Use Python 3.10 in Continuous Integration tests #1577
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Python 3.10 has been released on 7 October 2021, see changelog at https://docs.python.org/3.10/whatsnew/3.10.html. Updating all the GitHub Actions continuous integration workflows that used Python 3.9 to use Python 3.10 now. Also updated setup.py to include Python 3.10 classifier.
weiji14
commented
Oct 8, 2021
There was a problem hiding this comment.
The setup mamba step is erroring at https://github.com/GenericMappingTools/pygmt/runs/3833784779?check_suite_focus=true#step:4:795 with package python-3.10.0-h62f1059_0_cpython requires pip, but none of the providers can be installed, which is weird because pip on conda-forge is noarch so it should be installable. Will try again in the coming days.
|
Ok, I've changed the CI scripts to only install Python 3.10 on the "GMT Dev Tests" workflow because there isn't a Python 3.10 miniconda/mambaforge installer yet (the reason for why things didn't work as mentioned in #1577 (review)). The next problem is that Edit: Also need to wait for Python 3.10 migration on conda-forge (see conda-forge/conda-forge-pinning-feedstock#2008), because of Note that PyGMT should technically support Python 3.10 already since we've moved to noarch builds (conda-forge/pygmt-feedstock#13), so this Pull Request is just about making sure that our Continuous Integration tests pass on Python 3.10. |
Workaround missing Python 3.10 packages for dvc on conda-forge.
|
/test-gmt-dev Edit: there is something wrong with the |
I think |
|
/test-gmt-dev Edit: I thought 95e318c worked, but running |
|
One more step closer 😆 Have managed to resolve the There are some unit tests in _______________________ test_geopandas_info_geodataframe _______________________
gdf = geometry
multipolygon MULTIPOLYGON (((0.00000 0.00000, 20.0000... POLYGON ((20.00000 10.00000, 23.00000 10.00000...
linestring LINESTRING (20.00000 15.00000, 30.00000 15.00000)
def test_geopandas_info_geodataframe(gdf):
"""
Check that info can return the bounding box region from a
geopandas.GeoDataFrame.
"""
> output = info(data=gdf, per_column=True)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:47:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/info.py:87: in info
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: in tempfile_from_geojson
geojson.to_file(**ogrgmt_kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/geodataframe.py:1114: in to_file
_to_file(self, filename, driver, schema, index, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:355: in _to_file
_check_fiona("'to_file' method")
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
func = "'to_file' method"
def _check_fiona(func):
if fiona is None:
> raise ImportError(
f"the {func} requires the 'fiona' package, but it is not installed or does "
f"not import correctly.\nImporting fiona resulted in: {fiona_import_error}"
)
E ImportError: the 'to_file' method requires the 'fiona' package, but it is not installed or does not import correctly.
E Importing fiona resulted in: /usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/ogrext.cpython-310-x86_64-linux-gnu.so: undefined symbol: _PyGen_Send
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:80: ImportError
______________ test_geopandas_info_shapely[multipolygon-desired0] ______________
geojson = <shapely.geometry.multipolygon.MultiPolygon object at 0x7f605c927d90>
@contextmanager
def tempfile_from_geojson(geojson):
"""
Saves any geo-like Python object which implements ``__geo_interface__``
(e.g. a geopandas.GeoDataFrame or shapely.geometry) to a temporary OGR_GMT
text file.
Parameters
----------
geojson : geopandas.GeoDataFrame
A geopandas GeoDataFrame, or any geo-like Python object which
implements __geo_interface__, i.e. a GeoJSON.
Yields
------
tmpfilename : str
A temporary OGR_GMT format file holding the geographical data.
E.g. '1a2b3c4d5e6.gmt'.
"""
with GMTTempFile(suffix=".gmt") as tmpfile:
os.remove(tmpfile.name) # ensure file is deleted first
ogrgmt_kwargs = dict(filename=tmpfile.name, driver="OGR_GMT", mode="w")
try:
# Using geopandas.to_file to directly export to OGR_GMT format
> geojson.to_file(**ogrgmt_kwargs)
E AttributeError: 'MultiPolygon' object has no attribute 'to_file'
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: AttributeError
During handling of the above exception, another exception occurred:
gdf = geometry
multipolygon MULTIPOLYGON (((0.00000 0.00000, 20.0000... POLYGON ((20.00000 10.00000, 23.00000 10.00000...
linestring LINESTRING (20.00000 15.00000, 30.00000 15.00000)
geomtype = 'multipolygon', desired = [0.0, 35.0, 0.0, 20.0]
@pytest.mark.parametrize(
"geomtype,desired",
[
("multipolygon", [0.0, 35.0, 0.0, 20.0]),
("polygon", [20.0, 23.0, 10.0, 14.0]),
("linestring", [20.0, 30.0, 15.0, 15.0]),
],
)
def test_geopandas_info_shapely(gdf, geomtype, desired):
"""
Check that info can return the bounding box region from a shapely.geometry
object that has a __geo_interface__ property.
"""
geom = gdf.loc[geomtype].geometry
> output = info(data=geom, per_column=True)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:65:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/info.py:87: in info
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:140: in tempfile_from_geojson
import fiona
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
# -*- coding: utf-8 -*-
"""
Fiona is OGR's neat, nimble API.
Fiona provides a minimal, uncomplicated Python interface to the open
source GIS community's most trusted geodata access library and
integrates readily with other Python GIS packages such as pyproj, Rtree
and Shapely.
How minimal? Fiona can read features as mappings from shapefiles or
other GIS vector formats and write mappings as features to files using
the same formats. That's all. There aren't any feature or geometry
classes. Features and their geometries are just data.
A Fiona feature is a Python mapping inspired by the GeoJSON format. It
has `id`, 'geometry`, and `properties` keys. The value of `id` is
a string identifier unique within the feature's parent collection. The
`geometry` is another mapping with `type` and `coordinates` keys. The
`properties` of a feature is another mapping corresponding to its
attribute table. For example:
{'id': '1',
'geometry': {'type': 'Point', 'coordinates': (0.0, 0.0)},
'properties': {'label': u'Null Island'} }
is a Fiona feature with a point geometry and one property.
Features are read and written using objects returned by the
``collection`` function. These ``Collection`` objects are a lot like
Python ``file`` objects. A ``Collection`` opened in reading mode serves
as an iterator over features. One opened in a writing mode provides
a ``write`` method.
Usage
-----
Here's an example of reading a select few polygon features from
a shapefile and for each, picking off the first vertex of the exterior
ring of the polygon and using that as the point geometry for a new
feature writing to a "points.shp" file.
>>> import fiona
>>> with fiona.open('docs/data/test_uk.shp', 'r') as inp:
... output_schema = inp.schema.copy()
... output_schema['geometry'] = 'Point'
... with collection(
... "points.shp", "w",
... crs=inp.crs,
... driver="ESRI Shapefile",
... schema=output_schema
... ) as out:
... for f in inp.filter(
... bbox=(-5.0, 55.0, 0.0, 60.0)
... ):
... value = f['geometry']['coordinates'][0][0]
... f['geometry'] = {
... 'type': 'Point', 'coordinates': value}
... out.write(f)
Because Fiona collections are context managers, they are closed and (in
writing modes) flush contents to disk when their ``with`` blocks end.
"""
from contextlib import contextmanager
import logging
import os
import sys
import warnings
import platform
from six import string_types
try:
from pathlib import Path
except ImportError: # pragma: no cover
class Path:
pass
# TODO: remove this? Or at least move it, flake8 complains.
if sys.platform == "win32":
libdir = os.path.join(os.path.dirname(__file__), ".libs")
os.environ["PATH"] = os.environ["PATH"] + ";" + libdir
import fiona._loading
> with fiona._loading.add_gdal_dll_directories():
E AttributeError: partially initialized module 'fiona' has no attribute '_loading' (most likely due to a circular import)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/__init__.py:85: AttributeError
________________ test_geopandas_info_shapely[polygon-desired1] _________________
geojson = <shapely.geometry.polygon.Polygon object at 0x7f605c927730>
@contextmanager
def tempfile_from_geojson(geojson):
"""
Saves any geo-like Python object which implements ``__geo_interface__``
(e.g. a geopandas.GeoDataFrame or shapely.geometry) to a temporary OGR_GMT
text file.
Parameters
----------
geojson : geopandas.GeoDataFrame
A geopandas GeoDataFrame, or any geo-like Python object which
implements __geo_interface__, i.e. a GeoJSON.
Yields
------
tmpfilename : str
A temporary OGR_GMT format file holding the geographical data.
E.g. '1a2b3c4d5e6.gmt'.
"""
with GMTTempFile(suffix=".gmt") as tmpfile:
os.remove(tmpfile.name) # ensure file is deleted first
ogrgmt_kwargs = dict(filename=tmpfile.name, driver="OGR_GMT", mode="w")
try:
# Using geopandas.to_file to directly export to OGR_GMT format
> geojson.to_file(**ogrgmt_kwargs)
E AttributeError: 'Polygon' object has no attribute 'to_file'
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: AttributeError
During handling of the above exception, another exception occurred:
gdf = geometry
multipolygon MULTIPOLYGON (((0.00000 0.00000, 20.0000... POLYGON ((20.00000 10.00000, 23.00000 10.00000...
linestring LINESTRING (20.00000 15.00000, 30.00000 15.00000)
geomtype = 'polygon', desired = [20.0, 23.0, 10.0, 14.0]
@pytest.mark.parametrize(
"geomtype,desired",
[
("multipolygon", [0.0, 35.0, 0.0, 20.0]),
("polygon", [20.0, 23.0, 10.0, 14.0]),
("linestring", [20.0, 30.0, 15.0, 15.0]),
],
)
def test_geopandas_info_shapely(gdf, geomtype, desired):
"""
Check that info can return the bounding box region from a shapely.geometry
object that has a __geo_interface__ property.
"""
geom = gdf.loc[geomtype].geometry
> output = info(data=geom, per_column=True)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:65:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/info.py:87: in info
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:140: in tempfile_from_geojson
import fiona
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
# -*- coding: utf-8 -*-
"""
Fiona is OGR's neat, nimble API.
Fiona provides a minimal, uncomplicated Python interface to the open
source GIS community's most trusted geodata access library and
integrates readily with other Python GIS packages such as pyproj, Rtree
and Shapely.
How minimal? Fiona can read features as mappings from shapefiles or
other GIS vector formats and write mappings as features to files using
the same formats. That's all. There aren't any feature or geometry
classes. Features and their geometries are just data.
A Fiona feature is a Python mapping inspired by the GeoJSON format. It
has `id`, 'geometry`, and `properties` keys. The value of `id` is
a string identifier unique within the feature's parent collection. The
`geometry` is another mapping with `type` and `coordinates` keys. The
`properties` of a feature is another mapping corresponding to its
attribute table. For example:
{'id': '1',
'geometry': {'type': 'Point', 'coordinates': (0.0, 0.0)},
'properties': {'label': u'Null Island'} }
is a Fiona feature with a point geometry and one property.
Features are read and written using objects returned by the
``collection`` function. These ``Collection`` objects are a lot like
Python ``file`` objects. A ``Collection`` opened in reading mode serves
as an iterator over features. One opened in a writing mode provides
a ``write`` method.
Usage
-----
Here's an example of reading a select few polygon features from
a shapefile and for each, picking off the first vertex of the exterior
ring of the polygon and using that as the point geometry for a new
feature writing to a "points.shp" file.
>>> import fiona
>>> with fiona.open('docs/data/test_uk.shp', 'r') as inp:
... output_schema = inp.schema.copy()
... output_schema['geometry'] = 'Point'
... with collection(
... "points.shp", "w",
... crs=inp.crs,
... driver="ESRI Shapefile",
... schema=output_schema
... ) as out:
... for f in inp.filter(
... bbox=(-5.0, 55.0, 0.0, 60.0)
... ):
... value = f['geometry']['coordinates'][0][0]
... f['geometry'] = {
... 'type': 'Point', 'coordinates': value}
... out.write(f)
Because Fiona collections are context managers, they are closed and (in
writing modes) flush contents to disk when their ``with`` blocks end.
"""
from contextlib import contextmanager
import logging
import os
import sys
import warnings
import platform
from six import string_types
try:
from pathlib import Path
except ImportError: # pragma: no cover
class Path:
pass
# TODO: remove this? Or at least move it, flake8 complains.
if sys.platform == "win32":
libdir = os.path.join(os.path.dirname(__file__), ".libs")
os.environ["PATH"] = os.environ["PATH"] + ";" + libdir
import fiona._loading
> with fiona._loading.add_gdal_dll_directories():
E AttributeError: partially initialized module 'fiona' has no attribute '_loading' (most likely due to a circular import)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/__init__.py:85: AttributeError
_______________ test_geopandas_info_shapely[linestring-desired2] _______________
geojson = <shapely.geometry.linestring.LineString object at 0x7f605c926e60>
@contextmanager
def tempfile_from_geojson(geojson):
"""
Saves any geo-like Python object which implements ``__geo_interface__``
(e.g. a geopandas.GeoDataFrame or shapely.geometry) to a temporary OGR_GMT
text file.
Parameters
----------
geojson : geopandas.GeoDataFrame
A geopandas GeoDataFrame, or any geo-like Python object which
implements __geo_interface__, i.e. a GeoJSON.
Yields
------
tmpfilename : str
A temporary OGR_GMT format file holding the geographical data.
E.g. '1a2b3c4d5e6.gmt'.
"""
with GMTTempFile(suffix=".gmt") as tmpfile:
os.remove(tmpfile.name) # ensure file is deleted first
ogrgmt_kwargs = dict(filename=tmpfile.name, driver="OGR_GMT", mode="w")
try:
# Using geopandas.to_file to directly export to OGR_GMT format
> geojson.to_file(**ogrgmt_kwargs)
E AttributeError: 'LineString' object has no attribute 'to_file'
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: AttributeError
During handling of the above exception, another exception occurred:
gdf = geometry
multipolygon MULTIPOLYGON (((0.00000 0.00000, 20.0000... POLYGON ((20.00000 10.00000, 23.00000 10.00000...
linestring LINESTRING (20.00000 15.00000, 30.00000 15.00000)
geomtype = 'linestring', desired = [20.0, 30.0, 15.0, 15.0]
@pytest.mark.parametrize(
"geomtype,desired",
[
("multipolygon", [0.0, 35.0, 0.0, 20.0]),
("polygon", [20.0, 23.0, 10.0, 14.0]),
("linestring", [20.0, 30.0, 15.0, 15.0]),
],
)
def test_geopandas_info_shapely(gdf, geomtype, desired):
"""
Check that info can return the bounding box region from a shapely.geometry
object that has a __geo_interface__ property.
"""
geom = gdf.loc[geomtype].geometry
> output = info(data=geom, per_column=True)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:65:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/info.py:87: in info
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:140: in tempfile_from_geojson
import fiona
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
# -*- coding: utf-8 -*-
"""
Fiona is OGR's neat, nimble API.
Fiona provides a minimal, uncomplicated Python interface to the open
source GIS community's most trusted geodata access library and
integrates readily with other Python GIS packages such as pyproj, Rtree
and Shapely.
How minimal? Fiona can read features as mappings from shapefiles or
other GIS vector formats and write mappings as features to files using
the same formats. That's all. There aren't any feature or geometry
classes. Features and their geometries are just data.
A Fiona feature is a Python mapping inspired by the GeoJSON format. It
has `id`, 'geometry`, and `properties` keys. The value of `id` is
a string identifier unique within the feature's parent collection. The
`geometry` is another mapping with `type` and `coordinates` keys. The
`properties` of a feature is another mapping corresponding to its
attribute table. For example:
{'id': '1',
'geometry': {'type': 'Point', 'coordinates': (0.0, 0.0)},
'properties': {'label': u'Null Island'} }
is a Fiona feature with a point geometry and one property.
Features are read and written using objects returned by the
``collection`` function. These ``Collection`` objects are a lot like
Python ``file`` objects. A ``Collection`` opened in reading mode serves
as an iterator over features. One opened in a writing mode provides
a ``write`` method.
Usage
-----
Here's an example of reading a select few polygon features from
a shapefile and for each, picking off the first vertex of the exterior
ring of the polygon and using that as the point geometry for a new
feature writing to a "points.shp" file.
>>> import fiona
>>> with fiona.open('docs/data/test_uk.shp', 'r') as inp:
... output_schema = inp.schema.copy()
... output_schema['geometry'] = 'Point'
... with collection(
... "points.shp", "w",
... crs=inp.crs,
... driver="ESRI Shapefile",
... schema=output_schema
... ) as out:
... for f in inp.filter(
... bbox=(-5.0, 55.0, 0.0, 60.0)
... ):
... value = f['geometry']['coordinates'][0][0]
... f['geometry'] = {
... 'type': 'Point', 'coordinates': value}
... out.write(f)
Because Fiona collections are context managers, they are closed and (in
writing modes) flush contents to disk when their ``with`` blocks end.
"""
from contextlib import contextmanager
import logging
import os
import sys
import warnings
import platform
from six import string_types
try:
from pathlib import Path
except ImportError: # pragma: no cover
class Path:
pass
# TODO: remove this? Or at least move it, flake8 complains.
if sys.platform == "win32":
libdir = os.path.join(os.path.dirname(__file__), ".libs")
os.environ["PATH"] = os.environ["PATH"] + ";" + libdir
import fiona._loading
> with fiona._loading.add_gdal_dll_directories():
E AttributeError: partially initialized module 'fiona' has no attribute '_loading' (most likely due to a circular import)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/__init__.py:85: AttributeError
______________________ test_geopandas_plot_default_square ______________________
@pytest.mark.mpl_image_compare
def test_geopandas_plot_default_square():
"""
Check the default behavior of plotting a geopandas DataFrame with Point
geometry in 2d.
"""
point = shapely.geometry.Point(1, 2)
gdf = gpd.GeoDataFrame(geometry=[point])
fig = Figure()
> fig.plot(data=gdf, region=[0, 2, 1, 3], projection="X2c", frame=True)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:78:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:873: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/plot.py:273: in plot
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: in tempfile_from_geojson
geojson.to_file(**ogrgmt_kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/geodataframe.py:1114: in to_file
_to_file(self, filename, driver, schema, index, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:355: in _to_file
_check_fiona("'to_file' method")
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
func = "'to_file' method"
def _check_fiona(func):
if fiona is None:
> raise ImportError(
f"the {func} requires the 'fiona' package, but it is not installed or does "
f"not import correctly.\nImporting fiona resulted in: {fiona_import_error}"
)
E ImportError: the 'to_file' method requires the 'fiona' package, but it is not installed or does not import correctly.
E Importing fiona resulted in: /usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/ogrext.cpython-310-x86_64-linux-gnu.so: undefined symbol: _PyGen_Send
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:80: ImportError
______________________ test_geopandas_plot3d_default_cube ______________________
@pytest.mark.mpl_image_compare
def test_geopandas_plot3d_default_cube():
"""
Check the default behavior of plotting a geopandas DataFrame with
MultiPoint geometry in 3d.
"""
multipoint = shapely.geometry.MultiPoint([(0.5, 0.5, 0.5), (1.5, 1.5, 1.5)])
gdf = gpd.GeoDataFrame(geometry=[multipoint])
fig = Figure()
> fig.plot3d(
data=gdf,
perspective=[315, 25],
region=[0, 2, 0, 2, 0, 2],
projection="X2c",
frame=["WsNeZ1", "xag", "yag", "zag"],
zscale=1.5,
)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:91:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:873: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/plot3d.py:249: in plot3d
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: in tempfile_from_geojson
geojson.to_file(**ogrgmt_kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/geodataframe.py:1114: in to_file
_to_file(self, filename, driver, schema, index, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:355: in _to_file
_check_fiona("'to_file' method")
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
func = "'to_file' method"
def _check_fiona(func):
if fiona is None:
> raise ImportError(
f"the {func} requires the 'fiona' package, but it is not installed or does "
f"not import correctly.\nImporting fiona resulted in: {fiona_import_error}"
)
E ImportError: the 'to_file' method requires the 'fiona' package, but it is not installed or does not import correctly.
E Importing fiona resulted in: /usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/ogrext.cpython-310-x86_64-linux-gnu.so: undefined symbol: _PyGen_Send
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:80: ImportError
____________________ test_geopandas_plot_non_default_circle ____________________
@pytest.mark.mpl_image_compare
def test_geopandas_plot_non_default_circle():
"""
Check the default behavior of plotting geopandas DataFrame with Point
geometry in 2d.
"""
point = shapely.geometry.Point(1, 2)
gdf = gpd.GeoDataFrame(geometry=[point])
fig = Figure()
> fig.plot(data=gdf, region=[0, 2, 1, 3], projection="X2c", frame=True, style="c0.2c")
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:111:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:873: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/plot.py:273: in plot
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: in tempfile_from_geojson
geojson.to_file(**ogrgmt_kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/geodataframe.py:1114: in to_file
_to_file(self, filename, driver, schema, index, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:355: in _to_file
_check_fiona("'to_file' method")
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
func = "'to_file' method"
def _check_fiona(func):
if fiona is None:
> raise ImportError(
f"the {func} requires the 'fiona' package, but it is not installed or does "
f"not import correctly.\nImporting fiona resulted in: {fiona_import_error}"
)
E ImportError: the 'to_file' method requires the 'fiona' package, but it is not installed or does not import correctly.
E Importing fiona resulted in: /usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/ogrext.cpython-310-x86_64-linux-gnu.so: undefined symbol: _PyGen_Send
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:80: ImportError
___________________ test_geopandas_plot3d_non_default_circle ___________________
@pytest.mark.mpl_image_compare
def test_geopandas_plot3d_non_default_circle():
"""
Check the default behavior of plotting geopandas DataFrame with MultiPoint
geometry in 3d.
"""
multipoint = shapely.geometry.MultiPoint([(0.5, 0.5, 0.5), (1.5, 1.5, 1.5)])
gdf = gpd.GeoDataFrame(geometry=[multipoint])
fig = Figure()
> fig.plot3d(
data=gdf,
perspective=[315, 25],
region=[0, 2, 0, 2, 0, 2],
projection="X2c",
frame=["WsNeZ1", "xag", "yag", "zag"],
zscale=1.5,
style="c0.2c",
)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/tests/test_geopandas.py:124:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:805: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:873: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:586: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/decorators.py:726: in new_module
return module_func(*args, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/src/plot3d.py:249: in plot3d
with file_context as fname:
/usr/share/miniconda3/envs/pygmt/lib/python3.10/contextlib.py:135: in __enter__
return next(self.gen)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/pygmt/helpers/tempfile.py:134: in tempfile_from_geojson
geojson.to_file(**ogrgmt_kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/geodataframe.py:1114: in to_file
_to_file(self, filename, driver, schema, index, **kwargs)
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:355: in _to_file
_check_fiona("'to_file' method")
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
func = "'to_file' method"
def _check_fiona(func):
if fiona is None:
> raise ImportError(
f"the {func} requires the 'fiona' package, but it is not installed or does "
f"not import correctly.\nImporting fiona resulted in: {fiona_import_error}"
)
E ImportError: the 'to_file' method requires the 'fiona' package, but it is not installed or does not import correctly.
E Importing fiona resulted in: /usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/ogrext.cpython-310-x86_64-linux-gnu.so: undefined symbol: _PyGen_Send
/usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/geopandas/io/file.py:80: ImportError |
This reverts commit 2ce685e.
|
Another month, another update~ The Question: Do we want to get this pull request on testing Python 3.10 in CI merged now-ish, or wait until the GMT 6.3 bump goes through?
|
seisman
reviewed
Dec 7, 2021
| tomli | ||
| mamba install python=${{ matrix.python-version }} \ | ||
| ninja cmake libblas libcblas liblapack fftw libgdal \ | ||
| geopandas ghostscript libnetcdf hdf5 zlib curl pcre make |
There was a problem hiding this comment.
Do you think we should install geopandas using pip instead?
There was a problem hiding this comment.
Ideally yes, and I did try it (see 69d4e67), but pip install geopandas doesn't work on Python 3.10 because the fiona dependency doesn't have Python 3.10 wheels yet and the install is not functional:
E ImportError: the 'to_file' method requires the 'fiona' package, but it is not installed or does not import correctly.
E Importing fiona resulted in: /usr/share/miniconda3/envs/pygmt/lib/python3.10/site-packages/fiona/ogrext.cpython-310-x86_64-linux-gnu.so: undefined symbol: _PyGen_Send
So I had to revert back to using conda install geopandas in 0604c95.
There was a problem hiding this comment.
FYI, Python 3.10 support in fiona is being worked on at Toblerity/Fiona#1049. Seems like the Python 3.10 wheels might take a while to come out, so probably shouldn't wait.
There was a problem hiding this comment.
If we're waiting for the wheels to come out, why shouldn't we wait to upgrade to Python 3.10?
There was a problem hiding this comment.
If we're waiting for the wheels to come out, why shouldn't we wait to upgrade to Python 3.10?
If I'm reading your sentence correctly, no, we don't have to wait for the fiona Python 3.10 wheels to come out. The current state on the main branch is that fiona is installed indirectly via conda install geopandas. @seisman's suggestion was that we use pip install --pre geopandas instead, but that doesn't work because fiona doesn't have Python 3.10 wheels.
Since geopandas/fiona is an optional dependency for PyGMT, I think we can just push ahead with this PR as is (i.e. stick with conda install geopandas), but happy to wait too if there's a good reason to.
There was a problem hiding this comment.
It seems the new fiona release will take at least another month (Toblerity/Fiona#1053). I think we don't need to wait for it.
| @@ -76,7 +76,7 @@ jobs: | |||
| uses: conda-incubator/[email protected] | |||
| with: | |||
| activate-environment: pygmt | |||
| python-version: ${{ matrix.python-version }} | |||
| # python-version: ${{ matrix.python-version }} | |||
There was a problem hiding this comment.
Any special reason to comment out this line?
There was a problem hiding this comment.
The setup-miniconda action won't work with Python 3.10, because there isn't a miniconda or mambaforge version with Python 3.10 yet (see https://repo.anaconda.com/miniconda/ and https://github.com/conda-forge/miniforge/releases). The Python 3.10 install step happens later below.
seisman
approved these changes
Dec 25, 2021
seisman
added
the
final review call
willschlitzer
approved these changes
Dec 27, 2021
weiji14
removed
the
final review call
6 tasks
sixy6e
pushed a commit
to sixy6e/pygmt
that referenced
this pull request
Dec 21, 2022
…1577) Updating the "GMT Dev Tests" GitHub Actions continuous integration workflows that used Python 3.9 to use Python 3.10 now. * Put quotes around 3.10 so that it doesn't get read as Python 3.1 * Manually install Python 3.10 on ci_tests_dev.yaml * Use pip to install dvc on ci_tests_dev workflow Workaround missing Python 3.10 packages for dvc on conda-forge. * Install numpy before other deps since it is a build dependency for some * Prefer older binary pip packages over newer pip packages Save from having to compile Python 3.10 packages, and fixes installation issues for some libraries like `aiohttp` which have outdated pre-release versions. * Set minimum Python version to 3.8 in README.rst
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
Python 3.10 has been released on 7 October 2021, changelog is at https://docs.python.org/3.10/whatsnew/3.10.html. See previous PR for Python 3.9 at #689. This PR is part 2/2 for adding Python 3.10 support, see also the sister PR at #1591.
Note: Updating only the "GMT Dev Tests" GitHub Actions continuous integration workflows that used Python 3.9 to use Python 3.10 now.
Reminder: Set Python 3.10 Github Actions CI as a required check.Will do this once Python 3.10 gets more adoption across the Python ecosystem.Fixes #
Reminders
make formatandmake checkto make sure the code follows the style guide.doc/api/index.rst.Slash Commands
You can write slash commands (
/command) in the first line of a comment to performspecific operations. Supported slash commands are:
/format: automatically format and lint the code/test-gmt-dev: run full tests on the latest GMT development version