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Merge PR geoschem#251 (Update gcpy_env environment to install with Ma…
…mbaForge) This merge brings PR geoschem#251 (Update gcpy_env environment to install with MambaForge and to use latest package versions; Update scripts accordingly, by @yantosca) into the GCPy 1.4.0 development stream. This updates the docs/environments/environment.yml file to use more modern package versions, thus eliminating the dependence on Conda 4.12, and allowing installation with MambaForge. Several updates were also made to gcpy/util.py and gcpy/plot.py due to changes in Python packages. Furthermore, we have now abstracted some code out of the six_plot routine in gcpy/plot.py into separate functions. This should make the code easier to maintain and understand. See geoschem#251 for more information. Signed-off-by: Bob Yantosca <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,42 +1,58 @@ | ||
| # ====================================================================== | ||
| # GCPy environment file | ||
| # | ||
| # Recommended installation: with Mambaforge | ||
| # $ mamba env create -n gcpy_env --file=/path/to/gcpy/environment.yml | ||
| # | ||
| # Some package versions are not the most recent, but these | ||
| # have been proven to work together. (Bob Yantosca, 14 Aug 2023) | ||
| # ====================================================================== | ||
| name: gcpy_env | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| - nodefaults | ||
| dependencies: | ||
| - cartopy=0.19.0.post1 # Geospatial data processing | ||
| - awscli # Utilities for AWS cloud | ||
| - cartopy # Geospatial data processing | ||
| - cf_xarray # CF conventions for xarray | ||
| - dask # Parallel library; backend for xarray | ||
| - gridspec # Define Earth System Model grids | ||
| - ipython # Interactive Python (used by Jupyter) | ||
| - joblib # Parallelize python code | ||
| - jupyter # Jupyter Notebook | ||
| - matplotlib # Creates plots and visualizations | ||
| - netcdf4 # Python wrapper for netCDF | ||
| - netcdf-fortran # Python wrapper for netCDF-Fortran | ||
| - numpy # Optimized mathematical functions | ||
| - pandas # Tables/timeseries manipulation | ||
| - pip # Install packages from PyPi | ||
| - pylint # Python linter | ||
| - pyproj # Python map projections library | ||
| - python<3.10 # Any python version prior to 3.10 | ||
| - pypdf # PDF utilities (bookmarks, etc.) | ||
| - recommonmark # Dependency for Sphinx | ||
| - requests # HTTP library | ||
| - scipy # Scientific python package | ||
| - sparselt>=0.1.3 # Regridding earth system model data | ||
| - tabulate # Pretty-printing for column data | ||
| - xarray # Read data from netCDF etc files | ||
| # | ||
| # NOTE: These packages need to be pegged at specific versions | ||
| # in order to avoid an ImportError. | ||
| # -- Bob Yantosca (14 Aug 2023) | ||
| # | ||
| - esmf==8.1.1 # Earth system modeling framework | ||
| - esmpy==8.1.1 # Python wrapper for ESMF | ||
| - netcdf4==1.6.0 # Python wrapper for netCDF | ||
| - netcdf-fortran==4.5.4 # Python wrapper for netCDF-Fortran | ||
| - python==3.9.6 # Python version 3.9.6 | ||
| - pip==21.2.1 # Install packages from PyPi | ||
| - sparselt>=0.1.3 # Regridding earth system model data | ||
| - xesmf==0.5.1 # Universal regridder | ||
| - pip: | ||
| - awscli>=1.22.83 # Utilities for AWS cloud | ||
| - cf_xarray==0.7.4 # CF conventions for xarray | ||
| - dask==2021.7.1 # Parallel library; backend for xarray | ||
| - docutils==0.16 # Convert text to other formats | ||
| - h5netcdf==0.11.0 # Python interface to netCDF4/HDF5 | ||
| - h5py==3.3.0 # Python interface to HDF5 | ||
| - matplotlib==3.4.2 # Creates plots and visualizations | ||
| - ipython==8.11.0 # Interactive Python (used by Jupyter) | ||
| - jinja2==3.0.3 # Dependency for Sphinx | ||
| - joblib==1.0.1 # Parallelize python code | ||
| - jupyter==1.0.0 # Jupyter Notebook | ||
| - numpy==1.21.1 # Optimized mathematical functions | ||
| - pandas==1.3.1 # Tables/timeseries manipulation | ||
| - pycodestyle==2.9.1 # Python style checker (formerly PEP8) | ||
| - pyproj==3.6.0 # Python map projections library | ||
| - pylint==2.15.3 # Python linter | ||
| - pypdf2==1.26.0 # PDF utilities (bookmarks, etc.) | ||
| - recommonmark==0.7.1 # Dependency for Sphinx | ||
| - requests==2.26.0 # HTTP library | ||
| - scipy==1.7.0 # Scientific python package | ||
| - sphinx==3.5.4 # Generate ReadTheDocs output | ||
| - sphinx-autoapi==1.9.0 # Sphinx autodoc style documentation | ||
| - sphinx-autobuild==2021.3.14 # Build ReadTheDos live in browser | ||
| - sphinxcontrib-bibtex==2.2.0 # ReadTheDocs bibliography style | ||
| - sphinx_rtd_theme==0.5.2 # ReadTheDocs HTML theme files | ||
| - tabulate==0.8.9 # Pretty-printing for column data | ||
| - xarray==0.17.0 # Read data from netCDF etc files | ||
| # | ||
| # NOTE: These packages need to be pegged at specific versions | ||
| # or else the ReadTheDocs output won't render properly. | ||
| # -- Bob Yantosca (14 Aug 2023) | ||
| # | ||
| - docutils==0.16 # Convert text to other formats | ||
| - jinja2==3.0.3 # Dependency for Sphinx | ||
| - sphinx==3.5.4 # Generate ReadTheDocs output | ||
| - sphinx-autoapi==1.9.0 # Sphinx autodoc style documentation | ||
| - sphinx-autobuild==2021.3.14 # Build ReadTheDos live in browser | ||
| - sphinxcontrib-bibtex==2.2.0 # ReadTheDocs bibliography style | ||
| - sphinx_rtd_theme==0.5.2 # ReadTheDocs HTML theme files |
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