Merge branch 'main' of https://github.com/arafune/arpes

.github/workflows/python-app.yml

@@ -5,7 +5,7 @@ name: Python application
 
 on:
   push:
-    branches: ["main"]
+    branches: ["**"]
   pull_request:
     branches: ["main"]
 
@@ -37,4 +37,15 @@ jobs:
       - name: Rye activation
         run: |
           rye sync
-          rye run pytest tests
+
+      - name: test with rye
+        run: rye run pytest -vv --color=yes --cov=./  --cov-report=xml
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true # optional (default = false)
+          files: ./coverage.xml
+          flags: unittests # optional
+          name: codecov-umbrella # optional
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+          verbose: true # optional (default = false)

.github/workflows/ruff.yml

@@ -9,4 +9,5 @@ jobs:
       - uses: actions/checkout@v4
       - uses: chartboost/ruff-action@v1
         with:
+          src: "./src"
           python-version: "3.11"

README.rst

@@ -12,10 +12,8 @@
 
 .. |docs_status| image:: https://readthedocs.org/projects/arpes-v4/badge/?version=daredevil&style=flat
    :target: https://arpes-v4.readthedocs.io/en/daredevil/
-.. |coverage| image:: https://codecov.io/gh/chstan/arpes/branch/master/graph/badge.svg?token=mVrFuVRr3p
+.. |coverage| image:: https://codecov.io/gh/arafune/arpes/graph/badge.svg?token=TW9EPVB1VE
    :target:  https://app.codecov.io/gh/arafune/arpes
-.. |test_status| image:: https://github.com/arafune/arpes/actions/workflows/test.yml/badge.svg?branch=master
-   :target: https://github.com/arafune/arpes/actions/workflows/test.yml
 .. |code style| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black
 .. |code fromat| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json

docs/source/CHANGELOG.rst

@@ -9,11 +9,7 @@ Primary (X.-.-) version numbers are used to denote backwards
 incompatibilities between versions, while minor (-.X.-) numbers
 primarily indicate new features and documentation.
 
-4.0.1 ()
-
-New
-~~~
-
+4.0.1 (2024-07-21)
 
 
 Changed

pyproject.toml

@@ -10,28 +10,28 @@ readme = "README.rst"
 requires-python = ">= 3.11"
 
 dependencies = [
-  "holoviews>=1.16.0",
-  "astropy>=6.1",
-  "xarray>=2023.9.0",
-  "lmfit>=1.3.1",
-  "matplotlib>=3.8.0",
-  "pint>=0.22",
-  "h5py>=3.11.0",
-  "ase>=3.23.0",
-  "dill>=0.3.6",
-  "tqdm>=4.65.0",
-  "numba>=0.57.1",
-  "scikit-learn>=1.4.2",
-  "scikit-image>=0.20.0",
-  "netcdf4>=1.6.4",
-  "rx>=3.2.0",
-  "jupyter_server>=2.8",
-  "hvplot>=0.10",
-  "ipywidgets",
-  "ipykernel",
-  "more-itertools>=10.2.0",
-  "igorpy @ git+https://github.com/arafune/igorpy.git",
-  "titlecase>=2.4.1",
+    "holoviews>=1.16.0",
+    "astropy>=6.1",
+    "xarray>=2023.9.0",
+    "lmfit>=1.3.1",
+    "matplotlib>=3.8.0",
+    "pint>=0.22",
+    "h5py>=3.11.0",
+    "ase>=3.23.0",
+    "dill>=0.3.6",
+    "tqdm>=4.65.0",
+    "numba>=0.57.1",
+    "scikit-learn>=1.4.2",
+    "scikit-image>=0.20.0",
+    "rx>=3.2.0",
+    "jupyter_server>=2.8",
+    "hvplot>=0.10",
+    "ipywidgets",
+    "ipykernel",
+    "more-itertools>=10.2.0",
+    "igorpy @ git+https://github.com/arafune/igorpy.git",
+    "titlecase>=2.4.1",
+    "h5netcdf>=1.3.0",
 ]
 
 [build-system]

src/arpes/__init__.py

@@ -9,7 +9,7 @@
 if TYPE_CHECKING:
     from ._typing import ConfigSettings, ConfigType
 # Use both version conventions for people's sanity.
-VERSION = "4.0.0"
+VERSION = "4.0.1"
 __version__ = VERSION
 
 

src/arpes/endstations/plugin/example_data.py

@@ -9,7 +9,6 @@
 
 from __future__ import annotations
 
-import warnings
 from logging import DEBUG, INFO, Formatter, StreamHandler, getLogger
 from typing import TYPE_CHECKING, ClassVar
 
@@ -75,9 +74,6 @@ def load_single_frame(
 
         # Wrap into a dataset
         dataset = xr.Dataset({"spectrum": data})
-        warnings.warn(
-            'loaded data has not corrected by "offsets". You may need "S.apply_offsets"',
-            stacklevel=2,
-        )
+        dataset.S.apply_offsets(data.S.offsets)
 
         return dataset

src/arpes/xarray_extensions.py

@@ -2937,7 +2937,7 @@ def map(
         """
         return apply_dataarray(self._obj, np.vectorize(fn, **kwargs))
 
-    def shift_by(  # noqa: PLR0913
+    def shift_by(
         self,
         other: xr.DataArray | NDArray[np.float64],
         shift_axis: str = "",
@@ -3098,7 +3098,7 @@ def max_in_window(
 
         return destination
 
-    def first_exceeding(  # noqa: PLR0913
+    def first_exceeding(
         self,
         dim: str,
         value: float,

tests/conftest.py

@@ -6,17 +6,18 @@
 from pathlib import Path
 from typing import TYPE_CHECKING, TypedDict
 
+import pytest
+
 import arpes.config
 import arpes.endstations
-import pytest
 from arpes.io import example_data
-
 from tests.utils import cache_loader
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Iterator
 
     import xarray as xr
+
     from arpes._typing import ScanInfo, WorkSpaceType
 
 

tests/test_basic_data_loading.py

@@ -5,10 +5,11 @@
 import contextlib
 from typing import TYPE_CHECKING, Any, ClassVar
 
-import arpes.xarray_extensions  # pylint: disable=unused-import, redefined-outer-name  # noqa: F401
 import numpy as np
 import pytest
 import xarray as xr
+
+import arpes.xarray_extensions  # pylint: disable=unused-import, redefined-outer-name  # noqa: F401
 from arpes.utilities.conversion import convert_to_kspace
 
 if TYPE_CHECKING:

tests/test_bz_spec.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 import pytest
+
 from arpes.utilities import bz_spec