update notebook outputs - PAVICS image py311-250422 #562
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Should this be synchronized merge with Ouranosinc/PAVICS-e2e-workflow-tests#147 instead? |
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Apr 28, 2025
# Overview <!-- NOTE: Remember to tag 'release-py###-######' on the commit of this merge. --> ## Changes - Removes several obsolete `pip` and `conda` dependencies from the `environment.yml` and adds a lot more metadata to each entry. - The only remaining `PyPI`-provided libraries are now: - `figanos` → conda-forge/staged-recipes#29826 (comment) - `ipython-blocking` - `xncml` → plans to port to `conda-forge` - `Dockerfile` and `Dockerfile.testing`: Removed the `defaults` Anaconda channel and added `nodefaults` channel. - Relevant blog article: https://ubinfie.github.io/2024/10/15/anaconda-defaults.html - There is an issue with `miniforge`/`mambaforge` using a nonstandard location for setting `channels`. This makes it much harder to fully remove `defaults` in a docker-based environment. Setting `nodefaults` above `defaults` in the priority list is a workaround. Perhaps this will be fixed eventually. - Jupyter env changes: - Channels now includes `fortiers` for the `fstd2nc` library (previously installed via PyPI). - Relevant changes (alphabetical order): ```diff > - cf-units=3.3.0=py311h9f3472d_0 < - cf_xarray=0.10.0=pyhd8ed1ab_0 > - cf_xarray=0.10.5=pyhd8ed1ab_0 < - dash=2.18.1=pyhd8ed1ab_0 > - dash=3.0.3=pyhd8ed1ab_0 < - dask=2024.10.0=pyhd8ed1ab_0 < - dask-core=2024.10.0=pyhd8ed1ab_0 < - dask-expr=1.1.16=pyhd8ed1ab_0 > - dask=2025.4.0=pyhd8ed1ab_0 > - dask-core=2025.4.0=pyhd8ed1ab_0 < - distributed=2024.10.0=pyhd8ed1ab_0 > - distributed=2025.4.0=pyhd8ed1ab_0 # ECCC libraries < - fstd2nc==0.20240625.5=pypi < - fstd2nc-deps==0.20200304.6=pypi > - eccc_libburpc=1.17=0 > - eccc_libezinterpv=20.0.1.1=hdcf949b_2 > - eccc_librmn=20.0.3=0 > - eccc_libtdpack=1.6.3.1=0 > - eccc_libvgrid=6.9.3=0 > - eccc_rpnpy=2.2.0=py311h48b7412_1 > - eccc_support_libs=2023.12.0=0 < - eccodes=2.38.3=h8bb6dbc_1 > - eccodes=2.41.0=h8bb6dbc_0 < - esmf=8.6.1=nompi_h4441c20_3 < - esmpy=8.6.1=pyhc1e730c_0 > - esmf=8.8.1=mpi_mpich_h7cf99a1_100 > - esmpy=8.8.1=pyhecae5ae_0 < - figanos=0.3.0=pypi > - figanos=0.4.0=pypi < - fiona=1.9.5=py311hf8e0aa6_2 > - fiona=1.10.1=py311hf6089d3_3 < - flox=0.9.14=pyhd8ed1ab_0 > - flox=0.10.1=pyhd8ed1ab_0 < - gdal=3.8.5=py311hf92cf48_11 > - gdal=3.10.3=py311hef8459e_3 < - geoviews=1.13.0=hd8ed1ab_0 < - geoviews-core=1.13.0=pyha770c72_0 > - geoviews=1.14.0=hd8ed1ab_0 > - geoviews-core=1.14.0=pyha770c72_0 < - holoviews=1.20.0=pyhd8ed1ab_0 > - holoviews=1.20.2=pyhd8ed1ab_0 < - intake=0.7.0=pyhd8ed1ab_0 < - intake-esm=2024.2.6=pyhd8ed1ab_1 < - intake-geopandas=0.4.0=pyhd8ed1ab_0 < - intake-thredds=2024.3.1=pyhd8ed1ab_0 > - intake=2.0.8=pyhd8ed1ab_0 > - intake-esm=2025.2.3=pyhd8ed1ab_0 > - intake-geopandas=0.4.0=pyhd8ed1ab_1 > - intake-thredds=2025.2.18=pyhd8ed1ab_0 < - matplotlib=3.9.2=py311h38be061_2 < - matplotlib-base=3.9.2=py311h2b939e6_2 > - matplotlib=3.10.1=py311h38be061_0 > - matplotlib-base=3.10.1=py311h2b939e6_0 < - netcdf4=1.6.5=nompi_py311h74118c1_102 > - netcdf4=1.7.2=nompi_py311hae66bec_101 < - numba=0.60.0=py311h4bc866e_0 > - numba=0.61.2=py311h4e1c48f_0 # This is due to pinning in figanos for `numpy <2.0.0` < - numpy=1.26.4=py311h64a7726_0 > - numpy=1.26.4=pypi < - pint=0.23=pyhd8ed1ab_1 > - pint=0.24.4=pyhd8ed1ab_1 < - proj=9.4.0=hb784bbd_2 > - proj=9.6.0=h0054346_1 < - pyarrow=17.0.0=py311hbd00459_2 < - pyarrow-core=17.0.0=py311h4854187_2_cpu > - pyarrow=19.0.1=py311h38be061_0 > - pyarrow-core=19.0.1=py311h4854187_0_cpu < - pydantic==2.7.4=pypi < - pydantic-core==2.18.4=pypi > - pydantic=2.11.3=pyh3cfb1c2_0 > - pydantic-core=2.33.1=py311h687327b_0 < - pymetalink=6.5.2=pyhd8ed1ab_0 > - pymetalink=6.5.3=pyhd8ed1ab_0 < - pyogrio=0.7.2=py311hf8e0aa6_1 > - pyogrio=0.10.0=py311hf6089d3_1 < - pyproj=3.6.1=py311hc21b84f_7 > - pyproj=3.7.1=py311h0960b38_1 < - pytest-tornasync=0.6.0.post2=pypi > - pytest-tornasync=0.6.0.post2=pyhd8ed1ab_1 < - raven-hydro=0.3.2=py311h81cb690_1 > - raven-hydro=0.4.0=py311h81cb690_0 < - ravenpy=0.16.0=pyhd8ed1ab_0 > - ravenpy=0.18.1=pyhd8ed1ab_0 # Obsolete and archived < - roocs-utils=0.6.9=pyhd8ed1ab_0 < - s3fs=2024.10.0=pyhd8ed1ab_0 > - s3fs=2025.3.2=pyhd8ed1ab_0 < - scikit-image=0.24.0=py311h7db5c69_3 < - scikit-learn=1.5.2=py311h57cc02b_1 > - scikit-image=0.25.2=py311h7db5c69_0 > - scikit-learn=1.6.1=py311h57cc02b_0 < - scipy=1.14.1=py311he9a78e4_1 > - scipy=1.15.2=py311h8f841c2_0 < - shapely=2.0.4=py311h0bed3d6_1 > - shapely=2.1.0=py311h3dc67b8_0 # Downgrade < - streamlit=1.40.0=pyhd8ed1ab_0 > - streamlit=1.8.0=pyhd8ed1ab_0 < - xarray=2024.9.0=pyhd8ed1ab_1 > - xarray=2025.3.0=pyhd8ed1ab_0 < - xclim=0.53.2=pyhd8ed1ab_0 > - xclim=0.56.0=pyhd8ed1ab_0 < - xesmf=0.8.8=pyhd8ed1ab_0 > - xesmf=0.8.9=pyhd8ed1ab_0 < - xscen=0.10.1=pyhd8ed1ab_0 > - xscen=0.12.1=pyhd8ed1ab_0 < - xsdata=24.11=pypi > - xsdata=25.4=pyhd8ed1ab_0 # New requirement for xscen > - xsdba=0.4.0=pyhd8ed1ab_0 < - zarr=2.18.3=pyhd8ed1ab_0 > - zarr=2.18.7=pyhd8ed1ab_0 ``` ## Test - [x] Deployed as "gamma" image in p 8000 roduction for bokeh visualization performance regression testing. - [x] Manual test notebook https://github.com/Ouranosinc/PAVICS-landing/blob/master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-5Visualization.ipynb for bokeh visualization performance and it looks fine. - Jenkins build (only known intermittent esgf-dap.ipynb) https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/1ef212852e07fae3c1bc26de8501228df6f8e0e1/docker/saved_buildout/jenkins-buildlogs-default.txt - esgf-dap issue: Ouranosinc/pavics-sdi#353 ## Related Issue / Discussion - Matching notebook fixes: - Pavics-sdi: Ouranosinc/pavics-sdi#352 - Finch: N/A - PAVICS-landing: Ouranosinc/PAVICS-landing#107 - RavenPy: CSHS-CWRA/RavenPy#484 - Raven: Ouranosinc/raven#562 - Deployment to PAVICS: bird-house/birdhouse-deploy#526 - Other issues found while working on this one - `xesmf` 0.8.7 is incompatible with the latest versions of `xarray` (2025.3.0) and `numba` (61.0). `xesmf` 0.8.8 is broken and excluded via `xscen` dependency pins. - pangeo-data/xESMF#426 - The PyPI library for `fstd2nc` was replaced with the `conda` package (provided via `fortiers`). `fstd2nc==0.20250310.0_0` was found to be missing a necessary module. - neishm/fstd2nc#104 (comment) - Previous release: #137 ## Additional Information Full diff conda env export: release-py311-241111...1ef2128 Full new conda env export: https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/1ef212852e07fae3c1bc26de8501228df6f8e0e1/docker/saved_buildout/conda-env-export.yml DockerHub build log https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/1ef212852e07fae3c1bc26de8501228df6f8e0e1/docker/saved_buildout/docker-buildlogs.txt
Zeitsperre
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Apr 28, 2025
## Overview This PR updates the Jupyter env image with several new versions of dependencies. The Anaconda environment has been overhauled to rely more on native Anaconda packages and to remove many old/incompatible packages. ## Changes **The version in this PR has not yet been bumped** _Not adding things here under breaking/non-breaking, as I'm not certain what constitutes either type of change (though I would tend towards these being breaking changes for scientists)_ - Updates the Jupyter environment for PAVICS to py311-250423 - Anaconda channels now include `nodefaults` and `fortiers` (for `fstd2nc` library). - Many obsolete and incompatible plugins and dependencies have been removed, including many `PyPI`-provided packages. - The next major release will be built entirely (or almost entirely) from Anaconda packages. ## Related Issue / Discussion Ouranosinc/PAVICS-e2e-workflow-tests#147 ## Additional Information - Matching notebook fixes: - Pavics-sdi: Ouranosinc/pavics-sdi#352 - PAVICS-landing: Ouranosinc/PAVICS-landing#107 - RavenPy: CSHS-CWRA/RavenPy#484 - Raven: Ouranosinc/raven#562 ## CI Operations <!-- The test suite can be run using a different DACCS config with ``birdhouse_daccs_configs_branch: branch_name`` in the PR description. To globally skip the test suite regardless of the commit message use ``birdhouse_skip_ci`` set to ``true`` in the PR description. Using ``[<cmd>]`` (with the brackets) where ``<cmd> = skip ci`` in the commit message will override ``birdhouse_skip_ci`` from the PR description. Such commit command can be used to override the PR description behavior for a specific commit update. However, a commit message cannot 'force run' a PR which the description turns off the CI. To run the CI, the PR should instead be updated with a ``true`` value, and a running message can be posted in following PR comments to trigger tests once again. --> birdhouse_daccs_configs_branch: master birdhouse_skip_ci: false
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Overview
This PR fixes an issue with notebook outputs
Changes:
Related Issue / Discussion
This PR might not be needed, assuming that the latest fix removes this message.
Additional Information
Ouranosinc/PAVICS-e2e-workflow-tests#147