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20 hours ago •
altair-viz
altair-viz
Compatibility issues with Python 3.9.7 and altair 4.1.0?
I have some scripts I re-run weekly and they have been working fine for over a year now. That is until, I had to set up my computer completely new (new operating system: Mac OS Big Sur 11.6) which also prompted a series of installing newer versions (Upgrading Python from 3.7.2 to 3.9.7 and upgrading altair from 3.2.0 to 4.1.0). Since then my scripts don't work anymore and produce errors I can't figure out.
First, things that work:
- running altair sample code, eg from the Example Gallery (both for charts as well as for maps)
- creating my own charts that are not using alt.layer()
Things that don't work:
-
any kind of map that isn't sample code but self made
-
charts (eg line chart with multiple lines) with alt.layer()
Details on errors:
-
For the maps I get a
AttributeError: 'list' object has no attribute 'get'error, that is thrown atalt.mark_geoshape()and then moves on to defining the projection. The error message references altair/utils, the vegalite core and api as well as Python's jsonschema validator -- so I'm not sure whether it is an altair or a Python problem -
For the charts I get a
TypeError: Object of type set is not JSON serializableerror, although I'm not aware of any set I'm using/creating
Any pointers as to what is going on and / or how to fix it would be much appreciated. After three days of trying and googling, I'm out of ideas ;)
Complete error messages
- For maps:
AttributeError Traceback (most recent call last)
/var/folders/fk/_qbrt9ys18b6s2yb_kqblv1xt9_xg3/T/ipykernel_36594/216999948.py in <module>
8 center_values=[25,10]
9
---> 10 base = alt.Chart(countries).mark_geoshape(
11 fill='#D8DDE2',
12 stroke='white'
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/vegalite/v4/api.py in project(self, type, center, clipAngle, clipExtent, coefficient, distance, fraction, lobes, parallel, precision, radius, ratio, reflectX, reflectY, rotate, scale, spacing, tilt, translate, **kwds)
664
665 """
--> 666 projection = core.Projection(
667 center=center,
668 clipAngle=clipAngle,
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/vegalite/v4/schema/core.py in __init__(self, center, clipAngle, clipExtent, coefficient, distance, extent, fit, fraction, lobes, parallel, parallels, pointRadius, precision, radius, ratio, reflectX, reflectY, rotate, scale, size, spacing, tilt, translate, type, **kwds)
12124 size=Undefined, spacing=Undefined, tilt=Undefined, translate=Undefined, type=Undefined,
12125 **kwds):
> 12126 super(Projection, self).__init__(center=center, clipAngle=clipAngle, clipExtent=clipExtent,
12127 coefficient=coefficient, distance=distance, extent=extent,
12128 fit=fit, fraction=fraction, lobes=lobes, parallel=parallel,
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/utils/schemapi.py in __init__(self, *args, **kwds)
174
175 if DEBUG_MODE and self._class_is_valid_at_instantiation:
--> 176 self.to_dict(validate=True)
177
178 def copy(self, deep=True, ignore=()):
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/utils/schemapi.py in to_dict(self, validate, ignore, context)
335 if validate:
336 try:
--> 337 self.validate(result)
338 except jsonschema.ValidationError as err:
339 raise SchemaValidationError(self, err)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/utils/schemapi.py in validate(cls, instance, schema)
440 schema = cls._schema
441 resolver = jsonschema.RefResolver.from_schema(cls._rootschema or cls._schema)
--> 442 return jsonschema.validate(instance, schema, resolver=resolver)
443
444 @classmethod
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in validate(instance, schema, cls, *args, **kwargs)
963 cls.check_schema(schema)
964 validator = cls(schema, *args, **kwargs)
--> 965 error = exceptions.best_match(validator.iter_errors(instance))
966 if error is not None:
967 raise error
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/exceptions.py in best_match(errors, key)
352 """
353 errors = iter(errors)
--> 354 best = next(errors, None)
355 if best is None:
356 return
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/_validators.py in ref(validator, ref, instance, schema)
293
294 try:
--> 295 yield from validator.descend(instance, resolved)
296 finally:
297 validator.resolver.pop_scope()
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/_validators.py in properties(validator, properties, instance, schema)
327 for property, subschema in properties.items():
328 if property in instance:
--> 329 yield from validator.descend(
330 instance[property],
331 subschema,
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/_validators.py in ref(validator, ref, instance, schema)
293
294 try:
--> 295 yield from validator.descend(instance, resolved)
296 finally:
297 validator.resolver.pop_scope()
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/_validators.py in items(validator, items, instance, schema)
74 else:
75 for index in range(prefix, total):
---> 76 yield from validator.descend(
77 instance=instance[index],
78 schema=items,
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
212 return
213
--> 214 scope = id_of(_schema)
215 if scope:
216 self.resolver.push_scope(scope)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/jsonschema/validators.py in _id_of(schema)
88 if schema is True or schema is False:
89 return ""
---> 90 return schema.get("$id", "")
91
92
AttributeError: 'list' object has no attribute 'get'
- For charts:
TypeError Traceback (most recent call last)
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
968
969 if method is not None:
--> 970 return method(include=include, exclude=exclude)
971 return None
972 else:
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/vegalite/v4/api.py in _repr_mimebundle_(self, include, exclude)
1652 return {}
1653 else:
-> 1654 return renderers.get()(dct)
1655
1656 def display(self, renderer=Undefined, theme=Undefined, actions=Undefined, **kwargs):
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/utils/display.py in __call__(self, spec, **metadata)
178 kwargs = self.kwargs.copy()
179 kwargs.update(metadata)
--> 180 return spec_to_mimebundle(
181 spec, format="html", output_div=self.output_div, **kwargs
182 )
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/utils/mimebundle.py in spec_to_mimebundle(spec, format, mode, vega_version, vegaembed_version, vegalite_version, **kwargs)
60 return altair_saver.render(spec, format, mode=mode, **kwargs)
61 if format == "html":
---> 62 html = spec_to_html(
63 spec,
64 mode=mode,
~/.virtualenvs/DW_Data-QfWUG2cH/lib/python3.9/site-packages/altair/utils/html.py in spec_to_html(spec, mode, vega_version, vegaembed_version, vegalite_version, base_url, output_div, embed_options, json_kwds, fullhtml, requirejs, template)
219
220 return template.render(
--> 221 spec=json.dumps(spec, **json_kwds),
222 embed_options=json.dumps(embed_options),
223 mode=mode,
/usr/local/Cellar/[email protected]/3.9.7_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py in dumps(obj, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, default, sort_keys, **kw)
229 cls is None and indent is None and separators is None and
230 default is None and not sort_keys and not kw):
--> 231 return _default_encoder.encode(obj)
232 if cls is None:
233 cls = JSONEncoder
/usr/local/Cellar/[email protected]/3.9.7_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py in encode(self, o)
197 # exceptions aren't as detailed. The list call should be roughly
198 # equivalent to the PySequence_Fast that ''.join() would do.
--> 199 chunks = self.iterencode(o, _one_shot=True)
200 if not isinstance(chunks, (list, tuple)):
201 chunks = list(chunks)
/usr/local/Cellar/[email protected]/3.9.7_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py in iterencode(self, o, _one_shot)
255 self.key_separator, self.item_separator, self.sort_keys,
256 self.skipkeys, _one_shot)
--> 257 return _iterencode(o, 0)
258
259 def _make_iterencode(markers, _default, _encoder, _indent, _floatstr,
/usr/local/Cellar/[email protected]/3.9.7_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py in default(self, o)
177
178 """
--> 179 raise TypeError(f'Object of type {o.__class__.__name__} '
180 f'is not JSON serializable')
181
TypeError: Object of type set is not JSON serializable
Thanks for the report. This is due to the most recent release of jsonschema; see #2496. There is a fix in progress in #2503, until then you can pip install jsonschema==3.2 to fix the error.
Thank you SO MUCH! That definitely fixes problem 1 - which was the most pressing one. However, problem 2 with alt.layer() remains after your suggested fix, probably because seems not to be jsonschema-related (at least not to me / from the error message). Let me know if I should be submitting that separately.
Oh, sorry about that. Could you post a minimal example of code that reproduces the error?
Sure! It's produced when using this function, I already checked whether it being within the function is the problem, which it is not. Does this work for you in terms of example code? Happy to provide the data as well to enable re-running it if needed.
color_range = ['#00A5FF','#002D5A','#96BE00', '#F0C80F','#EC8C22','#BE232D']
def make_chart_cases_world(selected_countries):
# draw world line
base = alt.Chart(world_trend).mark_line(color='#9099A3', strokeDash=[4,4]).encode(
x='parsed_date:T',
y='world_roll_mean_per_population'
)
selected_countries_df = pd.DataFrame()
# filter dataframe for selected countries
for country in selected_countries:
temp_selection = jhu_daily_rolling[jhu_daily_rolling['ISO3code'] == country]
selected_countries_df = selected_countries_df.append(temp_selection)
min_date=datetime.strptime('2020-01-01', '%Y-%m-%d')
max_date=today
#plot development over time for selected countries
line_chart = alt.Chart(selected_countries_df).mark_line().encode(
alt.X('parsed_date:T',title='', axis=alt.Axis(), scale=alt.Scale(domain=[str(min_date), str(max_date)])),
alt.Y('roll_mean_cases_per_population:Q', title=''),
#color=alt.Color('ISO3code:N',scale=alt.Scale(domain=selected_countries,range=color_range)),
tooltip=['ISO3code', 'parsed_date:T', 'roll_mean_cases_per_population:Q']
)
layered_chart = alt.layer(base, line_chart)
return layered_chart.configure_axis(
grid=True
).configure_view(
strokeOpacity=0
)
make_chart_cases_world(['DEU', 'ZAF', 'USA', 'GBR', 'IND', 'BRA'])
Thanks - there are a number of variables undefined there, so it's hard for me to guess where the set object may have originated. I would suggest trying to create a Minimal reproducible example that someone else could run to reproduce the error you're seeing.
Thank you for teaching me about the Minimal reproducible example! That seems to be a great way to debug code, as now the original problem does not exist anymore, but I found new ones that are probably more related to my way of coding rather than to any bugs, I assume. So I'm closing this for now; in case I run into a dead end will submit a new issue with including a minimal reproducible example. Thanks again for your help and patience!
Hi, I'm having a similar issue which might be related to the same problem. Here's my code:
import pandas as pd
import numpy as np
import geopandas as gpd
import altair as alt
countries = gpd.read_file('https://raw.githubusercontent.com/nvkelso/natural-earth-vector/master/geojson/ne_110m_admin_0_countries.geojson')
alt.Chart(countries).mark_geoshape(
fill='lightgray',
stroke='darkgray',
strokeWidth=0.5
).properties(
width=600,
height=600
).project(
type='gnomonic',
rotate=[0,-90,0]
).configure_view(strokeWidth=0)
And here's the error that I'm getting:
AttributeError Traceback (most recent call last)
/var/folders/n2/39d7g3xs4qx_9qgpnp2c_cz40000gn/T/ipykernel_25742/2293139051.py in <module>
----> 1 alt.Chart(countries).mark_geoshape(
2 fill='lightgray',
3 stroke='darkgray',
4 strokeWidth=0.5
5 ).properties(
/usr/local/lib/python3.9/site-packages/altair/vegalite/v4/api.py in project(self, type, center, clipAngle, clipExtent, coefficient, distance, fraction, lobes, parallel, precision, radius, ratio, reflectX, reflectY, rotate, scale, spacing, tilt, translate, **kwds)
664
665 """
--> 666 projection = core.Projection(
667 center=center,
668 clipAngle=clipAngle,
/usr/local/lib/python3.9/site-packages/altair/vegalite/v4/schema/core.py in __init__(self, center, clipAngle, clipExtent, coefficient, distance, extent, fit, fraction, lobes, parallel, parallels, pointRadius, precision, radius, ratio, reflectX, reflectY, rotate, scale, size, spacing, tilt, translate, type, **kwds)
12124 size=Undefined, spacing=Undefined, tilt=Undefined, translate=Undefined, type=Undefined,
12125 **kwds):
> 12126 super(Projection, self).__init__(center=center, clipAngle=clipAngle, clipExtent=clipExtent,
12127 coefficient=coefficient, distance=distance, extent=extent,
12128 fit=fit, fraction=fraction, lobes=lobes, parallel=parallel,
/usr/local/lib/python3.9/site-packages/altair/utils/schemapi.py in __init__(self, *args, **kwds)
174
175 if DEBUG_MODE and self._class_is_valid_at_instantiation:
--> 176 self.to_dict(validate=True)
177
178 def copy(self, deep=True, ignore=()):
/usr/local/lib/python3.9/site-packages/altair/utils/schemapi.py in to_dict(self, validate, ignore, context)
335 if validate:
336 try:
--> 337 self.validate(result)
338 except jsonschema.ValidationError as err:
339 raise SchemaValidationError(self, err)
/usr/local/lib/python3.9/site-packages/altair/utils/schemapi.py in validate(cls, instance, schema)
440 schema = cls._schema
441 resolver = jsonschema.RefResolver.from_schema(cls._rootschema or cls._schema)
--> 442 return jsonschema.validate(instance, schema, resolver=resolver)
443
444 @classmethod
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in validate(instance, schema, cls, *args, **kwargs)
963 cls.check_schema(schema)
964 validator = cls(schema, *args, **kwargs)
--> 965 error = exceptions.best_match(validator.iter_errors(instance))
966 if error is not None:
967 raise error
/usr/local/lib/python3.9/site-packages/jsonschema/exceptions.py in best_match(errors, key)
352 """
353 errors = iter(errors)
--> 354 best = next(errors, None)
355 if best is None:
356 return
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
/usr/local/lib/python3.9/site-packages/jsonschema/_validators.py in ref(validator, ref, instance, schema)
296
297 try:
--> 298 yield from validator.descend(instance, resolved)
299 finally:
300 validator.resolver.pop_scope()
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
/usr/local/lib/python3.9/site-packages/jsonschema/_validators.py in properties(validator, properties, instance, schema)
330 for property, subschema in properties.items():
331 if property in instance:
--> 332 yield from validator.descend(
333 instance[property],
334 subschema,
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
/usr/local/lib/python3.9/site-packages/jsonschema/_validators.py in anyOf(validator, anyOf, instance, schema)
366 all_errors = []
367 for index, subschema in enumerate(anyOf):
--> 368 errs = list(validator.descend(instance, subschema, schema_path=index))
369 if not errs:
370 break
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
/usr/local/lib/python3.9/site-packages/jsonschema/_validators.py in ref(validator, ref, instance, schema)
296
297 try:
--> 298 yield from validator.descend(instance, resolved)
299 finally:
300 validator.resolver.pop_scope()
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
222
223 errors = validator(self, v, instance, _schema) or ()
--> 224 for error in errors:
225 # set details if not already set by the called fn
226 error._set(
/usr/local/lib/python3.9/site-packages/jsonschema/_validators.py in items(validator, items, instance, schema)
74 else:
75 for index in range(prefix, total):
---> 76 yield from validator.descend(
77 instance=instance[index],
78 schema=items,
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in descend(self, instance, schema, path, schema_path)
238
239 def descend(self, instance, schema, path=None, schema_path=None):
--> 240 for error in self.evolve(schema=schema).iter_errors(instance):
241 if path is not None:
242 error.path.appendleft(path)
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in iter_errors(self, instance, _schema)
212 return
213
--> 214 scope = id_of(_schema)
215 if scope:
216 self.resolver.push_scope(scope)
/usr/local/lib/python3.9/site-packages/jsonschema/validators.py in _id_of(schema)
88 if schema is True or schema is False:
89 return ""
---> 90 return schema.get("$id", "")
91
92
AttributeError: 'list' object has no attribute 'get'
I know the error goes away if I comment out the rotate attribute in the project property. And this error happens both on my local machine, running Python 3.9.9, Altair 4.1.0 and jsonschema 4.2.0 and on Google Colab with their default packages. Thank you.
The error you're seeing is unrelated to this issue, but it is reported here: #2496
You can either update to Altair version 4.2 (which is compatible with any jsonschema version), or you can downgrade to jsonschema<4.0 (which is compatible with Altair 4.1 and older)
Hi @jakevdp. Updating to Altair version 4.2 didn't help but downgrading jsonschema to 3.2 did. Any ideas? Thank you!
Thanks for checking – it looks like a bug in the schema validation, not related to the similar jsonschema issues
Note that it is specifically the rotate parameter that causes this issue and it is not present in the current development version of Altair (installable from Github) (tested with jsonschema 4.4).
Smaller mre:
import altair as alt
from vega_datasets import data
alt.Chart(data.us_10m.url).mark_geoshape().project(
rotate=[0, 0, 0] # Even this the default value raises an error with Altair 4.2
)
