Merge pull request #76 from mptino/cli

Entry point improvements & support for configs as relative/absolute paths

Author: nasserma

CONTRIBUTE.md

@@ -0,0 +1,6 @@
+# Contribution Policy
+
+* Open an issue in the shapelets [issue tracker](https://github.com/uw-comphys/shapelets/issues) and clearly describe your intentions on source code modifications
+* Ensure your modifications adhere to the existing standard of the shapelets library (i.e., do your docstrings follow the same format?) 
+* Test your modifications by running the shapelets unit tests from the command-line via ``shapelets-test``
+* Once the issue has been discussed with a library author, you may open a pull request

README.md

@@ -4,58 +4,62 @@
 
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.06058/status.svg)](https://doi.org/10.21105/joss.06058)
 
-[**Getting Started**](#getting-started)
-| [**Issues**](#issues)
+[**Main Features**](#main-features)
+| [**Getting Started**](#getting-started)
 | [**Contribute**](#contribute)
 | [**Citation**](#citation)
-| [**Authors**](#authors)
 
 ## What is shapelets? 
 
-Shapelets is a Python-based library that implements several shapelet functions and some of their applications in science and engineering. Shapelet functions are a complete and orthogonal set of localized basis functions with mathematical properties convenient for image analysis and manipulation. Applications include:
+Shapelets is a Python library that implements several shapelet functions and some of their applications in science and engineering. Shapelet functions are a complete and orthogonal set of localized basis functions with mathematical properties convenient for various image analyses. Existing applications from the literature include:
 
 * Astronomy/astrophysics ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x), [R. Massey (2005)](https://doi.org/10.48550/arXiv.astro-ph/0408445), [J. Berge (2019)](https://doi.org/10.48550/arXiv.1903.05837))
 * Nanostructure characterization ([R. Suderman (2015)](http://dx.doi.org/10.1103/PhysRevE.91.033307), [T. Akdeniz (2018)](https://doi.org/10.1088/1361-6528/aaf353), [M. P. Tino (2024)](http://dx.doi.org/10.1088/1361-6528/ad1df4))
 * Computational neuroscience ([J. D. Victor (2006)](https://doi.org/10.1152/jn.00498.2005), [T. O. Sharpee (2009)](https://doi.org/10.1007%2Fs10827-008-0107-5))
 * Medical imaging ([J. Weissman (2004)](https://doi.org/10.1364/OPEX.12.005760))
 
-The shapelets library provides reference code and documentation for the following shapelet functions:
+## Main features
 
-* Cartesian shapelets ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x))
+Shapelets provides implementations of the following shapelet functions from ``shapelets.core.functions``
+
+* Cartesian shapelets ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x)) 
 * Polar shapelets ([R. Massey (2005)](https://doi.org/10.48550/arXiv.astro-ph/0408445))
 * Exponential shapelets ([J. Berge (2019)](https://doi.org/10.48550/arXiv.1903.05837))
-* Orthonormal polar shapelets ([T. Akdeniz (2018)](https://doi.org/10.1088/1361-6528/aaf353), [M. P. Tino (2024)](https://hdl.handle.net/10012/20779))
+* Orthonormal polar shapelets with no radial extrema ([T. Akdeniz (2018)](https://doi.org/10.1088/1361-6528/aaf353))
+* Orthonormal polar shapelets with one degree of radial extrema ([M. P. Tino (2024)](https://hdl.handle.net/10012/20779))
+
+It also implements several shapelets applications, such as
+* The response distance method ([R. Suderman (2015)](http://dx.doi.org/10.1103/PhysRevE.91.033307)) - see [example 1](https://uw-comphys.github.io/shapelets/shapelets/docs/example_1.html)
+* The defect identification method ([M. P. Tino (2024)](http://dx.doi.org/10.1088/1361-6528/ad1df4)) - see [example 2](https://uw-comphys.github.io/shapelets/shapelets/docs/example_2.html)
+* The local pattern orientation method ([M. P. Tino (2024)](http://dx.doi.org/10.1088/1361-6528/ad1df4)) - see [example 3](https://uw-comphys.github.io/shapelets/shapelets/docs/example_3.html)
+* Galaxy decomposition and reconstruction ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x)) - see [example 4](https://uw-comphys.github.io/shapelets/shapelets/docs/example_4.html)
 
 ## Getting Started
 
 If you have Python 3.10+ installed on your machine, you can install the shapelets library via pip: 
 
     pip install shapelets
 
-Otherwise, consult the [official website](https://uw-comphys.github.io/shapelets/shapelets.html) for installation instructions.
-
-## Issues
-
-If you encounter any **problems** with shapelets, please create a post using the [issue tracker](https://github.com/uw-comphys/shapelets/issues). Provide a clear and concise description of the problem with images/code-snippets where appropriate. We will address these problems as fast as possible.
+Otherwise, consult the [installation guide](https://uw-comphys.github.io/shapelets/shapelets/docs/installation_guide.html).
+If you plan to use the shapelets library for your own work, please cite appropriately using this [citation](#citation).
+For any problems, create a post using the [issue tracker](https://github.com/uw-comphys/shapelets/issues). 
 
 ## Contribute
 
-The authors of the shapelets library welcome contributions to the source code. Please follow the contribution policy:
-
-* Open an issue on the library [issue tracker](https://github.com/uw-comphys/shapelets/issues) clearly describing your intentions on code modifications
-* Ensure your modifications or additions adhere to the existing standard of the shapelets library (i.e. how are your docstrings?) 
-* Test your modifications to ensure the integrity of the library is intact via the entry point: `shapelets-test`
-
-* Once the issue has been discussed with a library author, you may open a pull request containing your modifications
+The authors of the shapelets library welcome contributions to the source code. 
+Please follow the contribution policy [here](https://github.com/uw-comphys/shapelets/blob/main/CONTRIBUTE.md).
 
 ## Citation
-
-If you plan to use shapelets in your own work, please cite using the **Cite this repository** dropdown button on the top right of this page (under *About*).
-
-## Authors
-
-* Matthew Peres Tino (mptino@uwaterloo.ca)
-* Abbas Yusuf Abdulaziz 
-* Nasser Mohieddin Abukhdeir
-* Robert Suderman 
-* Thomas Akdeniz
+```
+@article{TinoShapelets2024,
+author = {Tino, Matthew Peres and Abdulaziz, Abbas Yusuf and Suderman, Robert and Akdeniz, Thomas and Abukhdeir, Nasser Mohieddin},
+title = {Shapelets: A Python package implementing shapelet functions and their applications},
+doi = {10.21105/joss.06058},
+journal = {Journal of Open Source Software},
+number = {95},
+pages = {6058},
+volume = {9},
+year = {2024},
+url = {https://joss.theoj.org/papers/10.21105/joss.06058}
+}
+```

WEBHOME.md

@@ -2,54 +2,46 @@
 
 ## What is shapelets? 
 
-Shapelets is a Python-based library that implements several shapelet functions and some of their applications in science and engineering. Shapelet functions are a complete and orthogonal set of localized basis functions with mathematical properties convenient for image analysis and manipulation. Applications include:
+Shapelets is a Python library that implements several shapelet functions and some of their applications in science and engineering. Shapelet functions are a complete and orthogonal set of localized basis functions with mathematical properties convenient for various image analyses. Existing applications from the literature include:
 
 * Astronomy/astrophysics ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x), [R. Massey (2005)](https://doi.org/10.48550/arXiv.astro-ph/0408445), [J. Berge (2019)](https://doi.org/10.48550/arXiv.1903.05837))
 * Nanostructure characterization ([R. Suderman (2015)](http://dx.doi.org/10.1103/PhysRevE.91.033307), [T. Akdeniz (2018)](https://doi.org/10.1088/1361-6528/aaf353), [M. P. Tino (2024)](http://dx.doi.org/10.1088/1361-6528/ad1df4))
 * Computational neuroscience ([J. D. Victor (2006)](https://doi.org/10.1152/jn.00498.2005), [T. O. Sharpee (2009)](https://doi.org/10.1007%2Fs10827-008-0107-5))
 * Medical imaging ([J. Weissman (2004)](https://doi.org/10.1364/OPEX.12.005760))
 
-The shapelets library provides reference code and documentation for the following shapelet functions:
+## Main features
 
-* Cartesian shapelets ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x))
+Shapelets provides implementations of the following shapelet functions from ``shapelets.core.functions``
+
+* Cartesian shapelets ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x)) 
 * Polar shapelets ([R. Massey (2005)](https://doi.org/10.48550/arXiv.astro-ph/0408445))
 * Exponential shapelets ([J. Berge (2019)](https://doi.org/10.48550/arXiv.1903.05837))
-* Orthonormal polar shapelets ([T. Akdeniz (2018)](https://doi.org/10.1088/1361-6528/aaf353), [M. P. Tino (2024)](https://hdl.handle.net/10012/20779))
+* Orthonormal polar shapelets with no radial extrema ([T. Akdeniz (2018)](https://doi.org/10.1088/1361-6528/aaf353))
+* Orthonormal polar shapelets with one degree of radial extrema ([M. P. Tino (2024)](https://hdl.handle.net/10012/20779))
+
+It also implements several shapelets applications, such as
+* The response distance method ([R. Suderman (2015)](http://dx.doi.org/10.1103/PhysRevE.91.033307)) - see [example 1](https://uw-comphys.github.io/shapelets/shapelets/docs/example_1.html)
+* The defect identification method ([M. P. Tino (2024)](http://dx.doi.org/10.1088/1361-6528/ad1df4)) - see [example 2](https://uw-comphys.github.io/shapelets/shapelets/docs/example_2.html)
+* The local pattern orientation method ([M. P. Tino (2024)](http://dx.doi.org/10.1088/1361-6528/ad1df4)) - see [example 3](https://uw-comphys.github.io/shapelets/shapelets/docs/example_3.html)
+* Galaxy decomposition and reconstruction ([A. Refregier (2003)](https://doi.org/10.1046/j.1365-8711.2003.05901.x)) - see [example 4](https://uw-comphys.github.io/shapelets/shapelets/docs/example_4.html)
 
 ## Getting Started
 
-1. If you have Python 3.10+ installed, you can install the shapelets library via pip:
+If you have Python 3.10+ installed, you can install the shapelets library via pip:
 ```
 pip install shapelets
 ```
-2. If you do not have Python 3.10+ installed, consult the [installation guide](https://uw-comphys.github.io/shapelets/shapelets/docs/installation_guide.html).
-3. Consult the [examples](https://uw-comphys.github.io/shapelets/shapelets/docs.html) to see how the library can be used.
-4. Checkout other documentation:
-    * [Custom Commands](https://uw-comphys.github.io/shapelets/shapelets/docs/custom_commands.html) 
-    * [Library Interface](https://uw-comphys.github.io/shapelets/shapelets/docs/library_interface.html)
-
-If you plan to use the shapelets library for your own work, please cite appropriately using the [citation](#citation) below.
+If you do not have Python 3.10+ installed, consult the [installation guide](https://uw-comphys.github.io/shapelets/shapelets/docs/installation_guide.html). Be sure to also checkout the [custom commands](https://uw-comphys.github.io/shapelets/shapelets/docs/custom_commands.html) and [examples](https://uw-comphys.github.io/shapelets/shapelets/docs.html) to see which shapelets applications are implemented and how to interact with the shapelets library.
 
-## Issues
-
-If you encounter any **problems** with shapelets, please create a post using the [issue tracker](https://github.com/uw-comphys/shapelets/issues). Provide a clear and concise description of the problem with images/code-snippets where appropriate. We will address these problems as fast as possible.
+If you plan to use the shapelets library for your own work, please cite appropriately using this [citation](#citation).
+For any problems, create a post using the [issue tracker](https://github.com/uw-comphys/shapelets/issues). 
 
 ## Contribute
 
-The authors of the shapelets library welcome contributions to the source code. Please follow the contribution policy:
-
-* Open an issue on the library [issue tracker](https://github.com/uw-comphys/shapelets/issues) clearly describing your intentions on code modifications
-* Ensure your modifications or additions adhere to the existing standard of the shapelets library (i.e. how are your docstrings?) 
-* Test your modifications to ensure the integrity of the library is intact via the entry point: 
-```
-shapelets-test
-```
-* Once the issue has been discussed with a library author, you may open a pull request containing your modifications
+The authors of the shapelets library welcome contributions to the source code. 
+Please follow the contribution policy [here](https://github.com/uw-comphys/shapelets/blob/main/CONTRIBUTE.md).
 
 ## Citation
-
-If you plan to use shapelets in your own work, please cite using the following bibtex citation:
-
 ```
 @article{TinoShapelets2024,
 author = {Tino, Matthew Peres and Abdulaziz, Abbas Yusuf and Suderman, Robert and Akdeniz, Thomas and Abukhdeir, Nasser Mohieddin},