MNT: Formatting and type annotations

.gitignore

@@ -1,5 +1,6 @@
 docs/source/examples
 docs/source/reference/generated
+docs/source/sg_execution_times.rst
 
 led / optimized / DLL files
 __pycache__/

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2018-2020 Greg Lucas
+Copyright (c) 2018 Greg Lucas
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/source/conf.py

@@ -19,10 +19,12 @@
 #
 import os
 import sys
+
 import pysecs
 
-sys.path.append(os.path.abspath('..'))
-sys.path.append('..')
+
+sys.path.append(os.path.abspath(".."))
+sys.path.append("..")
 
 
 # -- General configuration ---------------------------------------------
@@ -33,37 +35,36 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.githubpages',  # Helpful for publishing to gh-pages
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.napoleon',
-              'sphinx_gallery.gen_gallery',
-              ]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.githubpages",  # Helpful for publishing to gh-pages
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx_gallery.gen_gallery",
+]
 
 autosummary_generate = True
 
 napoleon_google_docstring = False
 
-intersphinx_mapping = {
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None)
-}
+intersphinx_mapping = {"numpy": ("https://numpy.org/doc/stable/", None)}
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'pysecs'
-copyright = "2018-2021, Greg Lucas"
+project = "pysecs"
+copyright = "2018-, Greg Lucas"
 author = "Greg Lucas"
 
 # The version info for the project you're documenting, acts as replacement
@@ -75,20 +76,13 @@
 # The full version, including alpha/beta/rc tags.
 release = pysecs.__version__
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'lovelace'
+pygments_style = "lovelace"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -99,12 +93,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 
 html_logo = "_static/pysecs.png"
 
 html_theme_options = {
-  "github_url": "https://github.com/greglucas/pysecs",
+    "github_url": "https://github.com/greglucas/pysecs",
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -116,16 +110,16 @@
 
 # Sphinx gallery
 sphinx_gallery_conf = {
-     'examples_dirs': '../../examples',   # path to example scripts
-     'gallery_dirs': 'examples',  # path for where to save generated output
-     'matplotlib_animations': True,
+    "examples_dirs": "../../examples",  # path to example scripts
+    "gallery_dirs": "examples",  # path for where to save generated output
+    "matplotlib_animations": True,
 }
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pysecsdoc'
+htmlhelp_basename = "pysecsdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -134,15 +128,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -152,21 +143,15 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pysecs.tex',
-     'pysecs Documentation',
-     'Greg Lucas', 'manual'),
+    (master_doc, "pysecs.tex", "pysecs Documentation", "Greg Lucas", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pysecs',
-     'pysecs Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pysecs", "pysecs Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -175,10 +160,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pysecs',
-     'pysecs Documentation',
-     author,
-     'pysecs',
-     'Spherical Elementary Current Systems in Python.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pysecs",
+        "pysecs Documentation",
+        author,
+        "pysecs",
+        "Spherical Elementary Current Systems in Python.",
+        "Miscellaneous",
+    ),
 ]

examples/plot_B_divergence_free.py

@@ -6,15 +6,18 @@
 an SECS pole placed at the north pole. Figure 2 from
 Amm and Viljanen 1999.
 """
+
 import matplotlib.pyplot as plt
 import numpy as np
+
 from pysecs import SECS
 
+
 # Radius of Earth
 R_E = 6378e3
 
 # Pole of the current system at the North Pole
-sec_loc = np.array([90., 0., R_E + 100e3])
+sec_loc = np.array([90.0, 0.0, R_E + 100e3])
 
 # Set up the system with a single SEC
 system_df = SECS(sec_df_loc=sec_loc)
@@ -33,27 +36,27 @@
 pred_loc = np.zeros(shape=(N, 3))
 angles = np.linspace(0, 45, N)
 
-pred_loc[:, 0] = 90-angles
+pred_loc[:, 0] = 90 - angles
 pred_loc[:, 2] = R_E
 
 B_pred = system_df.predict(pred_loc=pred_loc)
 
 # B_theta == -Bx == -B_pred[:,0]
 # Convert to nT (1e9)
-B_theta = -B_pred[:, 0]*1e9
+B_theta = -B_pred[:, 0] * 1e9
 # B_r == -Bz = -B_pred[:,2]
-B_r = -B_pred[:, 2]*1e9
+B_r = -B_pred[:, 2] * 1e9
 
 fig, ax = plt.subplots()
 
-ax.plot(angles, B_theta, c='b', label=r'B$_{\theta}$')
-ax.plot(angles, B_r, c='r', label=r'B$_r$')
-ax.legend(loc='upper right')
+ax.plot(angles, B_theta, c="b", label=r"B$_{\theta}$")
+ax.plot(angles, B_r, c="r", label=r"B$_r$")
+ax.legend(loc="upper right")
 ax.set_xlim(angles[0], angles[-1])
 ax.set_ylim(-5, 10)
-ax.set_xlabel('Angle from pole (deg)')
-ax.set_ylabel('B (nT)')
-ax.axhline(0., c='k', alpha=0.5, linewidth=0.5)
-ax.set_title('Amm and Viljanen (1999) Figure 2')
+ax.set_xlabel("Angle from pole (deg)")
+ax.set_ylabel("B (nT)")
+ax.axhline(0.0, c="k", alpha=0.5, linewidth=0.5)
+ax.set_title("Amm and Viljanen (1999) Figure 2")
 
 plt.show()

examples/plot_J_surface.py

@@ -5,16 +5,19 @@
 This example demonstrates the resulting current surfaces
 from the curl-free and divergence-free SEC poles.
 """
+
 import matplotlib.pyplot as plt
-from matplotlib.colors import LogNorm
 import numpy as np
+from matplotlib.colors import LogNorm
+
 from pysecs import SECS
 
+
 # Radius of Earth
 R_E = 6378e3
 
 # Pole of the current system at the North Pole
-sec_loc = np.array([90., 0., R_E + 100e3])
+sec_loc = np.array([90.0, 0.0, R_E + 100e3])
 
 # Set up the system with a single SEC
 system_df = SECS(sec_df_loc=sec_loc)
@@ -39,16 +42,16 @@
 lats = np.arange(lat_min, lat_max, delta)
 lons = np.arange(lon_min, lon_max, delta)
 
-lats2 = np.arange(lat_min-delta/2, lat_max+delta/2, delta)
-lons2 = np.arange(lon_min-delta/2, lon_max+delta/2, delta)
+lats2 = np.arange(lat_min - delta / 2, lat_max + delta / 2, delta)
+lons2 = np.arange(lon_min - delta / 2, lon_max + delta / 2, delta)
 
 nlat = len(lats)
 nlon = len(lons)
 
 xx, yy = np.meshgrid(lons, lats)
 xx2, yy2 = np.meshgrid(lons2, lats2)
 
-points = np.zeros((nlat*nlon, 3))
+points = np.zeros((nlat * nlon, 3))
 points[:, 0] = yy.ravel()
 points[:, 1] = xx.ravel()
 points[:, 2] = R_E
@@ -70,33 +73,38 @@
 J_cf_theta = np.linalg.norm(J_cf[:, :2], axis=1).reshape(nlat, nlon)
 J_cf_r = J_cf[:, 2].reshape(nlat, nlon)
 
-fig, (ax_cf, ax_df) = plt.subplots(figsize=(8, 3), ncols=2,
-                                   constrained_layout=True)
-fig.suptitle('Amm and Viljanen (1999) Figure 1')
+fig, (ax_cf, ax_df) = plt.subplots(figsize=(8, 3), ncols=2, constrained_layout=True)
+fig.suptitle("Amm and Viljanen (1999) Figure 1")
 
 # Limit quiver to only a few points
 nstep = 30
 
 norm = LogNorm(vmin=1e-5, vmax=1e-2)
 cax = ax_cf.pcolormesh(xx2, yy2, J_cf_theta, norm=norm)
-ax_cf.quiver(xx[nstep//2::nstep, nstep//2::nstep*2],
-             yy[nstep//2::nstep, nstep//2::nstep*2],
-             J_cf_y[nstep//2::nstep, nstep//2::nstep*2],
-             J_cf_x[nstep//2::nstep, nstep//2::nstep*2],
-             color='w', zorder=9)
-ax_cf.set_ylabel('Latitude (deg)')
-ax_cf.set_xlabel('Longitude (deg)')
+ax_cf.quiver(
+    xx[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    yy[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    J_cf_y[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    J_cf_x[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    color="w",
+    zorder=9,
+)
+ax_cf.set_ylabel("Latitude (deg)")
+ax_cf.set_xlabel("Longitude (deg)")
 
 cax = ax_df.pcolormesh(xx2, yy2, J_df_phi, norm=norm)
-ax_df.quiver(xx[nstep//2::nstep, nstep//2::nstep*2],
-             yy[nstep//2::nstep, nstep//2::nstep*2],
-             J_df_y[nstep//2::nstep, nstep//2::nstep*2],
-             J_df_x[nstep//2::nstep, nstep//2::nstep*2],
-             color='w', zorder=9)
-ax_df.set_ylabel('Latitude (deg)')
-ax_df.set_xlabel('Longitude (deg)')
-
-ax_cf.set_title('Curl Free')
-ax_df.set_title('Divergence Free')
+ax_df.quiver(
+    xx[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    yy[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    J_df_y[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    J_df_x[nstep // 2 :: nstep, nstep // 2 :: nstep * 2],
+    color="w",
+    zorder=9,
+)
+ax_df.set_ylabel("Latitude (deg)")
+ax_df.set_xlabel("Longitude (deg)")
+
+ax_cf.set_title("Curl Free")
+ax_df.set_title("Divergence Free")
 
 plt.show()