt.py", - "watch-test": "pytest -c pytest-config/pytest-watch.ini", - "watch-coverage": "pytest -c pytest-config/pytest-coverage.ini -f", - "coverage": "pytest -c pytest-config/pytest-coverage.ini", - "check-black": "black --config pyproject.toml --check", - "check-docstyle": "pydocstyle --config pyproject.toml", - "build-docs": "python scripts/build_docs.py", - "build-pypi": "python -m build --sdist --wheel .", - "build-conda": "yarn build-pypi && conda-build purge-all && conda-build ./conda -c anaconda -c conda-forge --output-folder conda-dist --numpy 1.20" - }, - "devDependencies": { - "@arkweid/lefthook": "^0.7.6" - } -} diff --git a/yarn.lock b/yarn.lock deleted file mode 100644 index c51521b4..00000000 --- a/yarn.lock +++ /dev/null @@ -1,8 +0,0 @@ -# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. -# yarn lockfile v1 - - -"@arkweid/lefthook@^0.7.6": - version "0.7.6" - resolved "https://registry.yarnpkg.com/@arkweid/lefthook/-/lefthook-0.7.6.tgz#0647f698a6ae9a42440846911a277a370359d861" - integrity sha512-dm8UE0+9sbDRFJ6BMYpOrg56W3/wpZq2eBkGsCM+iSBrEKQF8hXFZ4eEEBxo25yfEPNVZguN/FbZcRmkeCyRiA==