Merge pull request #90 from diffpy/next

Release py3 version and merge into main

Author: sbillinge

.travis.yml

@@ -7,6 +7,10 @@ os:
 
 env:
   - MYUSEMC=true MYPYTHON_VERSION=2.7
+  - MYUSEMC=true MYPYTHON_VERSION=3.7
+  - MYUSEMC=true MYPYTHON_VERSION=3.8
+  - MYUSEMC=true MYPYTHON_VERSION=3.9
+  - MYUSEMC=true MYPYTHON_VERSION=3.10
   - MYUSEMC=false
 
 matrix:
@@ -59,9 +63,6 @@ before_install:
   - $NOMC || conda create --name=testenv --yes python=${MYPYTHON_VERSION} coverage
   - $NOMC || conda config --add channels diffpy
 
-  # TODO - remove after update to wxpython 4
-  - $NOMC || conda config --set restore_free_channel true
-
   - $NOAPT || test "${TRAVIS_OS_NAME}" = "linux" || exit $?
   - $NOAPT || PATH="$(echo "$PATH" | sed 's,:/opt/pyenv/[^:]*,,g')"
   - $NOAPT || test "$(which python)" = "/usr/bin/python" || (
@@ -74,6 +75,7 @@ before_install:
   - $NOAPT || devutils/makesdist
   - $NOAPT || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
 
+
 install:
   - $NOMC || conda build --python=${MYPYTHON_VERSION} --no-test conda-recipe
   - $NOMC || conda render --python=${MYPYTHON_VERSION} --output conda-recipe |
@@ -93,6 +95,7 @@ install:
         exit 1;
     fi
 
+
 before_script:
   # provide shell functions to execute coverage with GUI support
   - case ${TRAVIS_OS_NAME} in
@@ -102,9 +105,11 @@ before_script:
         guicoverage() { pythonw -m coverage "$@"; } ;;
     esac
 
+
 script:
   - guicoverage run --source ${MYNAME} -m ${MYNAME}.tests.rundeps
 
+
 after_success:
   - pip install $MYPIPFLAGS codecov
   - codecov

CHANGELOG.md

@@ -0,0 +1,23 @@
+# Release notes
+
+Notable differences from version 1.1.2.
+
+## Version 2.0.0 – 2023-05-04
+
+### Added
+
+- Support for Python 3.8, 3.9, 3.10.
+- Use `.ddp3` instead of `.ddp` to store project files.
+
+### Changed
+
+- Update wxpython to 4.1.1 and remove incompatible align flags.
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+- Incompatible conversion between bytes and str from py2 to py3.
+- 

LICENSE.txt

@@ -1,5 +1,15 @@
-This program is part of the DiffPy and DANSE open-source projects
-and is available subject to the conditions and terms laid out below.
+This software was originally developed by the Billinge group as part
+of the Distributed Data Analysis of Neutron Scattering Experiments
+(DANSE) project funded by the US National Science Foundation under
+grant DMR-0520547. Developments of PDFfit2 were funded by NSF grant
+DMR-0304391 in the Billinge group, and with support from Michigan State
+University and Columbia University. Any opinions, findings, and conclusions
+or recommendations expressed in this material are those of the author(s)
+and do not necessarily reflect the views of the respective funding bodies.
+Subsequent development was done in the Billinge group at Columbia University
+and then in collaboration between the Billinge group at Columbia and Pavol
+Juhas at Brookhaven National Laboratory. Moving forward, PDFgui will be
+maintained as a community project with contributions welcomed from many people.
 
 If you use this program to do productive scientific research that leads
 to publication, we ask that you acknowledge use of the program by citing
@@ -10,9 +20,27 @@ the following paper in your publication:
     PDFgui: computer programs for studying nanostructure in
     crystals, J. Phys.: Condens.  Matter 19, 335219 (2007)
 
+Up to the release 1.1.2 (February 2017) the copyright was held by
+the institutions that hosted the work as follows:
 Copyright 2006-2007, Board of Trustees of Michigan State University,
-Copyright 2008-2017, Board of Trustees of Columbia University in the
-city of New York.  (Copyright holder indicated in each source file).
+Copyright 2008-2012, Board of Trustees of Columbia University in the
+city of New York.
+Copyright 2013, Brookhaven National Laboratory (Copyright holder
+indicated in each source file).
+
+As of February 2017, and the 1.1.2 release, PDFgui has moved to a shared copyright model.
+
+PDFgui uses a shared copyright model. Each contributor maintains copyright over their
+contributions to PDFgui. But, it is important to note that these contributions are
+typically only changes to the repositories. Thus, the PDFgui source code, in its entirety,
+is not the copyright of any single person or institution. Instead, it is the collective
+copyright of the entire PDFgui Development Team. If individual contributors want to
+maintain a record of what changes/contributions they have specific copyright on, they
+should indicate their copyright in the commit message of the change, when they commit
+the change to one of the PDFgui repositories.
+
+The PDFgui Development Team is the set of all contributors to the PDFgui project.
+A full list can be obtained from the git version control logs.
 
 For more information please visit the project web-page:
     https://www.diffpy.org

MANIFEST.in

@@ -20,4 +20,4 @@ exclude .coveragerc
 exclude .travis*
 prune conda-recipe
 prune devutils
-prune doc
+#prune doc

README.rst

@@ -20,12 +20,12 @@ is available in the doc/Farrow-jpcm-2007.pdf paper.
 REQUIREMENTS
 ------------------------------------------------------------------------
 
-PDFgui requires Python 2.7 and several third-party libraries
-that are used by PDFgui and its components.
+PDFgui requires Python 3.7, 3.8, 3.9, or 2.7 and several third-party
+libraries that are used by PDFgui and its components.
 
 * setuptools   - tools for installing Python packages
 * wxpython     - graphical user interface toolkit for Python
-* NumPy        - library for scientific computing with Python
+* numpy        - library for scientific computing with Python
 * matplotlib   - Python 2D plotting library
 * diffpy.pdffit2 - computational engine for PDFgui,
   https://github.com/diffpy/diffpy.pdffit2
@@ -36,34 +36,31 @@ that are used by PDFgui and its components.
 
 We recommend to use `Anaconda Python <https://www.anaconda.com/download>`_
 which allows to conveniently install PDFgui and all its software
-dependencies with a single command.  For other Python distributions
-it is necessary to install the required software separately.  As an
-example, on Ubuntu Linux some of the required software can be
-installed using ::
-
-   sudo apt-get install \
-      python-setuptools python-wxtools python-numpy \
-      python-matplotlib
-
-To install the remaining packages see the installation instructions
-at their respective web pages.
+dependencies with a single command.
 
+Please note that the Python3 PDFgui will read .ddp3 files. It is also
+possible for it to read .ddp files that were saved by the Python2 PDFgui
+but it will sometimes fail to read these. We are working on a solution
+that will be available in a future version.
 
 INSTALLATION
 ------------------------------------------------------------------------
 
 The preferred method is to use Anaconda Python and install from the
-"diffpy" channel of Anaconda packages ::
+"conda-forge" channel of Anaconda packages. `pdfgui` can be installed with `conda` ::
 
-   conda config --add channels diffpy
-   conda install diffpy.pdfgui
+   conda install -c conda-forge diffpy.pdfgui
 
 PDFgui can be then started from a terminal ("Anaconda Prompt" on
 Windows) by executing the "pdfgui" program.  An alternative
 method on Windows is to start PDFgui through the DiffPy start menu.
 
 If you don't use Anaconda or prefer to install from sources, make
-sure the required software is all in place and run ::
+sure the required software is all in place ::
+
+   conda install -c conda-forge diffpy.utils diffpy.pdffit2 matplotlib wxpython
+
+Then you are ready to install diffpy.pdfgui from source codes::
 
    python setup.py install
 
@@ -78,16 +75,36 @@ changing to the HOME directory and running ::
 
    python -m diffpy.pdfgui.tests.rundeps
 
+To use PDFgui, you can simply type `pdfgui`, or run the following command ::
+
+   python diffpy.pdfgui/src/diffpy/pdfgui/application/pdfgui.py
+
+If it shows some error like "This program needs access to the screen.". For Mac, you could install `python.app` from conda
+(`conda install python.app`), then run as follows ::
+
+   python.app diffpy.pdfgui/src/diffpy/pdfgui/application/pdfgui.py
+
 With Anaconda PDFgui can be later upgraded to the latest released
 version using ::
 
-   conda update diffpy.pdfgui
+   conda update -c conda-forge diffpy.pdfgui
 
 With other Python distributions the program can be upgraded to
 the latest version as follows ::
 
    easy_install --upgrade diffpy.pdfgui
 
+If you would like to use other Python distributions except Anaconda,
+it is necessary to install the required software separately. As an
+example, on Ubuntu Linux some of the required software can be
+installed using ::
+
+   sudo apt-get install \
+      python-setuptools python-wxtools python-numpy \
+      python-matplotlib
+
+To install the remaining packages see the installation instructions
+at their respective web pages.
 
 Other software
 ````````````````````````````````````````````````````````````````````````
@@ -97,6 +114,7 @@ structures.  We have tested with several structure viewers such as
 
 * AtomEye, http://li.mit.edu/A/Graphics/A/
 * PyMol, https://www.pymol.org
+* VESTA, http://jp-minerals.org/vesta/en/
 
 Other viewers should work as well, as long as they understand one of
 the output structure formats supported by PDFgui.

conda-recipe/conda_build_config.yaml

@@ -1,2 +1,6 @@
 python:
+  - 3.10
+  - 3.9
+  - 3.8
+  - 3.7
   - 2.7

conda-recipe/expandpdfguibase.py

@@ -9,6 +9,7 @@
 PDFGUIBASE = PDFGUIPATH[len(sys.prefix):].replace('\\', '/').strip('/')
 
 if __name__ == "__main__":
-    content = open(sys.argv[1]).read()
+    with open(sys.argv[1]) as fp:
+        content = fp.read()
     output = content.replace('@PDFGUIBASE@', PDFGUIBASE)
     sys.stdout.write(output)

conda-recipe/meta.yaml

@@ -35,6 +35,7 @@ requirements:
   run:
     - python
     - setuptools
+    - six
     - matplotlib
     - wxpython 4.*
     - menuinst                  [win]

doc/manual/acknowledgements.texinfo

@@ -0,0 +1,14 @@
+$PROJECT = 'diffpy.pdfgui'
+$ACTIVITIES = [
+              'tag',  # Creates a tag for the new version number
+              'push_tag',  # Pushes the tag up to the $TAG_REMOTE
+              'pypi',  # Sends the package to pypi
+              'ghrelease'  # Creates a Github release entry for the new tag
+               ]
+$PUSH_TAG_REMOTE = 'git@github.com:diffpy/diffpy.pdfgui.git'  # Repo to push tags to
+$GITHUB_ORG = 'diffpy'  # Github org for Github releases and conda-forge
+$GITHUB_REPO = 'diffpy.pdfgui'  # Github repo for Github releases  and conda-forge
+$GHRELEASE_PREPEND = """See [CHANGELOG.md](CHANGELOG.md) for detailed release notes.
+
+The release is also available at [PyPI](https://pypi.org/project/diffpy.pdfgui/) and [Conda](https://anaconda.org/conda-forge/diffpy.pdfgui).
+"""  # release message