Release notes

Version 2.2.1 - 2022-03-23

Added

• Added new API for accessing intermediate I(Q) plots as properties on PDFGetter instances via properties following a naming convention of PDFGetter.iq_<i>, where i is a zero-based index of the intermediate I(Q) to be returned. That is, rather than a single property returning an array of the I(Q)’s that would then be indexed, users may directly name an intermediate I(Q) (say, the first I(Q)) via a statement such as PDFGetter.iq_0.

Fixed

• Restored previous API behavior of PDFGetter.iq returning the I(Q) plot of the data. Since there are now multiple I(Q) plots (one after each subsequent background subtraction), this property now returns the final I(Q) data (i.e., the result of applying all background subtractions).

• Fixed formatting of authors list on PDFgetXNS3_manual.pdf cover page.

Version 2.2.0 - 2022-02-10

Added

• Support for Python 3.10

• Support for Python 3.9

• Unittests for testing CLI functionality.

• Tutorial example for multiple background subtractions (see diffpy.pdfgetx/doc/examples/Multiple_Background_Subtraction).

• New functionality for allowing multiple backgrounds to be subtracted from a dataset accessed via using the plural name equivalent of any previously singularly named variable (i.e., bgscale->bgscales, backgroundfile-> backgroundfiles, etc.) in both static config files (i.e., *.cfg) and interactive plotting sessions. Each set of parameters corresponding to a given background subtraction can also be manipulated by a set of sliders present in the tuneconfig window of an interactive shell session. In total, the multiple background subtraction functionality should work identically to the previous single background subtraction functionality except that the multiple background files and initial scale values cannot be specified through a pure CLI command (i.e., it must be specified either in a config file or added/modified during an interactive plotting session).

• Added extra test cases for testing the PDFGetter class.

• Added extra test cases for testing the PDFConfig class.

Changed

• Changed python versions specified in requirements.txt files to be in the range of the respective minor version rather than fixed to the Python X.Y.0 version

• Python version support policy now follows NEP 29

• Changed versions used in conda-recipe/build.sh to reflect currently supported Python versions.

• Changed Sphinx dependency m2r to m2r2.

• Added Connor J. Bracy and Zach Thatcher to contributors in AUTHORS.txt

• Added Connor J. Bracy to internal authors list and PDFgetXNS3_manual.pdf

Removed

• Support for Python 3.5 and 3.6.

Version 2.1.2 - 2021-12-24

Fixed

• Fixed the command provided to the users in the installation instructions which incorrectly instructed them to setup a Python environment in which pdfgetx could be installed by using the flag --python=3.8 to the correct usage of this flag as python=3.8.

Version 2.1.1 - 2020-09-01

Added

• Support for Python 3.8

Version 2.1.0 – 2020-07-15

Added

• New mode sas for processing Small Angle Scattering data and for using custom scattering factors.

• qmax-pushes-qmin coupling of sliders in the tuneconfig tool.

• New program pdfgets3 and IPython magic %pdfgets3.

Changed

• Software distribution format to a universal Python wheel.

• tuneconfig dialog to access full Q-range with all qmin, qmax, and qmaxinst sliders. Increased range for the rpoly slider.

Deprecated

• Software distribution in setuptools egg package.

Removed

• Support for Python 3.4.

Fixed

• Support backslash in the --find option path argument on Windows. Both forward and back slashes are allowed on Windows, but other platforms must use forward slash.

• Recipe for platform-dependent Anaconda package.

• Bogus test failure when installed in symlinked directory.

Version 2.0.0 – 2018-11-02

Added

• New mode neutron for processing constant-wavelength neutron scattering data.

• Correction for an offset of diffractometer zero angle.

• Configuration parameter twothetazero and command-line option --twothetazero for position of the actual zero angle in diffractometer degrees.

• New program pdfgetn3 and IPython magic %pdfgetn3.

• Separate configuration file pdfgetn3.cfg for the pdfgetn3 program.

• New sub-package diffpy.pdfgetx.apps for entry points to all programs.

• Table of electron scattering factors from E. J. Kirkland, Advanced Computing in Electron Microscopy.

• The + operator for additive pattern groups when matching input files with pdfgetx3 --find.

• An optional slash-containing entry, e.g., dir/, to set the search path for pdfgetx3 --find. Each pattern group may have one path entry which affects the current and subsequent pattern groups. Pattern groups that have only the path entry reuse the previous file patterns, for example, dir1/ .dat$ + dir2/ + dir3/.

• The dotfiles flag argument to functs.findfiles to also find dot-starting files without an explicit pattern.

• Support for Python 3.7.

• Tutorial examples for constant-wavelength neutron diffraction data.

Changed

• Initialization arguments of PDFConfig to set initial configuration values.

• path argument of functs.findfiles to give one search path instead of a list of paths.

• pdfgetx3 --find to search only the current directory and stop searching in --datapath.

• Improved PDF accuracy by removing repeated Q-grid interpolation.

• Handling of dot files by pdfgetx3 --find and the functs.findfiles function. The dotfiles are by default ignored unless explicitly selected by a "^." pattern.

• Return type of functs.findfiles from IPython SList to a simple list.

• Rename camel case interactive functions to lowercase, i.e., to loaddata, processfiles, clearsession.

• Use config.datapath lookup in processfiles(filename).

Deprecated

• Function cromermann.felectronatq for electron scattering factors calculation using Mott-Bethe approximate formula.

• IPython extension module diffpy.pdfgetx.ipy_pdfgetx3. Use diffpy.pdfgetx.ipy_magics instead.

• Camel case functions loadData, processFiles, clearSession.

Removed

• Support for Python 2.6.

• Processing of environment variable PDFGETX3PATH.

• Support for IPython 0.x.

• Obsolete variable __gitsha__ from the version module.

• Processing of command line options in PDFConfig class.

• Implicit loading of configuration files in PDFConfig instantiation.

Fixed

• Import of all objects from matplotlib.pyplot into an interactive session started by plotdata.

• Inaccurate G interpolation when rstep is comparable to pi / qmax.

• Lone anchor patterns ^, $ to match everything.

Version 1.2 – 2018-01-12

Added

• Support for Python 3.4, 3.5, 3.6 in addition to Python 2.6 and 2.7.

• Support for IPython 5.0 with preserved compatibility with IPython 0.10 and later.

• Support for matplotlib 2.0.

• New option --log=LOG for the plotdata program to set logarithmic scale for either of x or y axis. The plotdata() function learnt a new log argument with the same purpose.

• New argument ax for the plotdata() function that select a specific matplotlib axis for plotting.

• Support for Unicode filenames and values in the config interactive variable.

• Processing of parentheses and fractional stoichiometries in chemical formulas as in Pb (Ti Zr)1/2 O3.

• Explanatory error message when PDFgetX3 was installed for unsupported Python.

Changed

• The egg package file was enhanced to support all Python versions. The software is now distributed in a single egg rather than multiple eggs per each Python version.

• PDFgetX3 option --force to take a boolean argument (yes, no, true, etc.) or once. The configuration parameter force can be likewise set to a bool or to a string "once". This enables a safer one-time overwrite of existing output files.

• Plot labels to use a proper Unicode “Å” (Ångström) symbols. The “Å” symbol is also used within units in output files.

• The usecols argument of the loadData() function to also accept scalars, open-end slice objects and string-denoted slices such as "1:3" or "1:".

• The plotdata program and plotdata() function to accept open-end slices for the y-columns selection.

• The IPython magic function %pdfgetx3 to set the _exit_code variable as do generic shell commands run from IPython.

• Inline documentation to use NumPy-style Napoleon format, which is human readable and can be included in the manual.

• Release scripts to build software package bundles and documentation in binary-reproducible way.

Deprecated

• Compatibility with Python 2.6.

• Support for IPython 0.x.

• Variable __gitsha__ in the version module which was renamed to __git_commit__.

Removed

• The hold argument of the plotdata() function, because it was deprecated in matplotlib.

• Support for multiple x-columns in plotdata program and plotdata() function.

• Import of all objects from numpy module into the interactive session. NumPy is available under the np name instead.

Fixed

• Avoid duplicate “.gr.gr” extension when pdfgetx3 is run with option --output=f.gr.

• Crash on loading custom configuration section from a local file, when that section is missing in global configuration.

• Missing checkbox in the tuneconfig dialog caused by matplotlib bug.