GCPy 1.4.2 release

This is the release of GCPy 1.4.2, which includes: - PR #286 (Github Action for GCPy environment) - PR #287 (Fix dictionary key error for benchmark plotting) - PR #289 (Use pegged versions in environment.yml; update GitHub actions Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Jan 26, 2024 · 4bd730f · 4bd730f
2 parents a056352 + 70d649a
commit 4bd730f
Show file tree

Hide file tree

Showing 17 changed files with 422 additions and 73 deletions.
diff --git a/.github/workflows/build-gcpy-environment.yml b/.github/workflows/build-gcpy-environment.yml
@@ -0,0 +1,38 @@
+---
+#
+# GitHub action to build the GCPy production environment with micromamba
+# See: https://github.com/marketplace/actions/setup-micromamba
+#
+name: build-gcpy-environment
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main", "dev" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - name: Checkout the GCPy repository
+        uses: actions/checkout@v2
+      - name: Create "gcpy_env" environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: 'latest'
+          environment-file: docs/environment_files/environment.yml
+          init-shell: bash
+          cache-environment: true
+          generate-run-shell: true
+          post-cleanup: 'all'
+      - name: Test if "import gcpy" works
+        run: python -c "import gcpy"
+        shell: micromamba-shell {0}
+      - name: Test if we can create a plot
+        run: python -m gcpy.examples.plotting.create_test_plot
+        shell: micromamba-shell {0}
diff --git a/.github/workflows/build-test-environment.yml b/.github/workflows/build-test-environment.yml
@@ -0,0 +1,38 @@
+---
+#
+# GitHub action to build the GCPy test environment with micromamba
+# See: https://github.com/marketplace/actions/setup-micromamba
+#
+name: build-test-environment
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main", "dev" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+    steps:
+      - name: Checkout the GCPy repository
+        uses: actions/checkout@v2
+      - name: Create "testing" environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: 'latest'
+          environment-file: docs/environment_files/testing.yml
+          init-shell: bash
+          cache-environment: true
+          generate-run-shell: true
+          post-cleanup: 'all'
+      - name: Test if "import gcpy" works
+        run: python -c "import gcpy"
+        shell: micromamba-shell {0}
+      - name: Test if we can create a plot
+        run: python -m gcpy.examples.plotting.create_test_plot
+        shell: micromamba-shell {0}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,19 @@ All notable changes to GCPy will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.4.2] - 2024-01-26
+### Added
+- Example script `create_test_plot.py`, which can be used to check that GCPy has been installed properly
+- GitHub action `build-gcpy-environment` which tests installation of the mamba environment specified in in `docs/environment_files/environment.yml`
+- YAML file`docs/environment_files/testing.yml` for building an environment without pegged package versions (for testing)
+- GitHub action `build-test-environment` to test the environment specified in `testing.yml`
+
+### Changed
+- `build-gcpy-environment` GitHub action now runs with several Python versions 
+
+### Fixed
+- Prevent overwriting of the `results` variable when parallel plotting is deactivated (`n_cores: 1`)
+
 ## [1.4.1] - 2023-12-08
 ### Fixed
 - Now use the proper default value for the `--weightsdir` argument to `gcpy/file_regrid.py`
@@ -157,7 +170,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
   - Now use restarts_subdir tag from YAML file for paths to restart files (@yantosca)
   - GCPy now uses proper year for dev in 1-yr benchmarks (@laestrada)
   - Fixed date string issue in benchmarking scripts (@lizziel)
-  - Updates for new GCHP restart file format (@lizziel)  
+  - Updates for new GCHP restart file format (@lizziel)
 - Updated environment.yml with package versions that work together (@yantosca)
 - Updated the AUTHORS.txt and LICENSE.txt files (@yantosca)
 

diff --git a/docs/environment_files/environment.yml b/docs/environment_files/environment.yml
@@ -1,59 +1,50 @@
+---
 # ======================================================================
 # 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)
+# These package versions have been proven to work together.
+# See: https://github.com/geoschem/gcpy/issues/284
 # ======================================================================
 name: gcpy_env
 channels:
-    - conda-forge
-    - nodefaults    
+  - conda-forge
+  - nodefaults
 dependencies:
-    - 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
-    - tk                              # Tcl/tk library
-    - 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
-    - xesmf==0.5.1                    # Universal regridder
-    # 
-    # 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
+  - awscli==2.13.39                 # Utilities for AWS cloud
+  - cartopy==0.22.0                 # Geospatial data processing
+  - cf_xarray==0.8.4                # CF conventions for xarray
+  - dask==2023.9.2                  # Parallel library; backend for xarray
+  - gridspec==0.1.0                 # Define Earth System Model grids
+  - ipython==8.15.0                 # Interactive Python (used by Jupyter)
+  - joblib==1.3.2                   # Parallelize python code
+  - jupyter==1.0.0                  # Jupyter Notebook
+  - matplotlib==3.8.0               # Creates plots and visualizations
+  - netcdf4==1.6.0                  # Python wrapper for netCDF
+  - netcdf-fortran==4.5.4           # Python wrapper for netCDF-Fortran
+  - numpy==1.26.0                   # Optimized mathematical functions
+  - pandas==2.1.1                   # Tables/timeseries manipulation
+  - pip==23.2.1                     # Install packages from PyPi
+  - pylint==2.17.5                  # Python linter
+  - pyproj==3.6.1                   # Python map projections library
+  - python==3.9.18                  # Any python version prior to 3.10
+  - pypdf==3.16.1                   # PDF utilities (bookmarks, etc.)
+  - recommonmark==0.7.1             # Dependency for Sphinx
+  - requests==2.31.0                # HTTP library
+  - scipy==1.11.2                   # Scientific python package
+  - sparselt==0.1.3                 # Regridding earth system model data
+  - tabulate==0.9.0                 # Pretty-printing for column data
+  - tk==8.6.12                      # Tcl/tk library
+  - xarray==2023.8.0                # Read data from netCDF etc files
+  - esmf==8.1.1                     # Earth system modeling framework
+  - esmpy==8.1.1                    # Python wrapper for ESMF
+  - xesmf==0.5.1                    # Universal regridder
+  - 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
diff --git a/docs/environment_files/testing.yml b/docs/environment_files/testing.yml
@@ -0,0 +1,52 @@
+---
+# ======================================================================
+# GCPy testing environment file.
+# Intended to be used by the GCST for testing purposes.
+#
+# GCPy users should build the environment from "environment.yml",
+# as this will specify package versions that are known to work.
+# See: https://github.com/geoschem/gcpy/issues/284
+# ======================================================================
+name: testing
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - 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>=3.8                 # 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                          # Any python version prior to 3.10
+  - pypdf                           # PDF utilities (bookmarks, etc.)
+  - recommonmark                    # Dependency for Sphinx
+  - requests                        # HTTP library
+  - scipy                           # Scientific python package
+  - sparselt                        # Regridding earth system model data
+  - tabulate                        # Pretty-printing for column data
+  - tk                              # Tcl/tk library
+  - xarray                          # Read data from netCDF etc files
+  #
+  # NOTE: These packages are known to work, so peg these versions
+  #
+  - esmf==8.1.1                     # Earth system modeling framework
+  - esmpy==8.1.1                    # Python wrapper for ESMF
+  - xesmf==0.5.1                    # Universal regridder
+  - 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
diff --git a/docs/source/Release_guide.rst b/docs/source/Release_guide.rst
@@ -17,9 +17,9 @@ versions of GCPy on Github, PyPi, and conda-forge.
    - :file:`setup.py`
    - :file:`gcpy/_version.py`
    - :file:`docs/source/conf.py`
-   - :file:`benchmark/run_benchmark.py`
-   - :file:`benchmark/modules/run_1yr_fullchem_benchmark.py`
-   - :file:`benchmark/modules/run_1yr_tt_benchmark.py`
+   - :file:`gcpy/benchmark/run_benchmark.py`
+   - :file:`gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py`
+   - :file:`gcpy/benchmark/modules/run_1yr_tt_benchmark.py`
      |br|
 
 #. Update :file:`CHANGELOG.md` |br|

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -22,7 +22,7 @@
 author = 'GEOS-Chem Support Team'
 
 # The full version, including alpha/beta/rc tags
-release = '1.4.1'
+release = '1.4.2'
 
 # -- General configuration ---------------------------------------------------
 

diff --git a/gcpy/_version.py b/gcpy/_version.py
@@ -1,2 +1,2 @@
+__version__ = '1.4.2'
 
-__version__ = '1.4.1'
diff --git a/gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py b/gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py
@@ -43,7 +43,7 @@
 
         https://github.com/ipython/ipython/issues/10627
 
-This script corresponds with GCPy 1.4.0. Edit this version ID if releasing
+This script corresponds with GCPy 1.4.2. Edit this version ID if releasing
 a new version of GCPy.
 """
 
@@ -694,8 +694,9 @@ def gcc_vs_gcc_mass_table(mon):
                     for mon in range(bmk_n_months)
                 )
             else:
+                results = []
                 for mon in range(bmk_n_months):
-                    results = gcc_vs_gcc_mass_table(mon)
+                    results.append(gcc_vs_gcc_mass_table(mon))
 
         # ==================================================================
         # GCC vs GCC operations budgets tables
@@ -741,8 +742,9 @@ def gcc_vs_gcc_ops_budg(mon):
                     for mon in range(bmk_n_months)
                 )
             else:
+                results = []
                 for mon in range(bmk_n_months):
-                    results = gcc_vs_gcc_ops_budg(mon)
+                    results.append(gcc_vs_gcc_ops_budg(mon))
 
         # ==================================================================
         # GCC vs GCC aerosols budgets/burdens tables
@@ -1255,8 +1257,9 @@ def gchp_vs_gcc_mass_table(mon):
                     for mon in range(bmk_n_months)
                 )
             else:
+                results = []
                 for mon in range(bmk_n_months):
-                    results = gchp_vs_gcc_mass_table(mon)
+                    results.append(gchp_vs_gcc_mass_table(mon))
 
         # ==================================================================
         # GCHP vs GCC operations budgets tables
@@ -1311,8 +1314,9 @@ def gchp_vs_gcc_ops_budg(mon):
                     for mon in range(bmk_n_months)
                 )
             else:
+                results = []
                 for mon in range(bmk_n_months):
-                    results = gchp_vs_gcc_ops_budg(mon)
+                    results.append(gchp_vs_gcc_ops_budg(mon))
 
         # ==================================================================
         # GCHP vs GCC aerosol budgets and burdens tables
@@ -1863,8 +1867,9 @@ def gchp_vs_gchp_mass_table(mon):
                     for mon in range(bmk_n_months)
                 )
             else:
+                results = []
                 for mon in range(bmk_n_months):
-                    results = gchp_vs_gchp_mass_table(mon)
+                    results.append(gchp_vs_gchp_mass_table(mon))
 
         # ==================================================================
         # GCHP vs GCHP operations budgets tables
@@ -1921,8 +1926,9 @@ def gchp_vs_gchp_ops_budg(mon):
                     for mon in range(bmk_n_months)
                 )
             else:
+                results = []
                 for mon in range(bmk_n_months):
-                    results = gchp_vs_gchp_ops_budg(mon)
+                    results.append(gchp_vs_gchp_ops_budg(mon))
 
         # ==================================================================
         # GCHP vs GCHP aerosol budgets and burdens tables