FEAT: Improvements throughout ✏️

.github/workflows/sync-to-readthedocs-repo.yaml

@@ -7,7 +7,6 @@ on:
       - main
       - latest
       - 'pre/*'
-      - dario/quick_patches_pre/2.6
   workflow_dispatch:
     inputs:
       env:

.gitignore

@@ -102,6 +102,7 @@ pip-log.txt
 
 # Sphinx documentation
 _docs
+_autosummary
 
 # Spyder project settings
 .spyderproject

.pre-commit-config.yaml

@@ -9,12 +9,4 @@ repos:
     rev: "v0.1.5"
     hooks:
      - id: ruff
-       args: [ --fix ]
-
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
-    hooks:
-      - id: codespell
-        args: [ --exclude-file=poetry.lock ]
-        additional_dependencies:
-          - tomli
+       args: [ --fix ]

CHANGELOG.md

@@ -798,12 +798,12 @@ which fields are to be projected is now determined automatically based on the me
 ### Added
 
 - New `grid_spec` Field in `Simulation` that allows more flexibility in defining the mesh.
-- `GridSpec1d` class defining how the meshing along each dimension should be done, with sublcasses `UniformGrid` and `CustomGrid` that cover the functionality 
+- `GridSpec1d` class defining how the meshing along each dimension should be done, with subclasses `UniformGrid` and `CustomGrid` that cover the functionality 
   previously offered by supplying a float or a list of floats to `Simulation.grid_size`. New functionality offered by `AutoGrid` subclass, with the 
   mesh automatically generated based on the minimum required steps per wavelength.
 - New `PointDipole` source.
 - Opacity kwargs for monitor and source in `sim.plot`.
-- Separated `plotly`-based requirements from core requrements file, can be added with `"pip install tidy3d-beta[plotly]"`.
+- Separated `plotly`-based requirements from core requirements file, can be added with `"pip install tidy3d-beta[plotly]"`.
 
 ### Changed
 - `Simulation.grid_spec` uses the default `GridSpec`, which has `AutoGrid(min_steps_per_wvl=10)` in each direction. To initialize a `Simulation` then it is no 
@@ -945,7 +945,7 @@ which fields are to be projected is now determined automatically based on the me
 - PML parameters and padding Grid with pml pixels by [@momchil-flex](https://github.com/momchil-flex) in #64
 - Documentation by [@tylerflex](https://github.com/tylerflex) in #63
 - Gds import from [@tylerflex](https://github.com/tylerflex) in #69
-- Loggin by [@tylerflex](https://github.com/tylerflex) in #70
+- Login, by [@tylerflex](https://github.com/tylerflex) in #70
 - Multi-pole Drude medium by [@weiliangjin2021](https://github.com/weiliangjin2021) in #73
 - Mode Solver: from [@tylerflex](https://github.com/tylerflex) in #74
 - Near2Far from [@tylerflex](https://github.com/tylerflex) in #77

docs/_static/css/custom.css

@@ -26,6 +26,8 @@ iframe {width: 100%;border: unset}
 
 .toctree-wrapper li[class^=toctree-l1]>a {font-size: 1.4em; text-decoration: none}
 .toctree-wrapper li[class^=toctree-l2]>a {font-size: 1em; text-decoration: none}
+.toctree-wrapper li[class^=toctree-l3]>a {font-size: 0.9em; text-decoration: none}
+.toctree-wrapper li[class^=toctree-l4]>a {font-size: 0.9em; text-decoration: none}
 
 html[data-theme="light"] {
     --pst-color-primary: #b5445b;
@@ -79,6 +81,10 @@ img {
     background-color: var(--sd-color-info-bg);
 }
 
+html[data-theme=dark] .dataframe {
+    background-color: var(--pst-color-primary);
+}
+
 /* TODO make sure this is only for the API tables */
 /*table {*/
 /*  border: solid;*/

docs/api/index.rst

@@ -1,6 +1,6 @@
-***
-API
-***
+***************
+API |:computer:|
+***************
 
 .. toctree::
     :hidden:

docs/changelog.rst

@@ -1,4 +1,5 @@
-Changelog
-=========
+********************
+Changelog |:rewind:|
+********************
 
-.. mdinclude:: ../../CHANGELOG.md
+.. mdinclude:: ../CHANGELOG.md

docs/conf.py

@@ -80,6 +80,7 @@
     "IPython.sphinxext.ipython_directive",
     "IPython.sphinxext.ipython_console_highlighting",
     "nbsphinx",  # Integrate Jupyter Notebooks and Sphinx
+    "m2r2",
     # "sphinxcontrib.divparams", # TODO FIX
     "sphinx.ext.autodoc",  # Core Sphinx library for auto html doc generation from docstrings
     "sphinx.ext.autosummary",  # Create neat summary tables for modules/classes/methods etc

docs/development/index.rst

@@ -1,6 +1,6 @@
-*****************
-Development Guide
-*****************
+********************************************************************
+Development Guide |:hammer_and_wrench:|
+********************************************************************
 
 Welecome to the ``tidy3d`` developers guide! These are just some recommendations I've compiled, but we can change anything as we think might help the development cycle more.
 

docs/development/installation.rst

@@ -60,7 +60,7 @@ If you rather install ``poetry``, ``pipx`` and ``pandoc`` yourself, you can run
 The Detailed Lane
 ^^^^^^^^^^^^^^^^^
 
-If you do not have any of the above tools already installed and want to install them manually, let's go through the process of setting things up from scatch:
+If you do not have any of the above tools already installed and want to install them manually, let's go through the process of setting things up from scratch:
 
 
 Environment Requirements

docs/development/usage.rst

@@ -58,6 +58,9 @@ There are a range of handy development functions that you might want to use to s
     * - Dual snapshot between the ``tidy3d`` and ``notebooks`` source and submodule repository.
       - Make sure you are on the correct git branches you wish to commit to on both repositories, and all `non-git-ignored` files will be added to the commit.
       - ``tidy3d develop commit <your message>``
+    * - Interactively convert all markdown files to rst (replacement for m2r2)
+      -
+      - ``poetry run tidy3d develop convert-all-markdown-to-rst``
     * - Running ``pytest`` commands inside the ``poetry`` environment.
       - Make sure you have already installed ``tidy3d`` in ``poetry`` and you are in the root directory.
       - ``poetry run pytest``
@@ -70,3 +73,4 @@ There are a range of handy development functions that you might want to use to s
     * - Update lockfile after updating a dependency in ``pyproject.toml``
       - Remember to install after this command.
       - ``poetry lock``
+

docs/faq.rst

@@ -1,4 +1,4 @@
-FAQ
+FAQ |:mag_right:|
 ==========================
 
 What is Tidy3D?

docs/howdoi.rst

@@ -2,8 +2,8 @@
 
 .. _howdoi:
 
-How do I ...
-============
+How do I ... |:eyes:|
+========================
 
 
 Work with the Tidy3d Package
@@ -48,7 +48,7 @@ Plot Tidy3D Components
    * - Change the object plotting characteristics (facecolor, edgecolor, etc).
      - Plotting keyword arguments can be supplied to ``plot()``, for example ``obj.plot(x=0, edgecolor='blue', fill=False)``.  These keyword arguments correspond to those fed to `Matplotlib Patches <https://tinyurl.com/2nf5c2fk>`__.
    * - Change the global plot characteristics (title, size, etc).
-     - The plotting function return a matplotlib ``Axes``, wihch can be manipulated, for example ``ax = obj.plot(x=0);  ax.set_title('my_title')``.
+     - The plotting function return a matplotlib ``Axes``, which can be manipulated, for example ``ax = obj.plot(x=0);  ax.set_title('my_title')``.
 
 Create Geometries
 -----------------
@@ -62,7 +62,7 @@ Create Geometries
    * - Load a structure from GDS format?
      - From a cell in the ``gdstk`` package, the ``ps = td.PolySlab.from_gds(gds_cell, ...)`` method will load the geometry into a :class:`PolySlab`.
    * - Create a complex geometry, such as a ring?
-     - While many complex geometries can be created by supplying the vertices to :class:`PolySlab`, simple geometries, such as rings, can be constructed by overlaying two structures with :class:`Cylinder` geomety with the inner cylinder defined with medium of air.  Note that structures later in the ``structures`` list will override previous structures, which can be leveraged to make more complex geometries.
+     - While many complex geometries can be created by supplying the vertices to :class:`PolySlab`, simple geometries, such as rings, can be constructed by overlaying two structures with :class:`Cylinder` geometry with the inner cylinder defined with medium of air.  Note that structures later in the ``structures`` list will override previous structures, which can be leveraged to make more complex geometries.
 
 Materials
 ---------
@@ -163,7 +163,7 @@ Submit Jobs to Server
    * - Submit my simulation to run on Flexcompute's servers?
      - ``sim_data = web.run(simulation, task_name='my_task', path='out/data.hdf5')`` or ``job = web.Job(simulation, task_name='my_task'); job.run(path='out/data.hdf5')``.
    * - Upload a job to the web without running it so I can inspect it first?
-     - Once you've created a :class:`tidy3d.web.container.Job`, you can upload it to our servers with ``job.upload()`` and it will not run until you excplicitly tell it to with ``job.start()``.
+     - Once you've created a :class:`tidy3d.web.container.Job`, you can upload it to our servers with ``job.upload()`` and it will not run until you explicitly tell it to with ``job.start()``.
    * - Monitor the progress of a simulation?
      - ``web.monitor(task_id)``, ``job.monitor()``, or ``batch.monitor()`` will display the progress of your simulation(s).
    * - Load the results of a simulation?
@@ -175,7 +175,7 @@ Submit Jobs to Server
    * - Loop through :class:`tidy3d.web.container.BatchData` without loading all of the data into memory?
      - ``for task_name, sim_data in batch_data.items():`` will give access to a :class:`SimulationData` instance for each :class:`tidy3d.web.container.Job` in the batch one by one, so you can perform your postprocessing in the loop body without loading each of the simulations' data into memory at once.
    * - Save or load a :class:`tidy3d.web.container.Job` or :class:`tidy3d.web.container.Batch` so I can work with it later?
-     - Like most other tidy3d objects, :class:`tidy3d.web.container.Job` and :class:`tidy3d.web.container.Batch` instances have ``.to_file(path)`` and ``.from_file(path)`` methods that will export and load thier metadata as .json files.  This is especially useful for loading batches for analysis long after they have run.
+     - Like most other tidy3d objects, :class:`tidy3d.web.container.Job` and :class:`tidy3d.web.container.Batch` instances have ``.to_file(path)`` and ``.from_file(path)`` methods that will export and load their metadata as .json files.  This is especially useful for loading batches for analysis long after they have run.
 
 Extensions
 ----------
@@ -190,7 +190,7 @@ Extensions
      - Refer to the `Dispersion tutorial <notebooks/Fitting.html>`_ on the :class:`tidy3d.plugins.DispersionFitter` plugin.
    * - Specify the modes for a :class:`ModeMonitor` or :class:`ModeSource`?
      - Refer to the `Mode Solver tutorial <notebooks/ModeSolver.html>`_ on the :class:`tidy3d.plugins.ModeSolver` plugin.
-   * - Projet electromagnetic near field data to the far field?
+   * - Project electromagnetic near field data to the far field?
      - Refer to the `FieldProjections tutorial <notebooks/FieldProjections.html>`_.
    * - Compute scattering matrix parameters for modeling my device?
      - Refer to the `S Matrix tutorial <notebooks/SMatrix.html>`_ on the :class:`tidy3d.plugins.ComponentModeler` plugin.

docs/install.rst

@@ -1,5 +1,5 @@
 *************************
-Installation
+Installation |:wave:|
 *************************
 
 Welcome to Tidy3D
@@ -113,14 +113,14 @@ and pasting the API key when prompted. Note that one can also specify the API ke
 
     tidy3d configure --apikey=XXX
 
-Note: Windows users will need to peform a slighlty different step to link the registration. From the anaconda prompt where tidy3d was pip installed, the following commands should be run instead
+Note: Windows users will need to perform a slightly different step to link the registration. From the anaconda prompt where tidy3d was pip installed, the following commands should be run instead
 
 .. code-block:: bash
 
     pip install pipx
     pipx run tidy3d configure --apikey=XXX
 
-Alternatively, the API key can be set up using the evironment variable ``SIMCLOUD_APIKEY`` as:
+Alternatively, the API key can be set up using the environment variable ``SIMCLOUD_APIKEY`` as:
 
 .. code-block:: bash
 

docs/lectures/index.rst

@@ -1,5 +1,5 @@
-Lectures
-#########
+Lectures |:book:|
+##################
 
 Welcome to our lecture series!
 

make_script.py

@@ -44,7 +44,7 @@ def main(args):
     # add the simulation body itself
     sim_string += sim.__repr__()
 
-    # new we need to get rid of all the "type" info that isnt needed
+    # new we need to get rid of all the "type" info that isn't needed
 
     # remove type='...', in middle
     pattern = r"type='([A-Za-z0-9_\./\\-]*)', "