BUGFIX: VFT;

change to src layout

doc/source/_templates/autosummary/class.rst

@@ -3,25 +3,36 @@
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
+   :exclude-members: {% for item in methods %}{%- if not item.startswith('_') or item in ['__call__'] %}{{ item }}, {% endif %}{%- endfor %}
 
-   {% block methods %}
-
+   {%- block methods %}
    {% if methods %}
-   .. rubric:: {{ _('Methods') }}
-
-   {% for item in methods %}
-   .. automethod:: {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: {{ _('Attributes') }}
+   .. rubric:: Methods
 
    .. autosummary::
-   {% for item in attributes %}
-      ~{{ name }}.{{ item }}
-   {%- endfor %}
+      :toctree:
+
+   {% for item in methods %}
+   {%- if not item.startswith('_') or item in ['__call__'] %}   ~{{ name }}.{{ item }}
    {% endif %}
-   {% endblock %}
+   {%- endfor %}
+   {%- endif %}
+   {%- endblock %}
+
+   {%- block attributes %}
+   {%- if attributes %}
+   .. rubric:: Properties
+
+   .. autosummary::
+      :toctree:
+
+   {% for item in attributes %}
+   {%- if not item.startswith('_') or item in ['__call__'] %}   ~{{ name }}.{{ item }}
+   {% endif %}
+   {%- endfor %}
+   {%- endif %}
+   {%- endblock %}
+
+.. _sphx_glr_backref_{{ fullname }}:
+.. minigallery:: {{ objname }}
+   :add-heading:

doc/source/api/distributions.rst

@@ -1,5 +1,2 @@
 .. automodule:: nmreval.distributions
    :members:
-   :inherited-members:
-   :undoc-members:
-

doc/source/api/index.rst

@@ -11,3 +11,4 @@ Reference
    models
    distributions
    nmr
+   math

doc/source/conf.py

@@ -12,7 +12,7 @@
 #
 import os
 import sys
-sys.path.append('/autohome/dominik/nmreval')
+sys.path.append(os.path.abspath('../../src'))
 import nmreval
 
 
@@ -43,6 +43,9 @@ extensions = [
     'sphinx.ext.viewcode',
     'sphinx.ext.intersphinx',
     'sphinx_gallery.gen_gallery',
+    'sphinx.ext.todo',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.mathjax',
 ]
 
 # configuration for intersphinx
@@ -56,7 +59,7 @@ intersphinx_mapping = {
 
 # # autodoc options
 autodoc_typehints = 'none'
-autodoc_class_signature = 'separated'
+# autodoc_class_signature = 'separated'
 autoclass_content = 'class'
 autodoc_member_order = 'groupwise'
 #
@@ -79,6 +82,7 @@ sphinx_gallery_conf = {
     'min_reported_time': 10000000000,
     'show_memory': False,
     'show_signature': False,
+    'line_numbers': True,
 }
 
 # The suffix(es) of source filenames.
@@ -151,15 +155,23 @@ todo_include_todos = False
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'
+html_theme = 'sphinx_material'  # 'sphinx_rtd_theme'  # 'pydata_sphinx_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    'collapse_navigation': False,
-    'show_prev_next': False,
-    'navbar_end': ['navbar-icon-links.html', 'search-field.html'],
+    'nav_title': 'nmreval',
+    # 'base_url': 'https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval',
+    'repo_url': 'https://chaos3.fkp.physik.tu-darmstadt.de/source/nmreval',
+    'repo_name': 'Repo',
+    'html_minify': True,
+    'css_minify': True,
+    'master_doc': False,
+    'globaltoc_depth': 3,
+    'globaltoc_collapse': True,
+    'globaltoc_includehidden': True,
+    'heroes': {'index': 'Fun for the whole family!!!!'}
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -183,10 +195,10 @@ html_static_path = ['_static']
 html_logo = '_static/logo.png'
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'**': ['sidebar-nav-bs.html']}
-# html_sidebars = {
-#     '**': ['localtoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'],
-# }
+html_sidebars = {
+    "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
+}
+
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
@@ -205,7 +217,7 @@ html_last_updated_fmt = ''
 html_additional_pages = {}
 
 # If false, no module index is generated.
-html_domain_indices = False
+html_domain_indices = True
 
 # If false, no index is generated.
 html_use_index = True
@@ -214,10 +226,10 @@ html_use_index = True
 html_split_index = False
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-# html_show_sphinx = True
+html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-# html_show_copyright = True
+html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the

doc/source/index.rst

@@ -10,15 +10,15 @@ NMREval documentation
 .. toctree::
    :maxdepth: 1
 
+   install.rst
    user_guide/index
    gallery/index
    api/index
 
 
 
-Indices and tables
-==================
+Indices
+=======
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+| :ref:`genindex`
+| :ref:`modindex`

doc/source/nmr/pake.rst

@@ -11,7 +11,8 @@ In general, time signals are calculated by integration of all orientations (see
 .. math::
    g(t) = \int f[\omega_\text{int}(\theta, \phi)t]\sin\theta\,\mathrm{d}\theta\,\mathrm{d}\phi
 
-with :math:`f(\theta, \phi, t) = \cos[\omega_\text{int}(\theta, \phi) t]` or :math:`\exp[i\omega_\text{int}(\theta) t]` and fourier transform for a spectrum.
+with :math:`f(\theta, \phi, t) = \cos[\omega_\text{int}(\theta, \phi) t]` or :math:`\exp[i\omega_\text{int}(\theta) t]`
+and fourier transform for a spectrum.
 However, summation over :math:`\theta`, :math:`\phi`, and calculating :math:`f(\theta, \phi, t)` for each orientation is time consuming.
 
 Alternatively, if the orientations are equidistant in :math:`\cos\theta`, one can get to the spectrum directly by creating a histogram of :math:`\omega_\text{int}(\theta, \phi)`, thus circumventing a lot of calculations.

doc/source/user_guide/fit.rst

@@ -4,10 +4,6 @@
 Fitting data
 ============
 
-.. image:: ../_static/fit_dialog.png
-    :scale: 80%
-    :align: center
-
 The picture gives an example of dialog to setup and start fits.
 First, there is the possibiity to fit different functions, called models to differentiate from the functions inside each
 model, to different data simultaneously.

doc/source/user_guide/index.rst

@@ -1,11 +1,13 @@
-==========
+**********
 User Guide
-==========
+**********
 
 
 .. toctree::
    :maxdepth: 2
 
-   read
+   gui/index
+   read/index
+   edit_signals
    fit
    shift_scale

doc/source/user_guide/read.rst

@@ -1,19 +0,0 @@
-.. _user_guide.read:
-
-*************
-Reading files
-*************
-
-Supported filetypes are
-
-   * Text files,
-   * DAMARIS HDF5 files,
-   * Grace images.
-   * HP alpha-analyzer EPS files
-   * NTNMR .tnt files
-
-DAMARIS HDF files
-=================
-
-After scanning the selected file the program shows a list of the available data.
-