Skip to content

Commit

Permalink
Merge pull request #829 from StingraySoftware/update_joss_paper
Browse files Browse the repository at this point in the history 
New JOSS paper draft
  • Loading branch information
@matteobachetti
matteobachetti authored Oct 25, 2024
2 parents ba8d06d + 8f5cfa7 commit 137d17d
Show file tree
Hide file tree
Showing 10 changed files with 661 additions and 228 deletions.
17 changes: 17 additions & 0 deletions CHANGELOG.rst
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,20 @@
v2.2.2 (2024-10-25)
-------------------

Docs
^^^^

- Add newly-accepted JOSS paper to docs, update citation information, and fresh new badges (`#829 <https://github.com/StingraySoftware/stingray/pull/829>`__)

v2.2.1 (2024-10-23)
-------------------

Bug Fixes
^^^^^^^^^

- Fix issue with FITS headers, especially for RXTE data (`#853 <https://github.com/StingraySoftware/stingray/pull/853>`__)


v2.2 (2024-10-22)
-----------------

Expand Down
6 changes: 3 additions & 3 deletions README.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -89,16 +89,16 @@ The code is distributed under the MIT license; see `LICENSE.rst <LICENSE.rst>`_
:target: https://codecov.io/gh/StingraySoftware/stingray
.. |GitHub release| image:: https://img.shields.io/github/v/release/StingraySoftware/stingray
:target: https://github.com/StingraySoftware/stingray/releases/latest
.. |joss| image:: http://joss.theoj.org/papers/10.21105/joss.01393/status.svg
:target: https://doi.org/10.21105/joss.01393
.. |joss| image:: https://joss.theoj.org/papers/10.21105/joss.07389/status.svg
:target: https://doi.org/10.21105/joss.07389
.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1490116.svg
:target: https://doi.org/10.5281/zenodo.1490116
.. |Repo status| image:: https://www.repostatus.org/badges/latest/active.svg
:alt: Project Status: Active – The project has reached a stable, usable state and is being actively developed.
:target: https://www.repostatus.org/#active
.. |License| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
.. |pyOpenSci Peer-Reviewed| image:: https://pyopensci.org/badges/peer-reviewed.svg
.. |pyOpenSci Peer-Reviewed| image:: https://pyopensci.org/badges/peer-reviewed.svg
:target: https://github.com/pyOpenSci/software-review/issues/201

.. _Astropy: https://www.github.com/astropy/astropy
Expand Down
1 change: 0 additions & 1 deletion docs/changes/853.bugfix.rst
View file

This file was deleted.

82 changes: 67 additions & 15 deletions docs/citing.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ If this isn't possible — for example, because you worked with an unreleased v
Papers
======

Please cite both of the following papers:
If you are using Stingray 2.0 or newer, please cite both of the following papers:

.. raw:: html

Expand Down Expand Up @@ -54,17 +54,21 @@ Please cite both of the following papers:
}
function copyJossBib() {
var bibtex = `@ARTICLE{Huppenkothen2019,
doi = {10.21105/joss.01393},
url = {https://doi.org/10.21105/joss.01393},
year = {2019},
publisher = {The Open Journal},
volume = {4},
number = {38},
pages = {1393},
author = {Daniela Huppenkothen and Matteo Bachetti and Abigail Stevens and Simone Migliari and Paul Balm and Omar Hammad and Usman Mahmood Khan and Himanshu Mishra and Haroon Rashid and Swapnil Sharma and Evandro Martinez Ribeiro and Ricardo Valles Blanco},
title = {stingray: A modern Python library for spectral timing},
journal = {Journal of Open Source Software}
var bibtex = `@article{bachettiStingrayFastModern2024,
title = {Stingray 2: {{A}} Fast and Modern {{Python}} Library for Spectral Timing},
shorttitle = {Stingray 2},
author = {Bachetti, Matteo and Huppenkothen, Daniela and Stevens, Abigail and Swinbank, John and Mastroserio, Guglielmo and Lucchini, Matteo and Lai, Eleonora Veronica and Buchner, Johannes and Desai, Amogh and Joshi, Gaurav and Pisanu, Francesco and Pisupati, Sri Guru Datta and Sharma, Swapnil and Tripathi, Mihir and Vats, Dhruv},
year = {2024},
month = oct,
journal = {Journal of Open Source Software},
volume = {9},
number = {102},
pages = {7389},
issn = {2475-9066},
doi = {10.21105/joss.07389},
urldate = {2024-10-25},
abstract = {Bachetti et al., (2024). Stingray 2: A fast and modern Python library for spectral timing. Journal of Open Source Software, 9(102), 7389, https://doi.org/10.21105/joss.07389},
langid = {english}
}`;
const el = document.createElement('textarea');
el.value = bibtex;
Expand All @@ -82,9 +86,9 @@ Please cite both of the following papers:
[<a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...881...39H">ADS</a>]
[<a onclick="copyApjBib()">Copy BibTeX to clipboard</a>]</li>

<li>Huppenkothen et al., 2019. Journal of Open Source Software, 4(38), 1393.
[<a href="https://doi.org/10.21105/joss.01393">DOI</a>]
[<a href="https://joss.theoj.org/papers/10.21105/joss.01393#">JOSS</a>]
<li>Bachetti et al., 2024. Journal of Open Source Software, 9(102), 7389.
[<a href="https://doi.org/10.21105/joss.07389">DOI</a>]
[<a href="https://joss.theoj.org/papers/10.21105/joss.07389#">JOSS</a>]
[<a onclick="copyJossBib()">Copy BibTeX to clipboard</a>]</li>
</ul>

Expand All @@ -93,5 +97,53 @@ Other Useful References

.. raw:: html

<script type="text/javascript">
function copyOldJossBib() {
var bibtex = `@article{bachettiStingrayFastModern2024,
title = {Stingray 2: {{A}} Fast and Modern {{Python}} Library for Spectral Timing},
shorttitle = {Stingray 2},
author = {Bachetti, Matteo and Huppenkothen, Daniela and Stevens, Abigail and Swinbank, John and Mastroserio, Guglielmo and Lucchini, Matteo and Lai, Eleonora Veronica and Buchner, Johannes and Desai, Amogh and Joshi, Gaurav and Pisanu, Francesco and Pisupati, Sri Guru Datta and Sharma, Swapnil and Tripathi, Mihir and Vats, Dhruv},
year = {2024},
month = oct,
journal = {Journal of Open Source Software},
volume = {9},
number = {102},
pages = {7389},
issn = {2475-9066},
doi = {10.21105/joss.07389},
urldate = {2024-10-25},
abstract = {Bachetti et al., (2024). Stingray 2: A fast and modern Python library for spectral timing. Journal of Open Source Software, 9(102), 7389, https://doi.org/10.21105/joss.07389},
langid = {english}
}`;
const el = document.createElement('textarea');
el.value = bibtex;
document.body.appendChild(el);
el.select();
document.execCommand('copy');
document.body.removeChild(el);
}
function copyAsclBib() {
var bibtex = `@software{2016ascl.soft08001H,
author = {{Huppenkothen}, Daniela and {Bachetti}, Matteo and {Stevens}, Abigail L. and {Migliari}, Simone and {Balm}, Paul},
title = "{Stingray: Spectral-timing software}",
howpublished = {Astrophysics Source Code Library, record ascl:1608.001},
year = 2016,
month = aug,
eid = {ascl:1608.001},
adsurl = {https://ui.adsabs.harvard.edu/abs/2016ascl.soft08001H},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
}`;
const el = document.createElement('textarea');
el.value = bibtex;
document.body.appendChild(el);
el.select();
document.execCommand('copy');
document.body.removeChild(el);
}
</script>
Stingray is listed in the <a href="https://ascl.net/1608.001">Astrophysics Source Code Library</a>.
<a onclick="copyAsclBib()">Copy the corresponding BibTeX to clipboard</a>.

Our first JOSS paper, describing the development until 2019, is Huppenkothen et al. 2019b, "Stingray: a modern python library for spectral timing", <a href="https://joss.theoj.org/papers/10.21105/joss.01393">JOSS</a>; <a href="https://doi.org/10.21105/joss.01393">DOI: 10.21105/joss.01393'</a>.
<a onclick="copyOldJossBib()">Copy the corresponding BibTeX to clipboard</a>.
3 changes: 3 additions & 0 deletions docs/conf.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,7 @@
r"https://arxiv.org/",
r"https://.*adsabs.harvard.edu/",
r"https://zenodo.org/",
r"https://opensource.org/",
]

# -- Options for the edit_on_github extension ---------------------------------
Expand Down Expand Up @@ -236,6 +237,8 @@ def bibtex_url(self):
f.write(" - DOI\n")
f.write(" - Citation\n")
for r in sorted(releases, key=lambda r: r.version, reverse=True):
if "beta" in r.version or "rc" in r.version:
continue
f.write(f" * - `{r.version} <{r.github_url}>`__\n")
f.write(f" - `{r.doi} <{r.zenodo_url}>`__\n")
f.write(f" - `[Link to BibTeX] <{r.bibtex_url}>`__\n")
Expand Down
36 changes: 35 additions & 1 deletion docs/index.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,16 @@ Stingray: Next-Generation Spectral Timing
:alt: Stingray logo, outline of a stingray on top of a graph of the power spectrum of an X-ray binary
:align: center

.. csv-table::
:header: "Usage", "Release", "Development", "Community"
:widths: auto
:align: center

|Python version|, |GitHub release|, |Build Status Master|, |Slack|
|Docs|, |joss|, |Repo status|, |pyOpenSci Peer-Reviewed|
|License|, |doi|, |Coverage Status Master|, " "


Stingray is a Python library designed to perform times series analysis and related tasks on astronomical light curves.
It supports a range of commonly-used Fourier analysis techniques, as well as extensions for analyzing pulsar data, simulating data sets, and statistical modelling.
Stingray is designed to be easy to extend, and easy to incorporate into data analysis workflows and pipelines.
Expand All @@ -33,7 +43,7 @@ Current Capabilities
* Good Time Interval operations
* Filling gaps in light curves with statistically sound fake data

1. Fourier methods
2. Fourier methods
~~~~~~~~~~~~~~~~~~
* power spectra and cross spectra in Leahy, rms normalization, absolute rms and no normalization
* averaged power spectra and cross spectra
Expand Down Expand Up @@ -328,3 +338,27 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

.. |Python version| image:: https://img.shields.io/python/required-version-toml?tomlFilePath=https://raw.githubusercontent.com/stingraysoftware/stingray/main/pyproject.toml
:alt: Python Version from PEP 621 TOML
.. |Build Status Master| image:: https://github.com/StingraySoftware/stingray/workflows/CI%20Tests/badge.svg
:target: https://github.com/StingraySoftware/stingray/actions/
.. |Docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
:target: https://docs.stingray.science/
.. |Slack| image:: https://img.shields.io/badge/Join%20Our%20Community-Slack-blue
:target: https://join.slack.com/t/stingraysoftware/shared_invite/zt-49kv4kba-mD1Y~s~rlrOOmvqM7mZugQ
.. |Coverage Status Master| image:: https://codecov.io/gh/StingraySoftware/stingray/branch/master/graph/badge.svg?token=FjWeFfhU9F
:target: https://codecov.io/gh/StingraySoftware/stingray
.. |GitHub release| image:: https://img.shields.io/github/v/release/StingraySoftware/stingray
:target: https://github.com/StingraySoftware/stingray/releases/latest
.. |joss| image:: https://joss.theoj.org/papers/10.21105/joss.07389/status.svg
:target: https://doi.org/10.21105/joss.07389
.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1490116.svg
:target: https://doi.org/10.5281/zenodo.1490116
.. |Repo status| image:: https://www.repostatus.org/badges/latest/active.svg
:alt: Project Status: Active – The project has reached a stable, usable state and is being actively developed.
:target: https://www.repostatus.org/#active
.. |License| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
.. |pyOpenSci Peer-Reviewed| image:: https://pyopensci.org/badges/peer-reviewed.svg
:target: https://github.com/pyOpenSci/software-review/issues/201
Loading

0 comments on commit 137d17d

Please sign in to comment.