feat: merge numpy_v2_2 into logger_widget_panel (squashed)

.github/actions/setup_lfs/action.yml

@@ -11,11 +11,12 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - name: Clone tardis-sn/tardis-regression-data
+    - name: Clone atharva-2001/tardis-regression-data
       uses: actions/checkout@v4
       with:
-        repository: ${{ inputs.regression-data-repo }}
+        repository: atharva-2001/tardis-regression-data
         path: tardis-regression-data
+        ref: numpy_v2_2
 
     - name: Create LFS file list
       run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id

.github/workflows/release.yml

@@ -119,7 +119,7 @@ jobs:
         
       - name: Generate and process changelog
         run: |
-          CHANGELOG=$(git cliff --config pyproject.toml --unreleased | sed -n '/^## Changelog/,$p' | grep -vE '^(ERROR|WARN)')
+          CHANGELOG=$(git cliff --config pyproject.toml --unreleased --tag ${{ env.NEW_TAG }}| sed -n '/^## Changelog/,$p' | grep -vE '^(ERROR|WARN)')
           echo "CHANGELOG<<EOF" >> $GITHUB_ENV
           echo "$CHANGELOG" >> $GITHUB_ENV
           echo "EOF" >> $GITHUB_ENV

.mailmap

@@ -215,6 +215,8 @@ Stuart Sim <[email protected]> ssim <[email protected]>
 Stuart Sim <[email protected]> Stuart Sim <[email protected]>
 Stuart Sim <[email protected]> Stuart Sim <[email protected]>
 
+Swayam Shah <[email protected]> Sonu0305 <[email protected]>
+
 TARDIS Bot <[email protected]>
 TARDIS Bot <[email protected]> tardis-bot <[email protected]>
 TARDIS Bot <[email protected]> TARDIS Bot <[email protected]>

CHANGELOG.md

@@ -1,6 +1,20 @@
 ## Changelog
 
-### release-2024.12.08 (2024/12/07 20:08)
+### release-2025.01.12 (2025/01/11 20:04)
+- [2925](https://github.com/tardis-sn/tardis/pull/2925) give tag in git cliff command (2925) (@KasukabeDefenceForce)
+- [2923](https://github.com/tardis-sn/tardis/pull/2923) Moves non-physical input check outsode I/O module (2923) (@Sonu0305)
+- [2924](https://github.com/tardis-sn/tardis/pull/2924) Post-release 2025.01.05 (2924) (@tardis-bot)
+### release-2025.01.05 (2024/12/30 01:37)
+- [2915](https://github.com/tardis-sn/tardis/pull/2915) Post-release 2024.12.29 (2915) (@tardis-bot)
+### release-2024.12.29 (2024/12/23 04:39)
+- [2909](https://github.com/tardis-sn/tardis/pull/2909) Post-release 2024.12.22 (2909) (@tardis-bot)
+### release-2024.12.22 (2024/12/16 10:05)
+- [2901](https://github.com/tardis-sn/tardis/pull/2901) Update test docs (2901) (@KasukabeDefenceForce)
+- [2905](https://github.com/tardis-sn/tardis/pull/2905) Post-release 2024.12.15 (2905) (@tardis-bot)
+### release-2024.12.15 (2024/12/09 10:05)
+- [2902](https://github.com/tardis-sn/tardis/pull/2902) Fix Benchmarks Workflow (2902) (@atharva-2001)
+- [2900](https://github.com/tardis-sn/tardis/pull/2900) Post-release 2024.12.08 (2900) (@tardis-bot)
+### release-2024.12.08 (2024/12/04 12:24)
 - [2898](https://github.com/tardis-sn/tardis/pull/2898) Remove "labeled" from tests workflow triggers (2898) (@KasukabeDefenceForce)
 - [2865](https://github.com/tardis-sn/tardis/pull/2865) Rates matrix solver (2865) (@andrewfullard)
 - [2874](https://github.com/tardis-sn/tardis/pull/2874) Remove tau sobolevs from plasma (2874) (@andrewfullard)

CITATION.cff

@@ -3,8 +3,8 @@
 cff-version: 1.0.3
 message: If you use this software, please cite it using these metadata.
 # FIXME title as repository name might not be the best name, please make human readable
-title: 'tardis-sn/tardis: TARDIS v2024.12.08'
-doi: 10.5281/zenodo.14300679
+title: 'tardis-sn/tardis: TARDIS v2025.01.12'
+doi: 10.5281/zenodo.14633332
 # FIXME splitting of full names is error prone, please check if given/family name are correct
 authors:
 - given-names: Wolfgang
@@ -347,7 +347,7 @@ authors:
 - given-names: Atharwa
   family-names: Kharkar
   affiliation:
-version: release-2024.12.08
-date-released: 2024-12-08
+version: release-2025.01.12
+date-released: 2025-01-12
 repository-code: https://github.com/tardis-sn/tardis
 license: cc-by-4.0

README.rst

@@ -110,14 +110,14 @@ The following BibTeX entries are needed for the references:
           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
-.. |CITATION| replace:: kerzendorf_2024_14300679
+.. |CITATION| replace:: kerzendorf_2025_14633332
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14300679-blue
-                 :target: https://doi.org/10.5281/zenodo.14300679
+.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14633332-blue
+                 :target: https://doi.org/10.5281/zenodo.14633332
 
 .. code-block:: bibtex
 
-    @software{kerzendorf_2024_14300679,
+    @software{kerzendorf_2025_14633332,
       author       = {Kerzendorf, Wolfgang and
                       Sim, Stuart and
                       Vogl, Christian and
@@ -225,13 +225,13 @@ The following BibTeX entries are needed for the references:
                       Nayak U, Ashwin and
                       Kumar, Atul and
                       Kharkar, Atharwa},
-      title        = {tardis-sn/tardis: TARDIS v2024.12.08},
-      month        = dec,
-      year         = 2024,
+      title        = {tardis-sn/tardis: TARDIS v2025.01.12},
+      month        = jan,
+      year         = 2025,
       publisher    = {Zenodo},
-      version      = {release-2024.12.08},
-      doi          = {10.5281/zenodo.14300679},
-      url          = {https://doi.org/10.5281/zenodo.14300679}
+      version      = {release-2025.01.12},
+      doi          = {10.5281/zenodo.14633332},
+      url          = {https://doi.org/10.5281/zenodo.14633332},
     }
 
 *******

conda-linux-64.lock

@@ -202,7 +202,6 @@ https://conda.anaconda.org/conda-forge/noarch/babel-2.14.0-pyhd8ed1ab_0.conda#96
 https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.12.3-pyha770c72_1.conda#d48f7e9fdec44baf6d1da416fe402b04
 https://conda.anaconda.org/conda-forge/noarch/bleach-6.1.0-pyhd8ed1ab_0.conda#0ed9d7c0e9afa7c025807a9a8136ea3e
 https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2#9b347a7ec10940d3f7941ff6c460b551
-https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f907bb958910dc404647326ca80c263e
 https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py312hf06ca03_0.conda#56b0ca764ce23cc54f3f7e2a7b970f6d
 https://conda.anaconda.org/conda-forge/noarch/comm-0.2.2-pyhd8ed1ab_1.conda#74673132601ec2b7fc592755605f4c1b
 https://conda.anaconda.org/conda-forge/noarch/commonmark-0.9.1-py_0.tar.bz2#6aa0173c14befcd577ded130cf6f22f5

docs/contributing/development/running_tests.rst

@@ -22,39 +22,38 @@ tests, you can run this with:
     > pytest tardis
 
 
-Running the more advanced unit tests requires TARDIS Reference data that can be
+Running the more advanced unit tests requires TARDIS Regression data that can be
 downloaded
-(`tardis-refdata <https://github.com/tardis-sn/tardis-refdata>`_).
+(`tardis-regression-data <https://github.com/tardis-sn/tardis-regression-data>`_).
 `Git LFS <https://www.atlassian.com/git/tutorials/git-lfs>`_ is used
-to download the large refdata files in the tardis-refdata repository.
+to download the large regression data files in the tardis-regression-data repository.
 
-However, it is not required to download the entire repository. Firstly it is
-important to identify the refdata files that are needed. Sometimes, it is possible
-that a preused fixture that is also being used in the current tests is using some
-refdata. So, it is advised to check for such cases beforehand.
-
-After identifying the refdata files to be used in the unit tests, those particular
-files can be downloaded using ``git lfs`` 
 
 .. code-block:: shell
 
-    > git lfs pull --include=filename
+    > git lfs pull
+
 
-It is important to maintain the same directory structure as the tardis-refdata repo
-i.e. the lfs files should be in the same directory tree exactly as in tardis-refdata
-repository.
+The ``tardis-regression-data`` repository should be located outside of the main ``tardis`` repository, rather than being nested within it.
+
+.. warning::
+    We have migrated from ``tardis-refdata`` to``tardis-regression-data``.
 
 Finally, the tests can be run using the following command
 
 .. code-block:: shell
 
-    > pytest tardis --tardis-refdata=/path/to/tardis-refdata/
+    > pytest tardis --tardis-regression-data=/path/to/tardis-regression-data/
 
 Or, to run tests for a particular file or directory
 
 .. code-block:: shell
 
-    > pytest tardis/path/to/test_file_or_directory --tardis-refdata=/path/to/tardis-refdata/
+    > pytest tardis/path/to/test_file_or_directory --tardis-regression-data=/path/to/tardis-regression-data/
+
+
+.. warning::
+    In some cases you might have to update the regression data. The steps to update the regression data are outlined in the :ref:`update regression-data`.
 
 .. warning::
     The `tests workflow <https://github.com/tardis-sn/tardis/blob/master/.github/workflows/tests.yml>`_ runs on 
@@ -74,36 +73,4 @@ You can generate Plasma Reference by the following command:
 .. code-block:: shell
 
     > pytest -rs tardis/plasma/tests/test_complete_plasmas.py 
-    --tardis-refdata="/path/to/tardis-refdata/" --generate-reference
-
-Running the Integration Tests
-=============================
-
-These tests require reference files against which the results of the various
-tardis runs are tested. So you first need to either download the current
-reference files (`here <https://github.com/tardis-sn/tardis-refdata>`_)
-or generate new ones.
-
-Both of these require a configuration file for the integration tests:
-
-.. literalinclude:: integration.yml
-    :language: yaml
-
-Inside the atomic data directory there needs to be atomic data for each of
-the setups that are provided in the ``test_integration`` folder.
-If no references are given, the first step is to generate them.
-The ``--less-packets`` option is useful for debugging purposes and will just
-use very few packets to generate the references and thus make the process much
-faster --- THIS IS ONLY FOR DEBUGGING PURPOSES. The ``-s`` option ensures that
-TARDIS prints out the progress:
-
-.. code-block:: shell
-
-    > pytest --integration=integration.yml -m integration --generate-reference --less-packets
-
-To run the test after having run the ``--generate-references``, all that is
-needed is:
-
-.. code-block:: shell
-
-    > pytest --integration=integration.yml -m integration --less-packets --remote-data
+    --tardis-regression-data="/path/to/tardis-regression-data/" --generate-reference

docs/io/output/how_to_rpacket_tracking.ipynb

@@ -72,9 +72,9 @@
     "```yaml\n",
     "... \n",
     "montecarlo:\n",
-    "...\n",
-    "tracking:\n",
-    "    track_rpacket: true\n",
+    "    ...\n",
+    "    tracking:\n",
+    "        track_rpacket: true\n",
     "```"
    ]
   },

docs/physics/setup/model.ipynb

@@ -81,7 +81,7 @@
    "id": "cee054e9",
    "metadata": {},
    "source": [
-    "In the cell below, we set up a model. We use the [specific structure](../../io/configuration/components/models/index.rst#specific-structure) where we supply $t_\\mathrm{explosion}$, the velocity of the inner and outer boundaries of the supernova (labeled `start` and `stop`), and the number of shells (labeled `num`). The shells are then evenly spaced between the inner and outer boundaries of the supernova. The time after the explosion, the inner and outer velocities, and the number of shells can be varied to get different shell structures. The `SimulationState` object stores information about the model in the following attributes: `velocity` shows the velocity of the shell boundaries, `v_inner` shows the velocities of the inner boundaries of each shell, `v_outer` shows the velocity of the outer boundaries of each shell, and `v_middle` shows the velocity of the middle of each shell. Similarly, `radius`, `r_inner`, `r_outer`, and `r_middle` show the radii of each shell boundary, the inner boundaries, the outer boundaries, and the middles of each shell, respectively. `v_boundary_inner` shows the velocity of the inner boundary of the computational domain, and `v_boundary_outer` shows the velocity of the outer boundary of the computational domain. Finally, `volume` shows the volume of each shell, calculated via the formula of the volume of a spherical shell: $V=\\frac{4}{3}\\pi (r_\\mathrm{outer}^3-r_\\mathrm{inner}^3)$."
+    "In the cell below, we set up a model. We use the [specific structure](../../io/configuration/components/models/index.rst#specific-structure) where we supply $t_\\mathrm{explosion}$, the velocity of the inner and outer boundaries of the supernova (labeled `start` and `stop`), and the number of shells (labeled `num`). The shells are then evenly spaced between the inner and outer boundaries of the supernova. The time after the explosion, the inner and outer velocities, and the number of shells can be varied to get different shell structures. The `SimulationState` object stores information about the model in the following attributes: `velocity` shows the velocity of the shell boundaries, `v_inner` shows the velocities of the inner boundaries of each shell, `v_outer` shows the velocity of the outer boundaries of each shell, and `v_middle` shows the velocity of the middle of each shell. Similarly, `radius`, `r_inner`, `r_outer`, and `r_middle` show the radii of each shell boundary, the inner boundaries, the outer boundaries, and the middles of each shell, respectively. `v_inner_boundary` shows the velocity of the inner boundary of the computational domain, and `v_outer_boundary` shows the velocity of the outer boundary of the computational domain. Finally, `volume` shows the volume of each shell, calculated via the formula of the volume of a spherical shell: $V=\\frac{4}{3}\\pi (r_\\mathrm{outer}^3-r_\\mathrm{inner}^3)$."
    ]
   },
   {
@@ -111,8 +111,8 @@
     "print('v_inner:\\n', shell_simulation_state.v_inner)\n",
     "print('v_outer:\\n', shell_simulation_state.v_outer)\n",
     "print('v_middle:\\n', shell_simulation_state.v_middle)\n",
-    "print('v_boundary_inner:\\n', shell_simulation_state.v_boundary_inner)\n",
-    "print('v_boundary_outer:\\n', shell_simulation_state.v_boundary_outer)\n",
+    "print('v_inner_boundary:\\n', shell_simulation_state.v_inner_boundary)\n",
+    "print('v_outer_boundary:\\n', shell_simulation_state.v_outer_boundary)\n",
     "print('radius:\\n', shell_simulation_state.radius)\n",
     "print('r_inner:\\n', shell_simulation_state.r_inner)\n",
     "print('r_outer:\\n', shell_simulation_state.r_outer)\n",
@@ -125,7 +125,7 @@
    "id": "1ee56110",
    "metadata": {},
    "source": [
-    "Notice that `radius = velocity*time_explosion`, and similarly for `r_inner`, `r_outer`, and `r_middle`. You can get the radius of the photosphere via `v_boundary_inner*time_explosion` and outer edge of the supernova via `v_boundary_outer*time_explosion`.\n",
+    "Notice that `radius = velocity*time_explosion`, and similarly for `r_inner`, `r_outer`, and `r_middle`. You can get the radius of the photosphere via `v_inner_boundary*time_explosion` and outer edge of the supernova via `v_boundary_outer*time_explosion`.\n",
     "\n",
     "<div class=\"alert alert-info\">\n",
     "    \n",

docs/quickstart.ipynb

@@ -17,7 +17,7 @@
     "\n",
     "## Atomic Data\n",
     "\n",
-    "We recommend using the [kurucz_cd23_chianti_H_He.h5](https://dev.azure.com/tardis-sn/TARDIS/_apis/git/repositories/tardis-refdata/items?path=atom_data/kurucz_cd23_chianti_H_He.h5&resolveLfs=true) dataset."
+    "We recommend using the [kurucz_cd23_chianti_H_He.h5](https://github.com/tardis-sn/tardis-regression-data/raw/main/atom_data/kurucz_cd23_chianti_H_He.h5) dataset."
    ]
   },
   {

docs/resources/credits.rst

@@ -74,14 +74,14 @@ The following BibTeX entries are needed for the references:
           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
-.. |CITATION| replace:: kerzendorf_2024_14300679
+.. |CITATION| replace:: kerzendorf_2025_14633332
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14300679-blue
-                 :target: https://doi.org/10.5281/zenodo.14300679
+.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14633332-blue
+                 :target: https://doi.org/10.5281/zenodo.14633332
 
 .. code-block:: bibtex
 
-    @software{kerzendorf_2024_14300679,
+    @software{kerzendorf_2025_14633332,
       author       = {Kerzendorf, Wolfgang and
                       Sim, Stuart and
                       Vogl, Christian and
@@ -189,12 +189,12 @@ The following BibTeX entries are needed for the references:
                       Nayak U, Ashwin and
                       Kumar, Atul and
                       Kharkar, Atharwa},
-      title        = {tardis-sn/tardis: TARDIS v2024.12.08},
-      month        = dec,
-      year         = 2024,
+      title        = {tardis-sn/tardis: TARDIS v2025.01.12},
+      month        = jan,
+      year         = 2025,
       publisher    = {Zenodo},
-      version      = {release-2024.12.08},
-      doi          = {10.5281/zenodo.14300679},
-      url          = {https://doi.org/10.5281/zenodo.14300679}
+      version      = {release-2025.01.12},
+      doi          = {10.5281/zenodo.14633332},
+      url          = {https://doi.org/10.5281/zenodo.14633332},
     }