Merge branch 'dev0'

README.md

-# pyrst
-Python Robust Speckle Tracking (**pyrst**) is a library for wavefront metrology
+# pyrost
+Python Robust Speckle Tracking (**pyrost**) is a library for wavefront metrology
 and sample imaging based on ptychographic speckle tracking algorithm. This
 project takes over Andrew Morgan's [speckle_tracking](https://github.com/andyofmelbourne/speckle-tracking)
 project as an improved version aiming to add robustness to the optimisation
@@ -21,7 +21,7 @@ The documentation can be found on [Read the Docs](https://robust-speckle-trackin
 We recommend **not** building from source, but install the release from [pypi](https://test.pypi.org/project/rst/)
 with the pip package installer:
 
-    pip install pyrst
+    pip install pyrost
 
 Pre-build binary wheels for OS X are available in [pypi](https://test.pypi.org/project/rst/) as for now.
 
@@ -34,4 +34,4 @@ or:
 
     pip install -r requirements.txt -e . -v
 
-That cythonizes the Cython extensions and builds them into ``/pyrst/bin``.
\ No newline at end of file
+That cythonizes the Cython extensions and builds them into ``/pyrost/bin``.
\ No newline at end of file

docs/conf.py

@@ -17,7 +17,7 @@ sys.path.insert(0, os.path.abspath('..'))
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyrst'
+project = 'pyrost'
 copyright = '2020, Nikolay Ivanov'
 author = 'Nikolay Ivanov'
 

docs/index.rst

-.. pyrst documentation master file, created by
+.. pyrost documentation master file, created by
    sphinx-quickstart on Fri Oct 30 16:00:08 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-pyrst
-=====
+pyrost
+======
 
-Python Robust Speckle Tracking (**pyrst**) is a library for wavefront
+Python Robust Speckle Tracking (**pyrost**) is a library for wavefront
 metrology and sample imaging based on ptychographic speckle tracking
 algorithm. This project takes over Andrew Morgan's
 `speckle_tracking <https://github.com/andyofmelbourne/speckle-tracking>`_
@@ -19,7 +19,7 @@ algorithm, which yields an unabberated profile of the sample and the wavefront
 of the lens. Also it contains a set of auxiliary data processing
 routines, such as bad pixel masking, defocus sweep scan, wavefront
 reconstruction, phase model fitting, etc. All of them are listed in
-:class:`pyrst.STData`.
+:class:`pyrost.STData`.
 
 st_sim
 ======

docs/install.rst

@@ -3,7 +3,7 @@ Installation
 
 Dependencies
 ------------
-pyrst has the following **mandatory** runtime dependencies:
+pyrost has the following **mandatory** runtime dependencies:
 
 * `Python <https://www.python.org/>`_ 3.7 or later (Python 2.x is
   **not** supported).
@@ -17,32 +17,32 @@ pyrst has the following **mandatory** runtime dependencies:
 * `NumPy <https://numpy.org>`_ 1.19.0 or later.
 * `SciPy <https://scipy.org>`_ 1.5.2 or later.
 * `pyFFTW <https://github.com/pyFFTW/pyFFTW>`_ 0.12.0 or later, which is used
-  for the Fourier Transform wavefront reconstruction (:func:`pyrst.bin.ct_integrate`).
+  for the Fourier Transform wavefront reconstruction (:func:`pyrost.bin.ct_integrate`).
 
 Packages
 --------
-pyrst packages are available through `pypi <https://test.pypi.org/project/rst/>`_ on
+pyrost packages are available through `pypi <https://test.pypi.org/project/rst/>`_ on
 OS X as for now.
 
 pip
 ^^^
-pyrst is available on OS X via the `pip <https://pip.pypa.io/en/stable/>`_
+pyrost is available on OS X via the `pip <https://pip.pypa.io/en/stable/>`_
 package installer. Installation is pretty straightforward:
 
 .. code-block:: console
 
-    $ pip install pyrst
+    $ pip install pyrost
 
-If you want to install pyrst for a single user instead of
+If you want to install pyrost for a single user instead of
 system-wide, you can do:
 
 .. code-block:: console
 
-    $ pip install --user pyrst
+    $ pip install --user pyrost
 
 Installation from source
 ------------------------
-In order to install pyrst from source you will need:
+In order to install pyrost from source you will need:
 
 * a C++ compiler (gcc or clang will do).
 * `Python <https://www.python.org/>`_ 3.7 or later (Python 2.x is
@@ -57,19 +57,19 @@ In order to install pyrst from source you will need:
 * `NumPy <https://numpy.org>`_ 1.19.0 or later.
 
 After installing the dependencies, you can download the the source code from
-the `GitHub pyrst repository page <https://github.com/simply-nicky/pyrst>`_.
-Or you can download the last version of pyrst repository with ``git``:
+the `GitHub pyrost repository page <https://github.com/simply-nicky/pyrost>`_.
+Or you can download the last version of pyrost repository with ``git``:
 
 .. code-block:: console
 
-    $ git clone https://github.com/simply-nicky/pyrst.git
+    $ git clone https://github.com/simply-nicky/pyrost.git
 
-After downloading the pyrst's source code, ``cd`` into the repository root folder
+After downloading the pyrost's source code, ``cd`` into the repository root folder
 and build the C++ libraries using ``setuputils``:
 
 .. code-block:: console
 
-    $ cd pyrst
+    $ cd pyrost
     $ python setup.py install
 
 OR
@@ -80,6 +80,6 @@ OR
 
 Getting help
 ------------
-If you run into troubles installing pyrst, please do not hesitate
+If you run into troubles installing pyrost, please do not hesitate
 to contact me either through `my mail <nikolay.ivanov@desy.de>`_
-or by opening an issue report on `github <https://github.com/simply-nicky/pyrst/issues>`_.
\ No newline at end of file
+or by opening an issue report on `github <https://github.com/simply-nicky/pyrost/issues>`_.
\ No newline at end of file

docs/reference/ab_fit_ref.rst

-pyrst Abberations Fitting
-=========================
+pyrost Abberations Fitting
+==========================
 
-.. automodule:: pyrst.abberations_fit
+.. automodule:: pyrost.abberations_fit
 
 .. toctree::
     :maxdepth: 1

docs/reference/c_funcs/aperture_wp.rst

 aperture_wp
 ===========
 
-.. autofunction:: pyrst.bin.aperture_wp
\ No newline at end of file
+.. autofunction:: pyrost.bin.aperture_wp
\ No newline at end of file

docs/reference/c_funcs/barcode_profile.rst

 barcode_profile
 ===============
 
-.. autofunction:: pyrst.bin.barcode_profile
\ No newline at end of file
+.. autofunction:: pyrost.bin.barcode_profile
\ No newline at end of file

docs/reference/c_funcs/ct_integrate.rst

 ct_integrate
 ============
 
-.. autofunction:: pyrst.bin.ct_integrate
\ No newline at end of file
+.. autofunction:: pyrost.bin.ct_integrate
\ No newline at end of file

docs/reference/c_funcs/fraunhofer_1d.rst

 fraunhofer_1d
 =============
 
-.. autofunction:: pyrst.bin.fraunhofer_1d
\ No newline at end of file
+.. autofunction:: pyrost.bin.fraunhofer_1d
\ No newline at end of file

docs/reference/c_funcs/fraunhofer_1d_scan.rst

 fraunhofer_1d_scan
 ==================
 
-.. autofunction:: pyrst.bin.fraunhofer_1d_scan
\ No newline at end of file
+.. autofunction:: pyrost.bin.fraunhofer_1d_scan
\ No newline at end of file

docs/reference/c_funcs/lens_wp.rst

 lens_wp
 =======
 
-.. autofunction:: pyrst.bin.lens_wp
\ No newline at end of file
+.. autofunction:: pyrost.bin.lens_wp
\ No newline at end of file

docs/reference/c_funcs/make_frames.rst

 make_frames
 ===========
 
-.. autofunction:: pyrst.bin.make_frames
\ No newline at end of file
+.. autofunction:: pyrost.bin.make_frames
\ No newline at end of file

docs/reference/c_funcs/make_reference.rst

 make_reference
 ==============
 
-.. autofunction:: pyrst.bin.make_reference
\ No newline at end of file
+.. autofunction:: pyrost.bin.make_reference
\ No newline at end of file

docs/reference/c_funcs/make_whitefield.rst

 make_whitefield
 ===============
 
-.. autofunction:: pyrst.bin.make_whitefield
\ No newline at end of file
+.. autofunction:: pyrost.bin.make_whitefield
\ No newline at end of file

docs/reference/c_funcs/total_mse.rst

 total_mse
 =========
 
-.. autofunction:: pyrst.bin.total_mse
\ No newline at end of file
+.. autofunction:: pyrost.bin.total_mse
\ No newline at end of file

docs/reference/c_funcs/update_pixel_map_gs.rst

 update_pixel_map_gs
 ===================
 
-.. autofunction:: pyrst.bin.update_pixel_map_gs
\ No newline at end of file
+.. autofunction:: pyrost.bin.update_pixel_map_gs
\ No newline at end of file

docs/reference/c_funcs/update_pixel_map_nm.rst

 update_pixel_map_nm
 ===================
 
-.. autofunction:: pyrst.bin.update_pixel_map_nm
\ No newline at end of file
+.. autofunction:: pyrost.bin.update_pixel_map_nm
\ No newline at end of file

docs/reference/classes/abberations_fit.rst

 AbberationsFit
 ==============
 
-.. autoclass:: pyrst.AbberationsFit
+.. autoclass:: pyrost.AbberationsFit
     :members:
     :inherited-members:
\ No newline at end of file

docs/reference/classes/cxi_protocol.rst

 cxi_protocol
 ============
 
-.. autofunction:: pyrst.cxi_protocol
\ No newline at end of file
+.. autofunction:: pyrost.cxi_protocol
\ No newline at end of file

docs/reference/classes/loader.rst

 loader
 ======
 
-.. autofunction:: pyrst.loader
\ No newline at end of file
+.. autofunction:: pyrost.loader
\ No newline at end of file