Updates for release 0.8.0

.github/workflows/release.yml

@@ -83,30 +83,35 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: "3.13"
-    
+
     - name: Create Conda environment file
       run: |
         python -m pip install pyyaml
         python .github/make_ci_environ.py
       env:
         PYTHON_VERSION: "3.13"
+        FREE_THREADED: false
+        NO_DOC_BUILD: false
+        NO_NUMBA: true
         ENV_NAME: geoana-test
-        NO_NUMBA: "true"
 
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
-        environment-file: .github/environment_ci.yml
-        activate-environment: geoana-test 
+        environment-file: environment_ci.yml
+        activate-environment: geoana-test
+
     - name: Install Our Package
       run: |
         pip install --no-build-isolation --editable . --config-settings=setup-args="-Dwith_extensions=true"
+
     - name: Build documentation
       run: |
         cd docs
         make html
         cd ..
+
     - name: GitHub Pages
       uses: crazy-max/ghaction-github-pages@v2.5.0
       with:
@@ -136,14 +141,17 @@ jobs:
         pattern: cibw-*
         path: dist
         merge-multiple: true
+
     - name: Release to github
       uses: softprops/action-gh-release@v1
       with:
         files: dist/*
         generate_release_notes: true
         prerelease: false
+
     - name: Remove anywheel before pypi upload
       run: rm -f dist/geoana*none-any.whl
+
     - name: Upload wheels to pypi
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.github/workflows/test_with_conda.yml

@@ -37,7 +37,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: "3.13"
-    
+
     - name: Create Conda environment file
       run: |
         python -m pip install pyyaml

docs/api/geoana.kernels.rst

@@ -0,0 +1 @@
+.. automodule:: geoana.kernels

docs/api/index.rst

@@ -50,3 +50,4 @@ functions for performing useful operations.
   geoana.utils
   geoana.spatial
   geoana.plotting_utils
+  geoana.kernels

geoana/earthquake/oksar.py

@@ -27,6 +27,12 @@
 from datetime import datetime
 from geoana.utils import requires
 
+__all__ = [
+    "EarthquakeInterferogram",
+    "Oksar",
+    "example",
+]
+
 def _date_time_from_json(value):
     if len(value) == 10:
         return datetime.strptime(value.replace('-', '/'),'%Y/%m/%d')

geoana/em/base.py

@@ -1,13 +1,19 @@
 import numpy as np
 from scipy.constants import mu_0, epsilon_0
 
+__all__ = [
+    "BaseEM",
+    "BaseDipole",
+    "BaseElectricDipole",
+    "BaseMagneticDipole",
+    "BaseLineCurrent",
+]
 ###############################################################################
 #                                                                             #
 #                              Base Classes                                   #
 #                                                                             #
 ###############################################################################
 
-
 class BaseEM:
     """Base electromagnetics class.
 

geoana/em/fdem/base.py

@@ -2,6 +2,13 @@
 import numpy as np
 from scipy.constants import mu_0, epsilon_0
 
+__all__ = [
+    "omega",
+    "wavenumber",
+    "skin_depth",
+    "sigma_hat",
+    "BaseFDEM",
+]
 ###############################################################################
 #                                                                             #
 #                           Utility Functions                                 #

geoana/em/fdem/halfspace.py

@@ -4,6 +4,9 @@
 from geoana.em.base import BaseMagneticDipole
 from geoana.em.fdem.base import BaseFDEM
 
+__all__ = [
+    "MagneticDipoleHalfSpace",
+]
 
 class MagneticDipoleHalfSpace(BaseFDEM, BaseMagneticDipole):
     r"""Class for a harmonic magnetic dipole in a wholespace.

geoana/em/fdem/layered.py

@@ -5,6 +5,9 @@
 from geoana.kernels.tranverse_electric_reflections import rTE_forward
 import libdlf
 
+__all__ = [
+    "MagneticDipoleLayeredHalfSpace",
+]
 
 class MagneticDipoleLayeredHalfSpace(BaseFDEM, BaseMagneticDipole):
     """Simulation class for a harmonic magnetic dipole over a layered halfspace.

geoana/em/fdem/simple_functions.py

@@ -1,6 +1,10 @@
 import numpy as np
 from scipy.constants import mu_0
 
+__all__ = [
+    "vertical_magnetic_field_horizontal_loop",
+    "vertical_magnetic_flux_horizontal_loop",
+]
 
 def vertical_magnetic_field_horizontal_loop(
     frequencies, sigma=1.0, mu=mu_0, radius=1.0, current=1.0, turns=1, secondary=True

geoana/em/fdem/wholespace.py

@@ -3,6 +3,11 @@
 from geoana.utils import check_xyz_dim, append_ndim
 from geoana.em.base import BaseElectricDipole, BaseMagneticDipole
 
+__all__ = [
+    "ElectricDipoleWholeSpace",
+    "MagneticDipoleWholeSpace",
+    "HarmonicPlaneWave",
+]
 
 class ElectricDipoleWholeSpace(BaseFDEM, BaseElectricDipole):
     r"""Class for simulating the fields and fluxes for a harmonic electric dipole in a wholespace.

geoana/em/static/__init__.py

@@ -23,11 +23,13 @@
   PointCurrentWholeSpace
   PointCurrentHalfSpace
   DipoleHalfSpace
+  MagneticPrism
 """
 
-from geoana.em.static.sphere import ElectrostaticSphere
-
-from geoana.em.static.sphere import MagnetostaticSphere
+from geoana.em.static.sphere import (
+    ElectrostaticSphere,
+    MagnetostaticSphere,
+)
 
 from geoana.em.static.wholespace import (
     MagneticDipoleWholeSpace,

geoana/em/static/freespace.py

@@ -15,6 +15,9 @@
     prism_fxyz,
 )
 
+__all__ = [
+    "MagneticPrism",
+]
 
 class MagneticPrism(BasePrism):
     """Class for magnetic field solutions for a prism.

geoana/em/static/sphere.py

@@ -2,6 +2,10 @@
 from scipy.constants import epsilon_0
 from geoana.utils import check_xyz_dim
 
+__all__ = [
+    "ElectrostaticSphere",
+    "MagnetostaticSphere",
+]
 
 class ElectrostaticSphere:
     """Class for electrostatic solutions for a sphere in a wholespace.

geoana/em/static/wholespace.py

@@ -7,7 +7,8 @@
 
 __all__ = [
     "MagneticDipoleWholeSpace", "CircularLoopWholeSpace",
-    "MagneticPoleWholeSpace", "PointCurrentWholeSpace"
+    "MagneticPoleWholeSpace", "PointCurrentWholeSpace",
+    "LineCurrentWholeSpace"
 ]
 
 from ...kernels import prism_fzy

geoana/em/tdem/__init__.py

@@ -34,7 +34,19 @@
   magnetic_field_time_deriv_magnetic_dipole
   magnetic_flux_vertical_magnetic_dipole
   magnetic_flux_time_deriv_magnetic_dipole
-
+
+Reference Functions
+===================
+Useful reference functions from Ward and Hohmann.
+
+.. autosummary::
+  :toctree: generated/
+
+  reference.hz_from_vert_4_69a
+  reference.dhz_from_vert_4_70
+  reference.hp_from_vert_4_72
+  reference.dhp_from_vert_4_74
+
 """
 from geoana.em.tdem.base import peak_time, diffusion_distance, theta, BaseTDEM
 

geoana/em/tdem/base.py

@@ -2,6 +2,12 @@
 import numpy as np
 from scipy.constants import mu_0
 
+__all__ = [
+    "peak_time",
+    "diffusion_distance",
+    "theta",
+    "BaseTDEM",
+]
 
 ###############################################################################
 #                                                                             #

geoana/em/tdem/halfspace.py

@@ -6,6 +6,9 @@
 from geoana.em.tdem.simple_functions import magnetic_field_vertical_magnetic_dipole, magnetic_field_time_deriv_magnetic_dipole
 from geoana.utils import check_xyz_dim
 
+__all__ = [
+    "VerticalMagneticDipoleHalfSpace",
+]
 
 class VerticalMagneticDipoleHalfSpace(BaseTDEM, BaseMagneticDipole):
     """Transient of a vertical magnetic dipole in a half space.

geoana/em/tdem/reference.py

@@ -7,6 +7,13 @@
 from scipy.special import erf, ive, iv
 import numpy as np
 
+__all__ = [
+    "hz_from_vert_4_69a",
+    "dhz_from_vert_4_70",
+    "hp_from_vert_4_72",
+    "dhp_from_vert_4_74",
+]
+
 def hz_from_vert_4_69a(m, theta, rho):
     front = m / (4 * np.pi * rho**3)
     tp = theta * rho

geoana/em/tdem/simple_functions.py

@@ -6,6 +6,16 @@
 from geoana.em.tdem.base import theta
 from geoana.utils import append_ndim, check_xyz_dim
 
+__all__ = [
+  "vertical_magnetic_field_horizontal_loop",
+  "vertical_magnetic_flux_horizontal_loop",
+  "vertical_magnetic_field_time_deriv_horizontal_loop",
+  "vertical_magnetic_flux_time_deriv_horizontal_loop",
+  "magnetic_field_vertical_magnetic_dipole",
+  "magnetic_field_time_deriv_magnetic_dipole",
+  "magnetic_flux_vertical_magnetic_dipole",
+  "magnetic_flux_time_deriv_magnetic_dipole",
+]
 
 def vertical_magnetic_field_horizontal_loop(
     t, sigma=1.0, mu=mu_0, radius=1.0, current=1.0, turns=1

geoana/em/tdem/wholespace.py

@@ -6,6 +6,11 @@
 from geoana.utils import check_xyz_dim, append_ndim
 from geoana.em.base import BaseElectricDipole
 
+__all__ = [
+    "ElectricDipoleWholeSpace",
+    "TransientPlaneWave",
+]
+
 ###############################################################################
 #                                                                             #
 #                                  Classes                                    #

geoana/gravity.py

@@ -23,6 +23,11 @@
 from geoana.shapes import BasePrism
 from geoana.kernels import prism_f, prism_fz, prism_fzx, prism_fzy, prism_fzz
 
+__all__ = [
+    "PointMass",
+    "Sphere",
+    "Prism",
+]
 
 class PointMass:
     """Class for gravitational solutions for a point mass.

geoana/kernels/__init__.py

@@ -1,4 +1,42 @@
-"""This module contains kernals for (semi-)analytic geophysical responses
+"""
+===========================================
+Kernel Functions (:mod:`geoana.kernels`)
+===========================================
+.. currentmodule:: geoana.kernels
+
+This module contains kernals for (semi-)analytic geophysical responses
+These are optionally available as compiled extensions with fallback
+`numpy` implementations.
+
+Inverse Distance Integral Kernels
+==================================
+Kernels used to evaluate analytic integrals of the
+1/r volume integrand (and it's derivatives)
+
+Note that if `numba` is installed and `geoana` has compiled
+extensions, these are callable in no-python mode.
+
+.. autosummary::
+  :toctree: generated/
+
+  prism_f
+  prism_fz
+  prism_fzz
+  prism_fzx
+  prism_fzy
+  prism_fzzz
+  prism_fxxy
+  prism_fxxz
+  prism_fxyz
+
+Layered Electromagnetic Reflection Kernels
+==========================================
+.. autosummary::
+  :toctree: generated/
+
+  rTE_forward
+  rTE_gradient
+
 """
 from geoana.kernels.tranverse_electric_reflections import rTE_forward, rTE_gradient
 from geoana.kernels.potential_field_prism import (

geoana/kernels/potential_field_prism.py

@@ -1,6 +1,18 @@
 import numpy as np
 from scipy.special import xlogy
 
+__all__ = [
+    "prism_f",
+    "prism_fz",
+    "prism_fzz",
+    "prism_fzx",
+    "prism_fzy",
+    "prism_fzzz",
+    "prism_fxxy",
+    "prism_fxxz",
+    "prism_fxyz",
+]
+
 
 def _prism_f(x, y, z):
     """