Merge pull request #97 from unifhy-org/nutrients

Merging nutrients components #14 into main, updating version to v1.0.0

.github/workflows/advanced_tests.yml

@@ -7,12 +7,12 @@ on:
 
 jobs:
 
-  run-basic-tests:
+  run-advanced-tests:
 
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest, macos-13]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
       fail-fast: false
 
     runs-on: ${{ matrix.os }}
@@ -25,7 +25,7 @@ jobs:
 
       # check out PR HEAD commit
       - name: check out PR HEAD commit
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
@@ -37,6 +37,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           auto-update-conda: true
           mamba-version: "*"
+          miniconda-version: "latest"          
           channels: conda-forge
           channel-priority: true
 
@@ -49,22 +50,44 @@ jobs:
 
       # build dummy components required for tests
       - name: make gfortran available (macos only)
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-13'
         run: |
-          sudo ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
+          sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
           sudo mkdir /usr/local/gfortran
-          sudo ln -s /usr/local/Cellar/gcc@10/*/lib/gcc/10 /usr/local/gfortran/lib
+          sudo ln -s /usr/local/Cellar/gcc@11*/lib/gcc/11 /usr/local/gfortran/lib
+          gfortran --version
 
       - name: build dummy C and Fortran components
         run: |
           (cd ./tests/tests/components && make)
 
+
+      # install latest cf-python package
+      - name: install package
+        run: |
+          pip install https://github.com/NCAS-CMS/cf-python/archive/main.zip          
+
       # install package
       - name: install package
         run: |
           pip install -e .
 
       # run tests
-      - name: run advanced test suite
+      - name: run advanced tests 1 (SameTimeSameSpace)
+        run: |
+          (cd ./tests && python run_stss_tests.py)
+
+      # run tests
+      - name: run advanced tests 2 (SameTimeDiffSpace)
+        run: |
+          (cd ./tests && python run_stds_tests.py)          
+
+      # run tests
+      - name: run advanced tests 3 (DiffTimeSameSpace)
+        run: |
+          (cd ./tests && python run_dtss_tests.py)
+
+      # run tests
+      - name: run advanced tests 4 (DiffTimeDiffSpace)
         run: |
-          (cd ./tests && python run_all_tests.py)
+          (cd ./tests && python run_dtds_tests.py)          

.github/workflows/basic_tests.yml

@@ -8,27 +8,27 @@ on:
 jobs:
 
   run-basic-tests:
-  
+
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest, macos-13]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
       fail-fast: false
-        
+
     runs-on: ${{ matrix.os }}
-    
+
     defaults:
       run:
         shell: bash -l {0}
-    
+
     steps:
-    
+
       # check out PR HEAD commit
       - name: check out PR HEAD commit
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
-          
+
       # set up a conda environment
       - name: set up miniconda environment
         uses: conda-incubator/setup-miniconda@v2
@@ -37,20 +37,26 @@ jobs:
           python-version: ${{ matrix.python-version }}
           auto-update-conda: true
           mamba-version: "*"
+          miniconda-version: "latest"
           channels: conda-forge
           channel-priority: true
-          
+
       # install dependencies on conda environment
       - name: install package dependencies
         run: |
           mamba install udunits2=2.2.25
           mamba install --file=requirements.txt
-          
+
+      # install latest cf-python package
+      - name: install package
+        run: |
+          pip install https://github.com/NCAS-CMS/cf-python/archive/main.zip
+
       # install package
       - name: install package
         run: |
           pip install -e .
-          
+
       # run tests
       - name: run basic test suite
         run: |

.github/workflows/build_docs.yml

@@ -73,7 +73,6 @@ jobs:
 
       - name: install dependencies for framework and its documentation
         run: |
-          mamba install --file=requirements.txt
           mamba install --file=requirements-docs.txt
 
       - name: setup git user info

.gitignore

@@ -2,6 +2,7 @@ __pycache__/
 *.pyc
 *.pyf
 *.so
+.pre-commit*
 
 # ignore documentation built because copied in docs/ root already
 docs/_doc_build

.zenodo.json

@@ -8,12 +8,17 @@
         {
             "name": "Richard J. Ellis",
             "affiliation": "UK Centre for Ecology and Hydrology, UK"
-        }
+        },
+        {
+            "name": "Matt Brown",
+            "affiliation": "UK Centre for Ecology and Hydrology, UK",
+            "orcid": "0000-0003-1127-0279"
+        }        
     ],
     "title": "unifhy",
     "description": "A Unified Framework for Hydrology.",
     "notes": "Funded by the Natural Environment Research Council (NERC) Hydro-JULES programme (NE/S017380/1).",
     "license": {
         "id": "BSD-3-Clause"
     }
-}
+}

README.rst

@@ -13,14 +13,14 @@ Unified Framework for Hydrology
 .. image:: https://img.shields.io/badge/fair-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow?style=flat-square
    :target: https://fair-software.eu
    :alt: FAIR Software Compliance
-.. image:: https://img.shields.io/github/workflow/status/unifhy-org/unifhy/Basic%20tests?style=flat-square&label=tests
+.. image:: https://img.shields.io/github/actions/workflow/status/unifhy-org/unifhy/basic_tests.yml?style=flat-square&label=tests
    :target: https://github.com/unifhy-org/unifhy/actions/workflows/basic_tests.yml
    :alt: Tests Status
 
-The Python package `unifhy` (Unified Framework for Hydrology) is a hydrological 
-modelling framework which combines interchangeable modelling components for the 
-surface layer, subsurface, and open water parts of the terrestrial water cycle. 
-By two-way coupling these three components, the framework provides a fully
+The Python package `unifhy` (Unified Framework for Hydrology) is a hydrological
+modelling framework which combines interchangeable modelling components for the
+surface layer, subsurface, and open water parts of the terrestrial water and nutrient cycles.
+By two-way coupling these six components, the framework provides a fully
 functional model for simulating the terrestrial water cycle. It is designed to
 foster collaborations between land surface, hydrological, and groundwater
 modelling communities by structuring their interactions around standardised

changelog.rst

@@ -1,10 +1,39 @@
 .. default-role:: obj
 
-..
-   latest
-   ------
 
-   Yet to be versioned and released. Only available from *dev* branch until then.
+v1.0.0
+------
+
+.. rubric:: Dependencies
+
+* add support for Python 3.10 and 3.11
+* support dropped for cf-python <=3.16.2
+
+.. rubric:: API changes
+
+* 3 new Components added to framework to allow modelling of nutrient cycle
+  (`#14 <https://github.com/unifhy-org/unifhy/issues/14>`_)
+* Unit tests updated to include the 3 new Components
+  (`#93 <https://github.com/unifhy-org/unifhy/issues/93>`_)
+
+.. rubric:: Bug fixes
+
+* fix `DataComponent`/`NullComponent` bug making them unusable as
+  substitute components in a `Model`
+  (`#87 <https://github.com/unifhy-org/unifhy/issues/87>`_)
+* fix broken grid cell area calculation with CF-Python version 3.14.0 and above 
+  (`#98 <https://github.com/unifhy-org/unifhy/issues/98>`_)
+* fix broken grid subsetting with CF-Python 3.16.2
+  (`#101 <https://github.com/unifhy-org/unifhy/issues/101>`_)
+
+
+.. rubric:: Documentation
+
+* Update documentation to include Nutrient Components
+  (`#99 <https://github.com/unifhy-org/unifhy/issues/99>`_)
+* Added Developer section to documentation to document how to add new transfers and Components to the framework
+  (`#96 <https://github.com/unifhy-org/unifhy/issues/96>`_)
+
 
 v0.1.1
 ------

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 296a6d03df30610eda09667a1e37e1ea
+config: 05958782197871c0315be596afe948ce
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.X.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.X
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.X
+.. autoattribute:: unifhy.BritishNationalGrid.X

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.X_bounds.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.X_bounds
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.X_bounds
+.. autoattribute:: unifhy.BritishNationalGrid.X_bounds

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.X_name.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.X_name
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.X_name
+.. autoattribute:: unifhy.BritishNationalGrid.X_name

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.Y.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.Y
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.Y
+.. autoattribute:: unifhy.BritishNationalGrid.Y

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.Y_bounds.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.Y_bounds
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.Y_bounds
+.. autoattribute:: unifhy.BritishNationalGrid.Y_bounds

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.Y_name.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.Y_name
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.Y_name
+.. autoattribute:: unifhy.BritishNationalGrid.Y_name

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.axes.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.axes
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.axes
+.. autoattribute:: unifhy.BritishNationalGrid.axes

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.cell_area.rst.txt

@@ -4,4 +4,4 @@
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.cell_area
+.. autoattribute:: unifhy.BritishNationalGrid.cell_area

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.flow_direction.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.flow_direction
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.flow_direction
+.. autoattribute:: unifhy.BritishNationalGrid.flow_direction

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.land_sea_mask.rst.txt

@@ -4,4 +4,4 @@
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.land_sea_mask
+.. autoattribute:: unifhy.BritishNationalGrid.land_sea_mask

docs/0.1.0/_sources/api/attributes/unifhy.BritishNationalGrid.shape.rst.txt

@@ -4,4 +4,4 @@ unifhy.BritishNationalGrid.shape
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.BritishNationalGrid.shape
+.. autoattribute:: unifhy.BritishNationalGrid.shape

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.X.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.X
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.X
+.. autoattribute:: unifhy.LatLonGrid.X

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.X_bounds.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.X_bounds
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.X_bounds
+.. autoattribute:: unifhy.LatLonGrid.X_bounds

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.X_name.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.X_name
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.X_name
+.. autoattribute:: unifhy.LatLonGrid.X_name

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.Y.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.Y
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.Y
+.. autoattribute:: unifhy.LatLonGrid.Y

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.Y_bounds.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.Y_bounds
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.Y_bounds
+.. autoattribute:: unifhy.LatLonGrid.Y_bounds

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.Y_name.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.Y_name
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.Y_name
+.. autoattribute:: unifhy.LatLonGrid.Y_name

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.axes.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.axes
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.axes
+.. autoattribute:: unifhy.LatLonGrid.axes

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.cell_area.rst.txt

@@ -4,4 +4,4 @@
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.cell_area
+.. autoattribute:: unifhy.LatLonGrid.cell_area

docs/0.1.0/_sources/api/attributes/unifhy.LatLonGrid.flow_direction.rst.txt

@@ -4,4 +4,4 @@ unifhy.LatLonGrid.flow_direction
 .. currentmodule:: unifhy
 .. default-role:: obj
 
-.. autoattribute:: unifhy.LatLonGrid.flow_direction
+.. autoattribute:: unifhy.LatLonGrid.flow_direction