diffpy / diffpy.pdfmorph Goto Github PK
View Code? Open in Web Editor NEWAn easy way to compare PDFs.
Home Page: https://www.diffpy.org/diffpy.pdfmorph/
License: Other
An easy way to compare PDFs.
Home Page: https://www.diffpy.org/diffpy.pdfmorph/
License: Other
Setup Travis-CI for this repo.
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.
used labpdfproc as template
See #67 (review)
@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:
Issue can be resolved after 0.0.1 release.
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.To be fixed in branch morph_sequence
--temperature
with --sort-by=FIELD
--reverse
tag--metadata-filename
; a user can store FIELD data in that metadata file which PDFmorph can read from--verbose
tag to condense outputmultiple_morphs
and single_morphs
functions more maintainableTo be fixed in in branch change_libraries
pkg_resources
complete #24 before completing
Not morphs, just transformations. Change names of classes to reflect it.
I don't think this passes flake8 yet, we should fix that.
Make python3 friendly
e.g., see here for an example:
https://github.com/regro/regolith
Need discussion on whether default for plot labels is to use file names or "target" and "morph".
pip
long_description
to setup.py@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.
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
in both documentation and also --help
--yes
to conda create -n pdfmorph_env python=3
commandconda config --add channels conda-forge
easy_install --update
to pip <command>
Also do testing to make sure bg-mpl-stylesheets
is installed properly when installing from source.
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.
Make HTML and PDF manual modeled after PDFgui HTML manual and PDFgui PDF manual with sources here
remove /tests directory from top level
critical for release
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