Make file continuum opacities optional (#197)

* fix benchmarks

* change to use mamba and move back to tardis_env3.yml

* use conda environment

* stop densities from being calculated if not requested

* remove benchmarks files from pr

* remove benchmarks config

* fix tests to use specifications from config

* atom data cleanup

* remove deepcopy import

stardis/conftest.py

@@ -38,6 +38,16 @@ def example_kurucz_atomic_data():
     return AtomData.from_hdf("kurucz_cd23_chianti_H_He.h5")
 
 
+@pytest.fixture(scope="session")
+def example_kurucz_atomic_data_broadening():
+    return AtomData.from_hdf("kurucz_cd23_chianti_H_He.h5")
+
+
+@pytest.fixture(scope="session")
+def example_kurucz_atomic_data_parllel():
+    return AtomData.from_hdf("kurucz_cd23_chianti_H_He.h5")
+
+
 @pytest.fixture(scope="session")
 def example_config():
     config_dict = validate_yaml(EXAMPLE_CONF_PATH, schemapath=SCHEMA_PATH)
@@ -93,6 +103,64 @@ def example_stellar_plasma(
     )
 
 
+@pytest.fixture(scope="session")
+def example_stellar_plasma_parallel(
+    example_stellar_model, example_kurucz_atomic_data_parallel, example_config_parallel
+):
+    example_kurucz_atomic_data_parallel.prepare_atom_data(
+        np.arange(
+            1,
+            np.min(
+                [
+                    len(
+                        example_stellar_model.composition.elemental_mass_fraction.columns.tolist()
+                    ),
+                    example_config_parallel.model.final_atomic_number,
+                ]
+            )
+            + 1,
+        ),
+        line_interaction_type="macroatom",
+        nlte_species=[],
+        continuum_interaction_species=[],
+    )
+    return create_stellar_plasma(
+        example_stellar_model,
+        example_kurucz_atomic_data_parallel,
+        example_config_parallel,
+    )
+
+
+@pytest.fixture(scope="session")
+def example_stellar_plasma_broadening(
+    example_stellar_model,
+    example_kurucz_atomic_data_broadening,
+    example_config_broadening,
+):
+    example_kurucz_atomic_data_broadening.prepare_atom_data(
+        np.arange(
+            1,
+            np.min(
+                [
+                    len(
+                        example_stellar_model.composition.elemental_mass_fraction.columns.tolist()
+                    ),
+                    example_config_broadening.model.final_atomic_number,
+                ]
+            )
+            + 1,
+        ),
+        line_interaction_type="macroatom",
+        nlte_species=[],
+        continuum_interaction_species=[],
+    )
+    return create_stellar_plasma(
+        example_stellar_model,
+        example_kurucz_atomic_data_broadening,
+        example_config_broadening,
+    )
+
+
 @pytest.fixture(scope="session")
 def example_stellar_radiation_field(
     example_stellar_model, example_config, example_tracing_nus, example_stellar_plasma
@@ -121,14 +189,14 @@ def example_stellar_radiation_field_broadening(
     example_stellar_model,
     example_config_broadening,
     example_tracing_nus,
-    example_stellar_plasma,
+    example_stellar_plasma_broadening,
 ):
     stellar_radiation_field = RadiationField(
         example_tracing_nus, blackbody_flux_at_nu, example_stellar_model
     )
 
     calc_alphas(
-        stellar_plasma=example_stellar_plasma,
+        stellar_plasma=example_stellar_plasma_broadening,
         stellar_model=example_stellar_model,
         stellar_radiation_field=stellar_radiation_field,
         opacity_config=example_config_broadening.opacity,
@@ -147,14 +215,14 @@ def example_stellar_radiation_field_parallel(
     example_stellar_model,
     example_config_parallel,
     example_tracing_nus,
-    example_stellar_plasma,
+    example_stellar_plasma_broadening,
 ):
     stellar_radiation_field = RadiationField(
         example_tracing_nus, blackbody_flux_at_nu, example_stellar_model
     )
 
     calc_alphas(
-        stellar_plasma=example_stellar_plasma,
+        stellar_plasma=example_stellar_plasma_broadening,
         stellar_model=example_stellar_model,
         stellar_radiation_field=stellar_radiation_field,
         opacity_config=example_config_parallel.opacity,

stardis/plasma/base.py

@@ -526,9 +526,12 @@ def create_stellar_plasma(
     )
     plasma_modules += helium_lte_properties
 
-    plasma_modules.append(HMinusDensity)
-    plasma_modules.append(H2Density)
-    plasma_modules.append(H2PlusDensity)
+    if hasattr(config.opacity.file, "Hminus_bf"):
+        plasma_modules.append(HMinusDensity)
+    if hasattr(config.opacity.file, "H2minus_bf"):
+        plasma_modules.append(H2Density)
+    if hasattr(config.opacity.file, "H2plus_bf"):
+        plasma_modules.append(H2PlusDensity)
 
     if config.opacity.line.vald_linelist.use_linelist:
         if config.opacity.line.vald_linelist.shortlist:

stardis/radiation_field/opacities/opacities_solvers/util.py

@@ -31,7 +31,9 @@ def sigma_file(tracing_lambdas, temperatures, fpath, opacity_source=None):
     if (
         opacity_source == "H2plus_bf"
     ):  # This section specifically ingests the Stancil 1994 h2_plus_bf_S1994.dat table found in data.
-        h2_plus_bf_table = pd.read_csv(fpath, delimiter="\s+", index_col=0, comment="#")
+        h2_plus_bf_table = pd.read_csv(
+            fpath, delimiter=r"\s+", index_col=0, comment="#"
+        )
         h2_plus_bf_table.replace({"-": "e-"}, regex=True, inplace=True)
         h2_plus_bf_table = h2_plus_bf_table.astype(float)
         file_wavelengths = (h2_plus_bf_table.index.values * u.nm).to(u.AA).value
@@ -53,7 +55,7 @@ def sigma_file(tracing_lambdas, temperatures, fpath, opacity_source=None):
     elif (
         opacity_source == "Hminus_ff"
     ):  # This section specifically ingests the Bell and Berrington 1987 h_minus_ff_B1987.dat table found in data.
-        h_minus_ff_table = pd.read_csv(fpath, delimiter="\s+", comment="#")
+        h_minus_ff_table = pd.read_csv(fpath, delimiter=r"\s+", comment="#")
         h_minus_ff_table.columns = h_minus_ff_table.columns.str.strip(",")
 
         file_wavelengths = h_minus_ff_table[h_minus_ff_table.columns[0]].values

stardis/tests/stardis_test_config_parallel.yml

@@ -1,5 +1,5 @@
 stardis_config_version: 1.0
-n_threads: -99
+n_threads: 0
 atom_data: kurucz_cd23_chianti_H_He.h5
 model:
     type: marcs