Update to version of tardis with new atom data (#209)

* fix plasma

* use aug 25 release

.github/workflows/benchmarks.yml

@@ -1,7 +1,7 @@
 name: benchmarks
 
 env:
-  TARDIS_VER: release-2024.08.12 # master 
+  TARDIS_VER: release-2024.08.25 # master 
 
 on:
   push:

.github/workflows/build-docs.yml

@@ -46,7 +46,7 @@ jobs:
         id: install-tardis
         # shell: bash -l {0}
         run: |
-          pip install git+https://github.com/tardis-sn/[email protected].12
+          pip install git+https://github.com/tardis-sn/[email protected].25
         
       - name: Install STARDIS
         id: install-stardis

.github/workflows/tests.yml

@@ -65,7 +65,7 @@ jobs:
         id: install-tardis
         # shell: bash -l {0}
         run: |
-          pip install git+https://github.com/tardis-sn/[email protected].12
+          pip install git+https://github.com/tardis-sn/[email protected].25
           
       - name: Install STARDIS
         id: install-stardis

docs/index.rst

@@ -10,7 +10,7 @@ This is the documentation for STARDIS.
    Quickstart <quickstart/quickstart>
    Downloading and Installation <installation>
    Physics of STARDIS <physics/physics_of_stardis>
-   Example Notebooks <example_notebooks>
+   Example Notebooks <example_notebooks/rotation_broadening>
    Contributing <contributing>
    Bibliography <bibliography>
 

docs/installation.rst

@@ -25,7 +25,7 @@ the following in the terminal (replacing ``{platform}`` with
    $ wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-{platform}.lock
    $ conda create --name stardis --file conda-{platform}.lock
    $ conda activate stardis
-   $ pip install git+https://github.com/tardis-sn/[email protected].12
+   $ pip install git+https://github.com/tardis-sn/[email protected].25
 
 The third command (``conda activate stardis``) activates the
 environment, which is necessary to correctly install STARDIS using the directions below.
@@ -38,7 +38,7 @@ If you are using Mamba, the steps are similar:
    $ wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-{platform}.lock
    $ mamba create --name stardis --file conda-{platform}.lock
    $ mamba activate stardis
-   $ pip install git+https://github.com/tardis-sn/[email protected].12
+   $ pip install git+https://github.com/tardis-sn/[email protected].25
    
 Downloading and Installing STARDIS
 ----------------------------------

stardis/plasma/base.py

@@ -203,7 +203,9 @@ def calculate(
 
         points = len(t_electrons)
 
-        linelist = atomic_data.linelist.rename(columns={"ion_charge": "ion_number"})[
+        linelist = atomic_data.linelist_atoms.rename(
+            columns={"ion_charge": "ion_number"}
+        )[
             [
                 "atomic_number",
                 "ion_number",
@@ -341,7 +343,9 @@ def calculate(
         ###TODO: handle other broadening parameters
         points = len(t_electrons)
 
-        linelist = atomic_data.linelist.rename(columns={"ion_charge": "ion_number"})[
+        linelist = atomic_data.linelist_atoms.rename(
+            columns={"ion_charge": "ion_number"}
+        )[
             [
                 "atomic_number",
                 "ion_number",
@@ -538,7 +542,6 @@ def create_stellar_plasma(
     return BasePlasma(
         plasma_properties=plasma_modules,
         dilute_planckian_radiation_field=radiation_field,
-        abundance=stellar_model.composition.elemental_mass_fraction,
         atomic_data=atom_data,
         number_density=stellar_model.composition.elemental_number_density,
         link_t_rad_t_electron=1.0,

stardis_env3.yml

@@ -41,7 +41,7 @@ dependencies:
   - qgrid =1.3.1=pyhd8ed1ab_4 # qgrid-feedstock/issues/18
 
   - pip:
-      - git+https://github.com/tardis-sn/[email protected].12
+      - git+https://github.com/tardis-sn/[email protected].25
 
   # --- Packages not required for conda-forge recipe ---
 

stardis_env3_cuda.yml

@@ -46,7 +46,7 @@ dependencies:
   - cupy
 
   - pip:
-      - git+https://github.com/tardis-sn/[email protected].12
+      - git+https://github.com/tardis-sn/[email protected].25
 
   # --- Packages not required for conda-forge recipe ---