Updated docs

docs/source/gui.rst

@@ -5,11 +5,6 @@ This section contains tutorials and helpful hints for the pymead GUI.
 
 .. toctree::
 
-   gui_help/gui_airfoil.rst
    gui_help/gui_bezier.rst
    gui_help/gui_continuity.rst
-   gui_help/gui_fp.rst
-   gui_help/gui_ap.rst
-   gui_help/gui_opt.rst
-   gui_help/gui_airfoil_matching.rst
    gui_help/gui_helpful_hints.rst

docs/source/gui_help/gui_ap.rst

@@ -25,123 +25,6 @@ are also part of the AnchorPoint branch.
 
    Bézier G\ :sup:`2` continuity
 
-The AnchorPoint feature is powerful because it allows for inter- and intra-airfoil
-positional constraints at locations other than the leading edge or trailing edge. This is
-particularly useful in multi-element airfoil applications with system-level constraints,
-such symmmetry, thickness at a point, or distance between two airfoil surface positions.
-To insert an AnchorPoint from the GUI, right-click on the desired airfoil in the
-Parameter Tree, which brings up a context menu as shown below:
-
-
-.. figure:: images/fp_ap_menu_dark.*
-   :align: center
-   :class: only-dark
-
-   Airfoil context menu
-
-
-.. figure:: images/fp_ap_menu_light.*
-   :align: center
-   :class: only-light
-
-   Airfoil context menu
-
-
-After left-clicking on "Add AnchorPoint," the following dialog appears:
-
-
-.. figure:: images/ap_menu_dark.*
-   :align: center
-   :class: only-dark
-
-   AnchorPoint menu
-
-.. figure:: images/ap_menu_light.*
-   :align: center
-   :class: only-light
-
-   AnchorPoint menu
-
-Here is a description of each of the ``AnchorPoint`` menu items:
-
-.. list-table::
-   :widths: 20 80
-   :header-rows: 1
-
-   * - Item
-     - Parameter
-   * - x
-     - Distance from the origin in the "Geometry" window along the x-axis
-   * - y
-     - Distance from the origin in the "Geometry" window along the y-axis
-   * - L
-     - Distance between the control points located immediately before and after the ``AnchorPoint``
-       in the counter-clockwise ordering divided by the chord length of the airfoil.
-   * - R
-     - Radius of curvature of the airfoil at the ``AnchorPoint`` divided by the chord length of the
-       airfoil.
-   * - r
-     - Ratio of the distance between the control point immediately upstream of the ``AnchorPoint`` and
-       the ``AnchorPoint`` itself to the distance between the control points located immediately before
-       and after the ``AnchorPoint``\ . Here, "upstream" means after the ``AnchorPoint`` in the
-       counter-clockwise ordering for an ``AnchorPoint`` on the upper surface and before the
-       ``AnchorPoint`` for an ``AnchorPoint`` on the lower surface. This is normally in the
-       range :math:`[0,1]`; however, this is not enforced.
-   * - phi
-     - "Tilt" of the line connecting the control points immediately before and after the ``AnchorPoint``.
-       Regardless of whether the ``AnchorPoint`` is located on the airfoil upper surface or lower surface,
-       positive values of "phi" tilt the line toward the leading edge, while negative values of "phi"
-       tilt the line away from the leading edge.
-   * - psi1
-     - Downstream curvature control arm angle. This angle corresponds to the angle :math:`\psi` shown
-       at the top of this page. This angle takes on the range :math:`(0, \pi)`. When :math:`\psi=0`, the control arm
-       is collapsed completely inward. When :math:`\psi=\pi`, the control arm is stretched fully
-       outward relative to the slope control segment. Stretching the curvature control arm past
-       this angle flips the sign of the radius of curvature.
-   * - psi2
-     - Upstream curvature control arm angle. This angle corresponds to the angle :math:`\psi`
-       closer to the leading edge than the downstream curvature control arm angle. Same range
-       as psi1.
-   * - Previous Anchor Point
-     - Parent ``AnchorPoint`` to which this ``FreePoint`` belongs. More specifically, the ``FreePoint``
-       will be inserted into the Bézier curve which has this ``AnchorPoint`` as its first ``ControlPoint``
-       using counter-clockwise ordering. For an airfoil with no custom ``AnchorPoint``\ s, inserting this
-       ``FreePoint`` with the Previous Anchor Point set to ``"te_1"`` corresponds to adding a control
-       point to the airfoil's upper surface, while inserting a ``FreePoint`` with the
-       Previous Anchor Point set to ``"le"`` corresponds to adding a control point to the airfoil's
-       lower surface. Note that ``"te_1"`` represents the upper trailing edge point,
-       which is distinct from the lower trailing edge point in the case of an airfoil with a blunt
-       trailing edge.
-   * - Previous Free Point
-     - Similar to the "Previous Anchor Point" item, this item sets the ``FreePoint`` insertion index
-       within the Bézier curve's control point matrix using counter-clockwise ordering. The
-       difference here is that an existing ``FreePoint`` is specified, rather than an ``AnchorPoint``.
-       Note that if no ``FreePoint``\ s have been added yet to the Bézier curve corresponding to the
-       ``AnchorPoint`` specified by "Previous Anchor Point", ``None`` is automatically selected.
-   * - Anchor Point Name
-     - Tag for the AnchorPoint. Must not be blank and must not match any another AnchorPoint name in
-       the current airfoil.
-
-
-The image below shows the default airfoil with an anchor point inserted. The values corresponding
-to the items in the table are shown in the Parameter Tree on the left of the image. Note that
-the airfoil is now comprised of three Bézier curves (rather than two), and the Bézier curves
-pass directly through the special control points marked by an "x," which correspond to the :math:`(x_0,y_0)`
-point as mentioned previously.
-
-.. figure:: images/anchor_point_insertion_dark.*
-   :align: center
-   :class: only-dark
-
-   FreePoint insertion
-
-
-.. figure:: images/anchor_point_insertion_light.*
-   :align: center
-   :class: only-light
-
-   FreePoint insertion
-
 
 ..
    This HTML code adds the "only-light" and "only-dark" class to the parent figures of

docs/source/install.rst

@@ -43,19 +43,6 @@ To accomplish this, first clone the directory using
 
   git clone https://github.com/mlau154/pymead.git
 
-If installing the most recent version of pymead, the branch corresponding to that version must be checked out.
-For instance, to checkout version 2.0.0, use
-
-.. code-block::
-
-  git checkout v2.0.0
-
-To see all available branches, use
-
-.. code-block::
-
-  git branch -a
-
 To pull the latest changes from the repository at some point after installation, use
 
 .. code-block::
@@ -76,15 +63,9 @@ Python. To check that the installation succeeded, run the following lines of cod
 
 .. code-block:: python
 
-  from pymead.core.airfoil import Airfoil
-  import matplotlib.pyplot as plt
-  fig, ax = plt.subplots()
-  a = Airfoil()
-  a.plot_airfoil(ax)
-  ax.set_aspect("equal")
-  plt.show()
+  import pymead
 
-If the installation was successful, an airfoil will appear on the screen.
+If the installation was successful, no errors will be thrown.
 
 Dependencies
 ============
@@ -93,22 +74,30 @@ Required
 --------
 
 Each of the following dependencies are required to use pymead. All packages listed in this section are automatically
-installed when using ``pip install pymead``. Alternatively, if cloning from the
-`pymead GitHub repo <https://github.com/mlau154/pymead>`_, these requirements can be installed using the included
-``requirements.txt`` file.
+installed when using Methods 1, 2, or 3 above. If using Method 4, the line ``pip install .`` installs these
+dependencies.
 
 - `scipy <https://scipy.org/>`_: Used for airfoil matching
-- `numpy <https://numpy.org/>`_: Used for linear algebra and random numbers
+- `numpy <https://numpy.org/>`_: Used for math, vector, and matrix computations
 - `shapely <https://shapely.readthedocs.io/en/stable/>`_: Computational geometry
 - `matplotlib <https://matplotlib.org/>`_: Static plotting
 - `requests <https://requests.readthedocs.io/en/latest/>`_: Downloading airfoil coordinate sets
   from `Airfoil Tools <http://airfoiltools.com/>`_
 - `PyQt5 <https://pypi.org/project/PyQt5/>`_: Graphical User Interface (GUI)
-- `pyqtgraph <https://www.pyqtgraph.org/>`_: Interactive plotting and parameter trees
+- `pyqtgraph <https://www.pyqtgraph.org/>`_: Interactive plots
 - `python-benedict <https://pypi.org/project/python-benedict/>`_: Dictionary utilities
 - `pandas <https://pandas.pydata.org/>`_: Data structures
-- `pymoo <https://pymoo.org/>`_: Aerodynamic shape optimization
+- `pymoo <https://pymoo.org/>`_: Genetic algorithms used for aerodynamic shape optimization
 - `numba <https://numba.pydata.org/>`_: Speed-up of inviscid lift coefficient calculation
+- `PyQtWebEngine <https://pypi.org/project/PyQtWebEngine/>`_: Internal GUI web-based help browser
+- `cmcrameri <https://www.fabiocrameri.ch/colourmaps/>`_: Perceptually uniform, color-vision-deficiency friendly color
+  maps by Fabio Crameri (used for flow visualization)
+- `JAX <https://jax.readthedocs.io/en/latest/>`_: Just-in-time compilation and automatic differentiation of non-linear
+  systems of geometric constraint equations for dynamic constraint editing
+- `jaxopt <https://jaxopt.github.io/stable/>`_: Root finding of non-linear systems of geometric constraint equations
+  using JAX's methods for just-in-time compilation and computation of the Jacobian using automatic differentiation
+- `networkx <https://networkx.org/documentation/stable/>`_: Analysis of the undirected graph describing the geometric
+  constraint system
 
 Optional
 --------

docs/source/todo.md

@@ -1,11 +1,14 @@
 Developer To-Dos
 ================
 
+Install
+-------
+- Add pip install option
+
 Planned feature additions
 -------------------------
 - Add the ability to fix points
 - Add absolute angle constraints
-- Add curvature continuity constraints
 - Add error handling for over-constrained/Jax shape/no solution in GCS
 
 Refactoring