Merge remote-tracking branch 'origin/main' into psf_model_fixes

.github/workflows/ci.yml

@@ -99,7 +99,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.cache/ctapipe
-          key: ctapipe-test-data
+          key: ctapipe-test-data-desy
 
       - name: Prepare mamba installation
         if: matrix.install-method == 'mamba' &&  contains(github.event.pull_request.labels.*.name, 'documentation-only') == false
@@ -207,9 +207,5 @@ jobs:
           git describe --tags
           python -c 'import ctapipe; print(ctapipe.__version__)'
 
-      - name: Produce Changelog
-        run: |
-          towncrier build --yes
-
       - name: Build docs
         run: make doc

.github/workflows/sonar.yml

@@ -19,12 +19,26 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event.workflow_run.conclusion == 'success'
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout branch or tag
+        uses: actions/checkout@v4
+        if: github.event.workflow_run.event != 'pull_request'
         with:
           repository: ${{ github.event.workflow_run.head_repository.full_name }}
           ref: ${{ github.event.workflow_run.head_branch }}
           fetch-depth: 0
 
+      - name: Checkout Pull Request merge result
+        uses: actions/checkout@v4
+        if: github.event.workflow_run.event == 'pull_request'
+        with:
+          ref: refs/pull/${{ github.event.workflow_run.pull_requests[0].number }}/merge
+          fetch-depth: 0
+
+      - name: Git info
+        run: |
+          git status
+          git log -n 5 --oneline
+
       - name: 'Download code coverage'
         uses: actions/github-script@v7
         with:

.mailmap

@@ -99,3 +99,5 @@ Vadym Voitsekhovskyi <[email protected]> <[email protected]>
 Tjark Miener <[email protected]>
 
 Michael Punch <[email protected]> <[email protected]>
+
+Christian Arauner <[email protected]> <[email protected]>

.readthedocs.yaml

@@ -1,7 +1,7 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   apt_packages:
     - ffmpeg
     - graphviz
@@ -14,3 +14,6 @@ python:
       path: .
       extra_requirements:
         - docs
+
+sphinx:
+  configuration: docs/conf.py

AUTHORS

@@ -6,8 +6,8 @@ Jean Jacquemier <[email protected]>
 Tino Michael <[email protected]>
 Lukas Nickel <[email protected]>
 Noah Biederbeck <[email protected]>
-Tomas Bylund <[email protected]>
 Lukas Beiske <[email protected]>
+Tomas Bylund <[email protected]>
 Georg Schwefer <[email protected]>
 Jonas Hackfeld <[email protected]>
 Christoph Toennis <[email protected]>
@@ -43,19 +43,20 @@ Thomas Gasparetto <[email protected]>
 Ruben Lopez-Coto <[email protected]>
 Orel Gueta <[email protected]>
 Tristan Carel <[email protected]>
+Daniel Morcuende <[email protected]>
 Daniel Nieto <[email protected]>
 Michael Punch <[email protected]>
 Miguel Nievas <[email protected]>
 Arnau Aguasca-Cabot <[email protected]>
 Christophe COSSOU <[email protected]>
 Cyril Alispach <[email protected]>
-Daniel Morcuende <[email protected]>
 Julien Lefaucheur <[email protected]>
 Konstantin Pfrang <[email protected]>
 Moritz Hütten <[email protected]>
 Thomas Armstrong <[email protected]>
 Alice Donini <[email protected]>
 Andrés Baquero <[email protected]>
+Christian Arauner <[email protected]>
 David Landriu <[email protected]>
 Gernot Maier <[email protected]>
 Henning Ptaszyk <[email protected]>

CHANGES.rst

@@ -1,3 +1,59 @@
+ctapipe v0.23.2 (2025-01-21)
+============================
+
+Bug Fixes
+---------
+
+- Fill ``ctapipe.containers.SimulatedCameraContainer.true_image_sum`` in
+  ``HDF5EventSource``. Always returned default value of -1 before the fix. [`#2680 <https://github.com/cta-observatory/ctapipe/pull/2680>`__]
+
+Maintenance
+-----------
+
+- Add compatibility with numpy>=2.1. [`#2682 <https://github.com/cta-observatory/ctapipe/pull/2682>`__]
+
+
+ctapipe v0.23.1 (2024-12-04)
+============================
+
+Bug Fixes
+---------
+
+- Fix ``<reconstruction_property>_uncert`` calculations in ``ctapipe.reco.StereoMeanCombiner``.
+  Add helper functions for vectorized numpy calculations as new ``ctapipe.reco.telescope_event_handling`` module. [`#2658 <https://github.com/cta-observatory/ctapipe/pull/2658>`__]
+
+- Fix error in ``ctapipe-process`` when in the middle of a simtel file
+  that has true images available, a telescope event is missing the true image.
+  This can happen rarely in case a telescope triggered on pure NSB or
+  is oversaturated to the point where the true pe didn't fit into memory constraints.
+
+  The error was due to the ``DataWriter`` trying to write a ``None`` into an
+  already setup table for the true images.
+
+  The ``SimTelEventSource`` will now create an invalid true image filled with ``-1``
+  for such events. [`#2659 <https://github.com/cta-observatory/ctapipe/pull/2659>`__]
+
+- In ``SimTelEventSource``, ignore telescope events that did not take part in the stereo event trigger.
+  This happens rarely in Prod6 files in conjunction with the random mono trigger system.
+
+- Fix the order in which ``Tool`` runs final operations to fix an issue
+  of provenance not being correctly recorded. [`#2662 <https://github.com/cta-observatory/ctapipe/pull/2662>`__]
+
+- Fix data type of ``tel_id`` in the output of ``SubarrayDescription.to_table``
+
+- Fixed a bug where if a configuration file with unknown file extension was passed
+  to a tool, e.g. ``--config myconf.conf`` instead of ``--config myconf.yaml``, it
+  was silently ignored, despite an info log saying "Loading config file
+  myconf.conf". Configuration files must now have one of the following extensions
+  to be recognized: yml, yaml, toml, json, py. If not a ``ToolConfigurationError``
+  is raised. [`#2666 <https://github.com/cta-observatory/ctapipe/pull/2666>`__]
+
+Maintenance
+-----------
+
+- Add support for astropy 7.0. [`#2639 <https://github.com/cta-observatory/ctapipe/pull/2639>`__]
+- Change data server for test datasets from in2p3 to DESY hosted server. [`#2664 <https://github.com/cta-observatory/ctapipe/pull/2664>`__]
+
 ctapipe v0.23.0 (2024-11-18)
 ============================
 

README.rst

@@ -2,14 +2,14 @@
  ctapipe |pypi| |conda| |doilatest| |ci| |sonarqube_coverage| |sonarqube_quality|
 ==================================================================================
 
-.. |ci| image:: https://github.com/cta-observatory/ctapipe/workflows/CI/badge.svg?branch=main
-    :target: https://github.com/cta-observatory/ctapipe/actions?query=workflow%3ACI+branch%3Amain
+.. |ci| image:: https://github.com/cta-observatory/ctapipe/actions/workflows/ci.yml/badge.svg?branch=main
+    :target: https://github.com/cta-observatory/ctapipe/actions/workflows/ci.yml
     :alt: Test Status
 .. |sonarqube_quality| image:: https://sonar-cta-dpps.zeuthen.desy.de/api/project_badges/measure?project=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs&metric=alert_status&token=sqb_a533204f382b350568e922385cab7c2394587458
     :target: https://sonar-cta-dpps.zeuthen.desy.de/dashboard?id=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs
     :alt: sonarqube quality gate
 .. |sonarqube_coverage| image:: https://sonar-cta-dpps.zeuthen.desy.de/api/project_badges/measure?project=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs&metric=coverage&token=sqb_a533204f382b350568e922385cab7c2394587458
-    :target: https://sonar-cta-dpps.zeuthen.desy.de/api/project_badges/measure?project=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs&metric=coverage&token=sqb_a533204f382b350568e922385cab7c2394587458)](https://sonar-cta-dpps.zeuthen.desy.de/dashboard?id=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs
+    :target: https://sonar-cta-dpps.zeuthen.desy.de/component_measures?metric=coverage&selected=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs%3Asrc%2Fctapipe&view=treemap&id=cta-observatory_ctapipe_AY52EYhuvuGcMFidNyUs
     :alt: sonarqube code coverage
 .. |conda| image:: https://anaconda.org/conda-forge/ctapipe/badges/version.svg
   :target: https://anaconda.org/conda-forge/ctapipe

docs/_static/switcher.json

@@ -10,9 +10,9 @@
     "url": "https://ctapipe.readthedocs.io/en/stable/"
   },
   {
-    "name": "v0.23.0",
-    "version": "v0.23.0",
-    "url": "https://ctapipe.readthedocs.io/en/v0.23.0/"
+    "name": "v0.23.2",
+    "version": "v0.23.2",
+    "url": "https://ctapipe.readthedocs.io/en/v0.23.2/"
   },
   {
     "name": "v0.22.0",

docs/changelog.rst

@@ -2,4 +2,8 @@
 Change Log
 **********
 
-.. include:: ../CHANGES.rst
+
+.. changelog::
+   :towncrier: ../
+   :changelog_file: ../CHANGES.rst
+   :towncrier-skip-if-empty:

docs/conf.py

@@ -60,6 +60,7 @@
     "sphinx_design",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinx_gallery.gen_gallery",
+    "sphinx_changelog",
 ]
 
 

docs/developer-guide/maintainer-info.rst

@@ -37,30 +37,31 @@ The docs are automatically built and deployed using readthedocs.
 How To Make a Release?
 ======================
 
-1. Open a new pull request to prepare the release.
+#. Open a new pull request to prepare the release.
    This should be the last pull request to be merged before making the actual release.
 
-   Run ``towncrier`` in to render the changelog:
+   #. Run ``towncrier`` to render the changelog:
 
-   .. code-block:: console
+      .. code-block:: console
 
-      $ git fetch
-      $ git switch -c prepare_<VERSION NUMBER> origin/main
-      $ towncrier build --version=<VERSION NUMBER>
+         $ git fetch
+         $ git switch -c prepare_<VERSION NUMBER> origin/main
+         $ towncrier build --version=<VERSION NUMBER>
 
-   Add the planned new version to the ``docs/_static/switcher.json`` file, so it will be
-   available from the version dropdown once the documentation is built.
+   #. Add the planned new version to the ``docs/_static/switcher.json`` file, so it will be
+      available from the version dropdown once the documentation is built.
 
-   Update the ``AUTHORS`` file using the following command:
+   #. Update the ``AUTHORS`` file using the following command:
 
-   .. code-block:: console
+      .. code-block:: console
 
-      $ bash -c "git shortlog -sne | grep -v dependabot | sed -E 's/^\s+[0-9]+\s+//' > AUTHORS"
+         $ bash -c "git shortlog -sne | grep -v dependabot | sed -E 's/^\s+[0-9]+\s+//' > AUTHORS"
 
-2. Create a new github release, a good starting point should already be made by the
-   release drafter plugin.
+#. Create a new GitHub release.
+   A good starting point should already be made by the release drafter plugin.
 
-3. The PyPI upload will be done automatically by Github Actions.
+#. The PyPI upload will be done automatically by GitHub Actions.
 
-4. conda packages are built by conda-forge, the recipe is maintained here: https://github.com/conda-forge/ctapipe-feedstock/
-   A pull request to update the recipe should be opened automatically by a conda-forge bot when a new version is published to PyPi. This can take a couple of hours.
+#. conda packages are built by conda-forge, the recipe is maintained here: https://github.com/conda-forge/ctapipe-feedstock/.
+   A pull request to update the recipe should be opened automatically by a conda-forge bot when a new version is published to PyPI. This can take a couple of hours.
+   You can make it manually to speed things up.

docs/developer-guide/style-guide.rst

@@ -23,7 +23,7 @@ All functions, classes, and modules should contain appropriate API
 documentation in their *docstrings*.  The *docstrings* should be
 written in ReStructuredText format (same as the Sphinx high-level
 documentation), and should follow the `NumPy Docstring Standards
-<https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_
+<https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard>`_
 
 Documentation for all algorithms should contain citations to external
 works, which should be collected in ``bibliography.rst``. An example of

docs/references.bib

@@ -156,3 +156,17 @@ @manual{ctao-software-standards
   institution={CTAO},
   url={https://redmine.cta-observatory.org/dmsf/files/8628/view},
 }
+
+@article{lst1-crab-paper,
+  doi = {10.3847/1538-4357/ace89d},
+  url = {https://dx.doi.org/10.3847/1538-4357/ace89d},
+  year = {2023},
+  month = {oct},
+  publisher = {The American Astronomical Society},
+  volume = {956},
+  number = {2},
+  pages = {80},
+  author = {LST},
+  title = {Observations of the Crab Nebula and Pulsar with the Large-sized Telescope Prototype of the Cherenkov Telescope Array},
+  journal = {The Astrophysical Journal},
+}

environment.yml

@@ -40,6 +40,7 @@ dependencies:
   - pydata-sphinx-theme
   - sphinx-design
   - sphinxcontrib-bibtex
+  - sphinx_changelog
   - tomli
   - towncrier
   - tqdm

pyproject.toml

@@ -88,6 +88,7 @@ docs = [
     "sphinx-gallery >= 0.16.0",
     "sphinx_automodapi",
     "sphinxcontrib-bibtex",
+    "sphinx-changelog",
     "tomli; python_version < '3.11'",
 ]
 

src/ctapipe/calib/camera/calibrator.py

@@ -204,7 +204,7 @@ def _calibrate_dl0(self, event, tel_id):
 
         dl0_pixel_status = r1.pixel_status.copy()
         # set dvr pixel bit in pixel_status for pixels kept by DVR
-        dl0_pixel_status[signal_pixels] |= PixelStatus.DVR_STORED_AS_SIGNAL
+        dl0_pixel_status[signal_pixels] |= np.uint8(PixelStatus.DVR_STORED_AS_SIGNAL)
         # unset dvr bits for removed pixels
         dl0_pixel_status[~signal_pixels] &= ~np.uint8(PixelStatus.DVR_STATUS)
 

src/ctapipe/coordinates/tests/test_impact_distance.py

@@ -75,15 +75,15 @@ def test_shower_impact_distance(reference_location):
     assert np.allclose(impact_distances, [0, 1, 2] * u.m)
 
     # alt=0  az=0 should be aligned to x-axis (north in ground frame)
-    # therefore the distances should also be just the y-offset of the telecope
+    # therefore the distances should also be just the y-offset of the telescope
     shower_geom = ReconstructedGeometryContainer(
         core_x=0 * u.m, core_y=0 * u.m, alt=0 * u.deg, az=0 * u.deg
     )
     impact_distances = shower_impact_distance(shower_geom=shower_geom, subarray=sub)
     assert np.allclose(impact_distances, [0, 1, 2] * u.m)
 
     # alt=0  az=90 should be aligned to y-axis (east in ground frame)
-    # therefore the distances should also be just the x-offset of the telecope
+    # therefore the distances should also be just the x-offset of the telescope
     shower_geom = ReconstructedGeometryContainer(
         core_x=0 * u.m, core_y=0 * u.m, alt=0 * u.deg, az=90 * u.deg
     )