Update some slides

.github/workflows/pkgdown.yaml

@@ -57,12 +57,17 @@ jobs:
             any::gridExtra
             local::.
           needs: website
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
         with:
-          environment-file: environment.yml
-          cache-environment: false
-          cache-downloads: false
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+                  run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       - name: Create public directory
         run: |
           mkdir public

.gitlab-ci.yml

@@ -53,16 +53,13 @@ build-image:
   - name: ${DEVOPS_REGISTRY}usgs/docker:29-dind
     alias: docker
   script:
-    - echo ${CI_REGISTRY_PASSWORD} | docker login -u ${CI_REGISTRY_USER} --password-stdin $CI_REGISTRY
+    - echo "${CI_REGISTRY_PASSWORD}" | docker login -u "${CI_REGISTRY_USER}" --password-stdin $CI_REGISTRY
     - docker pull ${CI_REGISTRY_IMAGE}:latest || true
-    - cp *.tar.gz docker/
-    - cd docker
-    - docker build
-        -t ${CI_REGISTRY_IMAGE}:latest
-        .
+    - docker build --cache-from ${CI_REGISTRY_IMAGE}:latest -t ${CI_REGISTRY_IMAGE}:latest -t ${CI_REGISTRY_IMAGE}:BUILD_${CI_COMMIT_SHORT_SHA} -f docker/Dockerfile .
+    # If this is building a git tag, also push the corresponding docker tag
+    - if [ -n "${CI_COMMIT_TAG}" ]; then docker tag "${CI_REGISTRY_IMAGE}:BUILD_${CI_COMMIT_SHORT_SHA}" "${CI_REGISTRY_IMAGE}:${CI_COMMIT_TAG}"; fi
     - docker push --all-tags ${CI_REGISTRY_IMAGE}
-  artifacts:
-    expire_in: 45 minutes
+
 
 buildcheck:
   image: ${CI_REGISTRY_IMAGE}:latest
@@ -135,11 +132,11 @@ longtest:
 pages:
   image: ${CI_REGISTRY_IMAGE}:latest
   stage: end
-  before_script:
-    - conda env create -n dataretrieval -f environment.yml
   dependencies:
     - build-image
     - buildcheck
+  variables:
+    RETICULATE_PYTHON: /usr/bin/python3
   script:
     - |
       Rscript -e '

docker/Dockerfile

@@ -1,54 +1,60 @@
 FROM code.chs.usgs.gov:5001/ctek/docker/r-lang/r-base:4.6
 
-# Change the name of this environment to something which pleases you, if you
-# so please. But the name will not be relevant for most cases, as reticulate
-# will be pointed to the environment no matter what it is named.
-ARG CONDA_ENVIRONMENT_NAME=dataretrieval
-
-RUN apt-get update \
-  && apt-get install -y --no-install-recommends \
-  wget \
+# System dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  python3 \
+  python3-pip \
+  python3-dev \
+  # These might already come with r-cran-sf binary, commenting out for now:
+  # libgdal-dev \
+  # libgeos-dev \
+  # libproj-dev \
   && rm -rf /var/lib/apt/lists/*
-
-ENV CONDA_DIR="/root/conda"
-ENV PATH=$CONDA_DIR/bin:$PATH
 
-RUN wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" &&  \
-    bash Miniforge3.sh -b -p "${HOME}/conda" && \
-    rm Miniforge3.sh
+# Python dependencies
+RUN pip3 install --no-cache-dir --break-system-packages \
+  dataretrieval \
+  matplotlib \
+  geopandas \
+  numpy \
+  pandas \
+  scipy \
+  folium>=0.12 \
+  mapclassify \
+  python-dateutil \
+  seaborn \
+  requests
 
-# Necessary R libraries
-RUN apt-get update -qq && apt-get -y --no-install-recommends install \
-    r-cran-rcmdcheck \
-    r-cran-testthat \
-    r-cran-covr \
-    r-cran-reticulate \
-    r-cran-curl \
-    r-cran-lubridate \
-    r-cran-xml2 \
-    r-cran-httr2 \
-    r-cran-whisker \
-    r-cran-dplyr \
-    r-cran-sf \
-    r-cran-data.table \
-    r-cran-jsonlite \
-    r-cran-readr \
-    r-cran-knitr \
-    r-cran-rmarkdown \
-    r-cran-dt \
-    r-cran-leaflet \
-    r-cran-readxl \
-    r-cran-pkgdown \
-    r-cran-ggplot2 \
-    r-cran-tidyr \
-    r-cran-purrr \
-    && rm -rf /var/lib/apt/lists/* 
+# R dependencies
+RUN apt-get update -qq && apt-get install -y --no-install-recommends \
+  r-cran-reticulate \
+  r-cran-curl \
+  r-cran-lubridate \
+  r-cran-xml2 \
+  r-cran-httr2 \
+  r-cran-dplyr \
+  r-cran-sf \
+  r-cran-ggplot2 \
+  r-cran-tidyr \
+  r-cran-purrr \
+  r-cran-jsonlite \
+  r-cran-knitr \
+  r-cran-rmarkdown \
+  r-cran-leaflet \
+  r-cran-data.table \
+  r-cran-readr \
+  r-cran-rcmdcheck \
+  r-cran-testthat \
+  r-cran-pkgdown \
+  r-cran-covr \
+  r-cran-readxl \
+  r-cran-dt \
+  && rm -rf /var/lib/apt/lists/*
 
-ENV RETICULATE_PYTHON=/root/conda/envs/${CONDA_ENVIRONMENT_NAME}/bin/python
+ENV RETICULATE_PYTHON=/usr/bin/python3
 
 COPY *.tar.gz /tmp/pkg.tar.gz
-
 RUN set -eux; \
-    R CMD INSTALL /tmp/pkg.tar.gz && \
-    Rscript -e "library(dataRetrieval)" && \
-    rm -f /tmp/*.tar.gz
+  R CMD INSTALL /tmp/pkg.tar.gz && \
+  Rscript -e "library(dataRetrieval)" && \
+  rm -f /tmp/*.tar.gz

environment.yml

@@ -1,8 +1,14 @@
 name: dataretrieval
 channels:
   - conda-forge
+  - defaults
 dependencies:
+  - python>=3.10
+  - pip
   - dataretrieval
-  - matplotlib
+  - matplotlib-base
   - geopandas
+  - pyqt
+  - folium>=0.12
+  - mapclassify
 prefix: /home/user/miniforge3/envs/dataretrieval

requirements.txt

@@ -1,17 +1,7 @@
-numpy<2
-pandas==2.*
-geopandas==1.1.2
-scipy
-python-dateutil
-requests
-requests-mock
-coverage
-pytest
-flake8
-sphinx
-sphinx-rtd-theme
-ipython
-ipykernel
-nbsphinx
-nbsphinx_link
+dataretrieval
 matplotlib
+geopandas
+folium
+mapclassify
+seaborn
+