Merge branch 'develop' into merge_nci_modules

.github/workflows/dive.yml

@@ -91,4 +91,4 @@ jobs:
         uses: wemake-services/docker-image-size-limit@master
         with:
           image: ${{ env.ORG }}/${{ env.IMAGE}}:_build
-          size: "7 GiB"
+          size: "8 GiB"

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:git-e4f55ab-jammy as sandbox-conda
+FROM mambaorg/micromamba:git-df79b72-jammy as sandbox-conda
 
 USER root
 COPY env.yaml /conf/
@@ -16,7 +16,7 @@ ENV CC=/env/bin/x86_64-conda_cos6-linux-gnu-gcc \
 RUN micromamba run -p /env pip install --no-cache-dir \
     --no-build-isolation -r /conf/requirements.txt
 
-FROM ubuntu:jammy-20230816
+FROM ubuntu:jammy-20240212
 
 ARG nb_user=jovyan
 ARG nb_uid=1000
@@ -38,7 +38,7 @@ ENV LC_ALL=C.UTF-8 \
 USER $nb_user
 # NOTE - JupyterLab extensions can now be distributed as prebuilt extensions and available to PyPI
 RUN echo "Enable jupyter lab extensions" \
-  && jupyter labextension install jupyterlab-theme-toggle \
+  && jupyter labextension install jupyterlab-topbar-extension jupyterlab-theme-toggle \
   && jupyter labextension list \
   && echo "...done"
 

docker/assets/sync_repo

@@ -15,9 +15,5 @@ BRANCH="${2:-master}"
     rm -rf "${WORKDIR}"/{.github,.gitignore,LICENSE,README.md,README.rst,CITATION.cff,USAGE.rst,docker-compose.yml,DEAfrica_notebooks_template.ipynb,DEA_notebooks_template.ipynb,Scientific_workflows,Tests} || true
     cp -Rv ${WORKDIR}/. ~/
     rm -rf "${WORKDIR}"
-    # Install Tools folder if available
-    if [ -e $HOME/Tools/setup.py ]; then
-        python -m pip install -e "$HOME/Tools" || true
-    fi
     rm -rf "$HOME/.git"
 }

docker/env.yaml

@@ -21,6 +21,7 @@ dependencies:
   - access
   - aiobotocore
   - boto3
+  - s5cmd
   - affine
   - aiohttp
   - aioitertools
@@ -52,7 +53,7 @@ dependencies:
   - datadog
   - deepdiff
   - defusedxml
-  - distributed
+  - distributed>=2023.11
   - docutils
   - ephem
   - eodatasets3
@@ -76,7 +77,7 @@ dependencies:
   - itsdangerous
   - Jinja2
   - jmespath
-  - jsonschema<4.18
+  - jsonschema>4.18
   - kiwisolver
   - lark
   - python-lmdb
@@ -113,7 +114,7 @@ dependencies:
   - pyrsistent
   - pystac
   - pystac-client
-  - pytest
+  - pytest!=8.1.0
   - python-dateutil
   - python-rapidjson
   - python-slugify
@@ -177,10 +178,10 @@ dependencies:
   - dask-ml
   - pathos
   - scikit-learn
-  - tensorflow=2.7
+  - tensorflow>=2.10
   - xgboost
   - zarr
-  - bokeh
+  - bokeh=3.2.2
   - descartes
   - matplotlib
   - seaborn
@@ -205,7 +206,7 @@ dependencies:
   - spyndex
   - urbanaccess
   - contextily
-  - pyTMD
+  - pyTMD<=2.1.0
 # jupyter things
   - autopep8
   - black
@@ -225,7 +226,8 @@ dependencies:
   - jupyterlab-topbar
   - jupyterlab-system-monitor
   - jupyterhub
-  - jupytext
+  - jupytext<1.16
+  - jupyterlab_pygments<0.3.0
   - jupyter-resource-usage
   - jupyter_server
   - jupyter-server-proxy

docker/requirements.txt

@@ -6,6 +6,9 @@ jupyterlab-logout
 jupyter-contrib-core
 jupyter-contrib-nbextensions
 jupyter-nbextensions-configurator
+# pin for jupyterlab=3.x
+jupyterlab-topbar-text==0.6.2
+jupyterlab-logout==0.5.0
 
 # ODC/DEA: these are installed in builder stage
 otps
@@ -17,12 +20,14 @@ s2cloudmask
 opencv-python-headless
 opencv-contrib-python-headless
 
-datacube[performance,s3]
+datacube[performance,s3] >= 1.8.17
+odc-algo @ git+https://github.com/opendatacube/odc-algo@b8dcfce
 odc-cloud[ASYNC]
 odc-stac
 odc-stats[ows]
 odc-ui
 odc-geo
+dea-tools
 
 thredds-crawler
 hdstats==0.1.8.post1