Responses to pyOpenSci review

.gitignore

@@ -11,6 +11,7 @@ __pycache__
 
 # Other generated files
 */version.py
+*/_version.py
 */cython_version.py
 htmlcov
 .coverage

CREDITS.rst

@@ -2,15 +2,23 @@
 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
 ============
 
@@ -22,17 +30,24 @@ 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
@@ -41,17 +56,11 @@ 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

MANIFEST.in

@@ -1,6 +1,5 @@
 include README.rst
 include CHANGES.rst
-include setup.cfg
 include LICENSE.rst
 include pyproject.toml
 

README.rst

@@ -2,7 +2,15 @@
 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
@@ -69,6 +77,8 @@ Copyright & Licensing
 All content © 2015 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
@@ -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

docs/changes/842.trivial.rst

@@ -0,0 +1 @@
+Moved configuration to pyproject.toml as recommended by PEP 621

docs/conf.py

@@ -37,11 +37,17 @@
     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 ----------------------------------------------------
 
@@ -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]
@@ -157,17 +163,13 @@
 
 # -- 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

docs/index.rst

@@ -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)
@@ -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.
@@ -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
 -----------------------------