Comments (13)
mmann1123
commented on May 24, 2024
Ok I will work on this now. Sorry about the delay.
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mmann1123
commented on May 24, 2024
@jgrss Ok after a lot of fumbling I figured it out I think. Should be resolved in #194
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mmann1123
commented on May 24, 2024
@jgrss I put together a dockerfile to show you what I mean about local testing passing. #196
FROM ubuntu:20.04
USER root
RUN apt update -y && apt upgrade -y && \
apt install -y software-properties-common && \
add-apt-repository ppa:ubuntugis/ppa && \
apt update -y && apt install -y \
gdal-bin \
geotiff-bin \
git \
libgdal-dev \
libgl1 \
libspatialindex-dev \
wget \
python-is-python3 \
pip \
g++
RUN pip install Cython numpy rasterio
RUN git clone https://github.com/jgrss/geowombat.git --branch fix--mmann1123/MLdata
RUN pip install -r /geowombat/requirements.txt
RUN pip install sklearn-xarray pip-tools rtree ipykernel
RUN cd geowombat && pip install --user -e .
# CMD cd geowombat && git pull &&
RUN echo ' # %% \n\
import sys \n\
sys.path.append("/") \n\
sys.path.append("/geowombat") \n\
import geowombat as gw \n # %%' > ./geowombat/src/debug_script.py
CMD cd geowombat/tests/ && python -m test_ml && bash
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mmann1123
commented on May 24, 2024
@jgrss any idea why this is failing but not the docker build?
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jgrss
commented on May 24, 2024
I haven't yet figured this one out. And it's not just Docker. The tests from your branch pass in a local venv but fail when I push to CI.
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mmann1123
commented on May 24, 2024
Ok well, it makes me feel better that it isn't just me.
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mmann1123
commented on May 24, 2024
Maybe sklearn_xarray doesn't pin a version for xarray that is needs? Not sure what else might be going wrong
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jgrss
commented on May 24, 2024
sklearn-xarray pins xarray=0.15.1 here, whereas we pin xarray=2022.6.0 here. However, geowombat should upgrade Xarray with:
RUN cd geowombat && pip install --user -e .
coming after
RUN pip install sklearn-xarray pip-tools rtree ipykernel
If I do a clean install of geowombat and then
python -c "import xarray as xr;print(xr.__version__)"
I get
2022.6.0Can you print the Xarray version that's installed in the Docker image?
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jgrss
commented on May 24, 2024
You can also reduce
RUN pip install sklearn-xarray pip-tools rtree ipykernel
to
RUN pip install pip-tools ipykernel
and do
RUN cd geowombat && pip install --user -e ."[ml,perf]"
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mmann1123
commented on May 24, 2024
Figured it might be worth looking at everything from the docker build - looks like xarray=2022.6.0. Well Im running out of ideas here, looks like you were playing with setuptools. Do we have access to the docker file they use to do the CI build?
Package Version Location
-------------------- -------------------- --------------
affine 2.3.1
aiosignal 1.2.0
asttokens 2.0.8
attrs 22.1.0
backcall 0.2.0
certifi 2019.11.28
cffi 1.15.1
cftime 1.6.1
chardet 3.0.4
click 8.1.3
click-plugins 1.1.1
cligj 0.7.2
cloudpickle 2.2.0
cryptography 38.0.1
cycler 0.11.0
Cython 0.29.32
dask 2022.9.0
dask-glm 0.2.0
dask-ml 2022.5.27
dbus-python 1.2.16
debugpy 1.6.3
decorator 5.1.1
distlib 0.3.6
distributed 2022.9.0
distro-info 0.23ubuntu1
entrypoints 0.4
executing 1.0.0
filelock 3.8.0
Fiona 1.8.21
fonttools 4.37.1
frozenlist 1.3.1
fsspec 2022.8.2
GDAL 3.3.2
geopandas 0.11.1
geowombat 2.0.0 /geowombat/src
grpcio 1.43.0
h5netcdf 1.0.2
h5py 3.7.0
HeapDict 1.0.1
idna 2.8
importlib-metadata 4.12.0
importlib-resources 5.9.0
ipykernel 6.15.2
ipython 8.5.0
jedi 0.18.1
Jinja2 3.1.2
joblib 1.1.0
jsonschema 4.16.0
jupyter-client 7.3.5
jupyter-core 4.11.1
kiwisolver 1.4.4
lightgbm 3.3.2
llvmlite 0.39.1
locket 1.0.0
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
msgpack 1.0.4
multipledispatch 0.6.0
munch 2.5.0
nest-asyncio 1.5.5
netCDF4 1.6.0
numba 0.56.2
numpy 1.23.3
opencv-python 4.6.0.66
packaging 21.3
pandas 1.5.0rc0
parso 0.8.3
partd 1.3.0
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
pip 20.0.2
pkgutil-resolve-name 1.3.10
platformdirs 2.5.2
prompt-toolkit 3.0.31
protobuf 3.20.1
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
pycparser 2.21
pygeos 0.13
Pygments 2.13.0
PyGObject 3.36.0
pyparsing 3.0.9
pyproj 3.4.0
pyrsistent 0.18.1
python-apt 2.0.0+ubuntu0.20.4.8
python-dateutil 2.8.2
pytz 2022.2.1
PyYAML 6.0
pyzmq 23.2.1
rasterio 1.3.2
ray 2.0.0
requests 2.22.0
requests-unixsocket 0.2.0
retry 0.9.2
Rtree 1.0.0
scikit-learn 1.1.2
scipy 1.9.1
setuptools 45.2.0
Shapely 1.8.4
six 1.14.0
sklearn-xarray 0.4.0
snuggs 1.4.7
sortedcontainers 2.4.0
stack-data 0.5.0
tblib 1.7.0
threadpoolctl 3.1.0
toolz 0.12.0
tornado 6.1
tqdm 4.64.1
traitlets 5.3.0
unattended-upgrades 0.1
urllib3 1.25.8
virtualenv 20.16.5
wcwidth 0.2.5
wheel 0.34.2
xarray 2022.6.0
zict 2.2.0
zipp 3.8.1
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jgrss
commented on May 24, 2024
Are we sure that sklearn-xarray requiring xarray==0.15.1 isn't causing a problem?
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mmann1123
commented on May 24, 2024
I think that has something to do with it, but based on it working locally and on docker, I am assuming it has to do with the way CI is building the image for testing.
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jgrss
commented on May 24, 2024
See #198
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