atharva-2001 · atharva-2001 · Jan 6, 2025 · Jan 8, 2025 · Jan 9, 2025 · Dec 30, 2024
diff --git a/.github/workflows/release.yml b/.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

diff --git a/.mailmap b/.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]>

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,8 @@
 ## Changelog
 
-### release-2024.12.29 (2024/12/28 20:05)
+### release-2025.01.05 (2025/01/04 20:05)
+- [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)

diff --git a/CITATION.cff b/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 v2024.12.29'
-doi: 10.5281/zenodo.14567778
+title: 'tardis-sn/tardis: TARDIS v2025.01.05'
+doi: 10.5281/zenodo.14600165
 # 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-2024.12.29
-date-released: 2024-12-29
+version: release-2025.01.05
+date-released: 2025-01-05
 repository-code: https://github.com/tardis-sn/tardis
 license: cc-by-4.0
diff --git a/README.rst b/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_14567778
+.. |CITATION| replace:: kerzendorf_2025_14600165
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14567778-blue
-                 :target: https://doi.org/10.5281/zenodo.14567778
+.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14600165-blue
+                 :target: https://doi.org/10.5281/zenodo.14600165
 
 .. code-block:: bibtex
 
-    @software{kerzendorf_2024_14567778,
+    @software{kerzendorf_2025_14600165,
       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 v2024.12.29},
-      month        = dec,
-      year         = 2024,
+      title        = {tardis-sn/tardis: TARDIS v2025.01.05},
+      month        = jan,
+      year         = 2025,
       publisher    = {Zenodo},
-      version      = {release-2024.12.29},
-      doi          = {10.5281/zenodo.14567778},
-      url          = {https://doi.org/10.5281/zenodo.14567778},
+      version      = {release-2025.01.05},
+      doi          = {10.5281/zenodo.14600165},
+      url          = {https://doi.org/10.5281/zenodo.14600165},
     }
 
 *******

diff --git a/docs/resources/credits.rst b/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_14567778
+.. |CITATION| replace:: kerzendorf_2025_14600165
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14567778-blue
-                 :target: https://doi.org/10.5281/zenodo.14567778
+.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.14600165-blue
+                 :target: https://doi.org/10.5281/zenodo.14600165
 
 .. code-block:: bibtex
 
-    @software{kerzendorf_2024_14567778,
+    @software{kerzendorf_2025_14600165,
       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 v2024.12.29},
-      month        = dec,
-      year         = 2024,
+      title        = {tardis-sn/tardis: TARDIS v2025.01.05},
+      month        = jan,
+      year         = 2025,
       publisher    = {Zenodo},
-      version      = {release-2024.12.29},
-      doi          = {10.5281/zenodo.14567778},
-      url          = {https://doi.org/10.5281/zenodo.14567778},
+      version      = {release-2025.01.05},
+      doi          = {10.5281/zenodo.14600165},
+      url          = {https://doi.org/10.5281/zenodo.14600165},
     }
 
diff --git a/docs/tardis_example.yml b/docs/tardis_example.yml
@@ -54,4 +54,4 @@ montecarlo:
 spectrum:
   start: 500 angstrom
   stop: 20000 angstrom
-  num: 10000
+  num: 10000
diff --git a/docs/workflows/luminosity.npy b/docs/workflows/luminosity.npy
diff --git a/docs/workflows/luminosity_integrated.npy b/docs/workflows/luminosity_integrated.npy
diff --git a/docs/workflows/luminosity_virtual.npy b/docs/workflows/luminosity_virtual.npy
diff --git a/docs/workflows/standard_workflow.ipynb b/docs/workflows/standard_workflow.ipynb
@@ -25,7 +25,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow = StandardTARDISWorkflow(config, show_convergence_plots=True,show_progress_bars=True,convergence_plots_kwargs={\"export_convergence_plots\":True})"
+    "workflow = StandardTARDISWorkflow(config, show_convergence_plots=False,show_progress_bars=False,convergence_plots_kwargs={\"export_convergence_plots\":True})"
    ]
   },
   {
@@ -37,6 +37,18 @@
     "workflow.run()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "np.save('luminosity.npy',workflow.spectrum_solver.spectrum_real_packets.luminosity.value)\n",
+    "np.save('luminosity_virtual.npy',workflow.spectrum_solver.spectrum_virtual_packets.luminosity.value)\n",
+    "np.save('luminosity_integrated.npy',workflow.spectrum_solver.spectrum_integrated.luminosity.value)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,

diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py
@@ -449,7 +449,8 @@ def prepare_lines(self):
             )
         ]
 
-        self.lines = self.lines.sort_values(by="wavelength")
+        # self.lines = self.lines.sort_values(by="wavelength")
+        self.lines = self.lines.sort_values(by=["wavelength"], kind="mergesort")
 
     def prepare_line_level_indexes(self):
         levels_index = pd.Series(

diff --git a/tardis/io/model/parse_radiation_field_configuration.py b/tardis/io/model/parse_radiation_field_configuration.py
@@ -8,6 +8,7 @@
     parse_structure_from_config,
 )
 from tardis.plasma.radiation_field import DilutePlanckianRadiationField
+from tardis.radiation_field.validate_radiation_field import validate_radiative_temperature
 
 logger = logging.getLogger(__name__)
 
@@ -113,12 +114,7 @@ def parse_radiation_field_state_from_csvy(
             geometry, packet_source
         )
 
-    if np.any(t_radiative < 1000 * u.K):
-        logging.critical(
-            "Radiative temperature is too low in some of the shells, temperatures below 1000K "
-            f"(e.g., T_rad = {t_radiative[np.argmin(t_radiative)]} in shell {np.argmin(t_radiative)} in your model) "
-            "are not accurately handled by TARDIS.",
-        )
+    validate_radiative_temperature(t_radiative)
 
     if hasattr(csvy_model_data, "columns") and (
         "dilution_factor" in csvy_model_data.columns

diff --git a/tardis/io/model/readers/generic_readers.py b/tardis/io/model/readers/generic_readers.py
@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 from astropy import units as u
-from numpy import recfromtxt
+from numpy import genfromtxt
 from radioactivedecay import Nuclide
 from radioactivedecay.utils import Z_DICT, elem_to_Z
 
@@ -44,12 +44,13 @@ def read_simple_ascii_density(
         time_of_model_string = fh.readline().strip()
         time_of_model = parse_quantity(time_of_model_string)
 
-    data = recfromtxt(
-        fname,
-        skip_header=1,
-        names=("index", "velocity", "density"),
-        dtype=(int, float, float),
-    )
+    data = genfromtxt(
+            fname,
+            skip_header=1,
+            names=("index", "velocity", "density"),
+            encoding='utf-8',
+        )
+    np.savetxt("data.txt", data)
     velocity = (data["velocity"] * u.km / u.s).to("cm/s")
     mean_density = (data["density"] * u.Unit("g/cm^3"))[1:]
 

diff --git a/tardis/radiation_field/validate_radiation_field.py b/tardis/radiation_field/validate_radiation_field.py
@@ -0,0 +1,31 @@
+import logging
+import numpy as np
+from astropy import units as u
+
+logger = logging.getLogger(__name__)
+
+def validate_radiative_temperature(t_radiative):
+    """
+    Validates the radiative temperature to ensure it is physically reasonable.
+
+    Parameters
+    ----------
+    t_radiative : Quantity
+        The radiative temperature array.
+
+    Raises
+    ------
+    ValueError
+        If any radiative temperature is below 1000 K.
+    """
+    if np.any(t_radiative < 1000 * u.K):
+        min_t_rad = t_radiative[np.argmin(t_radiative)]
+        min_shell = np.argmin(t_radiative)
+        logging.critical(
+            "Radiative temperature is too low in some of the shells, temperatures below 1000K "
+            f"(e.g., T_rad = {min_t_rad} in shell {min_shell} in your model) "
+            "are not accurately handled by TARDIS."
+        )
+        raise ValueError(
+            f"Radiative temperature below 1000 K detected: T_rad = {min_t_rad} in shell {min_shell}."
+        )
diff --git a/tardis/transport/montecarlo/tests/test_rpacket_tracker.py b/tardis/transport/montecarlo/tests/test_rpacket_tracker.py
@@ -138,7 +138,7 @@ def test_boundary_interactions(rpacket_tracker, regression_data):
     # Hard coding the number of columns
     # Based on the largest size of boundary_interaction array (60)
     obtained_boundary_interaction = np.full(
-        (no_of_packets, 64),
+        (no_of_packets, 77),
         [-1],
         dtype=rpacket_tracker[0].boundary_interaction.dtype,
     )

diff --git a/tardis/visualization/tools/convergence_plot.py b/tardis/visualization/tools/convergence_plot.py
@@ -16,12 +16,12 @@
 # Added the below as a (temporary) workaround to the latex
 # labels on the convergence plots not rendering correctly.
 import plotly
-from IPython.display import display, HTML
+# from IPython.display import display, HTML
 
-plotly.offline.init_notebook_mode()
-display(HTML(
-    '<script type="text/javascript" async src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_SVG"></script>'
-))
+# plotly.offline.init_notebook_mode()
+# display(HTML(
+#     '<script type="text/javascript" async src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_SVG"></script>'
+# ))
 
 
 def transition_colors(length, name="jet"):

diff --git a/tardis/workflows/standard_tardis_workflow.py b/tardis/workflows/standard_tardis_workflow.py
@@ -166,7 +166,7 @@ def get_convergence_estimates(self, transport_state):
                 "Absorbed": [absorbed_luminosity.value, "value"],
                 "Requested": [self.luminosity_requested.value, "value"],
             }
-        self.update_convergence_plot_data(plot_data)
+            self.update_convergence_plot_data(plot_data)
 
         logger.info(
             f"\n\tLuminosity emitted   = {emitted_luminosity:.3e}\n"

diff --git a/tardis/workflows/standard_workflow_runnner.py b/tardis/workflows/standard_workflow_runnner.py
@@ -0,0 +1,35 @@
+import os
+# import sys
+# print(f"Working Directory: {os.getcwd()}")
+# print(f"PYTHONPATH: {sys.path}")
+# print(f"Environment: {dict(os.environ)}")
+import time
+# time.sleep(10)
+
+from tardis.io.configuration.config_reader import Configuration
+from tardis.workflows.standard_tardis_workflow import StandardTARDISWorkflow
+
+
+yaml_file_path = '/Users/atharva/workspace/code/tardis-main/tardis/docs/tardis_example.yml'
+print(f"Current working directory: {os.getcwd()}")
+print(f"About to load YAML config from: {yaml_file_path}")  # If yaml_file_path exists
+
+
+# Create configuration from YAML file
+config = Configuration.from_yaml(
+    yaml_file_path
+)
+
+# Set debug configuration
+config.debug = {}
+config.debug.log_level = "WARNING"
+config.debug.specific_log_level = "WARNING"
+
+# Initialize and run workflow
+workflow = StandardTARDISWorkflow(
+    config,
+    show_convergence_plots=False,
+    show_progress_bars=False,
+    convergence_plots_kwargs={"export_convergence_plots": True}
+)
+workflow.run()