Merge remote-tracking branch 'upstream/main' into plugin-fix

.dockerignore

@@ -0,0 +1,2 @@
+.dockerignore
+.venv

.github/workflows/release.yml

@@ -0,0 +1,57 @@
+name: Release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'New version'
+        required: true
+
+jobs:
+  update-and-build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Update pyproject.toml version
+        run: |
+          sed -i "s/^version = .*/version = \"${{ github.event.inputs.version }}\"/" pyproject.toml
+          git config --global user.name 'GitHub Actions'
+          git config --global user.email '[email protected]'
+          git commit -am "ci: Version bump ${{ github.event.inputs.version }}"
+          git push
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ vars.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Build and push Docker Image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          platforms: linux/amd64 #,linux/arm64 future ;)
+          push: true
+          tags: ${{ vars.DOCKER_IMAGE_NAME }}:${{ github.event.inputs.version }}, ${{ secrets.DOCKER_IMAGE_NAME }}:latest
+
+      - name: Push version bump commit
+        run: |
+          git tag ${{ github.event.inputs.version }}
+          git push origin ${{ github.event.inputs.version }}
+          git push
+
+      - name: Create GitHub Release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.event.inputs.version }}
+          release_name: Release ${{ github.event.inputs.version }}
+          draft: false
+          prerelease: false

.gitignore

@@ -13,3 +13,4 @@ docs/build
 .venv
 dist
 *~
+.python-version

Dockerfile

@@ -1,39 +1,27 @@
-FROM dssat/dssat-csm
+FROM dssat/dssat-csm:v4.8.2.0
 
-COPY . /app/pythia
-RUN ln -sf /bin/bash /bin/sh && \
-# install pre-reqs for pyenv installed pythons
-apt-get install -y build-essential libssl-dev zlib1g-dev libbz2-dev \
-libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
-xz-utils tk-dev libffi-dev liblzma-dev python-openssl git libspatialindex-dev && \
-# setup pyenv
-curl https://pyenv.run | bash && \                          
-echo 'export PATH="/root/.pyenv/bin:/root/.local/bin:$PATH"' >> ~/.bashrc && \
-echo 'eval "$(pyenv init -)"' >> ~/.bashrc && \
-echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.bashrc && \
-export PATH="/root/.pyenv/bin:/root/.local/bin:$PATH" && \
-eval "$(pyenv init -)" && \
-eval "$(pyenv virtualenv-init i)" && \
-# install python 3.7.9
-pyenv install 3.7.9 && \
-pyenv rehash && \
-pyenv virtualenv 3.7.9 pythia-3.7.9 && \
-pyenv activate pythia-3.7.9 && \
-pip install --upgrade pip && \
-pip install pipenv && \
-# install dependencies
-cd /app/pythia && \
-pipenv install && \
-echo "#!/bin/bash" > /app/pythia.sh && \
-echo "" >> /app/pythia.sh && \
-echo 'export PATH="/root/.pyenv/bin:/root/.local/bin:$PATH"' >> /app/pythia.sh && \
-echo 'export PYENV_VIRTUALENV_DISABLE_PROMPT=1' >> /app/pythia.sh && \
-echo 'eval "$(pyenv init -)"' >> /app/pythia.sh && \
-echo 'eval "$(pyenv virtualenv-init -)"' >> /app/pythia.sh && \
-echo "pyenv activate pythia-3.7.9" >> /app/pythia.sh && \
-echo "python /app/pythia/pythia.py \$@" >> /app/pythia.sh && \
-echo "pyenv deactivate" && \
-chmod 755 /app/pythia.sh
+RUN apt-get update && apt-get install -y \
+    python3.11 \
+    python3.11-dev \
+    python3-pip \
+    python3-venv \
+    python3-poetry \
+    python3-virtualenv \
+    curl \
+    gdal-bin=3.6.2+dfsg-1+b2 \
+    libgdal-dev=3.6.2+dfsg-1+b2 \
+    && rm -rf /var/lib/apt/lists/*
 
-ENTRYPOINT ["/app/pythia.sh"]
-CMD ["-h"]
+ENV GDAL_VERSION 3.6.2
+ENV C_INCLUDE_PATH=/usr/include/python3.11/cpython
+ENV CPLUS_INCLUDE_PATH=/usr/include/python3.11/cpython
+
+WORKDIR /app/pythia
+
+COPY pyproject.toml poetry.toml poetry.lock ./
+RUN POETRY_VIRTUALENVS_CREATE=false poetry install --no-interaction --no-ansi
+
+COPY . ./
+ENV PATH="${PATH}:/app/pythia/bin"
+
+ENTRYPOINT ["pythia"]

bin/pythia

@@ -1,3 +1,4 @@
-#!/usr/bin/env sh
+#!/usr/bin/env bash
 
-python -m pythia $@
+source .venv/bin/activate
+python3 -m pythia $@

docs/about.rst

@@ -1,7 +1,7 @@
 What is Pythia?
 ===============
 
-Pythia is a simple framework to assist users in running DSSAT over a spatial area based on grid points. Pythia can use any DSSAT v4.7 build. The inputs to the framework are:
+Pythia is a simple framework to assist users in running DSSAT over a spatial area based on grid points. Pythia can use any DSSAT v4.7 build or greater. The inputs to the framework are:
 
 - A JSON configuration file
 - Shape files

docs/conf.py

@@ -17,24 +17,23 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'Pythia'
-copyright = '2020, DSSAT Foundation'
-author = 'Christopher Villalobos'
+project = "Pythia"
+copyright = "2020 - 2022, DSSAT Foundation"
+author = "Christopher Villalobos"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = "1.0.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-]
+extensions = []
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -47,15 +46,15 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # -- RTD Settings -------------------------------------------------------------
 
 # It seems that RTD needs to have this set in order for the build to occur.
 #
-master_doc = 'index'
+master_doc = "index"