diffpy / diffpy.pdfmorph Goto Github PK

Issue can be resolved after 0.0.1 release.

• Need to determine behavior at psize for MorphISpheroid. Do we (1) set to zero or (2) divide by characteristic function. Current test data has set to zero, but _spheroidalCF does not set the characteristic function to zero at the boundary.
• Add prolate spheroid test data.

used labpdfproc as template

@CJ-Wright - Please remove the tarball aset 0.0.1.tar.gz from
https://github.com/diffpy/diffpy.pdfmorph/releases/tag/0.0.1.
The github-generated archive has the same content, but downloads
with a correct name (diffpy.pdfmorph-0.0.1.tar.gz) and starts with a correct
diffpy.pdfmorph-0.0.1/ prefix directory.

Also please add release tag v0.0.1 and remove tag 0.0.1 to be consistent with changelog.

• Add --yes to conda create -n pdfmorph_env python=3 command
• Remove duplicated conda config --add channels conda-forge
• Change easy_install --update to pip <command>
• Replace travis badge with gh status badge

Also do testing to make sure bg-mpl-stylesheets is installed properly when installing from source.

See #67 (review)

• Chris Farrow is probably not interested in maintaining this package - replace with Matthew?
• remove download_url
• update install_requires list so we can install with pip
• add long_description to setup.py

I don't think this passes flake8 yet, we should fix that.

I may just not know how to use the software, but is there no way to output the values it used for the morphing? Add values to the output.

@RomanMatthew - can you please fix whitespace problems reported by

$ git diff --check df96a1599

AUTHORS.rst:5: trailing whitespace.
+Chia-Hao (Timothy) Liu, Timur Davis, S. Matthew Román, Simon J.L. 
AUTHORS.rst:10: trailing whitespace.
+For a list of contributors, visit 
CHANGELOG.rst:13: new blank line at EOF.
README.rst:12: trailing whitespace.
+PDFmorph is a Python software package designed to increase the insight 
README.rst:13: trailing whitespace.
+researchers can obtain from measured atomic pair distribution functions 
...

all - please use git pre-commit check to avoid whitespace errors:

$ cd .git/hooks
$ cp pre-commit.sample pre-commit

We need some docs:

• change docs over to numpy
• setup sphinx
• setup doctr
• setup description

Make python3 friendly

I have added new branch master-svn-import with a complete import of project history from subversion. The only difference from the current master 243661a is in expansion of svn keywords.

Can we reset master to 6b1816f and rebase all PRs on that commit?

Need discussion on whether default for plot labels is to use file names or "target" and "morph".

remove /tests directory from top level

Make HTML and PDF manual modeled after PDFgui HTML manual and PDFgui PDF manual with sources here

Setup Travis-CI for this repo.

Current proposal:

objective -> morphed : data will be manipulated
reference -> target: data will stay unchanged.

The obj-ref language propagates across the repo (like xref, yobj etc), but the convention is rather clear and self-consistent as we always see xref, yref remain unchanged in the code.

The first order fix could be changing the language in pdfmorph function and app since they are user facing.

cc: @sbillinge @pavoljuhas

complete #24 before completing

in both documentation and also --help

critical for release

e.g., see here for an example:
https://github.com/regro/regolith

To be fixed in branch morph_sequence

• Replace --temperature with --sort-by=FIELD
• Add --reverse tag
• Add --metadata-filename; a user can store FIELD data in that metadata file which PDFmorph can read from
• Add --verbose tag to condense output
• Make multiple_morphs and single_morphs functions more maintainable

To be fixed in in branch change_libraries

• Move to Pytest rather than Unittest
• Refactor test file names to specify which module is being tested
• Fix deprecation with pkg_resources

Not morphs, just transformations. Change names of classes to reflect it.

We are still using pylab syntax with matplotlib, it would be nice to use pyplot API as suggested by official doc.

easy_install and pip have conflicting way of handling namespaced packages (diffpy functions as a namespace only and is not a real package) and a mixed installation then may not work:

$ conda create -n xx36 -c diffpy diffpy.utils
$ conda activate xx36
$ python -c 'import diffpy.utils' # OK
$ pip install https://github.com/diffpy/diffpy.pdfmorph/archive/master.tar.gz
$ python -c 'import diffpy.utils' # FAILS
Traceback (most recent call last):
File "", line 1, in
ModuleNotFoundError: No module named 'diffpy.utils'
This actually happens because of an outdated definition of namespace package in diffpy/init.py which is specific to setuptools (easy_install) and does not work well with pip. Other diffpy packages have that code updated, e.g., diffpy.structure/src/diffpy/init.py, and then it seems to work with both easy_install and pip.

fix namespace package handling in diffpy/init.py as in diffpy.structure and
check if mixed easy_install, pip installation of several diffpy packages works OK
and if it does, update README to suggest pip as the installation tool