version 0.4 (#7)

* Initial commit for the baseline package This package includes the code that was used in the publication of : L. P. René de Cotret and B. J. Siwick, A general method for baseline-removal in ultrafast electron powder diffraction data using the dual-tree complex wavelet transform, Struct. Dyn. 4 (2016) * Initial documentation for the baseline package * Removed links to PyUp and saythanks * Added installation of NumPy before setup.py can be run on Appveyor * Revert "Added installation of NumPy before setup.py can be run on Appveyor" This reverts commit dd4ab54. * FIX: appveyor builds failing fue to numpy not being * Removed TOX dependency in Appveyor CI * FIX: Install numpy & friends from conda on appveyor CI * FIX: remove optional installation of conda * FIX: typo in appveyor.yml * FIX: Escape characters * FIX: Yet another typo * f * Installation of skimage through conda * UTF-8 encoding * appveyor.yml typo * build_sphinx command * Not installign the right python version * f * 23rd time's the charm * Refactoring of the baseline package Iterative baseline functions are pretty similar, and they now share a common implementation for the 1D case. * Documentation setup based on SHAMPOO * DOC: updated documentation to reflect the pywavelets dependency * Sphinx RTD theme added * Appveyor testing via unittest * FIX: appveyor.yml typo * FIX: Python 3.5 install from Miniconda3s * FIX: Appveyor.yml typo * CI overhaul - Removed travis CI - switched Appveyor testing to a modified version of Astropy's CI-Helpers * FIX: appveyor os not found * FIX: code climate and readme * Angular average and tutorial (#3) * Continuous integration and documentation (#2) * Initial commit for the baseline package This package includes the code that was used in the publication of : L. P. René de Cotret and B. J. Siwick, A general method for baseline-removal in ultrafast electron powder diffraction data using the dual-tree complex wavelet transform, Struct. Dyn. 4 (2016) * Initial documentation for the baseline package * Removed links to PyUp and saythanks * Added installation of NumPy before setup.py can be run on Appveyor * Revert "Added installation of NumPy before setup.py can be run on Appveyor" This reverts commit dd4ab54. * FIX: appveyor builds failing fue to numpy not being * Removed TOX dependency in Appveyor CI * FIX: Install numpy & friends from conda on appveyor CI * FIX: remove optional installation of conda * FIX: typo in appveyor.yml * FIX: Escape characters * FIX: Yet another typo * f * Installation of skimage through conda * UTF-8 encoding * appveyor.yml typo * build_sphinx command * Not installign the right python version * f * 23rd time's the charm * Refactoring of the baseline package Iterative baseline functions are pretty similar, and they now share a common implementation for the 1D case. * Documentation setup based on SHAMPOO * DOC: updated documentation to reflect the pywavelets dependency * Sphinx RTD theme added * Appveyor testing via unittest * FIX: appveyor.yml typo * FIX: Python 3.5 install from Miniconda3s * FIX: Appveyor.yml typo * CI overhaul - Removed travis CI - switched Appveyor testing to a modified version of Astropy's CI-Helpers * FIX: appveyor os not found * FIX: code climate and readme * Initial commit * pseudo-voigt and friends * DOC: angular_average tutorial * DOC: References * DOC: baseline tutorial * API: angular_average returns intensity and radius * DOC: angular_average tutorial * Plot utils: spectrum (rainbow) colors * Parallel utils: pmap Parallel map that reduces to the use of map() for a single process. * Structure package (#4) * Affine transforms module First commit for the affine transforms module, containing functions to create affine transforms and transform points and other transforms. * Initial commit for the core structure package * Atom class tutorial * structure tutorial enhancements Added an example of crystal potential * Find center of polycrystalline diffraction patterns via correlation * ENH: powder center finding in noisy data The correlation of image and its mirror is post-processed for better peak-finding. This is not optimal yet, but better than before * Alignment procedures using scikit-image * DOC: fixed some documentation * Exposed dt_max_level to skued.baseline package Since baseline_dt can take a level = 'max' argument, the dt_max_level function can be used to determine what level is 'max' * FIX: dual-tree wavelet data was not included in setup.py * FIX: odd-length signals alogn axis for baseline functions Arrays with odd length along an axis would be mangled by the numpy.resize function. Added better resizing using numpy.swapaxes * Added a form-factors parameters module This module contains (partially) the atomic scattering factor parametrization from the International Table for Crystallography Vol.C Table 4.3.2.2 * simulation package skued.simulation package has been created with the powder diffraction routine powdersim * Added preduce function Parallel reduce function * FIX: plot_utils documentation * Parametrization of electron form factors for all neutral atoms z < 103 The same parametrization is used for atomic potential and electron form factors. From Kirkland 2010 Appendix C * Tranformable is now an abstract base class * Added quantities module for physical quantities The quantities module helps calculating electron properties based on electron energy * Encoding on .py files * Encoding * Code cleanup * 2D baseline_dwt * FIX: CIF Parser cif_parser module was not correctly interpreting CIF files due to multiple possible values of space groups. Next step is a better parser module * Better cif (#6) * CIF Parser based on cif2cell * Moved cif2cell outside of package * Bump up version to 0.4 * Removed diffracted intensity normalization from Crystal class No use case I could think of right now * FIX: doc references Numbered references are autogenerated with .. [#] * DOC: better autodocumentation of classes in skued.structure * DOCS: tweaks to autoclass directive
LaurentRDC · May 26, 2017 · b03ed2f · b03ed2f
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diff --git a/.mention-bot b/.mention-bot
diff --git a/README.rst b/README.rst
@@ -1,5 +1,5 @@
 scikit-ued
-=======
+==========
 
 .. image:: https://img.shields.io/appveyor/ci/LaurentRDC/scikit-ued/master.svg
     :target: https://ci.appveyor.com/project/LaurentRDC/scikit-ued
@@ -23,13 +23,7 @@ To install the latest development version from `Github <https://github.com/Laure
 
 If your current Python installation doesn't have pip available, try `get-pip.py <bootstrap.pypa.io>`_
 
-After installing scikit-ued you can use it like any other Python module.
-Soon, there'll be a simple example here:
-
-.. code-block:: python
-
-    import skued
-    # come back later, this package is empty
+After installing scikit-ued you can use it like any other Python module as :code:`skued`.
 
 API Reference
 -------------

diff --git a/RELEASE.rst b/RELEASE.rst
@@ -1,5 +1,5 @@
 Steps to Release scikit-ued
-=========================
+===========================
 
 These are the steps to take to create a release of the module ``skued``:
 

diff --git a/cif2cell-1.2.10/ESPInterfaces.py b/cif2cell-1.2.10/ESPInterfaces.py
diff --git a/cif2cell-1.2.10/HOWTOCITE b/cif2cell-1.2.10/HOWTOCITE
@@ -0,0 +1,28 @@
+Please use the following citation information:
+
+Torbjorn Bjorkman, "CIF2Cell: Generating geometries for electronic structure programs", 
+Computer Physics Communications 182, 1183-1186 (2011)
+doi: 10.1016/j.cpc.2011.01.013
+
+My name is rendered in ascii above, bonus points for getting umlauts over both of the o's.
+See also below for a BibTeX entry for use with LaTeX, but which should also be readable
+for most scientific reference handling software.
+
+Thank you for citing and happy computing!
+Torbjorn Bjorkman
+
+
+
+
+@article{cif2cell,
+title = "CIF2Cell: Generating geometries for electronic structure programs",
+journal = "Computer Physics Communications",
+volume = "182",
+number = "5",
+pages = "1183 - 1186",
+year = "2011",
+issn = "0010-4655",
+doi = "10.1016/j.cpc.2011.01.013",
+url = "http://www.sciencedirect.com/science/article/pii/S0010465511000336",
+author = "Torbj\"orn Bj\"orkman"
+}
diff --git a/cif2cell-1.2.10/LICENSE b/cif2cell-1.2.10/LICENSE
diff --git a/cif2cell-1.2.10/PKG-INFO b/cif2cell-1.2.10/PKG-INFO
@@ -0,0 +1,11 @@
+Metadata-Version: 1.1
+Name: cif2cell
+Version: 1.2.10
+Summary: Construct a unit cell from CIF data
+Home-page: http://cif2cell.sourceforge.net/
+Author: Torbjorn Bjorkman
+Author-email: torbjornb@gmail.com
+License: GNU General Public License version 3
+Description: A command-line tool to generate the geometrical setup for various electronic structure codes from a CIF format file.
+Platform: UNKNOWN
+Requires: CifFile
diff --git a/cif2cell-1.2.10/PyCifRW-3.3.tar.gz b/cif2cell-1.2.10/PyCifRW-3.3.tar.gz
diff --git a/cif2cell-1.2.10/README b/cif2cell-1.2.10/README
@@ -0,0 +1,112 @@
+Copyright 2010, Torbjorn Bjorkman
+
+CIF2CELL
+
+A tool to generate the geometrical setup for various electronic 
+structure codes from a CIF (Crystallographic Information 
+Framework) file. The code will generate the crystal structure for 
+the primitive cell or the conventional cell.
+
+CURRENTLY SUPPORTS
+
+               |  alloy  |
+code           | support |   output files
+---------------|---------|-----------------------------------
+ASE                no      positions.py
+VASP              VCA      POSCAR
+ABINIT             no      [compoundname].in
+Siesta             no      [compoundname].fdf
+CPMD               no      [compoundname].inp
+CASTEP            VCA      [compoundname].cell
+Crystal09          no      [compoundname].d12
+quantum espresso   no      [compoundname].in
+FHI-aims           no      geometry.in
+RSPt               no      symt.inp
+Fleur              no      inp_[compoundname]
+hutsepot           no      [compoundname].sys
+cellgen            no      cellgen.inp
+elk                no      GEOMETRY.OUT
+exciting           no      input.xml
+spacegroup         no      spacegroup.in
+ncol               no      [spacegroupname/compoundname].dat 
+                           for bstr.
+emto               yes     [spacegroupname/compoundname].dat 
+                           for kstr, bmdl, shape, kgrn and kfcd
+                           in separate directories.
+spr-kkr            yes     [compoundname].sys
+xyz                no      [compoundname].xyz
+
+CONTENTS
+The distribution includes:
+* This README file.
+* The file LICENSE with the GPLv3 license.
+* The python files cif2cell, uctools.py and spacegroupdata.py
+* Installation files, setup.py and MANIFEST.
+* A manual.
+* The directory cifs/ containing a set of example CIF files 
+  as well as the crystal structures of the full periodic table 
+  from COD, the Crystallography Open Database <http://www.crystallography.net>
+  and also a few from ICSD (with permission).
+* The file PyCifRW-3.3.tar.gz, containing the PyCifRW package needed for
+  parsing CIF files.
+
+
+INSTALLATION INSTRUCTIONS
+
+Prerequisites: The program requires Python 2.4 or higher and the
+               PyCIFRW python package (which will be installed 
+               automatically if not present, see below for manual 
+   	       installation instructions). Note however that the output
+               may be slightly different (but formally equivalent) 
+	       with Python 2.4 than with later versions.
+
+To install the program in your systems standard location, simply type:
+python setup.py install 
+To choose a different location, add 
+--prefix=where/you/want/it 
+to the above line. For help and more options type
+python setup.py --help
+
+The installation will also create a directory $PREFIX/lib/cif2cell
+that contains the manual and sample cif files.
+
+
+DOCUMENTATION
+
+The setup will install the manual, cif2cell.pdf, into the 
+$PREFIX/lib/cif2cell/docs directory. 
+
+
+RUNNING
+
+Run 'cif2cell -h' to get a listing of the different options.
+Example:
+cif2cell Ni20Mn3P6.cif -p vasp --vasp-cartesian-positions
+will generate a POSCAR file for VASP with the positions in cartesian format.
+
+
+LICENSE INFORMATION
+
+cif2cell is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+cif2cell is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with cif2cell.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+Happy computing!
+
+Torbjorn Bjorkman
+COMP, Aaalto University School ofScience and Technology, 
+Department of Applied Physics, 
+Espoo, Finland
+torbjorn@cc.hut.fi
+