From ec7604ba3878a87ba633ae4471849411c4db3916 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 1 Jul 2026 00:12:27 +0000 Subject: [PATCH 1/2] build(deps): bump the pip-dependencies group in /docker with 5 updates Bumps the pip-dependencies group in /docker with 5 updates: | Package | From | To | | --- | --- | --- | | [geopandas](https://github.com/geopandas/geopandas) | `1.1.2` | `1.1.3` | | [jupyterlab](https://github.com/jupyterlab/jupyterlab) | `4.5.9` | `4.6.0` | | [pandas](https://github.com/pandas-dev/pandas) | `2.3.3` | `3.0.3` | | [pydeck](https://github.com/visgl/deck.gl) | `0.9.1` | `0.9.2` | | [rasterio](https://github.com/rasterio/rasterio) | `1.4.4` | `1.5.0` | Updates `geopandas` from 1.1.2 to 1.1.3 - [Release notes](https://github.com/geopandas/geopandas/releases) - [Changelog](https://github.com/geopandas/geopandas/blob/main/CHANGELOG.md) - [Commits](https://github.com/geopandas/geopandas/compare/v1.1.2...v1.1.3) Updates `jupyterlab` from 4.5.9 to 4.6.0 - [Release notes](https://github.com/jupyterlab/jupyterlab/releases) - [Changelog](https://github.com/jupyterlab/jupyterlab/blob/main/RELEASE.md) - [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.5.9...@jupyterlab/lsp@4.6.0) Updates `pandas` from 2.3.3 to 3.0.3 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](https://github.com/pandas-dev/pandas/compare/v2.3.3...v3.0.3) Updates `pydeck` from 0.9.1 to 0.9.2 - [Release notes](https://github.com/visgl/deck.gl/releases) - [Changelog](https://github.com/visgl/deck.gl/blob/master/CHANGELOG.md) - [Commits](https://github.com/visgl/deck.gl/commits) Updates `rasterio` from 1.4.4 to 1.5.0 - [Release notes](https://github.com/rasterio/rasterio/releases) - [Changelog](https://github.com/rasterio/rasterio/blob/main/CHANGES.txt) - [Commits](https://github.com/rasterio/rasterio/compare/1.4.4...1.5.0) --- updated-dependencies: - dependency-name: geopandas dependency-version: 1.1.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip-dependencies - dependency-name: jupyterlab dependency-version: 4.6.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip-dependencies - dependency-name: pandas dependency-version: 3.0.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pip-dependencies - dependency-name: pydeck dependency-version: 0.9.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: pip-dependencies - dependency-name: rasterio dependency-version: 1.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pip-dependencies ... Signed-off-by: dependabot[bot] --- docker/requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docker/requirements.txt b/docker/requirements.txt index 4bf9cd048bb..c1b9f5def5e 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -1,16 +1,16 @@ attrs descartes fiona==1.10.1 -geopandas==1.1.2 +geopandas==1.1.3 ipykernel ipywidgets -jupyterlab==4.5.9 +jupyterlab==4.6.0 jupyterlab-widgets==3.0.16 keplergl==0.3.7 matplotlib numpy==1.26.4 -pandas==2.3.3 +pandas==3.0.3 py4j==0.10.9.9 -pydeck==0.9.1 -rasterio==1.4.4 +pydeck==0.9.2 +rasterio==1.5.0 shapely==2.1.2 From 0ade48284c99fc03a21a98d247210914cccbc3ee Mon Sep 17 00:00:00 2001 From: Jia Yu Date: Sat, 11 Jul 2026 20:07:26 -0700 Subject: [PATCH 2/2] Move numpy to 2.x and fix the Debian-numpy uninstall failure rasterio 1.5.0 requires numpy>=2, so the group's rasterio bump cannot resolve while numpy is pinned to 1.26.4. Bump numpy to 2.2.6, and add --ignore-installed to the requirements pip install: install-spark.sh installs GDAL, which pulls in Debian's python3-numpy, and pip cannot uninstall a distro-managed package ('RECORD file not found'). --ignore-installed installs into /usr/local, which precedes dist-packages on sys.path. Hold pandas at 2.3.3 (3.0 is a breaking major not yet validated against PySpark 4.0's pandas API and Sedona). --- docker/requirements.txt | 4 ++-- docker/sedona-docker.dockerfile | 7 ++++++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/docker/requirements.txt b/docker/requirements.txt index c1b9f5def5e..39d8bfd70ea 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -8,8 +8,8 @@ jupyterlab==4.6.0 jupyterlab-widgets==3.0.16 keplergl==0.3.7 matplotlib -numpy==1.26.4 -pandas==3.0.3 +numpy==2.2.6 +pandas==2.3.3 py4j==0.10.9.9 pydeck==0.9.2 rasterio==1.5.0 diff --git a/docker/sedona-docker.dockerfile b/docker/sedona-docker.dockerfile index 4156fa36c3b..361ec7c2950 100644 --- a/docker/sedona-docker.dockerfile +++ b/docker/sedona-docker.dockerfile @@ -49,8 +49,13 @@ RUN chmod +x ${SEDONA_HOME}/docker/install-spark.sh RUN ${SEDONA_HOME}/docker/install-spark.sh ${spark_version} ${hadoop_s3_version} ${aws_sdk_version} # Install Python dependencies +# --ignore-installed is required because install-spark.sh installs GDAL +# (gdal-bin/libgdal-dev), which pulls in Debian's python3-numpy. Upgrading numpy +# then fails with "Cannot uninstall numpy ... RECORD file not found" because pip +# cannot remove a distro-managed package. --ignore-installed skips that uninstall +# and installs into /usr/local, which precedes dist-packages on sys.path. COPY docker/requirements.txt /opt/requirements.txt -RUN pip3 install --no-cache-dir -r /opt/requirements.txt --break-system-packages +RUN pip3 install --no-cache-dir -r /opt/requirements.txt --break-system-packages --ignore-installed # Copy local compiled jars and python code to the docker environment