Merge branch 'main' into format

.gitignore

@@ -85,6 +85,7 @@ gammapy/gammapy.cfg
 docs/_generated
 docs/gen_modules
 docs/api
+docs/sg_execution_times.rst
 .coverage
 
 dev/crab

README.rst

@@ -1,37 +1,43 @@
 .. image:: https://anaconda.org/conda-forge/gammapy/badges/license.svg
-    :target: https://github.com/gammapy/gammapy/blob/master/LICENSE.rst
-    :alt: Licence
+   :target: https://github.com/gammapy/gammapy/blob/master/LICENSE.rst
+   :alt: Licence
 
 .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
-    :target: http://www.astropy.org/
-
+   :target: http://www.astropy.org/
+|
 .. image:: https://anaconda.org/conda-forge/gammapy/badges/platforms.svg
-    :target: https://anaconda.org/conda-forge/gammapy
-
+   :target: https://anaconda.org/conda-forge/gammapy
+|
 .. image:: http://img.shields.io/pypi/v/gammapy.svg?text=version
-    :target: https://pypi.org/project/gammapy/
-    :alt: Latest release
+   :target: https://pypi.org/project/gammapy/
+   :alt: Latest release
 
 .. image:: https://img.shields.io/pypi/dm/gammapy?label=downloads%20%7C%20pip&logo=PyPI
    :alt: PyPI - Downloads
 
 .. image:: https://anaconda.org/conda-forge/gammapy/badges/version.svg
-    :target: https://anaconda.org/conda-forge/gammapy
+   :target: https://anaconda.org/conda-forge/gammapy
 
 .. image:: https://img.shields.io/conda/dn/conda-forge/gammapy?label=downloads%20%7C%20conda&logo=Conda-Forge
-    :target: https://anaconda.org/conda-forge/gammapy
+   :target: https://anaconda.org/conda-forge/gammapy
 
 .. image:: https://img.shields.io/badge/launch-binder-579aca.svg?logo=data:image/png;base64,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
    :target: mybinder.org
-
+|
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4701488.svg?style=flat
-    :target: https://doi.org/10.5281/zenodo.4701488
+   :target: https://doi.org/10.5281/zenodo.4701488
 
 .. image:: https://archive.softwareheritage.org/badge/origin/https://github.com/gammapy/gammapy/
-    :target: https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/gammapy/gammapy
+   :target: https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/gammapy/gammapy
 
+.. image:: https://archive.softwareheritage.org/badge/swh:1:snp:11e81660a96c3252c4afa4d48b58d1d2f78ea80a/
+   :target: https://archive.softwareheritage.org/swh:1:snp:11e81660a96c3252c4afa4d48b58d1d2f78ea80a;origin=https://github.com/gammapy/gammapy
+|
 .. image:: https://img.shields.io/badge/A&A-Published-Green.svg
-    :target: https://doi.org/10.1051/0004-6361/202346488
+   :target: https://doi.org/10.1051/0004-6361/202346488
+|
+.. image:: https://img.shields.io/badge/Matomo-3152A0?style=for-the-badge&logo=Matomo&logoColor=white
+   :target: https://matomo.org/
 
 Gammapy
 =======

codemeta.json

@@ -253,18 +253,31 @@
         }
     ],
     "codeRepository": "https://github.com/gammapy/gammapy",
-    "datePublished": "2024-02-29",
+    "dateCreated": "2013-08-19",
+    "datePublished": "2014-08-25",
+    "dateModified": "2024-02-29",
     "description": "Gammapy analyzes gamma-ray data and creates sky images, spectra and lightcurves, from event lists and instrument response information; it can also determine the position, morphology and spectra of gamma-ray sources. It is used to analyze data from H.E.S.S., Fermi-LAT, HAWC, and the Cherenkov Telescope Array (CTA).",
     "identifier": "https://doi.org/10.5281/zenodo.4701488",
     "keywords": [
         "Astronomy",
         "Gamma-rays",
-        "Data analysis"
+        "Data analysis",
+        "Scientific/Engineering"
     ],
     "license": "https://spdx.org/licenses/BSD-3-Clause",
     "name": "Gammapy: Python toolbox for gamma-ray astronomy",
     "url": "https://gammapy.org/",
     "softwareVersion": "v1.2",
+    "applicationCategory": "Astronomy",
+    "applicationSubCategory": "Very-high-energy gamma rays",
+    "programmingLanguage": "Python 3",
+    "operatingSystem": "Linux, Mac OS, Windows",
+    "referencePublication": "https://doi.org/10.1051/0004-6361/202346488",
+    "audience": {
+        "@id": "/audience/science-research",
+        "@type": "Audience",
+        "audienceType": "Science/Research"
+    },
     "maintainer": {
         "@id": "https://orcid.org/0000-0003-4568-7005",
         "@type": "Person",

dev/codemeta.py

@@ -4,6 +4,7 @@
 import logging
 from configparser import ConfigParser
 import click
+from datetime import date
 
 log = logging.getLogger(__name__)
 
@@ -24,6 +25,10 @@ def update_codemeta(maintainer, filename, setup_file=None):
     data["developmentStatus"] = ("active",)
     data["email"] = "[email protected]"
 
+    modified_date = str(date.today())
+    data["dateModified"] = modified_date
+
+
     if setup_file:
         # complete with software requirements from setup.cfg
         cf = ConfigParser()

dev/github_summary.py

@@ -198,7 +198,7 @@ def list_merged_PRs(filename, milestones, from_backports):
     table = Table.read(filename)
 
     # Keep only merged PRs
-    table = table[table["is_merged"] is True]
+    table = table[table["is_merged"] == True]
 
     # Keep the requested milestones
     valid = np.zeros((len(table)), dtype="bool")

docs/_static/custom.css

@@ -88,7 +88,7 @@ p {
   color: white;
 }
 
-#navbar-icon-links i.fa-twitter-square::before {
+#navbar-icon-links i.fa-square-x-twitter::before {
   color: white;
 }
 

docs/_static/matomo.js

@@ -0,0 +1,15 @@
+//  Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+// Matomo Tracking Code
+    var _paq = window._paq = window._paq || [];
+    /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+    _paq.push(['trackPageView']);
+    _paq.push(['enableLinkTracking']);
+    (function() {
+        var u="https://apcstatview.in2p3.fr/";
+        _paq.push(['setTrackerUrl', u+'matomo.php']);
+        _paq.push(['setSiteId', '3']);
+        var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+        g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
+    })();
+

docs/conf.py

@@ -26,6 +26,8 @@
 # be accessible, and the documentation will not build correctly.
 
 import datetime
+import sys
+import os
 
 # Get configuration information from setup.cfg
 from configparser import ConfigParser
@@ -35,7 +37,7 @@
 from sphinx_astropy.conf import *
 
 # Sphinx-gallery config
-from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
+from sphinx_gallery.sorting import ExplicitOrder
 
 # Load utils docs functions
 from gammapy.utils.docs import SubstitutionCodeBlock, gammapy_sphinx_ext_activate
@@ -56,6 +58,8 @@ def setup(app):
 conf.read([os.path.join(os.path.dirname(__file__), "..", "setup.cfg")])
 setup_cfg = dict(conf.items("metadata"))
 
+sys.path.insert(0, os.path.dirname(__file__))
+
 linkcheck_anchors_ignore = []
 linkcheck_ignore = [
     "http://gamma-sky.net/#",
@@ -70,6 +74,8 @@ def setup(app):
     "https://www.hawc-observatory.org/",  # invalid certificate
     "https://ipython.org",  # invalid certificate
     "https://jupyter.org",  # invalid certificate
+    "https://hess-confluence.desy.de/confluence/display/HESS/HESS+FITS+data", # private page
+    "https://hess-confluence.desy.de/"
 ]
 
 # the buttons link to html pages which are auto-generated...
@@ -111,7 +117,6 @@ def setup(app):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns.append("_templates")
-exclude_patterns.append("_static")
 exclude_patterns.append("**.ipynb_checkpoints")
 exclude_patterns.append("user-guide/model-gallery/*/*.ipynb")
 exclude_patterns.append("user-guide/model-gallery/*/*.md5")
@@ -220,7 +225,7 @@ def setup(app):
         {
             "name": "Twitter",
             "url": "https://twitter.com/gammapyST",
-            "icon": "fab fa-twitter-square",
+            "icon": "fab fa-square-x-twitter",
         },
         {
             "name": "Slack",
@@ -234,6 +239,10 @@ def setup(app):
     },
     "navbar_end": ["version-switcher", "theme-switcher", "navbar-icon-links"],
     "navigation_with_keys": True,
+    # footers
+    "footer_start": ["copyright"],
+    "footer_center": ["last-updated"],
+    "footer_end": ["sphinx-version", "theme-version"]
 }
 
 
@@ -314,7 +323,7 @@ def setup(app):
     "exclude_implicit_doc": {},
     "filename_pattern": r"\.py",
     "reset_modules": ("matplotlib",),
-    "within_subsection_order": FileNameSortKey,
+    "within_subsection_order": "sphinxext.TutorialExplicitOrder",
     "download_all_examples": True,
     "capture_repr": ("_repr_html_", "__repr__"),
     "nested_sections": False,
@@ -328,11 +337,12 @@ def setup(app):
 }
 
 html_static_path = ["_static"]
-
-html_css_files = [
-    "custom.css",
-]
+html_css_files = ["custom.css"]
+html_js_files = ["matomo.js"]
 
 html_context = {
     "default_mode": "light",
 }
+
+# Add-on to insert the Matomo tracker
+templates_path = ['_templates']

docs/development/dev_howto.rst

@@ -70,9 +70,12 @@ Notes:
   Gammapy names defined here, to the names used in the formats.
   Of course, where formats are not set in stone yet, we advocate and encourage
   the use of the names chosen here.
-* Finally, we realise that eventually probably CTA will define this, and Gammapy
-  is only a prototype. So if CTA chooses something else, probably we will follow
-  suite and do one more backward-incompatible change at some point to align with CTA.
+* Finally, CTAO has proposed a full data model associated to the needed quantities. And
+  the community is working to create a data format for very-high-energy data produced by gamma-ray
+  and neutrino experiments within the open initiative `Very-high-energy Open Data Format`_. This format
+  aims to respect the CTAO data model, to respect the `FAIR principles`_ and to follow as much as
+  possible the `IVOA`_ recommendations. In order to handle past, current and old formats,
+  Gammapy should follow the `FAIR4RS principles`_ by proposing a user-friendly interface.
 
 Clobber or overwrite?
 +++++++++++++++++++++

docs/development/doc_howto.rst

@@ -144,7 +144,7 @@ following command.
 
     pytest --doctest-modules --ignore-glob=*/tests gammapy
 
-If you get a zsh error try using putting to ignore block inside quotes 
+If you get a zsh error try using putting to ignore block inside quotes
 
 .. code-block:: bash
 
@@ -157,6 +157,7 @@ The documentation built-in process uses the `sphinx-gallery <https://sphinx-gall
 extension to build galleries of illustrated examples on how to use Gammapy (i.e.
 :ref:`model-gallery`). The Python scripts used to produce the model gallery are placed in
 ``examples/models`` and ``examples/tutorials``. The configuration of the ``sphinx-gallery`` module is done in ``docs/conf.py``.
+The tutorials are order using a python dictionary stored in ``docs/sphinxext.py``.
 
 
 Choose a thumbnail and tooltip for the tutorial gallery
@@ -179,9 +180,9 @@ choose the thumbnail for the tutorial by adding a comment before the plot:
     plt.show()
 
 The example is taken from the `sphinx-gallery documentation <https://sphinx-gallery.github.io/stable/auto_examples/plot_4_choose_thumbnail.html>`__,
-please refer to it for more details. 
+please refer to it for more details.
 
-The tooltip is the text that appears when you hover over the thumbnail. It is taken from the first line 
+The tooltip is the text that appears when you hover over the thumbnail. It is taken from the first line
 of the docstring of the tutorial. You can change it by editing the docstring. See e.g.
 `Analysis 1 Tutorial <https://github.com/gammapy/gammapy/blob/main/examples/tutorials/starting/analysis_1.py#L5>`__.
 
@@ -194,7 +195,7 @@ Links in tutorials are just handled via normal RST syntax.
 Links to other tutorials
 ++++++++++++++++++++++++
 
-From docstrings and RST documentation files in Gammapy you can link to other tutorials 
+From docstrings and RST documentation files in Gammapy you can link to other tutorials
 and gallery examples by using RST syntax like this:
 
 .. code-block:: rst
@@ -217,7 +218,7 @@ To make a reference to a heading within an RST file, first you need to define an
     ==============
 
 
-The reference is the rendered as ``datasets``. 
+The reference is the rendered as ``datasets``.
 To link to this in the documentation you can use:
 
 .. code-block:: rst

docs/development/release.rst

@@ -90,9 +90,8 @@ Steps for the day to announce the release:
    (decide on a case by case basis, if it's relevant to the group of people):
 
     * https://groups.google.com/forum/#!forum/astropy-dev
-    * https://lists.nasa.gov/mailman/listinfo/open-gamma-ray-astro
-    * CTA DATA list ([email protected])
-    * hess-analysis
+    * CTAO AS WG list (cta-wg-as [at] cta-observatory [dot] org)
+    * hess-forum list (hess-forum [at] lsw.uni-heidelberg [dot] de)
 #. Make sure the release milestone and issue is closed on GitHub
 #. Update these release notes with any useful infos / steps that you learned
    while making the release (ideally try to script / automate the task or check,

docs/getting-started/index.rst

@@ -45,7 +45,9 @@ environment using either conda or mamba.** Here are two methods to quickly insta
         Update existing version? Working with virtual environments? Installing a specific version? Check the advanced
         installation page.
 
-        .. button-ref:: install
+        +++
+
+        .. button-ref:: installation
             :ref-type: ref
             :click-parent:
             :color: secondary
@@ -66,15 +68,15 @@ Tutorials Overview
     :link: ../tutorials/data/cta.html
 
 Gammapy can read and access data from multiple gamma-ray instruments. Data from
-Imaging Atmospheric Cherenkov Telescopes, such as `CTA`_, `H.E.S.S.`_, `MAGIC`_
+Imaging Atmospheric Cherenkov Telescopes, such as `CTAO`_, `H.E.S.S.`_, `MAGIC`_
 and `VERITAS`_, is typically accessed from the **event list data level**, called "DL3".
 This is most easily done using the `~gammapy.data.DataStore` class. In addition data
 can also be accessed from the **level of binned events and pre-reduced instrument response functions**,
 so called "DL4". This is typically the case for `Fermi-LAT`_ data or data from
 Water Cherenkov Observatories. This data can be read directly using the
 `~gammapy.maps.Map` and `~gammapy.irf.core.IRFMap` classes.
 
-:bdg-link-primary:`CTA data tutorial <../tutorials/data/cta.html>`
+:bdg-link-primary:`CTAO data tutorial <../tutorials/data/cta.html>`
 :bdg-link-primary:`HESS data tutorial <../tutorials/data/hess.html>`
 :bdg-link-primary:`Fermi-LAT data tutorial <../tutorials/data/fermi_lat.html>`
 

docs/getting-started/usage.rst

@@ -48,8 +48,7 @@ Gammapy is a Python package, so you can of course import and use it from Python:
     Type "help", "copyright", "credits" or "license" for more information.
     >>> from gammapy.stats import CashCountsStatistic
     >>> CashCountsStatistic(n_on=10, mu_bkg=4.2).sqrt_ts
-    2.397918129147546
-
+    np.float64(2.397918129147546)
 
 IPython
 -------

docs/index.rst

@@ -18,7 +18,7 @@ Gammapy
 
 
 Gammapy is a community-developed, open-source Python package for gamma-ray
-astronomy built on Numpy, Scipy and Astropy. **It is the core library for the** `CTA`_ **Science Tools**
+astronomy built on Numpy, Scipy and Astropy. **It is the core library for the** `CTAO`_ **Science Tools**
 but can also be used to analyse data from existing imaging atmospheric Cherenkov telescopes
 (IACTs), such as `H.E.S.S.`_, `MAGIC`_ and `VERITAS`_. It also provides some support
 for `Fermi-LAT`_ and `HAWC`_ data analysis.

docs/references.txt

@@ -59,7 +59,7 @@
 
 .. _Python for gamma-ray astronomy 2015: http://gammapy.github.io/PyGamma15/
 
-.. _CTA: https://www.cta-observatory.org/
+.. _CTAO: https://www.ctao.org/
 .. _H.E.S.S.: https://www.mpi-hd.mpg.de/hfm/HESS/
 .. _HAWC: https://www.hawc-observatory.org/
 .. _VERITAS: https://veritas.sao.arizona.edu/
@@ -69,6 +69,7 @@
 .. _FermiPy: https://github.com/fermiPy/fermipy
 .. _gadf: https://gamma-astro-data-formats.readthedocs.io/
 .. _Gamma Astro Data Formats: https://gamma-astro-data-formats.readthedocs.io/
+.. _Very-high-energy Open Data Format: https://vodf.readthedocs.io/en/latest/index.html
 
 .. _April 2016 IACT data meeting: https://github.com/open-gamma-ray-astro/2016-04_IACT_DL3_Meeting/
 
@@ -135,3 +136,7 @@
 .. _A Whirlwind tour of Python: https://nbviewer.org/github/jakevdp/WhirlwindTourOfPython/blob/master/Index.ipynb
 .. _Python data science handbook: https://jakevdp.github.io/PythonDataScienceHandbook/
 .. _Astropy Hands-On Tutorial: https://github.com/Asterics2020-Obelics/School2019/tree/master/astropy
+
+.. _FAIR principles: https://www.go-fair.org/fair-principles/
+.. _FAIR4RS principles: https://www.rd-alliance.org/group_output/fair-principles-for-research-software-fair4rs-principles/
+.. _IVOA: https://ivoa.net/