Merge pull request #100 from earthlab/upgrade-to-3.9

Upgrade to 3.11
earthlab · Sep 30, 2024 · d414461 · d414461
2 parents 2b98909 + f1b63a3
commit d414461
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diff --git a/.github/workflows/build-for-docker.yml b/.github/workflows/build-for-docker.yml
@@ -5,7 +5,7 @@ on: workflow_dispatch
 jobs:
   runtests:
     name: "Set up environment"
-    runs-on: "ubuntu-latest"
+    runs-on: "ubuntu-20.04"
     defaults:
       run:
         shell: bash -l {0}

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
@@ -10,6 +10,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
+        with:
+          ref: upgrade-to-3.9
 
       - name: Login to DockerHub
         uses: docker/login-action@v1
@@ -19,12 +21,12 @@ jobs:
 
       - name: Build and push image
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5.1.0
         with:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: earthlab/earth-analytics-python-env:${GITHUB_REF##*/}
+          tags: earthlab/earth-analytics-dev-env:latest
 
       - name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}
diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
@@ -9,21 +9,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        os: 
+          - "ubuntu-latest"
+          - "macos-13"
+          - "macos-latest"
+          - "windows-latest"
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -el {0}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/[email protected]
+        with:
+            ref: ${{ github.head_ref || github.ref_name }}
       - uses: conda-incubator/[email protected]
         with:
-          miniconda-version: 'latest'
-          channels: conda-forge
-          channel-priority: true
-          auto-update-conda: false
           auto-activate-base: false
           environment-file: environment.yml
           activate-environment: earth-analytics-python
       - run: conda list
       - run: python -c "import earthpy"
-      - run: python -c "import rasterio"
+      - run: python -c "import geopandas"
+      - run: python -c "import rioxarray"
diff --git a/Dockerfile b/Dockerfile
@@ -1,16 +1,32 @@
-FROM jupyter/minimal-notebook
+FROM jupyter/minimal-notebook:python-3.11
 
-MAINTAINER Leah Wasser <[email protected]>
+# Installing package for libmamba
+USER root
+RUN apt-get update && \
+    apt-get install -y \
+    libfmt-dev \ 
+    libtiff5
 
-COPY environment.yml environment.yml
+USER jovyan
 
-RUN conda env update --name base --file environment.yml \
-  && conda info --envs \
-  && conda list \
-  && rm environment.yml
+# Set up conda
+RUN conda update conda 
+RUN conda config --remove channels conda-forge
+RUN conda config --add channels conda-forge
+#RUN conda config --set channel_priority strict
+#RUN conda config --set solver classic
 
-ENV PROJ_LIB $CONDA_DIR/share/proj
+# Create environment
+COPY environment.yml /home/jovyan/ 
+RUN conda env update -n base -f /home/jovyan/environment.yml
 
-# Test imports
-RUN python -c "import rasterio"
-RUN python -c "import earthpy"
+# Activating environment
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
+    echo "conda deactivate" >> /home/jovyan/.bash_profile && \
+    echo "conda activate base" >> /home/jovyan/.bash_profile
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base
+# using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
+RUN source /home/jovyan/.bash_profile
+
+# Install dev version of Earthpy
+RUN pip install git+https://github.com/earthlab/earthpy@apppears
diff --git a/environment.yml b/environment.yml
@@ -4,55 +4,69 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.8
+  - python=3.11
   - pip
+
   # Core scientific python
   - numpy
-  - pyqt
-  - tqdm
-  - kiwisolver
-
-  # Plotting
-  - matplotlib
-  - plotly
-  - seaborn
+  - pandas
+  - scipy
 
-  # Spatial packages
-  - pysal
+  # Geospatial libraries
+  # Coordinates and CRSs
   - pyproj>=3.0
-  - rasterstats
   - geopy
   - cartopy
-  - descartes
-  - contextily
-  - earthpy
-  - folium
+  # Vector data
+  - geopandas
   - geojson
-  - mapboxgl
-  - hydrofunctions
-  - geocoder
-  - tweepy
+  - pyogrio
+  # Raster data
   - xarray
-  - rioxarray>=0.3.0
-  - scipy
+  - h5py
   - netcdf4
-  - nc-time-axis
+  - rioxarray>=0.3.0
+  - xarray-spatial
   - regionmask
-
-  # Natural language processing
-  - nltk
-  - textblob
-
-  # Jupyter Environment
-  - papermill
-  - autopep8
+
+  # Interactive computing
+  - ipython
   - jupyterlab
   - notebook
-  - ipython
-  - jupyter_contrib_nbextensions
-  - nbclean
+  - tqdm
   - nbresuse
+  - papermill
+  - nbclean
+
+  # ML and modeling
+  - scikit-learn
+  - scikit-fuzzy
+
+  # Data access
+  - earthpy
+  - earthaccess
+  - pystac-client
 
-  # Autograding
-  - matplotcheck>=0.1.3
-  - nbgrader
+  # Plotting
+  # Matplotlib
+  - matplotlib
+  - nc-time-axis
+  - descartes
+  - contextily
+  - seaborn
+  # Holoviews
+  - hvplot
+  - geoviews>=1.10
+  - selenium
+  - phantomjs
+  - jupyter_bokeh
+  # Folium
+  - folium
+
+  # QA
+  - flake8
+  - flake8-import-order
+  - black
+  - autopep8
+  - pydocstyle
+  - nbqa