From f5a0c2c20be85d229a1e0d44b2827f744e7c0c9c Mon Sep 17 00:00:00 2001 From: Ryuichi Arafune Date: Sun, 11 Feb 2024 16:07:30 +0900 Subject: [PATCH] =?UTF-8?q?=F0=9F=8E=A8=20=20Bump=20up=20the=20version=20t?= =?UTF-8?q?o=204.0.0.beta1?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 🎉 Restructure the layout of the project --- .gitignore | 2 +- Changes.md | 33 +- arpes/experiment/__init__.py | 311 -- docs/source/CHANGELOG.rst | 45 +- docs/source/index.rst | 15 +- .../building-from-source.md | 0 {conda => legacy_files/conda}/meta.yaml | 0 {conda => legacy_files/conda}/run_test.py | 0 .../environment-readthedocs.yml | 0 .../environment-update-test.yml | 0 package.json => legacy_files/package.json | 0 .../pypi-readme.rst | 0 package-lock.json | 3526 ----------------- pyproject.toml | 42 +- requirements.txt | 2 - {arpes => src/arpes}/__init__.py | 2 +- {arpes => src/arpes}/_typing.py | 0 {arpes => src/arpes}/analysis/__init__.py | 0 {arpes => src/arpes}/analysis/align.py | 0 {arpes => src/arpes}/analysis/background.py | 0 .../arpes}/analysis/band_analysis.py | 0 .../arpes}/analysis/band_analysis_utils.py | 0 .../arpes}/analysis/decomposition.py | 0 .../arpes}/analysis/deconvolution.py | 10 +- {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}/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}/corrections/background.py | 0 .../corrections/fermi_edge_corrections.py | 0 .../arpes}/deep_learning/__init__.py | 0 .../arpes}/deep_learning/formatters.py | 0 .../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}/deep_learning/transforms.py | 0 {arpes => src/arpes}/endstations/__init__.py | 0 .../arpes}/endstations/fits_utils.py | 0 .../arpes}/endstations/igor_utils.py | 0 .../arpes}/endstations/nexus_utils.py | 0 .../arpes}/endstations/plugin/ALG_main.py | 0 .../arpes}/endstations/plugin/ALG_spin_ToF.py | 0 .../arpes}/endstations/plugin/ANTARES.py | 0 .../arpes}/endstations/plugin/BL10_SARPES.py | 0 .../plugin/Elettra_spectromicroscopy.py | 0 .../arpes}/endstations/plugin/HERS.py | 0 .../arpes}/endstations/plugin/IF_UMCS.py | 0 .../arpes}/endstations/plugin/MAESTRO.py | 0 .../arpes}/endstations/plugin/MBS.py | 0 .../arpes}/endstations/plugin/SPD_main.py | 0 .../arpes}/endstations/plugin/SSRF_NSRL.py | 0 .../arpes}/endstations/plugin/SToF_DLD.py | 0 .../arpes}/endstations/plugin/__init__.py | 0 .../arpes}/endstations/plugin/example_data.py | 0 .../arpes}/endstations/plugin/fallback.py | 0 .../arpes}/endstations/plugin/igor_export.py | 0 .../arpes}/endstations/plugin/igor_plugin.py | 0 .../arpes}/endstations/plugin/kaindl.py | 0 .../arpes}/endstations/plugin/merlin.py | 0 .../arpes}/endstations/prodigy_itx.py | 0 .../arpes}/endstations/prodigy_xy.py | 0 .../example_data/GrIr_111_20230410_1.sp2 | 0 {arpes => src/arpes}/example_data/cut.fits | 0 .../arpes}/example_data/example_itx_data.itx | 0 .../arpes}/example_data/fermi_surface.nc | Bin {arpes => src/arpes}/example_data/nano_xps.nc | Bin .../arpes}/example_data/photon_energy.nc | Bin .../example_data/temperature_dependence.nc | Bin {arpes => src/arpes}/exceptions.py | 0 {arpes => src/arpes}/fits/__init__.py | 0 {arpes => src/arpes}/fits/broadcast_common.py | 0 .../arpes}/fits/fit_models/__init__.py | 0 .../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}/fits/fit_models/fermi_edge.py | 0 .../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}/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/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/annotations.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 .../bz_tool/CoordinateOffsetWidget.py | 0 .../bz_tool/RangeOrSingleValueWidget.py | 0 .../arpes}/plotting/bz_tool/__init__.py | 0 {arpes => src/arpes}/plotting/dispersion.py | 0 {arpes => src/arpes}/plotting/dos.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}/plotting/fermi_surface.py | 0 .../arpes}/plotting/fit_tool/__init__.py | 0 .../plotting/fit_tool/fit_inspection_plot.py | 0 {arpes => src/arpes}/plotting/fits.py | 0 {arpes => src/arpes}/plotting/movie.py | 0 {arpes => src/arpes}/plotting/parameter.py | 0 .../arpes}/plotting/qt_ktool/__init__.py | 0 .../arpes}/plotting/qt_tool/AxisInfoWidget.py | 0 .../plotting/qt_tool/BinningInfoWidget.py | 0 .../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 .../preparation/hemisphere_preparation.py | 0 .../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}/utilities/__init__.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 => src/arpes}/utilities/combine.py | 0 .../arpes}/utilities/conversion/__init__.py | 0 .../arpes}/utilities/conversion/base.py | 0 .../conversion/bounds_calculations.py | 0 .../utilities/conversion/calibration.py | 0 .../arpes}/utilities/conversion/core.py | 0 .../utilities/conversion/fast_interp.py | 0 .../arpes}/utilities/conversion/forward.py | 3 +- .../arpes}/utilities/conversion/grids.py | 0 .../utilities/conversion/kx_ky_conversion.py | 0 .../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 .../utilities/qt/data_array_image_view.py | 0 .../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 tests/test_prodigy_itx.py | 2 +- 191 files changed, 113 insertions(+), 3880 deletions(-) delete mode 100644 arpes/experiment/__init__.py rename building-from-source.md => legacy_files/building-from-source.md (100%) rename {conda => legacy_files/conda}/meta.yaml (100%) rename {conda => legacy_files/conda}/run_test.py (100%) rename environment-readthedocs.yml => legacy_files/environment-readthedocs.yml (100%) rename environment-update-test.yml => legacy_files/environment-update-test.yml (100%) rename package.json => legacy_files/package.json (100%) rename pypi-readme.rst => legacy_files/pypi-readme.rst (100%) delete mode 100644 package-lock.json delete mode 100644 requirements.txt rename {arpes => src/arpes}/__init__.py (98%) rename {arpes => src/arpes}/_typing.py (100%) rename {arpes => src/arpes}/analysis/__init__.py (100%) rename {arpes => src/arpes}/analysis/align.py (100%) rename {arpes => src/arpes}/analysis/background.py (100%) rename {arpes => src/arpes}/analysis/band_analysis.py (100%) rename {arpes => src/arpes}/analysis/band_analysis_utils.py (100%) rename {arpes => src/arpes}/analysis/decomposition.py (100%) rename {arpes => src/arpes}/analysis/deconvolution.py (98%) rename {arpes => src/arpes}/analysis/derivative.py (100%) rename {arpes => src/arpes}/analysis/filters.py (100%) rename {arpes => src/arpes}/analysis/gap.py (100%) rename {arpes => src/arpes}/analysis/general.py (100%) rename {arpes => src/arpes}/analysis/kfermi.py (100%) rename {arpes => src/arpes}/analysis/mask.py (100%) rename {arpes => src/arpes}/analysis/moire.py (100%) rename {arpes => src/arpes}/analysis/path.py (100%) rename {arpes => src/arpes}/analysis/pocket.py (100%) rename {arpes => src/arpes}/analysis/resolution.py (100%) rename {arpes => src/arpes}/analysis/sarpes.py (100%) rename {arpes => src/arpes}/analysis/savitzky_golay.py (100%) rename {arpes => src/arpes}/analysis/self_energy.py (100%) rename {arpes => src/arpes}/analysis/shirley.py (100%) rename {arpes => src/arpes}/analysis/statistics.py (100%) rename {arpes => src/arpes}/analysis/tarpes.py (100%) rename {arpes => src/arpes}/analysis/xps.py (100%) rename {arpes => src/arpes}/bootstrap.py (100%) rename {arpes => src/arpes}/config.py (100%) rename {arpes => src/arpes}/constants.py (100%) rename {arpes => src/arpes}/corrections/__init__.py (100%) rename {arpes => src/arpes}/corrections/background.py (100%) rename {arpes => src/arpes}/corrections/fermi_edge_corrections.py (100%) rename {arpes => src/arpes}/deep_learning/__init__.py (100%) rename {arpes => src/arpes}/deep_learning/formatters.py (100%) rename {arpes => src/arpes}/deep_learning/interpret.py (100%) rename {arpes => src/arpes}/deep_learning/io.py (100%) rename {arpes => src/arpes}/deep_learning/models/__init__.py (100%) rename {arpes => src/arpes}/deep_learning/models/regression.py (100%) rename {arpes => src/arpes}/deep_learning/transforms.py (100%) 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/IF_UMCS.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/SPD_main.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/prodigy_itx.py (100%) rename {arpes => src/arpes}/endstations/prodigy_xy.py (100%) rename {arpes => src/arpes}/example_data/GrIr_111_20230410_1.sp2 (100%) rename {arpes => src/arpes}/example_data/cut.fits (100%) rename {arpes => src/arpes}/example_data/example_itx_data.itx (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}/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/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/annotations.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/dispersion.py (100%) rename {arpes => src/arpes}/plotting/dos.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_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/movie.py (100%) rename {arpes => src/arpes}/plotting/parameter.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}/utilities/__init__.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/combine.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 (99%) 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/.gitignore b/.gitignore index 53625bc7..fa71b07c 100644 --- a/.gitignore +++ b/.gitignore @@ -41,7 +41,7 @@ cache/*.keep .idea/ -local_config.py +src/local_config.py !datasets/Misc !experiments/Misc diff --git a/Changes.md b/Changes.md index 8cc515c1..93b4d3c0 100644 --- a/Changes.md +++ b/Changes.md @@ -1,20 +1,31 @@ Major Changes from 3.0.1 -- Introdcue a new attrs, "energy_notation" is introduced, which determines eithe "Kinetic" energy or "Binding" energy - - Add new method: S.switch_energy_notation(self, nonlinear_order=1) -- Use correct method to convert from the angle to mthe omentum. (Original approach was found to be incorrect) -- filters.boxcar: skip_nan has been removed -- Dataset.S.spectra returns the list of the xr.DataArrays whose dims contains "eV". (See xarray_extensions.py) -- Provide SPD_main.py & prodigy_itx.py -- Add a new method S.swap_angle_unit() to change the angle unit (deg <-> radian) -- Do not carelessly set deafult=None +- Most important change: -- Replace algorithms to make them simpler and more efficient + - Use correct method to convert from the angle to moementum. (Original approach was found to be incorrect) + +- New feature + - Provide SPD_main.py & prodigy_itx.py + - Provide IF\_\_UMCS.py & prodigy_xy.py + - Introduce Type annotation, which is major trend in the current python coding. + - Users are requested to know type of the object treated. Especially, the users should know the difference between xr.DataArray & xr.Dataset + - Introduce a new attrs, "energy_notation", which determines either "Kinetic" energy or "Binding" energy + - Add new method: S.switch_energy_notation(self, nonlinear_order=1) + +* Dataset.S.spectra returns the list of the xr.DataArrays whose dims contains "eV". (See xarray_extensions.py) + Add a new method S.swap_angle_unit() to change the angle unit (deg <-> radian) + +- Coding guide line + +* Do not carelessly set default=None +* Replace algorithms to make them simpler and more efficient - stack_plot.py/flat_stack_plot - analysis/general.py/rebin -- Removing +* Removing + + Many files/methods/class have been removed because of inconsistency, legacy style, useless. Here is just a short list the ones I remember now: - Remove arpes.all @@ -46,7 +57,7 @@ Major Changes from 3.0.1 - Remove original_id method, as I cannot figure out the purpose. - Remove lmfit_plot.py. The original ModelResult.plot() is sufficiently useful, and no reason for keeping to maintain this patched version. - Remove condensed_attrs: We should not enfoce camelcase on attributes, while original version did. Rather, the snake_case would be better from the modern pythonic viewpoint. - - Remove `trace` arg for debuggin. This technique may be sharp, but not so well fitted the current python trend; typing oriented. + - Remove `trace` arg for debugging. This technique may be sharp, but not so well fitted the current python trend; typing oriented. Fix from 3.0.1 diff --git a/arpes/experiment/__init__.py b/arpes/experiment/__init__.py deleted file mode 100644 index 6c172160..00000000 --- a/arpes/experiment/__init__.py +++ /dev/null @@ -1,311 +0,0 @@ -"""Integrates PyARPES with data acquisition. - -This module is a work-in-progress. Ideally, we would one day like to offer -a simple graphical utility that can communicate with various ARPES DAQ hardware using -a file based interchange format. Currently, DAQ sequences roughly consistent with the -capabilities of the MAESTRO beamlines are supported via JSON. - -More capabilities are also available for Tr-ARPES (shuffling to prevent laser and drift -skewing datasets) with more to come. -""" - -from __future__ import annotations - -import json -from itertools import chain, product -from pathlib import Path -from typing import TYPE_CHECKING, Any, ClassVar - -import numpy as np - -if TYPE_CHECKING: - from collections.abc import Iterable, Iterator - - from _typeshed import Incomplete - -__all__ = ("JSONExperimentDriver", "linspace", "shuffled", "move", "comment", "collect") - - -def flatten(lists): - return chain.from_iterable([_ if np.iterable(_) else [_] for _ in lists]) - - -class ExperimentTreeItem: - def __add__(self, other): - if isinstance(other, ExperimentTreeItem): - return [self, other] - - return [self, *other] - - def __mul__(self, other): - return Product(self, other) - - -class Product(ExperimentTreeItem): - items = None - - def __init__(self, *args: Incomplete) -> None: - self.items = args - self._iter = None - - def __len__(self) -> int: - return np.prod([len(item) for item in self.items]) - - def __iter__(self): - def safeiter(item_or_iterable: Any | Iterable[Any]) -> Iterator[Any]: - try: - return iter(item_or_iterable) - except TypeError: - return iter([item_or_iterable]) - - self._iter = product(*[safeiter(i) for i in self.items]) - return self - - def __next__(self): - return next(self._iter) - - def __repr__(self) -> str: - front = "" - content = "\n[\n{}\n]\n".format(", \n".join(["\t" + repr(f) for f in self.items])) - - back = "" - - return front + content + back - - -class Collect(ExperimentTreeItem): - def __init__(self, duration, configuration) -> None: - self.duration = duration - self.configuration = configuration - - def __repr__(self) -> str: - return f"" - - -class Move(ExperimentTreeItem): - moveset = None - wait_after = 0 - measure_while_moving = False - backlash_compensate = False - - def __init__( - self, - wait_after=0, - measure_while_moving=False, - backlash_compensate=False, - **kwargs: Incomplete, - ) -> None: - self.moveset = kwargs - self.wait_after = wait_after - self.measure_while_moving = measure_while_moving - self.backlash_compensate = backlash_compensate - - def __repr__(self) -> str: - return "".format( - " ".join([f"{k}={v}" for k, v in self.moveset.items()]), - self.wait_after, - self.measure_while_moving, - self.backlash_compensate, - ) - - -class Comment(ExperimentTreeItem): - comment = "" - - def __init__(self, the_comment) -> None: - self.comment = the_comment - - -class Shuffled(ExperimentTreeItem): - values = None - - def __init__(self, values) -> None: - self.values = values - - def __repr__(self) -> str: - front = "" - try: - content = "\n[\n{}\n]\n".format( - ", \n".join(["\t" + repr(v) for v in list(flatten(self.values))]), - ) - except Exception: # pylint: disable=broad-except - content = repr(self.values) - - back = "" - return front + content + back - - -class Linspace(ExperimentTreeItem): - start = 0 - stop = 0 - num = 0 - endpoint = True - - def __init__(self, f, start, stop, num, endpoint=True) -> None: - self.f = f - self.start = start - self.stop = stop - self.num = num - self.endpoint = endpoint - - def __len__(self) -> int: - return self.num - - def __iter__(self): - return iter(self.values) - - @property - def values(self): - values = np.linspace(self.start, self.stop, self.num) - return [self.f(v) for v in values] - - def __repr__(self) -> str: - front = " {}, {} steps endpoint={}>".format( - self.start, - self.stop, - self.num, - self.endpoint, - ) - content = "\n[\n{}\n]\n".format(", \n".join(["\t" + repr(f) for f in self.values])) - back = "" - return front + content + back - - -# pylint: disable=invalid-name - -linspace = Linspace -shuffled = Shuffled -move = Move -comment = Comment -collect = Collect - -# pylint: enable=invalid-name - - -class ExperimentDriver: - queue_location = None - seconds_per_frame = 1 - - # units / second - movement_speed: ClassVar[dict[str, float]] = { - "temp": 0.03, # deg kelvin per second - "x": 1, # mm / sec - "y": 1, - "z": 1, - "theta": np.deg2rad(1), - "beta": np.deg2rad(1), - "chi": np.deg2rad(1), - "alpha": np.deg2rad(0.1), - "psi": 100, - } - - def __init__(self, queue_location=None) -> None: - self.queue_location = queue_location - - @property - def ext(self): - return "drive" - - def dump(self, file, input_object, **kwargs: Incomplete): - file.write(self.dumps(input_object, **kwargs)) - - def dumps(self, input_object, desired_total_time=None): - return "" - - def dump_to_queue(self, name, input_object, **kwargs: Incomplete): - if self.queue_location is None: - msg = "Must supply a queue location." - raise ValueError(msg) - - dump_path = Path(self.queue_location) / f"{name}.{self.ext}" - with Path(dump_path).open("w") as f: - self.dump(f, input_object, **kwargs) - - def calculate_overhead(self, o): - return self.calculate_duration(o)[1:] - - def calculate_duration(self, o) -> tuple[float, float, float, float]: - """Returns the anticipated scan duration. - - For this purpose, the duration is taken inclusive of the - time spent in movement or idle/overhead time, and performing synthetic - acquisitions like spectrometer sweeping. - - Example: - If you received [600, 0.1, 0, 0.25] from a call to this function - this means that the scan will take about 10 minutes, of which - 60 seconds (10%) of the time is spent in movement overhead, and - no extra time is anticipated to be spent adjusting voltages - in the spectrometer, and only 75% of the data recorded by - the spectrometer will be kept. - """ - raise NotImplementedError - - -class ExperimentEncoder(json.JSONEncoder): - def default(self, obj): # pylint: disable=method-hidden - if isinstance(obj, Product): - return { - "type": "product", - "items": obj.items, - } - if isinstance(obj, Linspace): - return { - "type": "linspace", - "start": obj.start, - "stop": obj.stop, - "num": obj.num, - "endpoint": obj.endpoint, - "values": obj.values, - } - if isinstance(obj, Move): - return { - "type": "move", - "wait_after": obj.wait_after, - "measure_while_moving": obj.measure_while_moving, - "backlash_compensate": obj.backlash_compensate, - "moveset": obj.moveset, - } - if isinstance(obj, Collect): - return { - "type": "collect", - "duration": obj.duration, - "configuration": obj.configuration, - } - return super().default(obj) - - -class FlatExperimentEncoder(json.JSONEncoder): - def default(self, obj): # pylint: disable=method-hidden - if isinstance(obj, Product): - return flatten(iter(obj)) - if isinstance(obj, Linspace): - return flatten(obj.values) - if isinstance(obj, Move): - return { - "type": "move", - "wait_after": obj.wait_after, - "measure_while_moving": obj.measure_while_moving, - "backlash_compensate": obj.backlash_compensate, - "moveset": obj.moveset, - } - if isinstance(obj, Collect): - return { - "type": "collect", - "duration": obj.duration, - "configuration": obj.configuration, - } - return super().default(obj) - - -class JSONExperimentDriver(ExperimentDriver): - """An ExperimentDriver which supports JSON serialization.""" - - def dumps(self, o, desired_total_time=None): - """Dumps the experiment sequence and performs a flattening pass.""" - initial_pass = json.dumps({"sequence": o, "configuration": {}}, cls=FlatExperimentEncoder) - - # we do an extra flattening pass here - dict_values = json.loads(initial_pass) - dict_values["sequence"] = flatten(dict_values["sequence"]) - return json.dumps(dict_values) diff --git a/docs/source/CHANGELOG.rst b/docs/source/CHANGELOG.rst index 1ff8d8ec..b3cf313c 100644 --- a/docs/source/CHANGELOG.rst +++ b/docs/source/CHANGELOG.rst @@ -9,6 +9,49 @@ Primary (X.-.-) version numbers are used to denote backwards incompatibilities between versions, while minor (-.X.-) numbers primarily indicate new features and documentation. + +4.0.0 (2024-01-01) + +New +~~~ + +Non-original author update. + +* Provide SPD_main.py and prodigy_itx.py to load the data measured with SPECS prodigy. +* A new method S.swap_angle_unit() to change the angle unit (deg <-> radian) + +Changed +~~~~~~~ +* Required python version >= 3.11 +* Introduce type hints. + - Type annotation sometimes limits the python's flexibility, but for induces the robustness, which is essentially useful for scientific analyais. + - Because of the same reason, drop the "flexibile" (from a certain view points, it may be pythonic) codes. +* Drop PyQt5, use PySide6 instead. +* Drop the Bokeh based functionalities because they are not compatible with the current jupyter. + - curvature_tool, comparison_tool + - While some of them might be useful, but at least when I started to use this, the compatibility was broken. I don't know how these were useful. +* Remove arpes.all +* And many! + * Remove G.extent + * Remove overlapped_stack_dispersion_plot + - use stack_dispersion_plot_with_appropriate_args + * Revise the k-conversion. The origianl version is correct from the view of the coding, but incorrect from the physics! + * introduce new attrs, "energy_notation". if not specified, attrs["energy_notation"] = "Binding" is assumed to keep the consistency from the previous version. + + * see Changes.md for others + +In coding style: + +* Drop carelessly set default=None + +Fixed +~~~~~ +* broadcast_model concatenation error #18 (https://github.com/chstan/arpes/issues/18) +* Fix error in BZ plot due to the recent version of ASE #20 +* Fix the import error in BZ plotting example #7 + + + 3.0.1 (2021-07-27) New @@ -220,7 +263,7 @@ New approximated Minor -~~~~~~ +^^^^^ 1. Some wrappers around getting Jupyter/IPython state 2. ``imread`` wrapper that chooses backend between ``imageio`` and diff --git a/docs/source/index.rst b/docs/source/index.rst index e4e43999..68cde754 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,6 +1,19 @@ PyARPES ======= -**Non maintainer update** +**V4 Release: Non maintainer update** +After V3 release, the origiinal author/maintainer seems to have relinquished maintenance of PyArpes. +While I have posted several pull-requests and comments, but very unfortunately, he have not responded at all. +Furthermore, he does not seems to conduct ARPES related scientific work. +That's would be main reason why he have not maintain it. There is no motivation to maintain codes those are not used. + +And after previous version release, python ecosystem has been improved. +Conda is not necessarilly the best system, especially for Mac users. +Rather, I believe that it has some adverse effects that tend to cause confusion. +Thus I have decided to drop the conda related. +I strongly recommend to use "rye", instead. + +While I have added many type hints in the codes, I still feel that the current package is not so easy to use for the less experienced Python users. +I still recommended igor to analyze, especially to the student. diff --git a/building-from-source.md b/legacy_files/building-from-source.md similarity index 100% rename from building-from-source.md rename to legacy_files/building-from-source.md diff --git a/conda/meta.yaml b/legacy_files/conda/meta.yaml similarity index 100% rename from conda/meta.yaml rename to legacy_files/conda/meta.yaml diff --git a/conda/run_test.py b/legacy_files/conda/run_test.py similarity index 100% rename from conda/run_test.py rename to legacy_files/conda/run_test.py diff --git a/environment-readthedocs.yml b/legacy_files/environment-readthedocs.yml similarity index 100% rename from environment-readthedocs.yml rename to legacy_files/environment-readthedocs.yml diff --git a/environment-update-test.yml b/legacy_files/environment-update-test.yml similarity index 100% rename from environment-update-test.yml rename to legacy_files/environment-update-test.yml diff --git a/package.json b/legacy_files/package.json similarity index 100% rename from package.json rename to legacy_files/package.json diff --git a/pypi-readme.rst b/legacy_files/pypi-readme.rst similarity index 100% rename from pypi-readme.rst rename to legacy_files/pypi-readme.rst diff --git a/package-lock.json b/package-lock.json deleted file mode 100644 index 480c1cbf..00000000 --- a/package-lock.json +++ /dev/null @@ -1,3526 +0,0 @@ -{ - "name": "python3", - "version": "3.0.0", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "name": "python3", - "version": "3.0.0", - "license": "GPL-3.0", - "dependencies": { - "lefthook": "^1.5.1", - "neovim": "^4.10.1", - "npm": "^10.2.0" - }, - "devDependencies": { - "@arkweid/lefthook": "^0.7.6" - } - }, - "node_modules/@arkweid/lefthook": { - "version": "0.7.7", - "resolved": "https://registry.npmjs.org/@arkweid/lefthook/-/lefthook-0.7.7.tgz", - "integrity": "sha512-Eq30OXKmjxIAIsTtbX2fcF3SNZIXS8yry1u8yty7PQFYRctx04rVlhOJCEB2UmfTh8T2vrOMC9IHHUvvo5zbaQ==", - "cpu": [ - "x64", - "arm64", - "ia32" - ], - "deprecated": "@arkweid/lefthook has been renamed to @evilmartians/lefthook, please upgrade to it. 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{ name = "Conrad Stansbury", email = "chstan@berkeley.edu" }, - { name = "Ryuichi Arafune", email = "ryuichi.arafune@gmail.com" }, -] -readme = "README.rst" -requires-python = ">= 3.10" [build-system] requires = ["hatchling"] build-backend = "hatchling.build" + [tool.rye] managed = true dev-dependencies = [ @@ -54,13 +57,15 @@ dev-dependencies = [ [tool.hatch.metadata] allow-direct-references = true +[tool.hatch.build.targets.wheel] +packages = ["src/arpes"] + [tool.coverge.run] -include = ["arpes"] omit = [ "tests/*", - "arpes/plotting/*", - "arpes/deep_learning/*", - "arpes/widgets.py", + "src/arpes/plotting/*", + "src/arpes/deep_learning/*", + "src/arpes/widgets.py", ] [tool.coverge.report] @@ -100,11 +105,11 @@ convention = "google" [tool.ruff.lint.per-file-ignores] -"__init__.py" = ["F401"] # unused-import -"arpes/__init__.py" = ["T201"] # print used -"arpes/experiment/__init__.py" = ["ALL"] -"arpes/workflow.py" = ["T201", "T203"] -"arpes/fits/lmfit_html_repr.py" = ["SLF001"] # private member accecced +"__init__.py" = ["F401"] # unused-import +"src/arpes/__init__.py" = ["T201"] # print used +"src/arpes/experiment/__init__.py" = ["ALL"] +"src/arpes/workflow.py" = ["T201", "T203"] +"src/arpes/fits/lmfit_html_repr.py" = ["SLF001"] # private member accecced [tool.mypy] ignore_missing_imports = true @@ -117,6 +122,5 @@ name = "cz_emoji" version = "0.0.1" tag_format = "$version" - [tool.coverage.report] exclude_also = ["if TYPE_CHECKING:"] 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/arpes/__init__.py b/src/arpes/__init__.py similarity index 98% rename from arpes/__init__.py rename to src/arpes/__init__.py index 06e0f69b..639e42bc 100644 --- a/arpes/__init__.py +++ b/src/arpes/__init__.py @@ -6,7 +6,7 @@ import warnings # Use both version conventions for people's sanity. -VERSION = "3.1.0daredevil" +VERSION = "4.0.0 beta1" __version__ = VERSION diff --git a/arpes/_typing.py b/src/arpes/_typing.py similarity index 100% rename from arpes/_typing.py rename to src/arpes/_typing.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/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 98% rename from arpes/analysis/deconvolution.py rename to src/arpes/analysis/deconvolution.py index 56ad03ba..5756499a 100644 --- a/arpes/analysis/deconvolution.py +++ b/src/arpes/analysis/deconvolution.py @@ -40,7 +40,7 @@ def deconvolve_ice( psf: NDArray[np.float_], n_iterations: int = 5, deg: int | None = None, -) -> DataType: +) -> xr.DataArray | NDArray[np.float_]: """Deconvolves data by a given point spread function (PSF). The iterative convolution extrapolation method is used. @@ -55,8 +55,8 @@ def deconvolve_ice( Returns: The deconvoled data in the same format. """ - data = data if isinstance(data, xr.DataArray) else normalize_to_spectrum(data).values - arr = data.values + data = data if isinstance(data, xr.DataArray) else normalize_to_spectrum(data) + arr: NDArray[np.float_] = data.values if deg is None: deg = n_iterations - 3 iteration_steps = list(range(1, n_iterations + 1)) @@ -65,10 +65,10 @@ def deconvolve_ice( for _ in range(n_iterations - 1): iteration_list.append(scipy.ndimage.convolve(iteration_list[-1], psf)) - iteration_list = np.asarray(iteration_list) + iteration_array = np.asarray(iteration_list) deconv = arr * 0 - for t, series in enumerate(iteration_list.T): + for t, series in enumerate(iteration_array.T): coefs = np.polyfit(iteration_steps, series, deg=deg) poly = np.poly1d(coefs) deconv[t] = poly(0) 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 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a/arpes/preparation/hemisphere_preparation.py b/src/arpes/preparation/hemisphere_preparation.py similarity index 100% rename from arpes/preparation/hemisphere_preparation.py rename to src/arpes/preparation/hemisphere_preparation.py diff --git a/arpes/preparation/tof_preparation.py b/src/arpes/preparation/tof_preparation.py similarity index 100% rename from arpes/preparation/tof_preparation.py rename to src/arpes/preparation/tof_preparation.py diff --git a/arpes/provenance.py b/src/arpes/provenance.py similarity index 100% rename from arpes/provenance.py rename to src/arpes/provenance.py diff --git a/arpes/repair.py b/src/arpes/repair.py similarity index 100% rename from arpes/repair.py rename to src/arpes/repair.py diff --git a/arpes/simulation.py b/src/arpes/simulation.py similarity index 100% rename from arpes/simulation.py rename to src/arpes/simulation.py diff --git a/arpes/utilities/__init__.py b/src/arpes/utilities/__init__.py similarity index 100% rename from arpes/utilities/__init__.py rename to src/arpes/utilities/__init__.py diff --git a/arpes/utilities/bz.py b/src/arpes/utilities/bz.py similarity index 100% rename from arpes/utilities/bz.py rename to src/arpes/utilities/bz.py diff --git a/arpes/utilities/bz_spec.py b/src/arpes/utilities/bz_spec.py similarity index 100% rename from arpes/utilities/bz_spec.py rename to src/arpes/utilities/bz_spec.py diff --git a/arpes/utilities/collections.py b/src/arpes/utilities/collections.py similarity index 100% rename from arpes/utilities/collections.py rename to src/arpes/utilities/collections.py diff --git a/arpes/utilities/combine.py b/src/arpes/utilities/combine.py similarity index 100% rename from arpes/utilities/combine.py rename to src/arpes/utilities/combine.py diff --git a/arpes/utilities/conversion/__init__.py b/src/arpes/utilities/conversion/__init__.py similarity index 100% rename from arpes/utilities/conversion/__init__.py rename to src/arpes/utilities/conversion/__init__.py diff --git a/arpes/utilities/conversion/base.py b/src/arpes/utilities/conversion/base.py similarity index 100% rename from arpes/utilities/conversion/base.py rename to src/arpes/utilities/conversion/base.py diff --git a/arpes/utilities/conversion/bounds_calculations.py b/src/arpes/utilities/conversion/bounds_calculations.py similarity index 100% rename from arpes/utilities/conversion/bounds_calculations.py rename to src/arpes/utilities/conversion/bounds_calculations.py diff --git a/arpes/utilities/conversion/calibration.py b/src/arpes/utilities/conversion/calibration.py similarity index 100% rename from arpes/utilities/conversion/calibration.py rename to src/arpes/utilities/conversion/calibration.py diff --git a/arpes/utilities/conversion/core.py b/src/arpes/utilities/conversion/core.py similarity index 100% rename from arpes/utilities/conversion/core.py rename to src/arpes/utilities/conversion/core.py diff --git a/arpes/utilities/conversion/fast_interp.py b/src/arpes/utilities/conversion/fast_interp.py similarity index 100% rename from arpes/utilities/conversion/fast_interp.py rename to src/arpes/utilities/conversion/fast_interp.py diff --git a/arpes/utilities/conversion/forward.py b/src/arpes/utilities/conversion/forward.py similarity index 99% rename from arpes/utilities/conversion/forward.py rename to src/arpes/utilities/conversion/forward.py index 8d8f64a4..4e493cdd 100644 --- a/arpes/utilities/conversion/forward.py +++ b/src/arpes/utilities/conversion/forward.py @@ -48,7 +48,7 @@ LOGLEVELS = (DEBUG, INFO) -LOGLEVEL = LOGLEVELS[1] +LOGLEVEL = LOGLEVELS[0] logger = getLogger(__name__) fmt = "%(asctime)s %(levelname)s %(name)s :%(message)s" formatter = Formatter(fmt) @@ -228,6 +228,7 @@ def convert_through_angular_pair( # noqa: PLR0913 # perform the conversion logger.debug("Performing final momentum conversion.") + logger.debug("transverse_specification : {transverse_specification}") converted_data = convert_to_kspace( data, **transverse_specification, diff --git a/arpes/utilities/conversion/grids.py b/src/arpes/utilities/conversion/grids.py similarity index 100% rename from arpes/utilities/conversion/grids.py rename to src/arpes/utilities/conversion/grids.py diff --git a/arpes/utilities/conversion/kx_ky_conversion.py b/src/arpes/utilities/conversion/kx_ky_conversion.py similarity index 100% rename from arpes/utilities/conversion/kx_ky_conversion.py rename to src/arpes/utilities/conversion/kx_ky_conversion.py diff --git a/arpes/utilities/conversion/kz_conversion.py b/src/arpes/utilities/conversion/kz_conversion.py similarity index 100% rename from arpes/utilities/conversion/kz_conversion.py rename to src/arpes/utilities/conversion/kz_conversion.py diff --git a/arpes/utilities/conversion/remap_manipulator.py b/src/arpes/utilities/conversion/remap_manipulator.py similarity index 100% rename from arpes/utilities/conversion/remap_manipulator.py rename to src/arpes/utilities/conversion/remap_manipulator.py diff --git a/arpes/utilities/conversion/trapezoid.py b/src/arpes/utilities/conversion/trapezoid.py similarity index 100% rename from arpes/utilities/conversion/trapezoid.py rename to src/arpes/utilities/conversion/trapezoid.py diff --git a/arpes/utilities/dict.py b/src/arpes/utilities/dict.py similarity index 100% rename from arpes/utilities/dict.py rename to src/arpes/utilities/dict.py diff --git a/arpes/utilities/excepthook.py b/src/arpes/utilities/excepthook.py similarity index 100% rename from arpes/utilities/excepthook.py rename to src/arpes/utilities/excepthook.py diff --git a/arpes/utilities/funcutils.py b/src/arpes/utilities/funcutils.py similarity index 100% rename from arpes/utilities/funcutils.py rename to src/arpes/utilities/funcutils.py diff --git a/arpes/utilities/geometry.py b/src/arpes/utilities/geometry.py similarity index 100% rename from arpes/utilities/geometry.py rename to src/arpes/utilities/geometry.py diff --git a/arpes/utilities/image.py b/src/arpes/utilities/image.py similarity index 100% rename from arpes/utilities/image.py rename to src/arpes/utilities/image.py diff --git a/arpes/utilities/jupyter.py b/src/arpes/utilities/jupyter.py similarity index 100% rename from arpes/utilities/jupyter.py rename to src/arpes/utilities/jupyter.py diff --git a/arpes/utilities/math.py b/src/arpes/utilities/math.py similarity index 100% rename from arpes/utilities/math.py rename to src/arpes/utilities/math.py diff --git a/arpes/utilities/normalize.py b/src/arpes/utilities/normalize.py similarity index 100% rename from arpes/utilities/normalize.py rename to src/arpes/utilities/normalize.py diff --git a/arpes/utilities/qt/__init__.py b/src/arpes/utilities/qt/__init__.py similarity index 100% rename from arpes/utilities/qt/__init__.py rename to src/arpes/utilities/qt/__init__.py diff --git a/arpes/utilities/qt/app.py b/src/arpes/utilities/qt/app.py similarity index 100% rename from arpes/utilities/qt/app.py rename to src/arpes/utilities/qt/app.py diff --git a/arpes/utilities/qt/data_array_image_view.py b/src/arpes/utilities/qt/data_array_image_view.py similarity index 100% rename from arpes/utilities/qt/data_array_image_view.py rename to src/arpes/utilities/qt/data_array_image_view.py diff --git a/arpes/utilities/qt/help_dialogs.py b/src/arpes/utilities/qt/help_dialogs.py similarity index 100% rename from arpes/utilities/qt/help_dialogs.py rename to src/arpes/utilities/qt/help_dialogs.py diff --git a/arpes/utilities/qt/utils.py b/src/arpes/utilities/qt/utils.py similarity index 100% rename from arpes/utilities/qt/utils.py rename to src/arpes/utilities/qt/utils.py diff --git a/arpes/utilities/qt/windows.py b/src/arpes/utilities/qt/windows.py similarity index 100% rename from arpes/utilities/qt/windows.py rename to src/arpes/utilities/qt/windows.py diff --git a/arpes/utilities/region.py 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 diff --git a/tests/test_prodigy_itx.py b/tests/test_prodigy_itx.py index 7f6d6bdc..57bc1881 100644 --- a/tests/test_prodigy_itx.py +++ b/tests/test_prodigy_itx.py @@ -8,7 +8,7 @@ from arpes.endstations.prodigy_itx import ProdigyItx, load_sp2 -data_dir = Path(__file__).parent.parent / "arpes" / "example_data" +data_dir = Path(__file__).parent.parent / "src" / "arpes" / "example_data" @pytest.fixture()