Release 0.2.0 preparation

alpaca/VERSION

@@ -1 +1 @@
-0.2.0b1
+0.2.0

doc/authors.rst

@@ -8,7 +8,7 @@ The following people have contributed code and/or ideas to the current version
 of Alpaca. The institutional affiliations are those at the time of the
 contribution, and may not be the current affiliation of a contributor.
 
-* Cristiano Köhler (orcid: 0000-0003-0503-5264) [1, 2]
+* Cristiano André Köhler (orcid: 0000-0003-0503-5264) [1, 2]
 * Danylo Ulianych (orcid: 0000-0003-3489-0542) [1]
 * Michael Denker (orcid: 0000-0003-1255-7300) [1]
 

doc/citation.rst

@@ -0,0 +1,29 @@
+*************
+Citing Alpaca
+*************
+To refer to the Alpaca software package in publications, please use:
+
+Alpaca (`doi:10.5281/zenodo.10276510 <https://doi.org/10.5281/zenodo.10276510>`_; `RRID:SCR_023739 <https://scicrunch.org/resolver/RRID:SCR_023739>`_)
+
+To cite a specific version of Alpaca please see version-specific DOIs at:
+
+ `doi:10.5281/zenodo.10276510 <https://doi.org/10.5281/zenodo.10276510>`_
+
+To cite Alpaca, please use:
+
+**Köhler CA, Ulianych D, Grün S, Decker S, Denker M (2023)
+Facilitating the sharing of electrophysiology data analysis results through in-depth provenance capture. arXiv:2311.09672.
+doi:10.48550/arXiv.2311.09672**
+
+A BibTeX entry for LaTeX users is:
+
+.. code-block:: none
+
+    @misc{alpaca23,
+          title={Facilitating the sharing of electrophysiology data analysis results through in-depth provenance capture},
+          author={Cristiano André Köhler and Danylo Ulianych and Sonja Grün and Stefan Decker and Michael Denker},
+          year={2023},
+          eprint={2311.09672},
+          archivePrefix={arXiv},
+          primaryClass={q-bio.NC}
+    }

doc/index.rst

@@ -14,7 +14,8 @@ based on the `W3C PROV format <https://www.w3.org/TR/prov-overview/>`_.
 
 Examples are provided for the analysis of electrophysiology data, using the
 open source packages `Neo <https://neuralensemble.org/neo>`_ and
-`Elephant <https://python-elephant.org>`_.
+`Elephant <https://python-elephant.org>`_. See `Köhler et al. (2023) <https://doi.org/10.48550/arXiv.2311.09672>`_
+for a detailed description on how to capture and interpret provenance trails generated by Alpaca.
 
 Visit the `project page on GitHub <https://github.com/INM-6/alpaca>`_, to
 report bugs and issues, or to make contributions to the source code.
@@ -30,9 +31,10 @@ Table of Contents
    install
    examples
    api
-   authors
    release_notes
    acknowledgments
+   authors
+   citation
    open_software_licenses
 
 

doc/install.rst

@@ -23,7 +23,7 @@ Alpaca requires `Python <http://python.org/>`_ 3.8 or higher.
 
            .. code-block:: sh
 
-              conda create --name alpaca python=3.9
+              conda create --name alpaca python=3.11
 
         2. Activate your environment:
 

doc/release_notes.rst

@@ -2,7 +2,32 @@
 Release Notes
 =============
 
-Alpaca 0.1.0 release notes
-**************************
+Release 0.2.0
+*************
+
+New functionality and features
+------------------------------
+* Added functionality to capture and serialize object values (e.g., values of integers, booleans, floats, complex numbers, NumPy numeric objects, or any other object type defined by the user) (#27).
+* Added support for adding semantic annotations in the captured provenance using ontologies (#26).
+* Added option to select levels captured in nested container outputs (#10, #25).
+* Extended attribute selection for graph aggregation (#24).
+* Improved logging and progress bar output (#14).
+* Improved performance when generating the provenance graph (#13).
+* Optimize attribute selection for graph visualization (#16).
+* Added ability to merge multiple provenance sources into a single visualization graph (#22).
+* Implemented functionality to add a suffix to the base file name in `get_file_name` utility function (#21).
+* Improved tracking of Python objects (#20).
+
+Bug fixes
+---------
+* Fixed error when tracking provenance of static methods in objects (#23).
+* Added support to other form of comprehensions (e.g., dictionaries, sets) as functions executed inside comprehensions other than list were not tracked (#19).
+* Fixed error when getting the module version when tracking a method descriptor (#17).
+* Added option to not store the list of members (i.e., all nodes that were aggregated in a super node) during graph aggregation, as in large graphs this resulted in an error when loading the graph in Gephi (#15).
+* Added support to track functions called as an attribute of a module (i.e., in the form `module.function(input)`), as they were not tracked by the decorator (#12).
+* Changed `save_provenance` function to avoid error when not capturing provenance (e.g., when the provenance capture was deactivated and the function called at the end of the script) (#11).
+
+Release 0.1.0
+*************
 
 This release constitutes the initial Alpaca release.