Added csvy parser

tardis/io/parsers/csvy.py

@@ -0,0 +1,84 @@
+import yaml
+import pandas as pd
+from tardis.io.util import YAMLLoader
+
+YAML_DELIMITER = '---'
+def load_csvy(fname):
+    """
+    Parameters
+    ----------
+
+    fname : string
+            Path to csvy file
+
+    Returns
+    -------
+    yaml_dict : dictionary
+                YAML part of the csvy file
+
+    data : pandas.dataframe
+           csv data from csvy file
+    """
+    with open(fname) as fh:
+        yaml_lines = []
+        yaml_end_ind = -1
+        for i, line in enumerate(fh):
+            if i == 0:
+                assert line.strip() == YAML_DELIMITER, 'First line of csvy file is not \'---\''
+            yaml_lines.append(line)
+            if i > 0 and line.strip() == YAML_DELIMITER:
+                yaml_end_ind = i
+                break
+        else:
+            raise ValueError('End %s not found'%(YAML_DELIMITER)) 
+        yaml_dict = yaml.load(''.join(yaml_lines[1:-1]), YAMLLoader)
+        try:
+            data = pd.read_csv(fname, skiprows=yaml_end_ind + 1)
+        except pd.io.common.EmptyDataError as e:
+            data = None
+
+    return yaml_dict, data
+
+def load_yaml_from_csvy(fname):
+    """
+    Parameters
+    ----------
+
+    fname : string
+            Path to csvy file
+
+    Returns
+    -------
+    yaml_dict : dictionary
+                YAML part of the csvy file
+    """
+    with open(fname) as fh:
+        yaml_lines = []
+        yaml_end_ind = -1
+        for i, line in enumerate(fh):
+            if i == 0:
+                assert line.strip() == YAML_DELIMITER, 'First line of csvy file is not \'---\''
+            yaml_lines.append(line)
+            if i > 0 and line.strip() == YAML_DELIMITER:
+                yaml_end_ind = i
+                break
+        else:
+            raise ValueError('End %s not found'%(YAML_DELIMITER)) 
+        yaml_dict = yaml.load(''.join(yaml_lines[1:-1]), YAMLLoader)
+    return yaml_dict
+
+def load_csv_from_csvy(fname):
+    """
+    Parameters
+    ----------
+
+    fname : string
+            Path to csvy file
+
+    Returns
+    -------
+    data : pandas.dataframe
+           csv data from csvy file
+    """
+    yaml_dict, data = load_csvy(fname)
+    return data

tardis/io/schemas/csvy_model.yml

@@ -0,0 +1,143 @@
+$schema: http://json-schema.org/draft-04/schema#
+type: object
+additionalProperties: false
+properties:
+  name: 
+    type: string
+    description: name of the model being run
+
+  description:
+    type: string
+    description: description of the model being run
+
+  tardis_model_config_version:
+    type: string
+    description: Version of the configuration file
+
+# datatype name used for consistency with astropy ecsv files.
+  datatype:
+    type: object
+    description: fields found in csv part of csvy file
+    additionalProperties: False
+    properties:
+      fields:
+        type: array
+
+  v_inner_boundary:
+    type: quantity
+    description: velocity of the inner boundary
+
+  v_outer_boundary:
+    type: quantity
+    description: velocity of the outer boundary of the last shell
+
+  velocity:
+    type: object
+    properties:
+      start:
+        type: quantity
+      stop:
+        type: quantity
+      num:
+        type: number
+        multipleOf: 1.0
+
+  density:
+    oneOf:
+    - $ref: '#/definitions/density/branch85_w7'
+    - $ref: '#/definitions/density/exponential'
+    - $ref: '#/definitions/density/power_law'
+    - $ref: '#/definitions/density/uniform'
+
+  abundance:
+    $ref: '#/definitions/abundance/uniform'
+
+required:
+- tardis_model_config_version
+
+definitions:
+  density:
+    branch85_w7:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - branch85_w7
+        w7_time_0:
+          type: quantity
+          default: 0.000231481 day
+          description: This needs no change - DO NOT TOUCH
+        w7_rho_0:
+          type: quantity
+          default: 3e29 g/cm^3
+          description: This needs no change - DO NOT TOUCH
+        w7_v_0:
+          type: quantity
+          default: 1 km/s
+          description: This needs no change - DO NOT TOUCH
+    exponential:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - exponential
+        time_0:
+          type: quantity
+          description: Time at which the pure model densities are right
+        rho_0:
+          type: quantity
+          description: density at time_0
+        v_0:
+          type: quantity
+          description: at what velocity the density rho_0 applies
+      required:
+      - rho_0
+      - v_0
+    power_law:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - power_law
+        time_0:
+          type: quantity
+          description: Time at which the pure model densities are right
+        rho_0:
+          type: quantity
+          description: density at time_0
+        v_0:
+          type: quantity
+          description: at what velocity the density rho_0 applies
+        exponent:
+          type: number
+          description: exponent for exponential density profile
+      required:
+      - rho_0
+      - v_0
+      - exponent
+    uniform:
+      type: object
+      additionalProperties: false
+      properties:
+        type:
+          enum:
+          - uniform
+        time_0:
+          type: quantity
+          description: Time at which the pure model densities are right
+        value:
+          type: quantity
+          description: value for uniform density
+      required:
+      - value
+  abundance:
+    uniform:
+      type: object
+      additionalProperties: true
+      properties:
+        type:
+          enum:
+          - uniform

tardis/io/setup_package.py

@@ -1,4 +1,4 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
 def get_package_data():
-    return {'tardis.io.tests': ['data/*.dat', 'data/*.yml', 'data/*.csv']}
+    return {'tardis.io.tests': ['data/*.dat', 'data/*.yml', 'data/*.csv', 'data/*.csvy']}

tardis/io/tests/data/csvy_full.csvy

@@ -0,0 +1,23 @@
+---
+name: csvy_full
+description: Example csvy config file for TARDIS.
+tardis_model_config_version: v1.0
+datatype:
+  fields:
+    -  name: velocity
+       unit: km/s
+       desc: velocities of shell outer bounderies.
+    -  name: density
+       unit: g/cm^3
+       desc: density of shell.
+    -  name: H
+       desc: fractional H abundance
+    -  name: He
+       desc: fractional He abundance
+
+v_inner_boundary: 9000 km/s
+v_outer_boundary: 15000 km/s
+---
+velocity,density,H,He
+10000, 5e-9, 0.3, 0.7
+11000, 2e-9, 0.6, 0.4

tardis/io/tests/data/csvy_missing.csvy

@@ -0,0 +1,19 @@
+---
+datatype:
+  fields:
+    -  name: velocity
+       unit: km/s
+    -  name: density
+       unit: g/cm^3
+       desc: density of shell.
+    -  name: H
+       desc: fractional H abundance
+    -  name: He
+       desc: fractional He abundance
+
+v_inner_boundary: 9000 km/s
+v_outer_boundary: 15000 km/s
+---
+velocity,density,H,He
+10000, 5e-9, 0.3, 0.7
+11000, 2e-9, 0.6, 0.4

tardis/io/tests/data/csvy_nocsv.csvy

@@ -0,0 +1,16 @@
+---
+name: csvy_nocsv
+description: Example csvy config file for TARDIS.
+tardis_model_config_version: v1.0
+
+velocity:
+  start: 9000 km/s
+  stop: 15000 km/s
+  num: 10
+density:
+  type: branch85_w7
+abundance:
+  type: uniform
+v_inner_boundary: 9000 km/s
+v_outer_boundary: 15000 km/s
+---

tardis/io/tests/test_csvy_reader.py

@@ -0,0 +1,45 @@
+import tardis
+from tardis.io.parsers import csvy
+from tardis.io.config_validator import validate_dict
+from jsonschema import exceptions as json_schema_exc
+import pytest
+import os
+from astropy import units as u
+import numpy.testing as npt
+
+
+DATA_PATH = os.path.join(tardis.__path__[0], 'io', 'tests', 'data')
+
+@pytest.fixture
+def csvy_full_fname():
+    return os.path.join(DATA_PATH, 'csvy_full.csvy')
+
+@pytest.fixture
+def csvy_nocsv_fname():
+    return os.path.join(DATA_PATH, 'csvy_nocsv.csvy')
+
+@pytest.fixture
+def csvy_missing_fname():
+    return os.path.join(DATA_PATH, 'csvy_missing.csvy')
+
+def test_csvy_finds_csv_first_line(csvy_full_fname):
+    yaml_dict, csv = csvy.load_csvy(csvy_full_fname)
+    npt.assert_almost_equal(csv['velocity'][0],10000)
+
+def test_csv_colnames_equiv_datatype_fields(csvy_full_fname):
+    yaml_dict, csv = csvy.load_csvy(csvy_full_fname)
+    datatype_names = [od['name'] for od in yaml_dict['datatype']['fields']]
+    for key in csv.columns:
+        assert key in datatype_names
+    for name in datatype_names:
+        assert name in csv.columns
+
+def test_csvy_nocsv_data_is_none(csvy_nocsv_fname):
+    yaml_dict, csv = csvy.load_csvy(csvy_nocsv_fname)
+    assert csv is None
+
+def test_missing_required_property(csvy_missing_fname):
+    yaml_dict, csv = csvy.load_csvy(csvy_missing_fname)
+    with pytest.raises(Exception):
+        vy = validate_dict(yaml_dict, schemapath=os.path.join(tardis.__path__[0], 'io', 'schemas',
+ 'csvy_model.yml'))