some spelling fixes in the docs (#2787)

* some spelling fixes in the docs found via codespell * update mailmap
tardis-sn · Aug 9, 2024 · f69fb44 · f69fb44
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diff --git a/.mailmap b/.mailmap
@@ -281,3 +281,5 @@ Gudur Krishna Chaitanya <[email protected]> KC210404 <[email protected]
 Israel Roldan <[email protected]> Israel Roldan <[email protected]>
 Israel Roldan <[email protected]> AirvZxf <[email protected]>
 Israel Roldan <[email protected]> airv_zxf <[email protected]>
+
+Michael Zingale <[email protected]>
diff --git a/docs/contributing/development/code_quality.rst b/docs/contributing/development/code_quality.rst
@@ -18,7 +18,7 @@ TARDIS follows the `PEP 8 <https://www.python.org/dev/peps/pep-0008/>`_ style gu
 
 Black
 -----
-`Black <https://black.readthedocs.io/en/stable/index.html>`_ is a PEP 8 compliant opinionated code formatter. At TARDIS. we use Black to automatically conform to PEP 8. It is already installed in the TARDIS conda environment, so all you have to do is to run Black before commiting your changes: ::
+`Black <https://black.readthedocs.io/en/stable/index.html>`_ is a PEP 8 compliant opinionated code formatter. At TARDIS. we use Black to automatically conform to PEP 8. It is already installed in the TARDIS conda environment, so all you have to do is to run Black before committing your changes: ::
 
     black {source_file_or_directory}
 
@@ -37,7 +37,7 @@ To run Ruff, use the following command: ::
     ruff check <source_file_or_directory> # Lints the code
     ruff check <source_file_or_directory> --fix # Lints and fixes any fixable errors
 
-Currently, Ruff is not integrated with the TARDIS CI and is not a requirement for merging a PR. However, it is recommended to run Ruff on your code before commiting it to ensure that new code already follows these rules.
+Currently, Ruff is not integrated with the TARDIS CI and is not a requirement for merging a PR. However, it is recommended to run Ruff on your code before committing it to ensure that new code already follows these rules.
 
 .. note :: We adopt the linting rules utilized by astropy. Permanent rules are defined in the ``pyproject.toml``, non-permanent rules are defined in the ``.ruff.toml`` file. If you want to add a new rule, please add it to the ``.ruff.toml`` file. If you want to add a permanent rule, please open a PR to the ``pyproject.toml``.
 

diff --git a/docs/contributing/development/continuous_integration.rst b/docs/contributing/development/continuous_integration.rst
@@ -16,7 +16,7 @@ Azure Repos
 
 Azure Repos is just another service to store Git repositories.
 Currently, we use Azure Repos to mirror ``tardis-refdata``
-repository since Azure does not impose limits on LFS bandwith
+repository since Azure does not impose limits on LFS bandwidth
 nor storage.
 
 **To clone this repository:**
@@ -25,7 +25,7 @@ nor storage.
 
   git clone https://[email protected]/tardis-sn/TARDIS/_git/tardis-refdata
 
-**To download a LFS file trough HTTPS:**
+**To download a LFS file through HTTPS:**
 
 .. code-block:: none
 
@@ -105,7 +105,7 @@ and works mostly in the same way.
 .. warning:: Triggers also can be set on the Azure's web interface
           too, but this action is discouraged, since it overrides
           any trigger specified in the YAML file and could lead to
-          confusing sitations.
+          confusing situations.
 
 There are more useful triggers such as the *cron* trigger, see the
 `Azure documentation section on triggers`_ for more information.
@@ -247,7 +247,7 @@ The common set of steps used across most TARDIS pipelines resides in the
 - Install TARDIS environment (optional).
 - Build and install TARDIS (optional).
 
-It was written to make pipelines easier to create and mantain. For example,
+It was written to make pipelines easier to create and maintain. For example,
 to start a new pipeline use::
 
   steps:
@@ -301,12 +301,12 @@ Authors pipeline
 
 This pipeline runs a notebook located in ``tardis-zenodo`` repository and
 pushes a new version of ``.zenodo.json`` to the root of ``tardis``
-repository if new commiters are found (or author order changes). The
+repository if new committers are found (or author order changes). The
 rendered notebook is uploaded to the pipeline results as an artifact.
 
 .. warning :: Fails if some author name is incomplete (due to an incomplete
-          GitHub profile) or duplicated (commited with more than one 
-          email adress). In both cases update ``.mailmap`` to fix it.
+          GitHub profile) or duplicated (committed with more than one 
+          email address). In both cases update ``.mailmap`` to fix it.
 
 In the near future we want to auto-update the citation guidelines in the
 ``README.rst`` and the documentation.

diff --git a/docs/contributing/development/git_workflow.rst b/docs/contributing/development/git_workflow.rst
@@ -352,7 +352,7 @@ When you are ready to ask for someone to review your code and consider a merge:
    pull request message.  This is still a good way to start a preliminary
    code review.
 
-The TARDIS documentation features interactive notebooks that run varius aspects of the code, as well as API documentation. To make sure that these notebooks remain up-to-date with the code, and that your docstrings are correctly incorporated into the API documentation, we ask that you build the documentation for your pull request following the instructions :ref:`here <doc-preview>`.
+The TARDIS documentation features interactive notebooks that run various aspects of the code, as well as API documentation. To make sure that these notebooks remain up-to-date with the code, and that your docstrings are correctly incorporated into the API documentation, we ask that you build the documentation for your pull request following the instructions :ref:`here <doc-preview>`.
 
 .. _using-virtualenv:
 

diff --git a/docs/contributing/development/update_refdata.rst b/docs/contributing/development/update_refdata.rst
@@ -10,10 +10,10 @@ in the reference data files.
 
 TARDIS stores reference data in the `tardis-refdata <https://github.com/tardis-sn/tardis-refdata>`_
 repository. This repository also has a mirror hosted in Azure Pipelines (synchronized automatically by a 
-GitHub workflow) since this Microsoft service does not have limitations in bandwith nor storage.
+GitHub workflow) since this Microsoft service does not have limitations in bandwidth nor storage.
 
 Sometimes, this data needs to be updated. The procedure to update these files manually is not trivial
-and has been automatized recently thanks to the `NumFOCUS <https://numfocus.org/>`_ support.
+and has been automated recently thanks to the `NumFOCUS <https://numfocus.org/>`_ support.
 
 
 =================

diff --git a/docs/io/configuration/components/supernova.rst b/docs/io/configuration/components/supernova.rst
@@ -10,7 +10,7 @@ The supernova component of the configuration file contains some key information
 
 As luminosity (in units of energy/s) is computed by integrating over the spectral luminosity (in units of energy/s/wavelength), TARDIS sums over all discrete energy packets to compute luminosity when ran, attempting to converge the output spectrum to match `luminosity_requested` (see :doc:`../../../physics/update_and_conv/update_and_conv`). `luminosity_requested` can be given in standard units, such as erg/s or J/s, or in logarithmic units such as log_lsun. The range over which TARDIS sums these energy packets is set by default from 0 to infinity via `luminosity_wavelength_start` and `luminosity_wavelength_end`, respectively, so as to generate a spectrum whose total luminosity across the entire spectrum is `luminosity_requested`. However, if in the event only the luminosity within a certain range of wavelengths is known, then `luminosity_wavelength_start` and `luminosity_wavelength_end` can be changed as necessary to reflect this, allowing TARDIS to attempt to create a spectrum whose luminosity within the set range will converge to the value defined in `luminosity_requested`.
 
-As an example, here is a sample code which will generate a specturm where only the luminosity of the visible light portion of the spectrum is given. Here, the output spectrum will have a luminosity of approximately :math:`10^{9.44}L_{sun}` within the visible range.  
+As an example, here is a sample code which will generate a spectrum where only the luminosity of the visible light portion of the spectrum is given. Here, the output spectrum will have a luminosity of approximately :math:`10^{9.44}L_{sun}` within the visible range.  
 
 .. code-block:: yaml
         

diff --git a/docs/io/visualization/using_widgets.rst b/docs/io/visualization/using_widgets.rst
@@ -37,7 +37,7 @@ You can interact with this GUI in the following ways:
 Edit Abundances
 ---------------
 There are two radio buttons which allow you to edit either single shell or 
-mutiple shells. The new input will be applied to selected shell(s) immediately 
+multiple shells. The new input will be applied to selected shell(s) immediately 
 and the plot is updated at the same time. If you want to edit multiple shells 
 at a time, remember to choose the second radio button and set the range of 
 shell number using int slider. The selected shell(s) is highlighted in the 

diff --git a/docs/physics/montecarlo/initialization.ipynb b/docs/physics/montecarlo/initialization.ipynb
@@ -261,7 +261,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# We set important quantites for making our histogram\n",
+    "# We set important quantities for making our histogram\n",
     "bins = 200\n",
     "nus_planck = np.linspace(min(packet_collection.initial_nus), max(packet_collection.initial_nus), bins).value\n",
     "bin_width = nus_planck[1] - nus_planck[0]\n",

diff --git a/docs/physics/setup/model.ipynb b/docs/physics/setup/model.ipynb
@@ -27,7 +27,7 @@
     "$v_\\mathrm{boundary\\_inner}$ and the velocity of the outer boundary $v_\\mathrm{boundary\\_outer}$ are\n",
     "supplied in the configuration file, as well as the time after the explosion for\n",
     "which TARDIS is calculating the spectrum ($t_\\mathrm{explosion}$). The radii of the inner and outer boundaries\n",
-    "are therefore calcuated by $r_\\mathrm{boundary\\_inner}=v_\\mathrm{boundary\\_inner}*t_\\mathrm{explosion}$ and\n",
+    "are therefore calculated by $r_\\mathrm{boundary\\_inner}=v_\\mathrm{boundary\\_inner}*t_\\mathrm{explosion}$ and\n",
     "$r_\\mathrm{boundary\\_outer}=v_\\mathrm{boundary\\_outer}*t_\\mathrm{explosion}$. Plasma at a distance $r$\n",
     "from the center of the supernova would then be traveling outward at a speed $v=\\frac{r}{r_\\mathrm{boundary\\_outer}}v_\\mathrm{boundary\\_outer} = \\frac{r}{t_\\mathrm{explosion}}$. This is\n",
     "also shown in the animation.\n",