Pixi installation

.gitattributes

@@ -1 +1,3 @@
 xmidas/_version.py export-subst
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -86,3 +86,6 @@ target/
 *.png
 *.nor
 *.ipynb
+# pixi environments
+.pixi/*
+!.pixi/config.toml

AUTHORS.rst

@@ -1,13 +1,17 @@
-=======
-Credits
-=======
-
-Maintainer
-----------
-
-* Brookhaven National Lab <>
-
-Contributors
-------------
-
-None yet. Why not be the first? See: CONTRIBUTING.rst
+=======
+Credits
+=======
+
+Maintainers
+----------
+
+- Ajith Pattammattel <pattammattel@bnl.gov>
+- Dmitri Gavrilov <dgavrilov@bnl.gov>
+
+*Brookhaven National Laboratory*
+
+
+Contributors
+------------
+
+None yet. Why not be the first? See: CONTRIBUTING.rst

CONTRIBUTING.rst

@@ -1,104 +1,104 @@
-============
-Contributing
-============
-
-Contributions are welcome, and they are greatly appreciated! Every
-little bit helps, and credit will always be given.
-
-You can contribute in many ways:
-
-Types of Contributions
-----------------------
-
-Report Bugs
-~~~~~~~~~~~
-
-Report bugs at https://github.com/dmgav/xmidas/issues.
-
-If you are reporting a bug, please include:
-
-* Any details about your local setup that might be helpful in troubleshooting.
-* Detailed steps to reproduce the bug.
-
-Fix Bugs
-~~~~~~~~
-
-Look through the GitHub issues for bugs. Anything tagged with "bug"
-is open to whoever wants to implement it.
-
-Implement Features
-~~~~~~~~~~~~~~~~~~
-
-Look through the GitHub issues for features. Anything tagged with "feature"
-is open to whoever wants to implement it.
-
-Write Documentation
-~~~~~~~~~~~~~~~~~~~
-
-XMidas could always use more documentation, whether
-as part of the official XMidas docs, in docstrings,
-or even on the web in blog posts, articles, and such.
-
-Submit Feedback
-~~~~~~~~~~~~~~~
-
-The best way to send feedback is to file an issue at https://github.com/dmgav/xmidas/issues.
-
-If you are proposing a feature:
-
-* Explain in detail how it would work.
-* Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
-
-Get Started!
-------------
-
-Ready to contribute? Here's how to set up `xmidas` for local development.
-
-1. Fork the `xmidas` repo on GitHub.
-2. Clone your fork locally::
-
-    $ git clone git@github.com:your_name_here/xmidas.git
-
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
-
-    $ mkvirtualenv xmidas
-    $ cd xmidas/
-    $ python setup.py develop
-
-4. Create a branch for local development::
-
-    $ git checkout -b name-of-your-bugfix-or-feature
-
-   Now you can make your changes locally.
-
-5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
-
-    $ flake8 xmidas tests
-    $ python setup.py test
-    $ tox
-
-   To get flake8 and tox, just pip install them into your virtualenv.
-
-6. Commit your changes and push your branch to GitHub::
-
-    $ git add .
-    $ git commit -m "Your detailed description of your changes."
-    $ git push origin name-of-your-bugfix-or-feature
-
-7. Submit a pull request through the GitHub website.
-
-Pull Request Guidelines
------------------------
-
-Before you submit a pull request, check that it meets these guidelines:
-
-1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
-   your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
-3. The pull request should work for Python 2.7, 3.3, 3.4, 3.5 and for PyPy. Check
-   https://travis-ci.org/dmgav/xmidas/pull_requests
-   and make sure that the tests pass for all supported Python versions.
-
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/dmgav/xmidas/issues.
+
+If you are reporting a bug, please include:
+
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "feature"
+is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+XMidas could always use more documentation, whether
+as part of the official XMidas docs, in docstrings,
+or even on the web in blog posts, articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/dmgav/xmidas/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `xmidas` for local development.
+
+1. Fork the `xmidas` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/xmidas.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv xmidas
+    $ cd xmidas/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 xmidas tests
+    $ python setup.py test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.7, 3.3, 3.4, 3.5 and for PyPy. Check
+   https://travis-ci.org/dmgav/xmidas/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+

LICENSE

@@ -1,29 +1,29 @@
-BSD 3-Clause License
-
-Copyright (c) 2021, Brookhaven National Lab
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-   may be used to endorse or promote products derived from this software
-   without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+BSD 3-Clause License
+
+Copyright (c) 2021, Brookhaven National Lab
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -1,18 +1,18 @@
-include AUTHORS.rst
-include CONTRIBUTING.rst
-include LICENSE
-include README.rst
-include requirements.txt
-
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.rst conf.py Makefile make.bat
-
-include versioneer.py
-include xmidas/_version.py
-recursive-include xmidas/uis *
-recursive-include xmidas/css *
-
-# If including data files in the package, add them like:
-# include path/to/data_file
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include LICENSE
+include README.rst
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat
+
+include versioneer.py
+include xmidas/_version.py
+recursive-include xmidas/uis *
+recursive-include xmidas/css *
+
+# If including data files in the package, add them like:
+# include path/to/data_file

README.rst

@@ -1,12 +1,14 @@
-======================================================
-XMidas (X-Ray Multimodal Image Data Analysis Software)
-======================================================
-
-.. image:: https://img.shields.io/pypi/v/xmidas.svg
-        :target: https://pypi.python.org/pypi/xmidas
-
-Software for analysis of imaging and spectrosocpy data collected at NSLS-II,
-Brookhaven National Laboratory
-
-* Free software: 3-clause BSD license
-* Documentation: https://nsls-ii.github.io/xmidas/.
+======================================================
+XMidas (X-Ray Multimodal Image Data Analysis Software)
+======================================================
+
+.. image:: https://img.shields.io/pypi/v/xmidas.svg
+        :target: https://pypi.python.org/pypi/xmidas
+
+Software for analysis of imaging and spectrosocpy data collected at NSLS-II,
+Brookhaven National Laboratory
+
+* Free software: 3-clause BSD license
+* Documentation: https://nsls-ii.github.io/xmidas/.
+
+* Citation: Ajith Pattammattel, Ryan Tappero, Dmitri Gavrilov, Hongqiao Zhang, Paul Aronstein, Henry Jay Forman, Peggy A O'Day, Hanfei Yan, Yong S Chu, Multimodal X-ray nano-spectromicroscopy analysis of chemically heterogeneous systems, Metallomics, Volume 14, Issue 10, October 2022, mfac078, https://doi.org/10.1093/mtomcs/mfac078