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cookiecutter: modified files pt2 by cadenmyers13 · Pull Request #154 · diffpy/diffpy.pdfgui · GitHub

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cookiecutter: modified files pt2 #154

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cookiecutter: modified files pt2 #154

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7ecc733
fix path
cadenmyers13 Aug 1, 2024
ade74ce
copyright update and run.py
cadenmyers13 Aug 1, 2024
7dc7029
fix capitalization
cadenmyers13 Aug 1, 2024
6c1a9f3
pkg_resources deprecation
cadenmyers13 Aug 1, 2024
e3db421
cookiecutter news file
cadenmyers13 Aug 1, 2024
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2 changes: 1 addition & 1 deletion README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ help menu and follow the tutorial instructions. A detailed description
is available in the doc/Farrow-jpcm-2007.pdf paper.


REQUIREMENTS
Requirements
------------------------------------------------------------------------

PDFgui requires Python 3.8+ or 2.7 and several third-party
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23 changes: 23 additions & 0 deletions news/cookiecutter.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
**Added:**

* <news item>

**Changed:**

* Package reformatted to comply with new Billinge Group package structure

**Deprecated:**

* pkg_resources replaced with importlib

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
2 changes: 1 addition & 1 deletion src/diffpy/pdfgui/control/pdfguimacros.py
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Original file line number Diff line number Diff line change
Expand Up @@ -381,7 +381,7 @@ def makeDopingSeries(control, fit, base, dopant, paths, doping):
from diffpy.pdfgui.control.pdfguicontrol import PDFGuiControl

control = PDFGuiControl()
control.load("../../tests/testdata/ni.ddp")
control.load("src/diffpy/pdfgui/tests/testdata/ni.ddp")

sbillinge Aug 2, 2024

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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

did you test this? It is unlikely to work because this is a relative file-path.
fit = control.fits[0]
olist = makeRSeries(control, fit, 5, 20, 5)
print("\n".join(f[0].name for f in olist))
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7 changes: 4 additions & 3 deletions src/diffpy/pdfgui/gui/pdfguiglobals.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,9 @@
"""This module contains global parameters needed by PDFgui."""

import os.path
from importlib import resources

from pkg_resources import Requirement, resource_filename
from pkg_resources import Requirement

sbillinge Aug 2, 2024

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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

I think pkg_resources is deprecated so we want to get rid of this. I would put pkg_resources fixes on a separate PR tbh.

from diffpy.pdfgui.gui import debugoptions

Expand All @@ -31,7 +32,7 @@
isAltered = False

# Resolve APPDATADIR base path to application data files.
_mydir = os.path.abspath(resource_filename(__name__, ""))
_mydir = os.path.abspath(str(resources.files(__name__).joinpath("")))

sbillinge Aug 2, 2024

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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

whenever we touch lines of code that do path munging, switch the code to using pathlib.Path. Then do it for the full module. This also on a separate PR because it will be harder to merge.
_upbasedir = os.path.normpath(_mydir + "/../../..")
_development_mode = os.path.basename(_upbasedir) == "src" and os.path.isfile(
os.path.join(_upbasedir, "../setup.py")
Expand All @@ -47,7 +48,7 @@
if _development_mode:
APPDATADIR = os.path.dirname(_mydir)
else:
APPDATADIR = os.path.join(resource_filename(_req, ""), "diffpy/pdfgui")
APPDATADIR = os.path.join(str(resources.files(_req, "")), "diffpy/pdfgui")

APPDATADIR = os.path.abspath(APPDATADIR)

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15 changes: 8 additions & 7 deletions src/diffpy/pdfgui/tests/debug.py
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Original file line number Diff line number Diff line change
@@ -1,15 +1,16 @@
#!/usr/bin/env python
##############################################################################
#
# diffpy.pdfgui Complex Modeling Initiative
# (c) 2016 Brookhaven Science Associates,
# Brookhaven National Laboratory.
# All rights reserved.
# (c) 2016 Brookhaven Science Associates, Brookhaven National Laboratory.
# (c) 2024 The Trustees of Columbia University in the City of New York.
# All rights reserved.
#
# File coded by: Pavol Juhas
# File coded by: Billinge Group members and community contributors.
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
# See GitHub contributions for a more detailed list of contributors.
# https://github.com/diffpy/diffpy.pdfgui/graphs/contributors
#
# See LICENSE.rst for license information.
#
##############################################################################

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42 changes: 19 additions & 23 deletions src/diffpy/pdfgui/tests/run.py
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Original file line number Diff line number Diff line change
@@ -1,38 +1,34 @@
#!/usr/bin/env python
##############################################################################
#
# diffpy.pdfgui by DANSE Diffraction group
# Simon J. L. Billinge
# (c) 2012-2024 Trustees of the Columbia University
# in the City of New York. All rights reserved.
# (c) 2012-2024 The Trustees of Columbia University in the City of New York.
# All rights reserved.
#
# File coded by: Pavol Juhas
# File coded by: Billinge Group members and community contributors.
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
# See GitHub contributions for a more detailed list of contributors.
# https://github.com/diffpy/diffpy.pdfgui/graphs/contributors
#
# See LICENSE.rst for license information.
#
##############################################################################

"""Convenience module for executing all unit tests with

python -m diffpy.pdfgui.tests.run
"""

import sys

if __name__ == "__main__":
import sys
import pytest

# show warnings by default
if not sys.warnoptions:
import os
import warnings

warnings.simplefilter("default")
# also affect subprocesses
os.environ["PYTHONWARNINGS"] = "default"
from diffpy.pdfgui.tests import test

# produce zero exit code for a successful test
sys.exit(not test().wasSuccessful())
if __name__ == "__main__":
# show output results from every test function
args = ["-v"]
# show the message output for skipped and expected failure tests
if len(sys.argv) > 1:
args.extend(sys.argv[1:])
print("pytest arguments: {}".format(args))
# call pytest and exit with the return code from pytest
exit_res = pytest.main(args)
sys.exit(exit_res)

# End of file
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