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Merge pull request #842 from StingraySoftware/pyOpensci-review-responses
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Responses to pyOpenSci review
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matteobachetti authored Sep 20, 2024
2 parents 0b1783a + db79270 commit c3e6dd3
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -11,6 +11,7 @@ __pycache__

# Other generated files
*/version.py
*/_version.py
*/cython_version.py
htmlcov
.coverage
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26 changes: 18 additions & 8 deletions CREDITS.rst
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Expand Up @@ -2,18 +2,27 @@
Authors and Credits
*******************

Stingray Project Coordinators
=============================
Stingray Founders
=================

* Matteo Bachetti
* Paul Balm
* Daniela Huppenkothen
* Simone Migliari
* Abigail Stevens

Current Maintainers
===================
* Matteo Bachetti
* Daniela Huppenkothen
* Guglielmo Mastroserio
* John Swinbank
* Matteo Lucchini

Contributors
============

* Johannes Buchner
* Riccardo Campana
* Meg Davis
* Amogh Desai
Expand All @@ -22,17 +31,24 @@ Contributors
* Nick Gorgone
* Anurag Hota
* Ajit Jadhav
* Gaurav Joshi
* Usman Khan
* Sambhav Kothari
* Abhinav Kumar
* Sandeep Kumar
* Utkarsh Kumar
* Eleonora Veronica Lai
* luzpaz
* Max Mahlke
* Kartik Mandar
* Evandro Martinez Ribeiro
* Himanshu Mishra
* Sashank Mishra
* Stuart Mumford
* paopaofi
* parkma99
* Francesco Pisanu
* Sri Guru Datta Pisupati
* Rashmi Raj
* Haroon Rashid
* Achilles Rasquinha
Expand All @@ -41,17 +57,11 @@ Contributors
* Swapnil Sharma
* Brigitta Sipocz
* Arfon Smith
* John Swinbank
* Akash Tandon
* Marta Mancosu
* Mihir Tripathi
* Ricardo Vallés Blanco
* Dhruv Vats
* Guglielmo Mastroserio
* Sri Guru Datta Pisupati
* Gaurav Joshi
* luzpaz
* Abhinav Kumar

If you have contributed to Stingray and your name is missing,
please send an email to the coordinators, or
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1 change: 0 additions & 1 deletion MANIFEST.in
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include README.rst
include CHANGES.rst
include setup.cfg
include LICENSE.rst
include pyproject.toml

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20 changes: 18 additions & 2 deletions README.rst
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Stingray
========

|Build Status Master| |Docs| |Slack| |joss| |doi| |Coverage Status Master| |GitHub release|
.. csv-table::
:header: "Usage", "Release", "Development", "Community"
:widths: 50, 50, 50, 50

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



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
X-Ray Spectral Timing Made Easy
Expand Down Expand Up @@ -66,9 +74,11 @@ If you find this package useful in your research, please provide appropriate ack
Copyright & Licensing
---------------------

All content © 2015 The Authors.
All content © 2024 The Authors.
The code is distributed under the MIT license; see `LICENSE.rst <LICENSE.rst>`_ for details.

.. |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
Expand All @@ -83,6 +93,12 @@ The code is distributed under the MIT license; see `LICENSE.rst <LICENSE.rst>`_
:target: https://doi.org/10.21105/joss.01393
.. |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

.. _Astropy: https://www.github.com/astropy/astropy
.. _Issues: https://www.github.com/stingraysoftware/stingray/issues
.. _Issue: https://www.github.com/stingraysoftware/stingray/issues
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1 change: 1 addition & 0 deletions docs/changes/842.trivial.rst
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Moved configuration to pyproject.toml as recommended by PEP 621
36 changes: 19 additions & 17 deletions docs/conf.py
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print("ERROR: the documentation requires the sphinx-astropy package to be installed")
sys.exit(1)

# Get configuration information from setup.cfg
conf = ConfigParser()
try:
import tomllib
except ImportError:
# Help users on older alphas
import tomli as tomllib
from pathlib import Path

# Grab minversion from pyproject.toml
with (Path(__file__).parents[1] / "pyproject.toml").open("rb") as f:
pyproject = tomllib.load(f)

conf.read([os.path.join(os.path.dirname(__file__), "..", "setup.cfg")])
setup_cfg = dict(conf.items("metadata"))

# -- General configuration ----------------------------------------------------

Expand All @@ -67,16 +73,16 @@
# -- Project information ------------------------------------------------------

# This does not *have* to match the package name, but typically does
project = setup_cfg["name"]
author = setup_cfg["author"]
copyright = "{0}, {1}".format(datetime.datetime.now().year, setup_cfg["author"])
project = pyproject["project"]["name"]
author = ",".join(pyproject["project"]["authors"][0]["name"])
copyright = "{0}, {1}".format(datetime.datetime.now().year, pyproject["project"]["authors"])

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.

import_module(setup_cfg["name"])
package = sys.modules[setup_cfg["name"]]
import_module(pyproject["project"]["name"])
package = sys.modules[pyproject["project"]["name"]]

# The short X.Y version.
version = package.__version__.split("-", 1)[0]
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# -- Options for the edit_on_github extension ---------------------------------

if setup_cfg.get("edit_on_github").lower() == "true":
extensions += ["sphinx_astropy.ext.edit_on_github"]

edit_on_github_project = setup_cfg["github_project"]
edit_on_github_branch = "master"
edit_on_github_branch = "main"

edit_on_github_source_root = ""
edit_on_github_doc_root = "docs"

# -- Resolving issue number to links in changelog -----------------------------
github_issues_url = "https://github.com/{0}/issues/".format(setup_cfg["github_project"])
github_issues_url = "https://github.com/{0}/issues/".format(
pyproject["project"]["urls"]["repository"]
)

# -- Configuration for nbsphinx -----------------------------------------------
# disable notebook execution
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6 changes: 5 additions & 1 deletion docs/index.rst
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Expand Up @@ -97,7 +97,6 @@ A **minimal installation** of Stingray requires the following dependencies:
In **typical** uses, requiring input/output, caching of results, and faster processing, we **recommend the following dependencies**:

+ numba (**highly** recommended)
+ tbb (needed by numba)
+ tqdm (for progress bars, always useful)
+ pyfftw (for the fastest FFT in the West)
+ h5py (for input/output)
Expand Down Expand Up @@ -125,6 +124,8 @@ For the Gaussian Process modeling in `stingray.modeling.gpmodeling`, you'll need
+ etils
+ typing_extensions

For the Bexvar calculations in `stingray.bexvar` and `stingray.lightcurve`, you'll need `UltraNest <https://johannesbuchner.github.io/UltraNest/index.html>`_.

Most of these are installed via ``pip``, but if you have an Nvidia GPU available, you'll want to take special care
following the installation instructions for jax and tensorflow(-probability) in order to enable GPU support and
take advantage of those speed-ups.
Expand Down Expand Up @@ -271,6 +272,9 @@ the stingray source directory.
Using Stingray
===============

The documentation below is built on top of Jupyter notebooks that can be run locally.
The easiest way to retrieve the notebooks is by `cloning the notebooks repository <https://github.com/StingraySoftware/notebooks>`_ and browsing the directories, which are conveniently divided by topic.

A Spectral timing exploration
-----------------------------

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