Merge branch 'develop' of https://github.com/GeoscienceAustralia/burn…

…-mapping into develop

Dockerfile

@@ -1,44 +1,29 @@
-ARG py_env_path=/env
-ARG V_BASE=3.3.0
+FROM osgeo/gdal:ubuntu-small-3.4.1
 
-FROM opendatacube/geobase-builder:${V_BASE} as env_builder
-ENV LC_ALL=C.UTF-8
-
-# Install our Python requirements
-COPY requirements.txt /conf/
-COPY constraints.txt /conf/
-ARG py_env_path
-RUN echo "" > /conf/constraints.txt
-RUN cat /conf/requirements.txt \
-  && env-build-tool new /conf/requirements.txt /conf/constraints.txt ${py_env_path} \
-  && rm -rf /root/.cache/pip \
-  && echo done
-
-# Below is the actual image that does the running
-FROM opendatacube/geobase-runner:${V_BASE}
 ENV DEBIAN_FRONTEND=noninteractive \
     LC_ALL=C.UTF-8 \
     LANG=C.UTF-8
 
-RUN apt-get update \
-    && apt-get install -y \
-         libtiff-tools \
-         git \
-         htop \
-         tmux \
-         wget \
-         curl \
-         nano \
-         unzip \
-         vim \
-         gcc \
-    && rm -rf /var/lib/apt/lists/*
-
-WORKDIR /tmp
-
-ARG py_env_path
-COPY --from=env_builder $py_env_path $py_env_path
-ENV PATH="${py_env_path}/bin:${PATH}"
+# Apt installation
+RUN apt-get update && \
+    apt-get install -y \
+      build-essential \
+      fish \
+      git \
+      vim \
+      htop \
+      wget \
+      unzip \
+      python3-pip \
+      libpq-dev python-dev \
+    && apt-get autoclean && \
+    apt-get autoremove && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}
+
+# Pip installation
+RUN mkdir -p /conf
+COPY requirements.txt /conf/
+RUN pip install -r /conf/requirements.txt
 
 # Copy source code and install it
 RUN mkdir -p /code
@@ -48,7 +33,7 @@ ADD . /code
 RUN echo "Installing dea-burn-cube through the Dockerfile."
 RUN pip install --extra-index-url="https://packages.dea.ga.gov.au" .
 
-RUN env && echo $PATH && pip freeze && pip check
+RUN pip freeze && pip check
 
 # Make sure it's working
 RUN dea-burn-cube --version

constraints.txt

@@ -1,149 +1,137 @@
-affine==2.3.1
+affine==2.4.0
 aiohttp==3.8.3
 aiosignal==1.3.1
 asttokens==2.2.1
 async-timeout==4.0.2
-attrs==22.1.0
+attrs==22.2.0
 backcall==0.2.0
-boto3==1.24.59
-botocore==1.27.59
+boto3==1.26.100
+botocore==1.29.100
 branca==0.6.0
-cachetools==5.2.1
+cachetools==5.3.0
 certifi==2022.12.7
-cffi==1.15.1
 cftime==1.6.2
 charset-normalizer==2.1.1
-ciso8601==2.2.0
+ciso8601==2.3.0
 click==8.1.3
 click-plugins==1.1.1
 cligj==0.7.2
-cloudpickle==2.2.0
-comm==0.1.2
-contourpy==1.0.6
-coverage==6.5.0
-cryptography==38.0.4
+cloudpickle==2.2.1
+contourpy==1.0.7
 cycler==0.11.0
-dask==2022.12.0
-dask-image==2022.9.0
+dask==2023.3.2
+dask-glm==0.2.0
+dask-image==2023.3.0
+dask-ml==2023.3.24
 datacube==1.8.9
-dea-tools==0.2.7
-debugpy==1.6.4
+dea-tools==0.2.8.dev47
 decorator==5.1.1
-distributed==2022.12.0
-entrypoints==0.4
-exceptiongroup==1.0.4
+distributed==2023.3.2
 executing==1.2.0
-folium==0.13.0
-fonttools==4.38.0
+Fiona==1.8.22
+folium==0.14.0
+fonttools==4.39.2
 frozenlist==1.3.3
-fsspec==2022.11.0
-GDAL==3.5.1
-geographiclib==1.52
+fsspec==2023.3.0
+GDAL==3.4.1
+GeoAlchemy2==0.13.1
+geographiclib==2.0
 geopandas==0.12.2
 geopy==2.3.0
-greenlet==2.0.1
+greenlet==2.0.2
+hdstats==0.2.1
 HeapDict==1.0.1
 idna==3.4
-imageio==2.22.4
-importlib-resources==5.10.1
-iniconfig==1.1.1
-ipykernel==6.19.2
+imageio==2.27.0
+importlib-metadata==6.1.0
+importlib-resources==5.12.0
 ipyleaflet==0.17.2
-ipython==8.7.0
-ipywidgets==8.0.3
+ipython==8.11.0
+ipywidgets==8.0.5
 jedi==0.18.2
 Jinja2==3.1.2
 jmespath==1.0.1
 joblib==1.2.0
 jsonschema==4.17.3
 jupyter-ui-poll==0.2.2
-jupyter_client==7.4.8
-jupyter_core==5.1.0
-jupyterlab-widgets==3.0.4
+jupyterlab-widgets==3.0.6
 kiwisolver==1.4.4
-lark-parser==0.12.0
+lark==1.1.5
+lazy-loader==0.2
+llvmlite==0.39.1
 locket==1.0.0
-lxml==4.9.1
-MarkupSafe==2.1.1
-matplotlib==3.6.2
+lxml==4.9.2
+MarkupSafe==2.1.2
+matplotlib==3.7.1
 matplotlib-inline==0.1.6
-moto==4.0.11
-msgpack==1.0.4
-multidict==6.0.3
+msgpack==1.0.5
+multidict==6.0.4
+multipledispatch==0.6.0
 munch==2.5.0
-nest-asyncio==1.5.6
-netCDF4==1.6.2
-networkx==2.8.8
+netCDF4==1.6.3
+networkx==3.0
+numba==0.56.4
 numexpr==2.8.4
 numpy==1.23.5
 odc-algo==0.2.3
 odc-ui==0.2.0a3
-OWSLib==0.27.2
-packaging==22.0
-pandas==1.5.2
+OWSLib==0.28.1
+packaging==23.0
+pandas==1.5.3
 parso==0.8.3
 partd==1.3.0
 pexpect==4.8.0
 pickleshare==0.7.5
-Pillow==9.3.0
+Pillow==9.4.0
 PIMS==0.6.1
-pkg_resources==0.0.0
-pkgutil_resolve_name==1.3.10
-platformdirs==2.6.0
-pluggy==1.0.0
-prompt-toolkit==3.0.36
+pkgutil-resolve-name==1.3.10
+prompt-toolkit==3.0.38
 psutil==5.9.4
 psycopg2==2.9.5
-psycopg2-binary==2.9.2
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pyarrow==10.0.1
-pycparser==2.21
-Pygments==2.13.0
+pyarrow==11.0.0
+Pygments==2.14.0
 pyparsing==3.0.9
 pyproj==3.2.1
-pyrsistent==0.19.2
-pytest==7.2.0
+pyrsistent==0.19.3
 python-dateutil==2.8.2
-pytz==2022.6
+pyTMD==1.1.3
+pytz==2023.2
 PyWavelets==1.4.1
 PyYAML==6.0
-pyzmq==24.0.1
-rasterio==1.3.4
-rasterstats==0.17.0
-requests==2.28.1
-responses==0.22.0
+rasterio==1.3.6
+rasterstats==0.18.0
+requests==2.28.2
 s3fs==0.4.2
 s3transfer==0.6.0
-scikit-image==0.19.3
-scikit-learn==1.2.0
-scipy==1.10.0
+scikit-image==0.20.0
+scikit-learn==1.2.2
+scipy==1.9.1
+setuptools-scm==7.1.0
 Shapely==1.8.5.post1
-simplejson==3.18.0
+simplejson==3.18.4
 six==1.16.0
 slicerator==1.1.0
 snuggs==1.4.7
 sortedcontainers==2.4.0
-SQLAlchemy==1.4.46
+SQLAlchemy==2.0.7
 stack-data==0.6.2
 tblib==1.7.0
 threadpoolctl==3.1.0
-tifffile==2022.10.10
-toml==0.10.2
+tifffile==2023.3.21
 tomli==2.0.1
 toolz==0.12.0
 tornado==6.2
-tqdm==4.64.1
-traitlets==5.7.0
+tqdm==4.65.0
+traitlets==5.9.0
 traittypes==0.2.1
-types-toml==0.10.8.1
-urllib3==1.26.13
-wcwidth==0.2.5
-Werkzeug==2.2.2
-widgetsnbextension==4.0.4
-xarray==2022.12.0
-xmltodict==0.13.0
-xyzservices==2022.9.0
+typing-extensions==4.5.0
+urllib3==1.26.15
+wcwidth==0.2.6
+widgetsnbextension==4.0.6
+xarray==2023.1.0
+xyzservices==2023.2.0
 yarl==1.8.2
 zict==2.2.0
-zipp==3.11.0
+zipp==3.15.0

requirements.txt

@@ -1,9 +1,15 @@
 aiohttp==3.8.3
+boto3
+botocore
+click
 datacube==1.8.9
 dea_tools==0.2.8.dev47
+fiona==1.8.22
+fsspec
+geopandas
 numpy==1.23.5
-psycopg2-binary==2.9.2
+pyarrow
 pyproj==3.2.1
 s3fs==0.4.2
+scipy==1.9.1
 Shapely==1.8.5.post1
-SQLAlchemy==1.4.46

setup.py

@@ -9,22 +9,6 @@
         name="dea-burn-cube",
         packages=["dea_burn_cube"],
         python_requires=">=3.8",
-        install_requires=[
-            "click",
-            "pytest",
-            "coverage",
-            "geopandas",
-            "datacube",
-            "boto3",
-            "botocore",
-            "pyarrow",
-            "fsspec",
-            "s3fs",
-            "moto[s3]",
-            "tqdm",
-            "dea-tools",
-            "aiohttp",
-        ],
         entry_points={
             "console_scripts": ["dea-burn-cube=dea_burn_cube.__main__:main"],
         },