filtered by pre-commit

.readthedocs.yaml

@@ -27,4 +27,3 @@ python:
     - requirements: ci/requirements_rtd.txt
     - method: pip
       path:  .
-

CHANGELOG.txt

@@ -1 +1 @@
-Please see doc/source/changelog.rst
+Please see doc/source/changelog.rst

CONTRIBUTING.md

@@ -1,9 +1,9 @@
 # Contributing
 
 When contributing to this repository, please first open an issue to discuss the change you wish to make.
-Mention you wish to help us improving this specific part of the project, we will be able to provide you guidance. 
+Mention you wish to help us improving this specific part of the project, we will be able to provide you guidance.
 
-If you have questions, the best is to subscribe to the associated mailing list. Direct contact with maintainers is 
+If you have questions, the best is to subscribe to the associated mailing list. Direct contact with maintainers is
 discouraged as we are few and may be unavailable (holidays, ...).
 
 ## Prepare your local working environment
@@ -16,7 +16,7 @@ discouraged as we are few and may be unavailable (holidays, ...).
 6. Build and test `python setup.py build test`
 
 This should take a few minutes and ensures everything is ready for developping within pyFAI.
-Later-on no recompilation will be needed unless you modify cython code. 
+Later-on no recompilation will be needed unless you modify cython code.
 In this case, recompilation can be accelerating by installing `ccache`.
 
 ## Pull Request Process
@@ -36,13 +36,12 @@ or to run any third party application using pyFAI (when the full path needs is p
 In one word, `bootstrap` is a great tool to help debugging, it re-compiles the code when needed but it is not perfect and corner cases probably exists.
 Note: it is forbidden to import pyFAI from the sources, to avoid bugs as many files will be missing or mis-placed.
 
-## Test locally your code 
+## Test locally your code
 
 The test suite of pyFAI can simply be triggered by running `./run_tests.py` which
-takes care of re-building what is needed. 
+takes care of re-building what is needed.
 This helper script has many option about coverage, selecting tests, debuging mode ...
 use `./run_tests.py -h` to visualize them all.
 
 
 Please note we have not yet decided for a code of conduct.
-

MANIFEST.in

@@ -43,4 +43,3 @@ recursive-exclude doc *.npz
 recursive-exclude doc *.npy
 recursive-exclude doc *.edf
 recursive-exclude doc *.edf
-

README.rst

@@ -39,7 +39,7 @@ As most Python packages, pyFAI is available via PIP::
 It is advised to run this in a vitural environment.
 Provide the *--user* to perform an installation local to your user (not recommended).
 Under UNIX, you may have to run the command via *sudo* to gain root access an
-perform a system wide installation (neither recommended). 
+perform a system wide installation (neither recommended).
 
 
 With conda
@@ -90,7 +90,7 @@ repository::
     git clone https://github.com/silx-kit/pyFAI.git
     cd pyFAI
     pip install --upgrade .
-    
+
 If you want pyFAI to make use of your graphic card, please install
 `pyopencl <http://mathema.tician.de/software/pyopencl>`_
 
@@ -158,13 +158,13 @@ using apt-get these can be installed as::
 MacOSX
 ------
 
-One needs to install `Python` (>=3.6) and `Xcode` prior to start installing pyFAI. 
+One needs to install `Python` (>=3.6) and `Xcode` prior to start installing pyFAI.
 The compiled extension will use only one core due to the limitation of the compiler.
-OpenCL is hence greately adviced on Apple systems. 
+OpenCL is hence greately adviced on Apple systems.
 Then install the missing dependencies with `pip`::
 
    pip install -r requirements.txt
-	
+
 
 Windows
 -------

build-deb.sh

@@ -37,7 +37,7 @@ deb_name=$(echo "$source_project" | tr '[:upper:]' '[:lower:]')
 
 # target system
 if [ -f /etc/debian_version ]
-then 
+then
     debian_version=$(cat /etc/debian_version | cut -d. -f1 | grep -o '[0-9]*')
     if [ -z $debian_version ]
     then
@@ -92,7 +92,7 @@ optional arguments:
     --help     show this help text
     --install  install the packages generated at the end of
                the process using 'sudo dpkg'
-    --stdeb-py3     Build using stdeb for python3           
+    --stdeb-py3     Build using stdeb for python3
     --debian9  Simulate a debian 9 Stretch system
     --debian10 Simulate a debian 10 Buster system
     --debian11 Simulate a debian 11 Bullseye system
@@ -165,7 +165,7 @@ clean_up()
 }
 
 build_deb() {
-    echo "Build for debian 9 or newer using actual packaging" 
+    echo "Build for debian 9 or newer using actual packaging"
     tarname=${project}_${debianversion}.orig.tar.gz
     clean_up
     python3 setup.py debian_src

ci/install_pyopencl.sh

@@ -1,14 +1,14 @@
 #!/bin/bash
 # Compile & install pyopencl
-if [ -f ci/intel_opencl_icd.sh ]; then 
+if [ -f ci/intel_opencl_icd.sh ]; then
 	source ci/intel_opencl_icd.sh
     git clone --depth=1 --shallow-submodules --recurse-submodules https://github.com/pyopencl/pyopencl
     pushd pyopencl
     pip install "setuptools<60.0.0"
-    pip install wheel pybind11 mako 
+    pip install wheel pybind11 mako
     CL_LIBRARY_PATH=$(python3 -c "import os; print(os.environ.get('LD_LIBRARY_PATH','').split(':')[-1])")
     CL_INCLUDE_PATH=$(python3 -c "import os; print(os.environ.get('C_INCLUDE_PATH','').split(':')[-1])")
-    echo CL_LIBRARY_PATH ${CL_LIBRARY_PATH} 
+    echo CL_LIBRARY_PATH ${CL_LIBRARY_PATH}
     echo CL_INCLUDE_PATH ${CL_INCLUDE_PATH}
     python3  configure.py  --cl-inc-dir=${CL_INCLUDE_PATH} --cl-lib-dir=${CL_LIBRARY_PATH}
     python3 setup.py build bdist_wheel

ci/requirements_appveyor.txt

@@ -14,4 +14,4 @@ matplotlib
 #mako
 #pyopencl
 numexpr
-silx
+silx

ci/requirements_gh.txt

@@ -18,6 +18,6 @@ scipy
 matplotlib
 #mako
 #pybind11
-#pyopencl 
+#pyopencl
 numexpr
 silx

doc/mathematica/geometry.txt

@@ -209,4 +209,4 @@ Out[50]//CForm=
    (2.*Sqrt(Power(d1*Cos(rot2)*Cos(rot3) + d2*(Cos(rot3)*Sin(rot1)*Sin(rot2) - Cos(rot1)*Sin(rot3)) + L*(Cos(rot1)*Cos(rot3)*Sin(rot2) + Sin(rot1)*Sin(rot3)),2) +
        Power(d1*Cos(rot2)*Sin(rot3) + L*(-(Cos(rot3)*Sin(rot1)) + Cos(rot1)*Sin(rot2)*Sin(rot3)) + d2*(Cos(rot1)*Cos(rot3) + Sin(rot1)*Sin(rot2)*Sin(rot3)),2))*
      (Power(L*Cos(rot1)*Cos(rot2) + d2*Cos(rot2)*Sin(rot1) - d1*Sin(rot2),2) + Power(d1*Cos(rot2)*Cos(rot3) + d2*(Cos(rot3)*Sin(rot1)*Sin(rot2) - Cos(rot1)*Sin(rot3)) +
-         L*(Cos(rot1)*Cos(rot3)*Sin(rot2) + Sin(rot1)*Sin(rot3)),2) + Power(d1*Cos(rot2)*Sin(rot3) + L*(-(Cos(rot3)*Sin(rot1)) + Cos(rot1)*Sin(rot2)*Sin(rot3)) + d2*(Cos(rot1)*Cos(rot3) + Sin(rot1)*Sin(rot2)*Sin(rot3)),2)))
+         L*(Cos(rot1)*Cos(rot3)*Sin(rot2) + Sin(rot1)*Sin(rot3)),2) + Power(d1*Cos(rot2)*Sin(rot3) + L*(-(Cos(rot3)*Sin(rot1)) + Cos(rot1)*Sin(rot2)*Sin(rot3)) + d2*(Cos(rot1)*Cos(rot3) + Sin(rot1)*Sin(rot2)*Sin(rot3)),2)))

doc/source/api/app/index.rst

@@ -3,4 +3,4 @@ pyFAI.app package
 
 The package pyFAI.app contains the code of the different command line scripts and programs.
 This code is not intended to be used by users of pyFAI as a library hence it makes little sense
-to document it here. 
+to document it here.

doc/source/api/gui/index.rst

@@ -3,7 +3,7 @@ pyFAI.gui package
 
 The package pyFAI.gui contains mainly the code of the graphical user interface widgets.
 This code is not intended to be used by users of pyFAI as a library hence it makes little sense
-to document it all here. Only documentation on the *Jupyter* tools are exposed. 
+to document it all here. Only documentation on the *Jupyter* tools are exposed.
 
 pyFAI.gui.cli_calibration module
 --------------------------------
@@ -36,4 +36,3 @@ pyFAI.gui.peak_picker module
     :members:
     :undoc-members:
     :show-inheritance:
-

doc/source/api/pyFAI.rst

@@ -147,6 +147,3 @@ Other sub-packages:
     opencl/index
     resources/index
     utils/index
-
-
-

doc/source/biblio.rst

@@ -75,4 +75,3 @@ Bibliography
    Benecke, G. et al., (2014)
    J. Appl. Cryst. 47,
    http://dx.doi.org/10.1107/S1600576714019773
-

doc/source/calibration.rst

@@ -143,4 +143,3 @@ Nevertheless its absolute value has no meaning, except the lower, the better.
 
 Subsequently, pyFAI offers some validation options in to check the quality of the fit.
 some of them global, some of them limited to given rings.
-

doc/source/changelog.rst

@@ -41,17 +41,17 @@ Bug-fix release with:
     - Implementation in Python, Cython and OpenCL with poissonian and azimuthal error-model
     - Sparsification, compression of single crystal data
 	- Application to peak-picking and quality assessement of SSX data
-	- Analysis of grid-scan to find single crystal 
+	- Analysis of grid-scan to find single crystal
 	- Single pass variance propagation in azimuthal bin
 	- Integration of the Jungfrau detector  (ID29)
 * 2D integration:
 	- New integrators with error propagation by default
 	- Full pixel splitting in addition to BBox and no splitting
-* Refactor of all LUT and CSR to share the same code base, makes tests more robust. 
+* Refactor of all LUT and CSR to share the same code base, makes tests more robust.
 * Calibration of experimental setup using Jupyter notebooks
 	- User interaction with plots in matplotlib (thanks Phil Hans)
 	- Factorize code between `pyFAI-calib` and jupyter calibration
-	- Tutorial as notebook and video recording 	
+	- Tutorial as notebook and video recording
 * Parallax correction for thick detector (still experimental, thanks to Vadim)
 * Improved tutorial on detector geometry calibration (based on Kabsch alignment)
 * Better performances on HPC nodes by limiting simple OpenMP to fewer cores
@@ -63,8 +63,8 @@ Bug-fix release with:
 -----------------
 * One year of development, about 500 commits & 370 files modified.
 * Generalization of the new generation 1D integrators (better error propagation)
-* Sigma clipping and sparsification of single crystal data (OpenCL only)  
-* Fix issue introduced with the scipy 1.15 (constrained calibration broken)  
+* Sigma clipping and sparsification of single crystal data (OpenCL only)
+* Fix issue introduced with the scipy 1.15 (constrained calibration broken)
 * Improved distortion correction (also on GPU, ...)
 * Major re-work of the documentation (thanks Thomas Kluyver and Loic Huder)
 * Improve the calibration of Pilatus and Eiger detectors based on a grid of holes.

doc/source/design/ai.rst

@@ -122,7 +122,7 @@ Two types of rebinning engines exists:
     Histograms loop over each individual pixel from the image, calculate the bin index and transfer the signal to the destination bin.
     This family of algorithms is rather easy to implement and provides good single threaded performances,
     but they are hard to parallelize (efficiently) due to the need of atomic operations for writing in the destination bin.
-    Note that several histograms are always needed, at least one for the signal and one for the count, plus one for the normalization factor and possibly one for the variance propagation. 
+    Note that several histograms are always needed, at least one for the signal and one for the count, plus one for the normalization factor and possibly one for the variance propagation.
 
 - Sparse matrix multiplication
 
@@ -140,13 +140,13 @@ Three levels of pixel splitting schemes are available within pyFAI:
 - No splitting
 
     The whole intensity is assigned to the center of the pixel and
-    rebinned using a simple histogram. 
+    rebinned using a simple histogram.
     Each pixel contributes to a single bin.
 
 - Bounding box pixel splitting
 
     The pixel is abstracted by a box surrounding it with, making calculation
-    easier but blurring a bit the image. Each pixel contributes to multiple bins. 
+    easier but blurring a bit the image. Each pixel contributes to multiple bins.
 
 - Tight pixel splitting
 

doc/source/design/index.rst

@@ -14,7 +14,7 @@ I would describe it as a stack of 5 layers, upper ones relying on lower ones:
 
 5. Graphical user interfaced application: ``pyFAI-calib2``, ``diff_map``, ...
 
-4. Command-line scripts: ``pyFAI-average``, ``pyFAI-benchmark``, ... 
+4. Command-line scripts: ``pyFAI-average``, ``pyFAI-benchmark``, ...
 
 3. Top level objects: ``AzimuthalIntegrator``, ``Distortion``, ...
 
@@ -24,12 +24,12 @@ I would describe it as a stack of 5 layers, upper ones relying on lower ones:
 
 0. Common basement: Python, Numpy, Cython, PyOpenCL and silx
 
-At level 5. are easy-to use applications, requiring no specific computing knowledge. 
-Levels 3. and 2. are heavily described in tutorials and should be accesible to 
+At level 5. are easy-to use applications, requiring no specific computing knowledge.
+Levels 3. and 2. are heavily described in tutorials and should be accesible to
 any Pythonistas. We try to keep the API on those levels consistent between versions.
 Level 1. is often written in Cython, or OpenCL and requires low-level expertise.
 
-Of course mastering level 1. provides faster analysis, but it is not of general use.     
+Of course mastering level 1. provides faster analysis, but it is not of general use.
 
 .. toctree::
    :maxdepth: 2

doc/source/detector.rst

@@ -111,4 +111,3 @@ you understanding the underlying mechanism:
 * **Distortion** which explains how to correct images for geometric distortion
 * **CCD-calibration** which explains how to calibrate such detectors for geometric
   distortion.
-

doc/source/ecosystem.rst

@@ -29,8 +29,8 @@ Program using pyFAI as a library
 --------------------------------
 
 `Github keeps track of dependant projects <https://github.com/silx-kit/pyFAI/network/dependents>`_ and 60 open source projects are
-explicitely dependant on pyFAI. 
-Those include data analysis in most synchrotrons in the world (NSLS-II, APS ...) but also on Free electron laser facilities and in electron microscopy.   
+explicitely dependant on pyFAI.
+Those include data analysis in most synchrotrons in the world (NSLS-II, APS ...) but also on Free electron laser facilities and in electron microscopy.
 Here is a list of friendly projects which developpers contributed back to pyFAI:
 
 
@@ -184,5 +184,3 @@ graphics for plotting data and it  incorporates a number of powerful
 packages for integrating 2D powder diffraction images, analyzing the
 curves to obtain PDFs and then tools for assessing the data and modeling
 it.  It is available from `diffpy.org <http://diffpy.org>`_.
-
-

doc/source/geometry.tex

@@ -12,9 +12,9 @@ \section{Geometry definition of \texttt{pyFAI}}
 by six variables, collectively called the PONI, for point of normal
 incidence. In addition, a detector calibration is provided in the
 PONI-file to convert pixel coordinates into real-space coordinates. In
-the simplest case this is a pixel size.  
+the simplest case this is a pixel size.
 
-\texttt{pyFAI} uses a coordinate system where the first axis (1)  is 
+\texttt{pyFAI} uses a coordinate system where the first axis (1)  is
 vertically up (or $y$), the second axis (2) is horizontal ($x$) towards the ring
 center (starboard), and the third axis (3) along the beam $z$. Note that
 in this order (1,2,3) is a right-handed coordinate system, which makes
@@ -55,7 +55,7 @@ \section{Geometry definition of \texttt{pyFAI}}
   \begin{bmatrix}
     \cos(\theta_3) & -\sin(\theta_3) & 0\\
     \sin(\theta_3) & \cos(\theta_3) & 0\\
-    0 & 0 & 1  
+    0 & 0 & 1
   \end{bmatrix}
   \\
   R(\theta_1, \theta_2, \theta_3)
@@ -143,7 +143,7 @@ \section{Geometry definition of \texttt{pyFAI}}
   \end{bmatrix}
   & =
   \begin{bmatrix}
-    A_1  \\ A_2 \\ A_3 
+    A_1  \\ A_2 \\ A_3
   \end{bmatrix}
   + \alpha
   \begin{bmatrix}
@@ -209,7 +209,7 @@ \section{Geometry definition of \texttt{ImageD11}}
   arranged on the detector. If, e.g., the detector is rotated by
   $90^{\circ}$, then $O=\begin{bmatrix} 0 & 1 \\ -1 &
   0\end{bmatrix}$. If left and right (or up and down) are inverted on the
-  detector, then $o_{22} = -1$ ($o_{11}=-1$). 
+  detector, then $o_{22} = -1$ ($o_{11}=-1$).
 \end{itemize}
 
 It appears that these conventions where defined under the assumption