Maintenance updates

.github/workflows/black.yml

@@ -0,0 +1,14 @@
+name: Black
+
+on: push
+
+jobs:
+  black:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - uses: psf/black@stable
+        with:
+          options: "--check"

.github/workflows/docker-publish.yml

@@ -10,10 +10,10 @@ on:
 jobs:
   publish:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Publish to Registry
         uses: docker/build-push-action@v1
         with:

.github/workflows/python-ci.yml

@@ -4,36 +4,38 @@ on: push
 
 jobs:
   test:
-
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ["3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Python dependencies
-      env:
-        PIP_INDEX_URL: https://pypi.pacificclimate.org/simple
-      run: |
-        pip install -r requirements.txt
-        pip install -e .[dev]
-    - name: Install R dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install --fix-missing libgit2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev libssl-dev
-        Rscript install_pkgs.R r_requirements.txt
-    - name: Test with pytest (full)
-      if: github.ref == 'refs/heads/master'
-      run: |
-        py.test -m "not online" -v
-    - name: Test with pytest (fast)
-      if: github.ref != 'refs/heads/master'
-      run: |
-        py.test -m "not online and not slow" -v
-    - name: Code Quality
-      run: black . --check
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y r-base libgit2-dev libudunits2-dev libnetcdf-dev libcurl4-openssl-dev libssl-dev libfontconfig1-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          export PATH="/root/.local/bin:$PATH"
+          poetry install --extras "dev"
+
+      - name: Set GITHUB_PAT env var for R
+        run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV
+
+      - name: Install R packages
+        run: Rscript install_pkgs.R
+
+      - name: Test with pytest (full)
+        if: github.ref == 'refs/heads/master'
+        run: |
+          poetry run py.test -m "not online" -v
+      - name: Test with pytest (fast)
+        if: github.ref != 'refs/heads/master'
+        run: |
+          poetry run py.test -m "not online and not slow" -v

Dockerfile

@@ -1,26 +1,26 @@
-FROM rocker/r-ver:4.0.3 AS build
+FROM rocker/r-ver:4.4 AS build
 
-COPY r_requirements.txt install_pkgs.R ./
+COPY pyproject.toml install_pkgs.R ./
 
 # Install python and R packages
 RUN apt-get update && \
   apt-get install -y --no-install-recommends \
-    libssl-dev \
-    libxml2-dev \
-    libudunits2-dev \
-    libnetcdf-dev \
-    libgit2-dev \
-    libfreetype6-dev \
-    libpng-dev \
-    libtiff5-dev \
-    libjpeg-dev \
-    libfontconfig1-dev \
-    libharfbuzz-dev \
-    libfribidi-dev \
-    libcurl4-openssl-dev && \
-  Rscript install_pkgs.R r_requirements.txt
-
-FROM rocker/r-ver:4.0.3
+  libssl-dev \
+  libxml2-dev \
+  libudunits2-dev \
+  libnetcdf-dev \
+  libgit2-dev \
+  libfreetype6-dev \
+  libpng-dev \
+  libtiff5-dev \
+  libjpeg-dev \
+  libfontconfig1-dev \
+  libharfbuzz-dev \
+  libfribidi-dev \
+  libcurl4-openssl-dev && \
+  Rscript install_pkgs.R
+
+FROM rocker/r-ver:4.4
 
 LABEL Maintainer="https://github.com/pacificclimate/quail" \
   Description="quail WPS" \
@@ -30,25 +30,31 @@ LABEL Maintainer="https://github.com/pacificclimate/quail" \
 WORKDIR /tmp
 
 # Copy R packages
-ARG R_FILEPATH=/root/R/x86_64-pc-linux-gnu-library/4.0
+ARG R_FILEPATH=/root/R/x86_64-pc-linux-gnu-library/4.4
 
 COPY --from=build ${R_FILEPATH}/PCICt ${R_FILEPATH}/PCICt
 COPY --from=build ${R_FILEPATH}/climdex.pcic ${R_FILEPATH}/climdex.pcic
 COPY --from=build ${R_FILEPATH}/Rcpp ${R_FILEPATH}/Rcpp
 
 # Add path to libR.so to the environment variable LD_LIBRARY_PATH
-ENV LD_LIBRARY_PATH=/usr/local/lib/R/lib:$LD_LIBRARY_PATH
+ENV LD_LIBRARY_PATH="/usr/local/lib/R/lib:${LD_LIBRARY_PATH}"
 ENV PIP_INDEX_URL="https://pypi.pacificclimate.org/simple/"
 
 COPY . /tmp
-COPY requirements.txt ./
+COPY pyproject.toml poetry.lock* ./
+
+ENV POETRY_HOME="/opt/poetry"
+ENV PATH="$POETRY_HOME/bin:$PATH"
 
-# Install Python
 RUN apt-get update && \
-  apt-get install -y --no-install-recommends python3.8 python3-pip && \
-  pip install -U pip && \
-  pip install -r requirements.txt && \
-  pip install gunicorn
+  apt-get install -y --no-install-recommends python3 python3-pip curl  && \
+  curl -sSL https://install.python-poetry.org | python3
+
+
+RUN poetry config virtualenvs.in-project true && \
+  poetry install
 
 EXPOSE 5000
-CMD gunicorn --bind=0.0.0.0:5000 quail.wsgi:application
+CMD ["poetry", "run", "gunicorn", "--bind=0.0.0.0:5000", "quail.wsgi:application"]
+
+

dev-component/DEVELOPMENT.md

@@ -1,11 +1,12 @@
 # Development
 
-This `docker-compose` is set up for development purposes. It will up a dev instance of `quail` with production settings. All you are required to do is to add the following lines to `birdhouse-config/env.local` running on `dev03`:
+This `docker-compose` is set up for development purposes. It will up a dev instance of `quail` with production settings. All you are required to do is to add the following lines to `birdhouse-config/env.local` running on `marble-dev01`:
 
 ```
 export EXTRA_CONF_DIRS="/storage/data/projects/comp_support/daccs/birdhouse-config
     ...
     /path/to/quail/dev-component"
 
 ...
-export QUAIL_DEV_IMAGE="pcic/quail:[your-tag]"
+export QUAIL_DEV_IMAGE="pcic/quail:[your-tag]"
+```