Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

xarray version update #323

Merged
merged 14 commits into from
May 12, 2023
Merged

xarray version update #323

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
0593a21
xarray version update
dabhicusp Apr 26, 2023
de97d97
Added test case for memory.
dabhicusp Apr 27, 2023
fcfc007
fixed lint errors.
dabhicusp Apr 27, 2023
735ae2d
Fixed CI/CD xarray version.
dabhicusp Apr 28, 2023
834a7de
Updated ci.yml cache value.
dabhicusp Apr 28, 2023
8321789
Revert "Updated ci.yml cache value."
dabhicusp Apr 28, 2023
8960314
Added flag for channel priority in ci.yml.
dabhicusp Apr 28, 2023
cd0e961
Revert "Added flag for channel priority in ci.yml."
dabhicusp Apr 28, 2023
8c57ae7
Fixed xarray issue in CI/CD.
dabhicusp Apr 28, 2023
3048a66
Fixed pip dependency in ci/cd.
dabhicusp Apr 28, 2023
6d95593
Updated NetCDF file Generation code.
dabhicusp May 4, 2023
f2eddef
Lint error resolved.
dabhicusp May 4, 2023
e657623
Context manager added in write_netcdf.
dabhicusp May 9, 2023
7d28454
bumping weather-mv version to v0.2.13
dabhicusp May 12, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion ci3.8.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,6 @@ dependencies:
- requests=2.28.1
- netcdf4=1.6.1
- rioxarray=0.12.2
- xarray=2022.10.0
- xarray-beam=0.3.1
- ecmwf-api-client=1.6.3
- fsspec=2022.10.0
Expand All @@ -31,5 +30,6 @@ dependencies:
- pygrib=2.1.4
- pip:
- earthengine-api==0.1.329
- xarray==2023.1.0
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

On second though: we may get weird link errors with our conda deploy if we don't include this as a conda dependency. Has this been published on conda forge yet?

Copy link
Collaborator Author

@dabhicusp dabhicusp May 9, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

While trying to install the xarray=2023.1.0 package in the CI/CD pipeline via the conda-forge channel, I encountered an error. However, the installation process worked without any issues when I tried it locally. Here's an error message that I received during the CI/CD run:
image
Link
Do you have any suggestions for resolving this issue?

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It looks like 2023.4.2 is available on conda (I think this is the latest release). How about we try upgrading to that version?

https://github.com/conda-forge/xarray-feedstock#current-release-info

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

As mentioned in the PR Description This is the last updated version of xarray that python 3.8 supported.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Maybe I'm getting ahead of myself. I'm happy to keep the pip (vs the conda) version, if we can test our local and docker deployment to prove that there are no link errors. Let's also create a follow-up CL to deprecate python 3.8 and include python 3.10. How does this sound?

Copy link
Collaborator Author

@dabhicusp dabhicusp May 11, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hello @alxmrs, I have tested both the local and docker deployments and did not encounter any errors.

Yes, this sounds good to me.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for confirming!

- ruff==0.0.260
- .[test]
2 changes: 1 addition & 1 deletion ci3.9.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,6 @@ dependencies:
- requests=2.28.1
- netcdf4=1.6.1
- rioxarray=0.12.2
- xarray=2022.10.0
- xarray-beam=0.3.1
- ecmwf-api-client=1.6.3
- fsspec=2022.10.0
Expand All @@ -31,5 +30,6 @@ dependencies:
- pygrib=2.1.4
- pip:
- earthengine-api==0.1.329
- xarray==2023.1.0
- ruff==0.0.260
- .[test]
2 changes: 1 addition & 1 deletion environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ dependencies:
- python=3.8.13
- apache-beam=2.40.0
- xarray-beam=0.3.1
- xarray=2022.11.0
- xarray=2023.1.0
- fsspec=2022.11.0
- gcsfs=2022.11.0
- rioxarray=0.12.2
Expand Down
2 changes: 1 addition & 1 deletion weather_dl/setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
"ecmwf-api-client==1.6.3",
"numpy>=1.19.1",
"pandas==1.5.1",
"xarray==2022.11.0",
"xarray==2023.1.0",
"requests>=2.24.0",
"urllib3==1.26.5",
"google-cloud-firestore==2.6.0",
Expand Down
47 changes: 46 additions & 1 deletion weather_mv/loader_pipeline/sinks_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,14 @@
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import contextlib
import datetime
import unittest
from functools import wraps
import numpy as np
import tempfile
import tracemalloc
import unittest
import xarray as xr

import weather_mv
from .sinks import match_datetime, open_dataset
Expand All @@ -38,6 +43,40 @@ def decorated(*args, **kwargs):
return decorated


@contextlib.contextmanager
def limit_memory(max_memory=30):
''''Measure memory consumption of the function.
'memory limit' in MB
'''
try:
tracemalloc.start()
yield
finally:
current, peak = tracemalloc.get_traced_memory()
tracemalloc.stop()
assert peak / 1024 ** 2 <= max_memory, f"Memory usage {peak / 1024 ** 2} exceeded {max_memory} MB limit."


@contextlib.contextmanager
def write_netcdf():
"""Generates temporary netCDF file using xarray."""
lat_dim = 3210
lon_dim = 3440
lat = np.linspace(-90, 90, lat_dim)
lon = np.linspace(-180, 180, lon_dim)
data_arr = np.random.uniform(low=0, high=0.1, size=(5, lat_dim, lon_dim))

ds = xr.Dataset(
{"var_1": (('time', 'lat', 'lon'), data_arr)},
coords={
"lat": lat,
"lon": lon,
})
with tempfile.NamedTemporaryFile() as fp:
ds.to_netcdf(fp.name)
yield fp.name


class OpenDatasetTest(TestDataBase):

def setUp(self) -> None:
Expand Down Expand Up @@ -67,6 +106,12 @@ def test_opens_tif_files(self):
self.assertIsNotNone(ds)
self.assertDictContainsSubset({'is_normalized': False}, ds.attrs)

def test_open_dataset__fits_memory_bounds(self):
alxmrs marked this conversation as resolved.
Show resolved Hide resolved
with write_netcdf() as test_netcdf_path:
with limit_memory(max_memory=30):
with open_dataset(test_netcdf_path) as _:
pass


class DatetimeTest(unittest.TestCase):

Expand Down
4 changes: 2 additions & 2 deletions weather_mv/setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
"dataclasses",
"numpy==1.22.4",
"pandas==1.5.1",
"xarray==2022.11.0",
"xarray==2023.1.0",
"cfgrib==0.9.10.2",
"netcdf4==1.6.1",
"geojson==2.5.0",
Expand All @@ -62,7 +62,7 @@
packages=find_packages(),
author='Anthromets',
author_email='[email protected]',
version='0.2.12',
version='0.2.13',
url='https://weather-tools.readthedocs.io/en/latest/weather_mv/',
description='A tool to load weather data into BigQuery.',
install_requires=beam_gcp_requirements + base_requirements,
Expand Down
2 changes: 1 addition & 1 deletion weather_sp/setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
"pygrib==2.1.4",
"eccodes",
"numpy>=1.20.3",
"xarray==2022.11.0",
"xarray==2023.1.0",
"scipy==1.9.3",
]

Expand Down