Update documentation

Correct sphinx warning

Author: kif

doc/source/api/ext/index.rst

@@ -73,14 +73,6 @@ pyFAI.ext.relabel module
     :undoc-members:
     :show-inheritance:
 
-pyFAI.ext.setup module
-----------------------
-
-.. automodule:: pyFAI.ext.setup
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pyFAI.ext.sparse_builder module
 -------------------------------
 
@@ -129,14 +121,6 @@ pyFAI.ext.splitPixel module
     :undoc-members:
     :show-inheritance:
 
-pyFAI.ext.splitPixelFull module
--------------------------------
-
-.. automodule:: pyFAI.ext.splitPixelFull
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pyFAI.ext.splitPixelFullCSR module
 ----------------------------------
 

doc/source/api/gui/utils.rst

@@ -49,14 +49,6 @@ pyFAI.gui.utils.projecturl module
     :undoc-members:
     :show-inheritance:
 
-pyFAI.gui.utils.setup module
-----------------------------
-
-.. automodule:: pyFAI.gui.utils.setup
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pyFAI.gui.utils.timeutils module
 --------------------------------
 

doc/source/api/gui/widgets.rst

@@ -73,14 +73,6 @@ pyFAI.gui.widgets.DetectorSelector module
     :undoc-members:
     :show-inheritance:
 
-pyFAI.gui.widgets.ElidedLabel module
-------------------------------------
-
-.. automodule:: pyFAI.gui.widgets.ElidedLabel
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pyFAI.gui.widgets.FileEdit module
 ---------------------------------
 

doc/source/api/modules.rst

@@ -10,7 +10,7 @@ expect after having launched *Jupyter notebook* (or ipython) and typed:
 
 The most important class is AzimuthalIntegrator which is an object containing
 both the geometry (it inherits from Geometry, another class)
-and exposes important methods (functions) like `integrate1d` and `integrate2d.
+and exposes important methods (functions) like `integrate1d` and `integrate2d`.
 
 .. toctree::
    :maxdepth: 2

doc/source/api/opencl/index.rst

@@ -49,14 +49,6 @@ pyFAI.opencl.preproc module
     :undoc-members:
     :show-inheritance:
 
-pyFAI.opencl.setup module
--------------------------
-
-.. automodule:: pyFAI.opencl.setup
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pyFAI.opencl.sort module
 ------------------------
 

doc/source/api/resources/index.rst

@@ -1,15 +1,14 @@
 pyFAI.resources package
 =======================
 
-pyFAI.resources.setup module
+pyFAI.resources.__init__ module
 ----------------------------
 
-.. automodule:: pyFAI.resources.setup
+.. automodule:: pyFAI.resources.__init__
     :members:
     :undoc-members:
     :show-inheritance:
 
-
 Module contents
 ---------------
 

doc/source/api/utils/index.rst

@@ -57,14 +57,6 @@ pyFAI.utils.orderedset module
     :undoc-members:
     :show-inheritance:
 
-pyFAI.utils.setup module
-------------------------
-
-.. automodule:: pyFAI.utils.setup
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 pyFAI.utils.shell module
 ------------------------
 

doc/source/man/diff_map.rst

@@ -122,6 +122,6 @@ Bugs:
 .....
 
 Bugs: Many, see hereafter: 1)If the number of files is too large, use
-double quotes "*.edf" 2)There is a known bug on Debian7 where importing
+double quotes "\*.edf" 2)There is a known bug on Debian7 where importing
 a large number of file can take much longer than the integration itself:
 consider passing files in the command line

doc/source/usage/cookbook/calibration_with_jupyter.ipynb

@@ -30,7 +30,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "04/10/2022"
+__date__ = "05/01/2023"
 __status__ = "stable"
 __docformat__ = 'restructuredtext'
 
@@ -3074,7 +3074,7 @@ def sigma_clip_ng(self, data,
 
         Keep only pixels with intensty:
 
-            |I - <I>| < thres * std(I)
+            \|I - <I>\| < thres * std(I)
 
         This enforces a gaussian distibution and is very good at extracting
         background or amorphous isotropic scattering out of Bragg peaks.

pyFAI/azimuthalIntegrator.py

@@ -36,7 +36,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "25/06/2020"
+__date__ = "05/01/2023"
 __status__ = "production"
 
 
@@ -116,10 +116,10 @@ def get_pixel_corners(self, correct_binning=False, use_cython=True):
         :param correct_binning: If True, check that the produced array have the right shape regarding binning
         :param use_cython: set to False for testing
         :return:  4D array containing:
-                    pixel index (slow dimension)
-                    pixel index (fast dimension)
-                    corner index (A, B, C or D), triangles or hexagons can be handled the same way
-                    vertex position (z,y,x)
+                  pixel index (slow dimension)
+                  pixel index (fast dimension)
+                  corner index (A, B, C or D), triangles or hexagons can be handled the same way
+                  vertex position (z,y,x)
         """
         if self._pixel_corners is None:
             with self._sem:

pyFAI/detectors/_non_flat.py

@@ -26,7 +26,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "13/07/2022"
+__date__ = "05/01/2023"
 __status__ = "development"
 
 import logging
@@ -175,6 +175,7 @@ def __init__(self,
         :param unit: the kind of radial units
         :param bin_center: position of the bin center
         :param mask_checksum: just a place-holder to track which mask was used
+
         Nota: bins value is deduced from the dimentionality of bin_centers
         """
         self.bin_centers = bin_centers
@@ -291,9 +292,10 @@ def sigma_clip(self, data, dark=None, dummy=None, delta_dummy=None,
         :param safe: Unused in this implementation
         :param error_model: Enum or str, "azimuthal" or "poisson"
         :param normalization_factor: divide raw signal by this value
-        :param cutoff: discard all points with |value - avg| > cutoff * sigma. 3-4 is quite common
+        :param cutoff: discard all points with \|value - avg\| > cutoff * sigma. 3-4 is quite common
         :param cycle: perform at maximum this number of cycles. 5 is common.
         :return: namedtuple with "position intensity error signal variance normalization count"
+
         """
         shape = data.shape
         error_model = ErrorModel.parse(error_model)

pyFAI/engines/CSR_engine.py

@@ -33,7 +33,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "28/03/2022"
+__date__ = "05/01/2023"
 __status__ = "production"
 
 import os
@@ -323,7 +323,7 @@ def _common_creation(self, points, gpt=None, ring=None):
         return gpt
 
     def onclick_new_grp(self, yx, ring):
-        " * new_grp Right-click (click+n):         try an auto find for a ring"
+        "new_grp Right-click (click+n):         try an auto find for a ring"
         # ydata is a float, and matplotlib display pixels centered.
         # we use floor (int cast) instead of round to avoid use of
         # banker's rounding
@@ -337,7 +337,7 @@ def onclick_new_grp(self, yx, ring):
             logger.warning("No peak found !!!")
 
     def onclick_single_point(self, yx, ring):
-        " * Right-click + Ctrl (click+b):  create new group with one single point"
+        "Right-click + Ctrl (click+b):  create new group with one single point"
         newpeak = self.massif.nearest_peak(yx)
         if newpeak:
             gpt = self._common_creation([newpeak], ring=ring)
@@ -346,7 +346,7 @@ def onclick_single_point(self, yx, ring):
             logger.warning("No peak found !!!")
 
     def onclick_append_more_points(self, yx, ring):
-        " * Right-click + m (click+m):     find more points for current group"
+        "Right-click + m (click+m):     find more points for current group"
         gpt = self.points.get(ring)
         if gpt:
             self.widget.remove_grp(gpt.label, update=False)
@@ -364,7 +364,8 @@ def onclick_append_more_points(self, yx, ring):
             self.onclick_new_grp(yx, ring)
 
     def onclick_append_1_point(self, yx, ring=None):
-        """ * Right-click + Shift (click+v): add one point to current group
+        """Right-click + Shift (click+v): add one point to current group
+
         :param xy: 2tuple of coordinates
         """
         gpt = self.points.get(ring)
@@ -382,7 +383,7 @@ def onclick_append_1_point(self, yx, ring=None):
             self.onclick_new_grp(yx, ring)
 
     def onclick_erase_grp(self, yx, ring):
-        " * Center-click or (click+d):     erase current group"
+        "Center-click or (click+d):     erase current group"
         gpt = self.points.pop(ring)
         if gpt:
             self.widget.remove_grp(gpt.label, update=True)
@@ -394,7 +395,7 @@ def onclick_erase_grp(self, yx, ring):
             logger.warning("No group of points for ring %s", ring)
 
     def onclick_erase_1_point(self, yx, ring):
-        " * Center-click + 1 or (click+1): erase closest point from current group"
+        "Center-click + 1 or (click+1): erase closest point from current group"
         gpt = self.points.get(ring)
         if not gpt:
             self.widget.remove_grp(gpt.label, update=True)

pyFAI/gui/peak_picker.py

@@ -42,7 +42,7 @@
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "04/10/2022"
+__date__ = "05/01/2023"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 
@@ -855,13 +855,14 @@ class FabioWriter(Writer):
     """
 
     def __init__(self, filename=None, extension=None, directory="", prefix=None, index_format="_%04d", start_index=0, fabio_class=None):
-        """
+        """Constructor of the class
+
         :param filename:
         :param extension:
         :param prefix: basename of the file
         :param index_format: "_%04s" gives "_0001" for example
         :param start_index: often 0 or 1
-        :param
+        :param fabio_class: type of file to write
         """
         Writer.__init__(self, filename, extension)
         self.header = {}

pyFAI/io/__init__.py

@@ -28,7 +28,7 @@
 
 __authors__ = ["Jérôme Kieffer", "Giannis Ashiotis"]
 __license__ = "MIT"
-__date__ = "17/11/2022"
+__date__ = "05/01/2023"
 __copyright__ = "2014-2021, ESRF, Grenoble"
 __contact__ = "jerome.kieffer@esrf.fr"
 
@@ -861,7 +861,7 @@ def sigma_clip(self, data, dark=None, dummy=None, delta_dummy=None,
         :param preprocess_only: return the dark subtracted; flat field & solidangle & polarization corrected image, else
         :param error_model: enum ErrorModel
         :param normalization_factor: divide raw signal by this value
-        :param cutoff: discard all points with |value - avg| > cutoff * sigma. 3-4 is quite common
+        :param cutoff: discard all points with ``|value - avg\| > cutoff * sigma``. 3-4 is quite common
         :param cycle: perform at maximum this number of cycles. 5 is common.
         :param out_avgint: destination array or pyopencl array for sum of all data
         :param out_sem: destination array or pyopencl array for uncertainty on mean value