Merge pull request #679 from British-Oceanographic-Data-Centre/675_scipy_integrate_cumtrapz_update

675 scipy integrate cumtrapz update
Update config files of COAsT toolbox so this tool can run with Python 3.9, 3.10, 3.11 and 3.12.

Author: MagdaJuarez

.github/workflows/build_package.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10' ]
+        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
 
     steps:
       - uses: actions/checkout@v4
@@ -36,6 +36,9 @@ jobs:
           ./build.sh
       - name: Test Package Install
         run: |
+          CONDA_BASE=$(conda info --base)
+          source "${CONDA_BASE}/etc/profile.d/conda.sh"
+          conda activate coast
           python -m pip install dist/coast-*.tar.gz
       - name: Generate Conda Metadata
         run: |

.github/workflows/unit_test_contents.yml

@@ -17,7 +17,11 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Generate contents.
         run: |
-          pip install . 
+          CONDA_BASE=$(conda info --base)
+          source "${CONDA_BASE}/etc/profile.d/conda.sh"
+          conda env update --prune --file environment.yml
+          conda activate coast
+          pip install .
           mkdir -p example_files
           sudo apt-get update
           sudo apt-get install -y libgeos-dev

.github/workflows/verify_package.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10' ]
+        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
 
     steps:
       - uses: actions/checkout@v4
@@ -34,6 +34,7 @@ jobs:
         run: |
           CONDA_BASE=$(conda info --base)
           source "${CONDA_BASE}/etc/profile.d/conda.sh"
+          conda config --set verbosity 3 --env
           conda env update --prune --file environment.yml 
           conda activate coast
           sudo apt-get update

build.sh

@@ -7,6 +7,9 @@ mkdir -p build dist
 echo "Cleaning up old versions..."
 rm -rf ./build/* ./dist/* ./Example_Python_Package.egg-info
 echo "Building package for distribution..."
-./venv/bin/python ./setup.py sdist bdist_wheel
+CONDA_BASE=$(conda info --base)
+source "${CONDA_BASE}/etc/profile.d/conda.sh"
+conda activate coast
+python ./setup.py sdist bdist_wheel
 
-echo "Done!"
+echo "Done!"

environment.yml

@@ -4,7 +4,7 @@ channels:
   - nodefaults
 dependencies:
   - python==3.10
-  - cython==3.1.1
+  - cython==0.29.37
   - cartopy==0.23.0
   - gsw==3.6.19
   - xarray[complete]==2023.7.0
@@ -31,5 +31,5 @@ dependencies:
   - spyder==6.0.7
   - jupyterlab==4.4.3
   - aiohttp==3.11.13
-  - PyYAML==6.0
+  - PyYAML==5.4.1
   - oyaml==1.0

generate_conda_meta.sh

@@ -1,3 +1,5 @@
 #!/bin/bash
-
+CONDA_BASE=$(conda info --base)
+source "${CONDA_BASE}/etc/profile.d/conda.sh"
+conda activate coast
 python setup.py conda

pyproject.toml

@@ -1,3 +1,3 @@
 [tool.black]
 line-length = 120
-target-version = ['py38', 'py39', 'py310']
+target-version = ['py38', 'py39', 'py310']

setup.py

@@ -31,7 +31,8 @@
         "keywords": ["NEMO", "shallow water", "ocean assessment"],
         "project_urls": {"documentation": "https://british-oceanographic-data-centre.github.io/COAsT/"},
         "install_requires": [
-            "PyYAML==6.0",
+            "cython==0.29.37",
+            "PyYAML==5.4.1",
             "oyaml==1.0",
             "pytest==7.1.1",
             "pytest-mock==3.7.0",
@@ -53,7 +54,6 @@
             "aiohttp==3.11.13",
             "tqdm==4.67.1",
             "pyproj==3.6.1",
-            "cython==3.1.1",
             "cartopy==0.23.0",
             "h5py==3.6.0",
             "zarr==2.18.2",
@@ -63,7 +63,7 @@
             # "xesmf>=0.3.0",  # Optional. Not part of main package
             # "esmpy>=8.0.0",  # Optional. Not part of main package
         ],
-        "python_requires": ">3.8,<3.11",
+        "python_requires": ">3.8,<3.13",
         "packages": ["coast", "coast.data", "coast._utils", "coast.diagnostics"],
         "include_package_data": True,
         "github": "British-Oceanographic-Data-Centre",

setup_environment.sh

@@ -5,13 +5,10 @@ cd "$(dirname "$0")"  # Set working directory
 
 echo "Cleaning up any existing virtual environment..."
 rm -rf ./venv
-echo "Creating new virtual environment..."
-python3 -m virtualenv ./venv
 echo "Installing required packages..."
-./venv/bin/pip install setuptools wheel twine
 CONDA_BASE=$(conda info --base)
 source "${CONDA_BASE}/etc/profile.d/conda.sh"
-conda env update --prune --file environment.yml 
 conda activate coast
+conda install -c conda-forge cython setuptools wheel twine
 
-echo "Done!"
+echo "Done!"