I/O Refactoring (#2652)

* Moves parse_input to IO and removes unused file

* Removes unused file and imports

* Separates parse_input into chunks

Also cleans up imports

* Deprecates old CMFGen reader and moves new one

* Fixes logging import

* Fixes import sorting

* Consistent file naming

* Consistent names and ordering for parsing functions

_from_config and _from_csvy to match typical class methods

Config first, CSVY second

* Abundances renamed to mass fractions in IO

With small extensions outside that area

* Pluralise

* Fixes mass fraction and density dimension mismatch for CSVY models

* Adds docstring

* black

* Adds dummy type variable to schema for convergence

Should fix read/write issue.

* Cleanup of structure config reading

Not really happy with it, but helps show some of the current problems with the config arrangement compared to the code

* Fixes error with density time point and black

* Fixes packet source re-init for custom sources

Also adjusts notebook to deal with quantity-based packet frequencies

* Resolve some escape sequence errors

* Plural mass fractions

* black

* Clarify docstrings

docs/io/optional/how_to_custom_source.ipynb

@@ -131,7 +131,6 @@
     "        truncation_frequency = (\n",
     "            u.Quantity(self.truncation_wavelength, u.Angstrom)\n",
     "            .to(u.Hz, equivalencies=u.spectral())\n",
-    "            .value\n",
     "        )\n",
     "\n",
     "        # Draw nus from blackbody distribution and reject based on truncation_frequency.\n",
@@ -220,7 +219,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

tardis/io/__init__.py

@@ -1,18 +1,3 @@
 """
-A collection of subpackages and submodules to handle input and output data. 
+A collection of subpackages and submodules to handle input and output data.
 """
-
-from tardis.io.configuration.config_internal import (
-    get_internal_configuration,
-    get_data_dir,
-)
-
-# readin model_data
-
-from tardis.io.model.readers.generic_readers import (
-    read_simple_ascii_abundances,
-)
-from tardis.io.model.readers.generic_readers import (
-    read_simple_ascii_density,
-)
-from tardis.io.model.readers.base import read_density_file

tardis/io/configuration/schemas/montecarlo_definitions.yml

@@ -55,6 +55,10 @@ definitions:
               description: specifies the threshold that is taken as convergence  (i.e.
                 0.05 means that the value does not change more than 5%)
               minimum: 0
+            type:
+              type: string
+              default: 'damped'
+              description: THIS IS A DUMMY VARIABLE DO NOT USE
         t_rad:
           type: object
           additionalProperties: false
@@ -69,6 +73,10 @@ definitions:
               description: specifies the threshold that is taken as convergence  (i.e.
                 0.05 means that the value does not change more than 5%)
               minimum: 0
+            type:
+              type: string
+              default: 'damped'
+              description: THIS IS A DUMMY VARIABLE DO NOT USE
           required:
           - threshold
         w:
@@ -85,6 +93,10 @@ definitions:
               description: specifies the threshold that is taken as convergence  (i.e.
                 0.05 means that the value does not change more than 5%)
               minimum: 0
+            type:
+              type: string
+              default: 'damped'
+              description: THIS IS A DUMMY VARIABLE DO NOT USE
           required:
           - threshold
         lock_t_inner_cycles:

tardis/io/model/__init__.py

@@ -1,4 +1,4 @@
 from tardis.io.model.readers.stella import read_stella_model
 
 # from tardis.io.model.stella import read_stella_model
-from tardis.io.model.cmfgen import read_cmfgen_model
+from tardis.io.model.readers.cmfgen import read_cmfgen_model