Merge pull request #23 from sunpy/cruft/update-1710843577

Updates from the package template

.codespellrc

@@ -0,0 +1,14 @@
+[codespell]
+skip = *.asdf,*.fits,*.fts,*.header,*.json,*.xsh,*cache*,*egg*,*extern*,.git,.idea,.tox,_build,*truncated,*.svg,.asv_env,.history
+ignore-words-list =
+    als,  # magex specific
+    alog,
+    nd,
+    nin,
+    observ,
+    ot,
+    te,
+    upto,
+    afile,
+    precessed,
+    precess,

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "8d590fba25722f382d4fb5554fa52dfec65952c9",
+  "commit": "3a8054de27a4af460d7cb737b2b1ec2621456e5f",
   "checkout": null,
   "context": {
     "cookiecutter": {

.flake8

@@ -22,6 +22,6 @@ exclude =
     __pycache__
     docs/conf.py
     build
-    sunkit-magex/__init__.py,
+    sunkit-magex/__init__.py
 rst-directives =
     plot

.isort.cfg

@@ -0,0 +1,16 @@
+[settings]
+balanced_wrapping = true
+skip =
+    docs/conf.py
+    sunkit_magex/__init__.py
+default_section = THIRDPARTY
+include_trailing_comma = true
+known_astropy = astropy, asdf
+known_sunpy = sunpy
+known_first_party = sunkit_magex
+length_sort = false
+length_sort_sections = stdlib
+line_length = 110
+multi_line_output = 3
+no_lines_before = LOCALFOLDER
+sections = STDLIB, THIRDPARTY, ASTROPY, SUNPY, FIRSTPARTY, LOCALFOLDER

.pre-commit-config.yaml

@@ -5,6 +5,11 @@ repos:
     hooks:
       - id: ruff
         args: ["--fix"]
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|sunkit_magex/extern)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
@@ -20,6 +25,11 @@ repos:
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|.json)$|^CITATION.rst$"
       - id: mixed-line-ending
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        args: [ "--write-changes" ]
 ci:
   autofix_prs: false
   autoupdate_schedule: "quarterly"

docs/conf.py

@@ -6,15 +6,16 @@
 
 import os
 import datetime
+
 # -- Project information -----------------------------------------------------
 
 # The full version, including alpha/beta/rc tags
 from sunkit_magex import __version__
 
 release = __version__
 project = "sunkit-magex"
-copyright = str(datetime.datetime.now().year) + " , The SunPy Community"  # noqa: A001
 author = "The SunPy Community"
+copyright = f"{datetime.datetime.now().year}, {author}"  # noqa: A001
 
 # -- General configuration ---------------------------------------------------
 

examples/finding_data/adapt_map_sequence.py

@@ -5,9 +5,12 @@
 Parse an ADAPT FITS file into a `sunpy.map.MapSequence`.
 """
 import matplotlib.pyplot as plt
-import sunpy.map
 from matplotlib import gridspec
+
 from astropy.io import fits
+
+import sunpy.map
+
 from sunkit_magex import pfss
 
 ###############################################################################

examples/internals/tracer_performance.py

@@ -6,10 +6,12 @@
 """
 import timeit
 
-import astropy.coordinates
-import astropy.units as u
 import matplotlib.pyplot as plt
 import numpy as np
+
+import astropy.coordinates
+import astropy.units as u
+
 import sunpy.map
 
 from sunkit_magex import pfss

examples/testing/helpers.py

@@ -1,15 +1,17 @@
-import functools
 import pathlib
+import functools
 
-import astropy.units as u
 import matplotlib.pyplot as plt
 import matplotlib.ticker as mticker
 import numpy as np
 import scipy.integrate
-import sunpy.map
 from sympy import acos, asin, cos, lambdify, sin
 from sympy.abc import x
 
+import astropy.units as u
+
+import sunpy.map
+
 import sunkit_magex.pfss.analytic as analytic
 import sunkit_magex.pfss.utils
 
@@ -19,7 +21,7 @@
 
 
 def theta_phi_grid(nphi, ns):
-    # Return a theta, phi grid with a given numer of points
+    # Return a theta, phi grid with a given number of points
     phi = np.linspace(0, 2 * np.pi, nphi)
     s = np.linspace(-1, 1, ns)
     s, phi = np.meshgrid(s, phi)

examples/testing/plot_error_map.py

@@ -5,16 +5,16 @@
 This script produces a map of errors between analytic field line equations
 and field lines numerically traced by `sunkit_magex.pfss`.
 """
-import astropy.constants as const
-import astropy.units as u
 import matplotlib.pyplot as plt
 import numpy as np
+
+import astropy.constants as const
+import astropy.units as u
 from astropy.coordinates import SkyCoord
 from astropy.visualization import quantity_support
 
-from sunkit_magex import pfss
-
 from examples.testing.helpers import pffspy_output, phi_fline_coords, theta_fline_coords
+from sunkit_magex import pfss
 
 quantity_support()
 

examples/testing/skip_open_flux_nr.py

@@ -4,7 +4,7 @@
 
 Comparing total unsigned flux to analytic solutions.
 
-This script caclulates the ratio of numeric to analytic total unsigned open
+This script calculates the ratio of numeric to analytic total unsigned open
 fluxes in PFSS solutions of spherical harmonics, as a function of the number of
 radial grid cells in the sunkit_magex.pfss grid.
 """

examples/testing/tracer_step_size.py

@@ -2,21 +2,16 @@
 Tracer step size (calculations)
 ===============================
 """
-import astropy.constants as const
-import astropy.units as u
 import numpy as np
 import pandas as pd
+
+import astropy.constants as const
+import astropy.units as u
 from astropy.coordinates import SkyCoord
 
+from examples.testing.helpers import pffspy_output, phi_fline_coords, result_dir, theta_fline_coords
 from sunkit_magex.pfss import tracing
 
-from examples.testing.helpers import (
-    pffspy_output,
-    phi_fline_coords,
-    result_dir,
-    theta_fline_coords,
-)
-
 l = 3
 m = 3
 nphi = 360

examples/using_pfsspy/plot_aia_overplotting.py

@@ -9,12 +9,14 @@
 
 import os
 
-import astropy.units as u
 import matplotlib.pyplot as plt
 import numpy as np
-import sunpy.map
+
+import astropy.units as u
 from astropy.coordinates import SkyCoord
 
+import sunpy.map
+
 import sunkit_magex.pfss
 import sunkit_magex.pfss.tracing as tracing
 from sunkit_magex.pfss.sample_data import get_gong_map

examples/using_pfsspy/plot_dipole.py

@@ -5,15 +5,17 @@
 A simple example showing how to use PFSS to compute the solution to a dipole
 source field.
 """
-import astropy.constants as const
-import astropy.units as u
 import matplotlib.patches as mpatch
 import matplotlib.pyplot as plt
 import numpy as np
-import sunpy.map
+
+import astropy.constants as const
+import astropy.units as u
 from astropy.coordinates import SkyCoord
 from astropy.time import Time
 
+import sunpy.map
+
 from sunkit_magex import pfss
 
 ###############################################################################

examples/using_pfsspy/plot_field_line_magnetic_field.py

@@ -5,12 +5,14 @@
 How to get the value of the magnetic field along a field line traced through
 the PFSS solution.
 """
+import matplotlib.pyplot as plt
+
 import astropy.constants as const
 import astropy.units as u
-import matplotlib.pyplot as plt
-import sunpy.map
 from astropy.coordinates import SkyCoord
 
+import sunpy.map
+
 from sunkit_magex import pfss
 
 ###############################################################################

examples/using_pfsspy/plot_gong.py

@@ -6,13 +6,15 @@
 """
 # sphinx_gallery_thumbnail_number = 4
 
-import astropy.constants as const
-import astropy.units as u
 import matplotlib.pyplot as plt
 import numpy as np
-import sunpy.map
+
+import astropy.constants as const
+import astropy.units as u
 from astropy.coordinates import SkyCoord
 
+import sunpy.map
+
 from sunkit_magex import pfss
 
 ###############################################################################

examples/using_pfsspy/plot_hmi.py

@@ -4,7 +4,7 @@
 
 Calculating a PFSS solution from a HMI synoptic map.
 
-This example shows how to calcualte a PFSS solution from a HMI synoptic map.
+This example shows how to calculate a PFSS solution from a HMI synoptic map.
 There are a couple of important things that this example shows:
 
 - HMI maps have non-standard metadata, so this needs to be fixed
@@ -13,8 +13,10 @@
 """
 import os
 
-import astropy.units as u
 import matplotlib.pyplot as plt
+
+import astropy.units as u
+
 import sunpy.map
 from sunpy.net import Fido
 from sunpy.net import attrs as a

examples/using_pfsspy/plot_open_closed_map.py

@@ -4,14 +4,16 @@
 
 Creating an open/closed field map on the solar surface.
 """
-import astropy.constants as const
-import astropy.units as u
 import matplotlib.colors as mcolor
 import matplotlib.pyplot as plt
 import numpy as np
-import sunpy.map
+
+import astropy.constants as const
+import astropy.units as u
 from astropy.coordinates import SkyCoord
 
+import sunpy.map
+
 from sunkit_magex import pfss
 
 ###############################################################################

pytest.ini

@@ -1,8 +1,8 @@
 [pytest]
 minversion = 7.0
 testpaths =
-  sunkit_magex
-  docs
+    sunkit_magex
+    docs
 norecursedirs =
     .tox
     build
@@ -26,7 +26,7 @@ filterwarnings =
     # add a comment or ideally a link to an issue that explains why the warning
     # is being ignored
     ignore:numpy.ndarray size changed, may indicate binary incompatibility:RuntimeWarning
-    # This seems to be a transitive faliure we should investigate
+    # This seems to be a transitive failure we should investigate
     ignore:unclosed event loop:ResourceWarning
     # https://github.com/pytest-dev/pytest-cov/issues/557
     # It was fixed and released but it does not seem to be fixed

sunkit_magex/pfss/__init__.py

@@ -1,10 +1,6 @@
 # Import this to register map sources
 import sunkit_magex.pfss.map as _
-from sunkit_magex.pfss import coords
-from sunkit_magex.pfss import fieldline
-from sunkit_magex.pfss import sample_data
-from sunkit_magex.pfss import tracing
-from sunkit_magex.pfss import utils
+from sunkit_magex.pfss import coords, fieldline, sample_data, tracing, utils
 from sunkit_magex.pfss.input import Input
 from sunkit_magex.pfss.output import Output
 from sunkit_magex.pfss.pfss import pfss

sunkit_magex/pfss/analytic.py

@@ -18,11 +18,12 @@
 Using this module requires ``sympy`` to be installed.
 """
 
-import astropy.units as u
 import numpy as np
 import scipy.special
 import sympy
 
+import astropy.units as u
+
 
 @u.quantity_input
 def _normalise_angles(theta: u.deg, phi: u.deg):
@@ -36,7 +37,7 @@ def _normalise_angles(theta: u.deg, phi: u.deg):
 
 def _Ynm(l, m, theta, phi):  # NOQA: E741
     """
-    Return values of spherical harmonic with numbers l, m at coordiantes
+    Return values of spherical harmonic with numbers l, m at coordinates
     theta, phi.
     """
     # Note swapped arguments phi, theta, as scipy has a different
@@ -73,7 +74,7 @@ def _spherical_harmonic_sympy(l, m):  # NOQA: E741
     theta, phi = sympy.symbols('theta, phi')
     harm = sympy.Ynm(L, M, theta, phi)
     if m < 0:
-        # Phase shift to align definition of Ymn with defnition in paper.
+        # Phase shift to align definition of Ymn with definition in paper.
         harm *= -1j
     harm = harm.subs([(L, l), (M, m)])
     return harm, theta, phi