formatting

.github/CONTRIBUTING.md

@@ -53,13 +53,13 @@ py -m install -v -e .[dev]
 
 If mamba isn't installed:
 
-```python
+```
 conda install mamba
 ```
 
 Then create the environment with the inclused Makefile commands:
 
-```python
+```
 make create
 conda activate invert4geom
 make install
@@ -75,7 +75,8 @@ pip install pre-commit # or brew install pre-commit on macOS
 pre-commit install # Will install a pre-commit hook into the git repo
 ```
 
-You can also/alternatively run `make lint` to check even without installing the hook.
+You can also/alternatively run `make lint` to check even without installing the
+hook.
 
 # Testing
 

README.md

@@ -1,6 +1,5 @@
 # invert4geom
 
-
 [![Actions Status][actions-badge]][actions-link]
 [![Documentation Status][rtd-badge]][rtd-link]
 
@@ -10,14 +9,20 @@
 
 [![GitHub Discussion][github-discussions-badge]][github-discussions-link]
 
-
 <!-- SPHINX-START -->
 
-**Invert4geom** is a Python library for performing 3D geometric gravity inversions, where the aim is to recover the geometry of a density contrast.
+**Invert4geom** is a Python library for performing 3D geometric gravity
+inversions, where the aim is to recover the geometry of a density contrast.
 
-Typical use cases include modeling the topography of the Moho, the sediment-basement contact, or bathymetry. These density contrasts are represented by a layer of vertical right-rectangular prisms. Since we use vertical prisms, they don't take the curvature of the Earth into account. For large-scale applications, such as continental studies, it would be better to use tesseroids instead of prisms.
+Typical use cases include modeling the topography of the Moho, the
+sediment-basement contact, or bathymetry. These density contrasts are
+represented by a layer of vertical right-rectangular prisms. Since we use
+vertical prisms, they don't take the curvature of the Earth into account. For
+large-scale applications, such as continental studies, it would be better to use
+tesseroids instead of prisms.
 
-See the [overview](overview.md) for further description of this package and what it can be used for.
+See the [overview](overview.md) for further description of this package and what
+it can be used for.
 
 The tutorials
 

docs/conf.py

@@ -61,4 +61,4 @@
 
 add_module_names = False
 
-add_function_parentheses = False
+add_function_parentheses = False

docs/index.md

@@ -28,32 +28,33 @@ Source code on GitHub <https://github.com/mdtanker/invert4geom>
 :start-after: <!-- SPHINX-START -->
 ```
 
-::::{grid} 2
-:::{grid-item-card}  {octicon}`rocket` Getting started?
-:text-align: center
-New to Invert4geom? Start here!
+::::{grid} 2 :::{grid-item-card} {octicon}`rocket` Getting started? :text-align:
+center New to Invert4geom? Start here!
+
 ```{button-ref} overview
     :click-parent:
     :color: primary
     :outline:
     :expand:
 ```
+
 :::
 
-:::{grid-item-card} {octicon}`comment-discussion` Need help?
-:text-align: center
+:::{grid-item-card} {octicon}`comment-discussion` Need help? :text-align: center
 Start a discussion on GitHub!
+
 ```{button-link} https://github.com/mdtanker/invert4geom/discussions
     :click-parent:
     :color: primary
     :outline:
     :expand:
     Discussions
 ```
+
 :::
 
-:::{grid-item-card} {octicon}`file-badge` Reference documentation
-:text-align: center
+:::{grid-item-card} {octicon}`file-badge` Reference documentation :text-align:
+center
 
 A list of modules and functions
 
@@ -63,6 +64,7 @@ A list of modules and functions
     :outline:
     :expand:
 ```
+
 :::
 
 :::{grid-item-card} {octicon}`bookmark` Using Invert4geom for research?
@@ -76,6 +78,7 @@ Citations help support our work
     :outline:
     :expand:
 ```
+
 :::
 
 ::::
@@ -102,8 +105,6 @@ how you can contribute to the project.
 *Many parts of this documentation was adapted from the* [Fatiando project](https://www.fatiando.org/).
 ```
 
-
-
 ## Indices and tables
 
 - {ref}`genindex`

docs/install.md

@@ -1 +1 @@
-# Install
+# Install

docs/overview.md

@@ -1 +1 @@
-# Overview
+# Overview

docs/template/module.rst_t

@@ -4,4 +4,4 @@
 .. automodule:: {{ qualname }}
 {%- for option in automodule_options %}
    :{{ option }}:
-{%- endfor %}
+{%- endfor %}

docs/template/package.rst_t

@@ -33,4 +33,4 @@ Module contents
 ---------------
 
 {{ automodule(pkgname, automodule_options) }}
-{% endif %}
+{% endif %}

docs/template/toc.rst_t

@@ -4,4 +4,4 @@
    :maxdepth: {{ maxdepth }}
 {% for docname in docnames %}
    {{ docname }}
-{%- endfor %}
+{%- endfor %}

src/invert4geom/inversion.py

@@ -103,19 +103,19 @@ def jacobian_annular(
     jac: NDArray,
 ) -> NDArray:
     """
-        Function to calculate the Jacobian matrix using the annular cylinder approximation
-        The resulting Jacobian is a matrix (numpy array) with a row per gravity observation
-        and a column per prism. This approximates the prisms as an annulus, and calculates
-        it's vertical gravity derivative.
-        Takes arrays from `jacobian`, feeds them into `grav_column_der`, and returns
-        the jacobian.
+        Function to calculate the Jacobian matrix using the annular cylinder
+        approximation. The resulting Jacobian is a matrix (numpy array) with a row per
+        gravity observation and a column per prism. This approximates the prisms as an
+        annulus, and calculates it's vertical gravity derivative. Takes arrays from
+        `jacobian`, feeds them into `grav_column_der`, and returns the jacobian.
 
     Parameters
     ----------
     grav_easting, grav_northing, grav_upward : NDArray
         coordinates of gravity observation points.
     prism_easting, prism_northing, prism_top, : NDArray
-        coordinates of prism's center in northing, easting, and upward directions, respectively
+        coordinates of prism's center in northing, easting, and upward directions,
+        respectively
     prism_density : NDArray
         density of prisms, in kg/m^3
     prism_spacing : float