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Toward 5.0 #24

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6cde41d
🎨 Simplify degrees_of_freedom
arafune May 8, 2024
fdc2e08
💡 Update Change.md
arafune May 8, 2024
5ae66f8
💡 Update ipynb
arafune May 8, 2024
6454179
🎨 Move is_subtracted to ARPESDataArrayAccessorBase
arafune May 8, 2024
588ba20
💡 Update doc
arafune May 9, 2024
14eef1f
🎨 Rearrange the methods in xarray_extensions.py
arafune May 10, 2024
cedabab
💬 Update type hints
arafune May 10, 2024
3c980f0
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune May 10, 2024
6a59ee9
🎨 Add category in warning.warn
arafune May 10, 2024
9c500ec
💬 Fix wrong type. get_coordintes can return like {"delay": np.array(…
arafune May 10, 2024
058f1ef
🎨 Add encoding arg to Path.open
arafune May 12, 2024
da457b6
💬 Update type hints
arafune May 12, 2024
ba18231
💬 Update type hints
arafune May 12, 2024
f278ab0
💬 Update type hints
arafune May 14, 2024
16ef1d9
💬 Update type hints
arafune May 16, 2024
815a332
💬 Update docments
arafune May 17, 2024
b61e88c
🔥 remove clean_attribute_names, clean_datavar_attribute_names becaus…
arafune May 20, 2024
a5e261b
💬 update type hints
arafune May 20, 2024
cef3b95
💬 Update type hints
arafune May 22, 2024
c9b47a9
💬 update type hints
arafune May 22, 2024
f586c1f
💬 update type hints
arafune May 22, 2024
e0cf659
🎨 Add TypeGuard
arafune May 22, 2024
d40a9e0
💬 update type hints
arafune May 22, 2024
a8a173b
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune May 22, 2024
d802319
💬 Update type hints
arafune May 22, 2024
704d2e6
💬 update type hints
arafune May 23, 2024
3d12eb0
💬 Update type hints
arafune May 23, 2024
863e1cc
💬 Update type hints
arafune May 23, 2024
630ca31
🔨 Just a tiny refactoring
arafune May 24, 2024
460f32c
💬
arafune May 26, 2024
6d5c241
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune May 26, 2024
7b125c5
🔥 Remove it, which does not seem to be so useful.
arafune May 28, 2024
c692f9d
💬 Update type hints
arafune May 29, 2024
6cdcf6d
💬 Update type hints
arafune May 29, 2024
d55af35
Merge branch 'daredevil' of https://github.com/arafune/arpes into dar…
arafune May 29, 2024
95bdba7
💬 Update type hints
arafune May 29, 2024
d1e1251
💬 update type hints
arafune May 29, 2024
2722f5a
💬 Add "PendingDeprecatedWarning"
arafune May 29, 2024
dfb8376
Merge branch 'daredevil' of https://github.com/arafune/arpes into dar…
arafune May 30, 2024
6a9d4a2
💬 Update type hints & add widget.py to the list for mypy ignore
arafune May 31, 2024
5e71d58
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune May 31, 2024
032085b
💬 Update type hints
arafune May 31, 2024
2f15d76
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune May 31, 2024
68e3e1a
💬 tryp to make XCompoisteModelMixin
arafune May 31, 2024
bd1f7b0
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune May 31, 2024
2b1cf03
🐛 (Fix)
arafune Jun 1, 2024
77bf3c0
🔧 Update required ase version.
arafune Jun 1, 2024
2fb95da
💬 (chroe): update type hints
arafune Jun 1, 2024
143e145
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 2, 2024
bf8aa6c
✅ add test_G_shift
arafune Jun 3, 2024
4365882
✅ Update conftest.py
arafune Jun 3, 2024
63e1245
✅ Add test for conversion/forward.py
arafune Jun 3, 2024
08a0871
Apply ruff --fix
arafune Jun 3, 2024
1242bb6
🐛 Typo fix
arafune Jun 3, 2024
ee99875
🚨 Remove a mypy warning
arafune Jun 3, 2024
f11ecf6
✅ Add test
arafune Jun 3, 2024
01e1d62
🔥 Remove fits/zones.py (Not used)
arafune Jun 3, 2024
7941a54
💬 Update type hits
arafune Jun 3, 2024
a59708a
💬 Update type hints around broadcast_model
arafune Jun 3, 2024
3aee94c
🔨 Stop using xarray.enumerate_dataarray.
arafune Jun 3, 2024
47a090d
💡 Update docs.
arafune Jun 3, 2024
2e8632c
🔨 G.iter_coords is simpler.
arafune Jun 3, 2024
711861d
💬 While I'm not 100% sure about the difference of "Iterator" and "Ge…
arafune Jun 3, 2024
c1c5c84
💡 Update docstrings
arafune Jun 3, 2024
1ae99e6
💡 latexpdf works well
arafune Jun 3, 2024
8cc3329
✏️
arafune Jun 3, 2024
79ea4f3
💬 Update type hints
arafune Jun 4, 2024
fb91924
⬆️ ase dependency
arafune Jun 4, 2024
4fe1f3f
✅ Test for G.shift_by
arafune Jun 4, 2024
5ebab85
✅ Add test for F.bands
arafune Jun 4, 2024
1ccacee
🚨 Add TypeGuard
arafune Jun 4, 2024
6ceed3e
✅ Test for parse_model
arafune Jun 4, 2024
058ecf9
💡 Update type hints
arafune Jun 4, 2024
d5d94d5
💬 Update type hints
arafune Jun 4, 2024
8c51792
💬 Update type hints
arafune Jun 4, 2024
474e77e
💬 Update type hints
arafune Jun 4, 2024
559c6d9
💡 Update docstring
arafune Jun 4, 2024
5b051f5
💬 Update doc
arafune Jun 4, 2024
6e205e6
🎨 Renname IF_UCMS to IF_UCMSEndstation for consistency
arafune Jun 4, 2024
d85329f
🎨 Raise the version to 4.0 beta2.
arafune Jun 5, 2024
d54055b
💡 Update documentation.
arafune Jun 5, 2024
8dd34d5
🔨 Rename tarpes.find_t0, as the definition of t=0 is not always true.
arafune Jun 5, 2024
9eff6d0
💬 Update type hints
arafune Jun 5, 2024
50cf146
💡 Update type hints
arafune Jun 5, 2024
eec5e52
💬 Update type hints
arafune Jun 5, 2024
d9f66db
💡 Update docs
arafune Jun 5, 2024
9933618
💡 Update docs
arafune Jun 5, 2024
58957fe
💡 Update docs.
arafune Jun 6, 2024
5c5cfee
💡 Update docs
arafune Jun 6, 2024
8d4bee1
💬 Update type hints
arafune Jun 7, 2024
24fb6f0
🔨 rename template -> results
arafune Jun 7, 2024
eb61c9f
💬 Update type hints
arafune Jun 7, 2024
1ebfa17
💬 Update type hints / docs
arafune Jun 7, 2024
f2dddb6
💥 arg name change with_attrs -> keep_attrs
arafune Jun 7, 2024
3c73057
💬 Update type hints
arafune Jun 7, 2024
1aac352
🔥 lmfit_html_repr is removed (move to legacy_files), because of unne…
arafune Jun 7, 2024
fd84edd
💬 Update type hints
arafune Jun 7, 2024
32b91d7
🔥 Remove normalize_to_dataset because of unneeded
arafune Jun 7, 2024
8817a99
🎨
arafune Jun 7, 2024
818a27a
🔥 Remove ParametersArgsFull
arafune Jun 7, 2024
b69c8c9
💬 Update type hints
arafune Jun 7, 2024
896047e
💬 Update type hints
arafune Jun 7, 2024
e7053c9
💬 Update type hints
arafune Jun 7, 2024
6ed1e77
💬
arafune Jun 7, 2024
16b91e9
💬 Update type hints
arafune Jun 7, 2024
e87ea93
💬 Update type hitns
arafune Jun 7, 2024
deea7ec
🐛
arafune Jun 8, 2024
acfa22a
💬 Update type hints
arafune Jun 8, 2024
51a9cab
💬 Update type hints
arafune Jun 8, 2024
551e8a5
💥 Change provenance in Dataset by broadcast_model.
arafune Jun 8, 2024
178fcd5
💬 Update docs
arafune Jun 8, 2024
7f6525b
💥 with_values method in "F" moves to "G".
arafune Jun 8, 2024
c1dc437
💬 Update type hints
arafune Jun 8, 2024
6e575cc
💥 S.with_values -> G.with_values
arafune Jun 8, 2024
1e47a52
🎨 Revise the helper function a bit.
arafune Jun 8, 2024
339180f
💬 Update doc string
arafune Jun 8, 2024
2c3f8ba
💡 Update docs
arafune Jun 8, 2024
bdac298
💡 Update docs
arafune Jun 9, 2024
c0a3836
🎨 Revise the helper function a bit.
arafune Jun 9, 2024
b5aaee8
💡 Update docs
arafune Jun 9, 2024
ee57982
🎨 Update inherit relationship in ARPESProperty
arafune Jun 10, 2024
cda7f21
🎨
arafune Jun 10, 2024
b1d8cc9
🎨 Rename variable / method
arafune Jun 10, 2024
2b38fc7
💬 Update type hints
arafune Jun 10, 2024
6c0a391
🎨 Hack unpack_band_from_fit.
arafune Jun 10, 2024
6cbbf96
🎨 with statement is recommended in using nditer
arafune Jun 10, 2024
3fa446c
💬 Update type hints
arafune Jun 11, 2024
debbec3
💡 Update docs
arafune Jun 11, 2024
38bb602
🔥 .F.bands will be deprecated.
arafune Jun 11, 2024
8b35eeb
💬 Update type hints
arafune Jun 11, 2024
8429e58
🎨 Try to remove ruff warning. Now, eventually, the codes are rurr-free.
arafune Jun 11, 2024
e3eadfb
💥 Parameter name of AffinneBroadenedFD: fd_center -> center, fd_widt…
arafune Jun 11, 2024
c9cbe2d
💬 Update type hints.
arafune Jun 11, 2024
fecbfeb
🎨 Revise _modelresults_to_array
arafune Jun 11, 2024
c7a4f4a
💡 Update doc
arafune Jun 11, 2024
f14dd90
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 11, 2024
8b13bea
💬 Revise docs (and considering refactor of the select_around_dta)
arafune Jun 12, 2024
3b37fad
🎨 Revise fat_sel a bit.
arafune Jun 12, 2024
ae80379
🔥 Remove S.fermi_surface, S.generic_fermi_surface
arafune Jun 13, 2024
d7e6191
🔥 Remove S.along that is the syntax sugar of slice_along_path
arafune Jun 13, 2024
5d7a719
🔥 Add DeprecatedWarning to plot_plane_bz, and process_kpath
arafune Jun 13, 2024
d389e4a
🎨 Update derivative1d and add test for it.
arafune Jun 13, 2024
85e8662
🎨 Change argument name in curvature2d directions -> dims to keep con…
arafune Jun 13, 2024
de24cb9
🎨 Store attrs in derivative analyis results.
arafune Jun 13, 2024
28c9382
✅ Add test for G.enumerate_iter_coords
arafune Jun 14, 2024
3e02e1b
🎨 G.shift_coords, G.scale_coords, and G.transform_coords is xr.Datas…
arafune Jun 14, 2024
95d9c04
♿️ Improving the code readability
arafune Jun 15, 2024
690e1e8
🎨 Remove verbose variable
arafune Jun 15, 2024
6c9e836
🔨 Use simple enumerate instead of np.nditer
arafune Jun 15, 2024
615b290
🚨
arafune Jun 15, 2024
a6bf997
🔨 Improve the readability
arafune Jun 15, 2024
5425ccd
💬 Update type hints
arafune Jun 15, 2024
8fe2e76
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 15, 2024
612f050
🔥 Remove description about iterate_axis which will be removed.
arafune Jun 16, 2024
8601410
🔥 Remove iterate_axis related methods but not iterate_axis itself
arafune Jun 16, 2024
65623a2
📝 Add about removal of G.iterate_axis
arafune Jun 16, 2024
fd0e4f5
🚨 Apply ruff to fix NPY201 error.
arafune Jun 16, 2024
4cd8918
✨ Preparation for removing xr.Dataset.F (all method should be only i…
arafune Jun 17, 2024
34f2577
🔥 Remove most methods in xr.Dataset.F
arafune Jun 17, 2024
964aeed
💬 Update type hints
arafune Jun 17, 2024
fbc4b15
🔥 Remove polarization_plot
arafune Jun 17, 2024
f71ff3e
💬 Update type hints
arafune Jun 17, 2024
c713887
💬 Update type hints
arafune Jun 17, 2024
e8fa591
🔧 Tidiy up pyproject.toml a bit
arafune Jun 17, 2024
e519b4b
💬 Update type hints
arafune Jun 17, 2024
12daed0
💬 update type hints
arafune Jun 17, 2024
1f6f5ac
💬 Update type hints
arafune Jun 17, 2024
aa1fe5f
Merge branch 'daredevil' of https://github.com/arafune/arpes into dar…
arafune Jun 18, 2024
a983f62
💬 Update type hints
arafune Jun 18, 2024
0de2109
Specify by kwargs
arafune Jun 18, 2024
4ba2206
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 18, 2024
bedc8a3
💬 Update type hints
arafune Jun 18, 2024
f422e07
Merge branch 'daredevil' of https://github.com/arafune/arpes into dar…
arafune Jun 18, 2024
51191e2
Fix ruff warning.
arafune Jun 18, 2024
eefe018
Merge branch 'daredevil' of https://github.com/arafune/arpes into dar…
arafune Jun 18, 2024
ab8d087
✅ Add test for stack_plot
arafune Jun 20, 2024
a7cf3dd
🔨 Just a very tiny refactoring
arafune Jun 20, 2024
304a17a
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 20, 2024
48d3291
✅ Add test for stack_plot
arafune Jun 21, 2024
0c08e57
✨ Add reverse arg to G.iter_coords
arafune Jun 21, 2024
bdfb407
🎨 Use G.iter_coords(reverse=True)
arafune Jun 21, 2024
80b4b79
just a tiny refactoring.
arafune Jun 24, 2024
4cffee8
⚡️ Re-implement plot_dos, plot_xps_spectrum and savitzky_golay funct…
arafune Jun 24, 2024
04b6afa
⚡️ Enable log plot
arafune Jun 24, 2024
0b3a400
🚨 These files have been ruff free.
arafune Jun 24, 2024
5967366
🔥 Remove no_ticks function which is just a reallly tiny wrapper
arafune Jun 25, 2024
452f416
➕ Add titlecase to the dependencies
arafune Jun 25, 2024
3939a2b
🔥 Remove the functions that I don't think it's useful.
arafune Jun 25, 2024
31a5843
✅ Add test for xps.py
arafune Jun 25, 2024
caa57e1
💬 Update type hints
arafune Jun 25, 2024
6058f4d
💬 Update type hints
arafune Jun 25, 2024
3a9c72c
🔧 Update pyproject.toml
arafune Jun 25, 2024
a92b113
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 25, 2024
babefce
🎨 the values in test are changed: To pass the test, require scipy>=1…
arafune Jun 26, 2024
0c1f827
⚡️ prodigy_itx accepts 4D itx data.
arafune Jun 26, 2024
9842dda
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 26, 2024
d09a9d2
🚨 some import lines move to top
arafune Jun 27, 2024
a29d106
🚨 Apply ruff check src --fix
arafune Jun 27, 2024
30f9ec8
🔨 A tiny refactoring
arafune Jun 27, 2024
1cd82e5
🐛 Avoid circularly importing...
arafune Jun 27, 2024
48d1781
⚡️ Record the file in the provenance
arafune Jun 28, 2024
d3ecc33
Update type hints
arafune Jun 28, 2024
75b187c
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jun 28, 2024
9ae8674
🚨 'import' moves to top region
arafune Jun 29, 2024
79a6a1a
💬 Update type hints
arafune Jul 1, 2024
66d7f74
💬 update type hints
arafune Jul 1, 2024
4b0a110
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jul 1, 2024
71bfb50
🐛 Fix bug in _parse_itx_head
arafune Jul 2, 2024
ef17465
💬 Update type hints
arafune Jul 3, 2024
ed0faf8
🚨
arafune Jul 3, 2024
2c58819
Drop G.to_unit_range
arafune Jul 5, 2024
2fe409a
🚚 Gathering the qt-based library into qt directory
arafune Jul 6, 2024
13453c2
fix ruff warning
arafune Jul 6, 2024
37a4ae9
Merge branch 'daredevil' of github.com:arafune/arpes into daredevil
arafune Jul 6, 2024
02d4f92
✨ new function: make_overview
arafune Jul 6, 2024
22f4b84
🎨 Modify format a bit.
arafune Jul 7, 2024
8e79271
💡 Update type hints
arafune Jul 7, 2024
5f7b03c
✨ Use holoview (it would be better way than direct use of bokeh.)
arafune Jul 7, 2024
677b565
💬 update crosshair_view
arafune Jul 8, 2024
cc9db4a
💡 Add docs
arafune Jul 8, 2024
0123d03
🚑 Fix in crosshair_view
arafune Jul 8, 2024
55f8369
🍻 Update parabolic band but not not fixed yet.
arafune Jul 8, 2024
8fcf211
🐛 Fix bug to show the kspace data.
arafune Jul 10, 2024
db28d91
Update formatting.
arafune Jul 10, 2024
110c75d
🎨
arafune Jul 10, 2024
07d63fe
🐛 Fix bug in x- and y- label
arafune Jul 10, 2024
db569b0
✅ Add test for crosshair_view
arafune Jul 10, 2024
853da00
🎨 DATA_PATH moves to __init__.py
arafune Jul 10, 2024
79f78d0
🎨
arafune Jul 10, 2024
c76667a
🎨
arafune Jul 10, 2024
7da47e8
🎨 CONFIG moves to __init__.py and pytest passes
arafune Jul 10, 2024
d62ba9e
🔥 Remove unneeded "import xarray_extension"
arafune Jul 10, 2024
3212308
🔥 Remove .S from files in endstations/
arafune Jul 10, 2024
7a9ceb8
💬 Remove unused args
arafune Jul 10, 2024
ad45e35
🎨 Just update the code following ruff suggestion.
arafune Jul 10, 2024
79cabd9
✨ Add a new_property parent_id
arafune Jul 10, 2024
8d95e77
✨ Use parent_id
arafune Jul 10, 2024
79f6f38
💡 Add memo for toward version 5.0
arafune Jul 11, 2024
2a461b7
💬 Update sort of import
arafune Jul 11, 2024
9c38ff4
🎨
arafune Jul 11, 2024
d243f46
Merge branch 'daredevil' into global_moves_to_init
arafune Jul 11, 2024
d299d0d
🚨
arafune Jul 11, 2024
6481cf3
✨ New feature fit_inspection by using holoview
arafune Jul 11, 2024
0c493a2
Rename crosshair_view -> profile_view
arafune Jul 11, 2024
bf3eefb
Show residual
arafune Jul 11, 2024
3fd3e40
Update profile view (font size change)
arafune Jul 11, 2024
ab1dc7b
Update api.rst
arafune Jul 11, 2024
3d597c9
🎨
arafune Jul 12, 2024
50ac968
Merge branch 'daredevil' of https://github.com/arafune/arpes into dar…
arafune Jul 12, 2024
2a1dc06
🎉 Release 4.0
arafune Jul 12, 2024
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💬 Update type hints
  • Loading branch information
arafune committed May 14, 2024
commit f278ab08c8eacdf31a3fa57fc301d8975bf70295
20 changes: 11 additions & 9 deletions src/arpes/bootstrap.py
Original file line number Diff line number Diff line change
@@ -33,12 +33,14 @@
from .utilities.region import normalize_region

if TYPE_CHECKING:
from collections.abc import Callable
from collections.abc import Callable, Iterable

import lmfit as lf
from _typeshed import Incomplete
from numpy.typing import NDArray

from arpes._typing import DataType

__all__ = (
"Normal",
"bootstrap",
@@ -85,17 +87,17 @@ def estimate_prior_adjustment(
Returns:
sigma / mu, the adjustment factor for the Poisson distribution
"""
data_array = data if isinstance(data, xr.DataArray) else normalize_to_spectrum(data)
data = data if isinstance(data, xr.DataArray) else normalize_to_spectrum(data)
if region is None:
region = "copper_prior"

region = normalize_region(region)

if "cycle" in data_array.dims:
data_array = data_array.sum("cycle")
if "cycle" in data.dims:
data = data.sum("cycle")

data_array = data_array.S.zero_spectrometer_edges().S.region_sel(region)
values = data_array.values.ravel()
data = data.S.zero_spectrometer_edges().S.region_sel(region)
values = data.values.ravel()
values = values[np.where(values)]
return np.std(values) / np.mean(values)

@@ -323,10 +325,10 @@ def bootstrap_intensity_polarization(data: xr.Dataset, n: int = 100) -> xr.Datas


def bootstrap(
fn: Callable[..., xr.Dataset | xr.DataArray],
skip: set[int] | list[int] | None = None,
fn: Callable[..., DataType],
skip: Iterable[int] | None = None,
resample_method: str | None = None,
) -> Callable[..., xr.DataArray | xr.Dataset]:
) -> Callable[..., DataType]:
"""Produces function which performs a bootstrap of an arbitrary function by sampling.

This is a functor which takes a function operating on plain data and produces one which
4 changes: 2 additions & 2 deletions src/arpes/plotting/dispersion.py
Original file line number Diff line number Diff line change
@@ -27,7 +27,7 @@
from matplotlib.figure import Figure, FigureBase
from numpy.typing import NDArray

from arpes._typing import PColorMeshKwargs, XrTypes
from arpes._typing import DataType, PColorMeshKwargs, XrTypes
from arpes.models.band import Band

__all__ = (
@@ -373,7 +373,7 @@ class LabeledFermiSurfaceParam(TypedDict, total=False):

@save_plot_provenance
def reference_scan_fermi_surface(
data: XrTypes,
data: DataType,
**kwargs: Unpack[LabeledFermiSurfaceParam],
) -> Path | Axes:
"""A reference plot for Fermi surfaces. Used internally by other code.
5 changes: 4 additions & 1 deletion src/arpes/workflow.py
Original file line number Diff line number Diff line change
@@ -242,7 +242,10 @@ def from_workspace(
workspace: WorkSpaceType | None = None,
) -> DataProvider:
if workspace is not None:
return cls(path=Path(workspace["path"]), workspace_name=workspace["name"])
return cls(
path=Path(workspace["path"]),
workspace_name=workspace.get("name", "no_name"),
)

return cls(path=Path(Path.cwd()), workspace_name=None)