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

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

tardis/io/atom_data/base.py

@@ -448,8 +448,11 @@ def prepare_lines(self):
                 self.selected_atomic_numbers, level="atomic_number"
             )
         ]
-
-        self.lines = self.lines.sort_values(by="wavelength")
+        # see https://github.com/numpy/numpy/issues/27725#issuecomment-2465471648
+        # with kind="stable" the returned array will maintain the relative order of a values which compare as equal.
+        # this is important especially after numpy v2 release
+        # https://numpy.org/doc/stable/release/2.0.0-notes.html#minor-changes-in-behavior-of-sorting-functions
+        self.lines = self.lines.sort_values(by=["wavelength", "line_id"], kind="stable")
 
     def prepare_line_level_indexes(self):
         levels_index = pd.Series(

tardis/io/model/readers/generic_readers.py

@@ -48,8 +48,8 @@ def read_simple_ascii_density(
         fname,
         skip_header=1,
         names=("index", "velocity", "density"),
-        dtype=None,
-        encoding=None,
+        dtype=[('index', 'i8'), ('velocity', 'f8'), ('density', 'f8')], 
+        encoding='utf-8',
     )
     velocity = (data["velocity"] * u.km / u.s).to("cm/s")
     mean_density = (data["density"] * u.Unit("g/cm^3"))[1:]

tardis/transport/montecarlo/tests/test_rpacket_tracker.py

@@ -135,10 +135,9 @@ def test_rpacket_tracker_properties(expected, obtained, request):
 def test_boundary_interactions(rpacket_tracker, regression_data):
     no_of_packets = len(rpacket_tracker)
 
-    # Hard coding the number of columns
-    # Based on the largest size of boundary_interaction array (60)
+    max_boundary_interaction_size = max([tracker.boundary_interaction.size for tracker in rpacket_tracker])
     obtained_boundary_interaction = np.full(
-        (no_of_packets, 64),
+        (no_of_packets, max_boundary_interaction_size),
         [-1],
         dtype=rpacket_tracker[0].boundary_interaction.dtype,
     )