From 439625c48e8799c178ba264ad22f58254f4bd481 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cristiano=20K=C3=B6hler?= <42555442+kohlerca@users.noreply.github.com> Date: Wed, 6 Dec 2023 12:06:55 +0100 Subject: [PATCH] Release 0.2.0 preparation (#28) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Cristiano Köhler --- alpaca/VERSION | 2 +- doc/authors.rst | 2 +- doc/citation.rst | 29 +++++++++++++++++++++++++++++ doc/index.rst | 6 ++++-- doc/install.rst | 2 +- doc/release_notes.rst | 29 +++++++++++++++++++++++++++-- 6 files changed, 63 insertions(+), 7 deletions(-) create mode 100644 doc/citation.rst diff --git a/alpaca/VERSION b/alpaca/VERSION index fdd0e66..341cf11 100644 --- a/alpaca/VERSION +++ b/alpaca/VERSION @@ -1 +1 @@ -0.2.0b1 \ No newline at end of file +0.2.0 \ No newline at end of file diff --git a/doc/authors.rst b/doc/authors.rst index 6ff5b5e..7de9f9b 100644 --- a/doc/authors.rst +++ b/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] diff --git a/doc/citation.rst b/doc/citation.rst new file mode 100644 index 0000000..68c6d22 --- /dev/null +++ b/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 `_; `RRID:SCR_023739 `_) + +To cite a specific version of Alpaca please see version-specific DOIs at: + + `doi: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} + } diff --git a/doc/index.rst b/doc/index.rst index 8544e9b..5f68723 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -14,7 +14,8 @@ based on the `W3C PROV format `_. Examples are provided for the analysis of electrophysiology data, using the open source packages `Neo `_ and -`Elephant `_. +`Elephant `_. See `Köhler et al. (2023) `_ +for a detailed description on how to capture and interpret provenance trails generated by Alpaca. Visit the `project page on GitHub `_, 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 diff --git a/doc/install.rst b/doc/install.rst index 606345d..63b2218 100644 --- a/doc/install.rst +++ b/doc/install.rst @@ -23,7 +23,7 @@ Alpaca requires `Python `_ 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: diff --git a/doc/release_notes.rst b/doc/release_notes.rst index e607557..15b9fce 100644 --- a/doc/release_notes.rst +++ b/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.