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thallor1 · Feb 6, 2025 · 7af55d3 · 7af55d3
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 4380c819bedbc942176f0465ba518747
+tags: 645f666f9bcd5a90fca523b33c5a78b7
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+#GitHub Pages
+
+Last update of sphinx html documentation from [ab6532e](https://github.com/thallor1/pyMACS/tree/ab6532ec8dfe46db341b6d223204bebf6ca45f31)
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diff --git a/_sources/api.rst.txt b/_sources/api.rst.txt
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+API Reference
+-------------
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
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+.. pyMACS documentation master file, created by
+   sphinx-quickstart on Fri May 10 17:02:58 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to pyMACS's documentation!
+==================================
+
+**pyMACS** is a python interface to a mcStas simulation of the MACS instrument. 
+There are a few steps to get the package running, but most importantly this must be run on a *unix machine with a bash shell*. See :doc:`installation` for further information.
+
+.. note::
+
+   This project is not under active development and is experimental.
+
+
+
+Installation
+-----------------
+
+.. toctree::
+   installation
+
+
+.. raw:: html
+
+   <hr>
+
+Notebook Tutorials
+-------------------
+
+.. toctree::
+   notebooks/introduction_notebook
+   notebooks/emulate_MACS_data
+   notebooks/resolution_example
+   notebooks/tio2_111
+   notebooks/sqw4_simulation
+   notebooks/cri3_plotting_example
+   notebooks/MACS_User_notebook
+
+Classes and Methods
+-------------------
+
+.. toctree::
+   virtualMACS
+   sample
+   kidney
+   monochromator
+   macsdata
+   scripting
+
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
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+Installation
+=======================
+
+Configuration of McStas environment
+------------------------------------
+
+.. note:: 
+
+	pyMACS requires a bash terminal. It is untested on any platform except Ubuntu, so use at your own risk. Windows users should use the Windows subshell for Linux. 
+
+Windows users should refer to `the WSL documentation <https://learn.microsoft.com/en-us/windows/wsl/install>`_ to configure a local Ubuntu environment. 
+
+While Mac is not natively supported, it should work so long as the bash terminal is used. Internally, pyMACS uses a virtual disk on memory which in linux is located at 
+
+.. code-block:: console
+
+	/dev/shm/
+
+This will need to be redefined to point to an alternate directory if using Mac - this step may be automated in a future update if needed, but for now please contact me if you need help with this. The software should run perfectly fine without this, but it may be bottlenecked by your hard disk.
+
+Please refer to the `McStas documentation <https://github.com/McStasMcXtrace/McCode/blob/mccode-legacy/INSTALL-McStas-3.x/Linux/README.md>`_ to get a working McStas 3.X installation. 
+
+Install with *pip*
+----------------------
+
+It is highly recommended to use a seperate virtual environment to run pyMACS and install its dependencies. This can be done simply asssuming one has a conda installtion, here for example I create an environment called "mcstas"
+
+.. code-block:: console
+
+	(base) $ conda create --name mcstas 
+	(base) $ conda activate mcstas
+
+
+To use pyMACS, simply install using pip:
+
+.. code-block:: console
+
+	(mcstas) $ install git+https://github.com/thallor1/pyMACS
+
+You will need to have a valid `git installation <https://git-scm.com/book/en/v2/Getting-Started-Installing-Git>`_ first. 
+
+There is one last step that is required which is the configuration of mcstasscript, which is a key dependency of pyMACS. Please refer to the `mcstasscript documentation <https://mads-bertelsen.github.io/getting_started/installation.html#configuration>`_ .
diff --git a/_sources/kidney.rst.txt b/_sources/kidney.rst.txt
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+kidney
+-------------------
+
+
+This is a python object that is the main wrapper for all of the methods of pyMACS. It requires only a few details to initialize - a .cif file to specify the sample being simulated, and a few instrumental settings. 
+
+.. autoclass:: pyMACS.kidney.Kidney
+	:members:
+	:show-inheritance:
+
+Create a list of object parameters, like n_mono.
diff --git a/_sources/macsdata.rst.txt b/_sources/macsdata.rst.txt
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+macsdata
+-------------------
+
+
+This is a python object that is the main wrapper for all of the methods of pyMACS. It requires only a few details to initialize - a .cif file to specify the sample being simulated, and a few instrumental settings. 
+
+.. autoclass:: pyMACS.macsdata.Data
+	:members:
+	:show-inheritance:
+
+Create a list of object parameters, like n_mono.
diff --git a/_sources/modules.rst.txt b/_sources/modules.rst.txt
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+pyMACS
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   pyMACS
diff --git a/_sources/monochromator.rst.txt b/_sources/monochromator.rst.txt
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+monochromator
+-------------------
+
+
+This is a python object that is the main wrapper for all of the methods of pyMACS. It requires only a few details to initialize - a .cif file to specify the sample being simulated, and a few instrumental settings. 
+
+.. autoclass:: pyMACS.monochromator.Monochromator
+	:members:
+	:show-inheritance:
+
+Create a list of object parameters, like n_mono.
diff --git a/_sources/notebooks/MACS_User_notebook.ipynb.txt b/_sources/notebooks/MACS_User_notebook.ipynb.txt
diff --git a/_sources/notebooks/cri3_plotting_example.ipynb.txt b/_sources/notebooks/cri3_plotting_example.ipynb.txt
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		#GitHub Pages

		Last update of sphinx html documentation from [ab6532e](https://github.com/thallor1/pyMACS/tree/ab6532ec8dfe46db341b6d223204bebf6ca45f31)