Fix dependencies issue

.github/workflows/test.yml

@@ -28,46 +28,62 @@ jobs:
     - name: install additional required packages
       run: |
         sudo apt-get install -y --no-install-recommends \
-        libudunits2-dev \
-        libproj-dev \
-        libgeos-dev \
-        libffi-dev \
-        cmake \
-        libgtest-dev \
-        build-essential \
-        curl \
-        libcurl4-openssl-dev
+          libudunits2-dev \
+          gdal-bin libgdal-dev \
+          libproj-dev \
+          libgeos-dev \
+          libffi-dev \
+          cmake \
+          libgtest-dev \
+          build-essential \
+          curl \
+          libcurl4-openssl-dev \
+          python3-numpy \
+          python3-shapely \
+          python3-cartopy
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install dependencies (inline, no external reqs)
       run: |
-        python -m pip install --upgrade pip==24.0
+        # 1. Pin pip & setuptools so distutils & flags work
+        python -m pip install --upgrade pip==24.0 setuptools==65.5.1 wheel setuptools_scm
 
-        # patch to solve dependency issues with celery / fiona / click / pytz
-        # download celery package 
+        # 2. Point pip at your IMOS PyPI repo (so aodntools>=1.3.1 is found)
+        export PIP_INDEX_URL="http://imos-artifacts.s3-website-ap-southeast-2.amazonaws.com/repo/pypi/${STAGE}/"
+        export PIP_EXTRA_INDEX_URL="https://pypi.org/simple/"
+        export PIP_TRUSTED_HOST="imos-artifacts.s3-website-ap-southeast-2.amazonaws.com"
+
+        # 3. Pre-install build-time deps so Cartopy/Matplotlib metadata steps pass
+        python -m pip install \
+          "numpy<1.24.0" \
+          "pandas<2.0" \
+          "matplotlib>=3.1,<3.6" --only-binary matplotlib
+
+        # 4. Patch & install Celery 5.1.2 (locks in click==7.1.2 & sane pytz)
         wget https://files.pythonhosted.org/packages/source/c/celery/celery-5.1.2.tar.gz
         tar -xzf celery-5.1.2.tar.gz
-        cd celery-5.1.2
-        # patch the requirements to use pytz>=2020.1 instead of pytz>dev which causes issues
+        pushd celery-5.1.2
         sed -i "s/pytz>dev/pytz>=2020.1/g" requirements/default.txt
-        sed -i "s/pytz>dev/pytz>=2020.1/g" celery.egg-info/requires.txt
         sed -i "s/pytz>dev/pytz>=2020.1/g" requirements/dev.txt
-        # install the package
         python setup.py install
-        cd ..
-        # remove downlaoded copy of celery
+        popd
         rm -rf celery-5.1.2 celery-5.1.2.tar.gz
 
-        pip install pytest-runner
-        pip install pyshp
-        pip install scipy
-        pip install -r stage_requirements.txt
-        pip install pytest-cov
+        # 5. build Shapely against system GEOS, but use Cartopy’s binary wheel
+        python -m pip install --no-binary shapely \
+          shapely==1.8.5.post1
+        # Cartopy has no Linux wheel on PyPI—build from source against system GEOS/PROJ:
+        python -m pip install --no-build-isolation --no-binary cartopy \
+          cartopy==0.20.3
 
+        # 6. Install your own package (and its private deps) + test extras & tools
+        python -m pip install -e .[testing]
+        python -m pip install pytest-runner pyshp scipy pytest-cov
       env:
         STAGE: ${{ matrix.stage }}
+
     - name: Test with pytest
       run: |
         pytest --cov=./ --cov-report=xml