Update config files

Update config files to install specific versions of cython and PyYAML depedencies. Also, activate conda environment in setup-environment, build-package and generate-conda-metadata steps

Author: MagdaJuarez

build.sh

@@ -7,11 +7,7 @@ mkdir -p build dist
 echo "Cleaning up old versions..."
 rm -rf ./build/* ./dist/* ./Example_Python_Package.egg-info
 echo "Building package for distribution..."
-CONDA_BASE=$(conda info --base)
-source "${CONDA_BASE}/etc/profile.d/conda.sh"
-conda create -n coast-toolbox python=3.10
-conda activate coast-toolbox
-conda install conda-forge::hdf5
-./venv/bin/python ./setup.py sdist bdist_wheel
+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<3.0.0
+  - 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 +1,3 @@
 #!/bin/bash
-
+conda activate coast
 python setup.py conda

setup.py

@@ -31,8 +31,8 @@
         "keywords": ["NEMO", "shallow water", "ocean assessment"],
         "project_urls": {"documentation": "https://british-oceanographic-data-centre.github.io/COAsT/"},
         "install_requires": [
-            "cython<3.0.0",
-            "PyYAML==6.0",
+            "cython==0.29.37",
+            "PyYAML==5.4.1",
             "oyaml==1.0",
             "pytest==7.1.1",
             "pytest-mock==3.7.0",

setup_environment.sh

@@ -5,14 +5,8 @@ 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 config --set verbosity 3 --env
-conda env update --prune --file environment.yml 
 conda activate coast
+conda install conda-forge::setuptools conda-forge::wheel conda-forge::twine
 
-echo "Done!"
+echo "Done!"