Added csvy parser #928

marxwillia · 2019-05-01T20:48:31Z

No description provided.

tardis/io/parsers/csvy.py

tardis/io/parsers/csvy_ex

wkerzendorf · 2019-05-01T22:41:19Z

Looks great @marxwillia! We need to use our special yaml parser to make sure it converts quantities strings to quantities - but we can work on this the next few days.

…tities.

marxwillia

Should the user have the flexibility to select a specific density profile and custom abundances? Or is a specific density profile only ever used with uniform abundances?

marxwillia · 2019-05-14T19:29:05Z

Just updated the csvy_model.yml schema file so that it includes the builtin options for density profiles and uniform abundance. I think we want the user to be able to run TARDIS this way in addition to the new flexibility of the csvy model file.

In the density and abundance definitions, the user can choose 'csvy' which has no subfields. My current plan is to make the user responsible for setting up the csv part of the model csvy file correctly, with help from some asserts.

This reverts commit 1ae1a8f.

tardis/io/parsers/csvy.py

tardis/io/schemas/csvy_model.yml

wkerzendorf

run the tests using python setup.py test

tardis/io/schemas/csvy_model.yml

wkerzendorf · 2019-05-21T14:23:21Z

tardis/io/tests/csvy_test.ipynb

@@ -0,0 +1,454 @@
+{


maybe this should go to the documentation?

tardis/io/tests/data/csvy_full.csvy

tardis/io/tests/test_csvy_reader.py

chvogl · 2019-05-22T16:04:26Z

tardis/io/schemas/csvy_model.yml

+    $ref: '#/definitions/abundance/uniform'
+
+  required:
+  - name


Do we want to require a name for the model?

nope - we should not. can the required key live within the node

I'm pretty sure that the required key cannot live within the node.

https://json-schema.org/understanding-json-schema/reference/object.html#required

tardis/io/tests/data/csvy_full.csvy

wkerzendorf · 2019-05-29T20:27:41Z

setup.py

@@ -113,6 +113,7 @@
 package_info['package_data'].setdefault(PACKAGENAME, [])
 package_info['package_data'][PACKAGENAME].append('data/*')
 package_info['package_data'][PACKAGENAME].append('io/schemas/*')
+package_info['package_data'][PACKAGENAME].append('io/tests/data/*')


use this https://github.com/tardis-sn/tardis/blob/master/tardis/io/setup_package.py for adding that.

wkerzendorf

there are three things still open - but then its good to merge.

wkerzendorf · 2019-05-29T20:28:08Z

tardis/io/schemas/csvy_model.yml

+    type: string
+    description: name of the model being run
+
+  description:


are these required keys?

Not currently.

wkerzendorf · 2019-05-29T20:28:22Z

tardis/io/schemas/csvy_model.yml

+    type: string
+    description: description of the model being run
+
+  tardis_model_config_version:


that should be required

tardis_model_config_version is now the only property required.

wkerzendorf · 2019-05-29T20:29:00Z

tardis/io/schemas/csvy_model.yml

+    $ref: '#/definitions/abundance/uniform'
+
+  required:
+  - name


nope - we should not. can the required key live within the node

tardis/io/tests/data/csvy_full.csvy

wkerzendorf · 2019-05-29T20:29:39Z

tardis/io/tests/test_csvy_reader.py

+import numpy.testing as npt
+
+
+DATA_PATH = os.path.join(tardis.__path__[0], 'io', 'tests', 'data')


could be a fixture as well.

Added csvy parser

d77f915

wkerzendorf reviewed May 1, 2019

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marxwillia added 6 commits May 2, 2019 14:32

Added two examples of TARDIS csvy files.

e19203d

Removed non-model related fields.

5da8003

Added TARDIS specific YAML loader to correctly interpret astropy quan…

e7169f7

…tities.

Tested TARDIS specific YAML loader.

56fe945

Fixed datatype fields being overwritten.

7d63e95

Added csvy_model schema. Work in progress.

90206f2

marxwillia commented May 8, 2019

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marxwillia added 2 commits May 8, 2019 15:33

Tested

77c5b76

Added option to run TARDIS with builtin density and uniform abundance

573e37a

marxwillia added 15 commits May 15, 2019 11:30

Added methods to load only the yaml or only the csv part of a csvy file.

1d4dda1

cleaned repo

49817af

cleaned repo

2d3b77d

Added 'model' to version field.

cfa5592

Added velocity to schema.

f96a2c6

Removed csvy option from structure and abundance fields.

0299482

Added ConfigurationNamespace from_csvy class method

5621d12

Started from_csvy for Radial1DModel

e91f034

Removed from_csvy

1ae1a8f

Revert "Removed from_csvy"

407c0fb

This reverts commit 1ae1a8f.

Removed from_csvy

2dae39f

Added datatype to schema

a097ee8

Added try except to load csvy with no csv

d8c4631

Fixed schema issue with csvy_nocsv

8908061

Added csvy unit tests

9c521be

marxwillia added 2 commits May 17, 2019 16:28

Removed from_csvy

b9ec8fa

run csvy unit tests

9ed0cc8

wkerzendorf reviewed May 21, 2019

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marxwillia added 5 commits May 22, 2019 11:35

Removed atom_data, Added comment for datatype name.

bace9c9

Removed description fields from schema

4968da4

Added docstring to load_csvy

fe32c28

Updated error messages

f989a71

Removed atom_data field

087f315

chvogl reviewed May 22, 2019

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marxwillia added 5 commits May 29, 2019 13:59

Used pytest fixtures

60c4392

Added docstrings

d6487e4

Updated required properties

5ccb902

Added tardis/io/tests/data/*

2f9404e

Replaced assert with assert_almost_equal

af4e85e

wkerzendorf reviewed May 29, 2019

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marxwillia added 5 commits May 29, 2019 17:18

Updated required properties. Fixed required alignment mistake.

4403073

Moved to docs

63dcf27

Moved load .csvy files from setup.py to io/setup_package

f008753

Added test that validation fails when missing required property in csvy

e85db2d

Replaced assert with pytest.raises(Exception)

de64084

wkerzendorf merged commit 153736a into tardis-sn:master May 29, 2019

dhomeier mentioned this pull request Jul 16, 2021

Add support for csvy in tables astropy/astropy#8650

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Added csvy parser #928

Added csvy parser #928

marxwillia commented May 1, 2019

wkerzendorf commented May 1, 2019

marxwillia left a comment

marxwillia commented May 14, 2019

wkerzendorf left a comment

wkerzendorf May 21, 2019

chvogl May 22, 2019

wkerzendorf May 29, 2019

marxwillia May 29, 2019

wkerzendorf May 29, 2019

wkerzendorf left a comment

wkerzendorf May 29, 2019

marxwillia May 29, 2019

wkerzendorf May 29, 2019

marxwillia May 29, 2019

wkerzendorf May 29, 2019

wkerzendorf May 29, 2019

		import numpy.testing as npt


		DATA_PATH = os.path.join(tardis.__path__[0], 'io', 'tests', 'data')

Added csvy parser #928

Added csvy parser #928

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