Introduce icon4py model (#221)

Introduces the icon4py.model namespace which contains the common namespace package and the atmosphere.dycore namespace package.

---------

Co-authored-by: Enrique G. Paredes <18477+egparedes@users.noreply.github.com>

.github/workflows/icon4py-qa.yml

@@ -29,16 +29,18 @@ jobs:
               uses: actions/setup-python@v3
               with:
                   python-version: "3.10"
-            - name: Install dependencies
+            - name: Install icon4py-atmosphere-dycore
+              working-directory: model/atmosphere/dycore
               run: |
                   python -m pip install --upgrade pip setuptools wheel
-                  python -m pip install $(cat ./base-requirements-dev.txt | grep pre-commit)
-                  pre-commit install-hooks
-                  # mypy hook uses local repo and thus requires installing icon4py & gt4py
-                  python -m pip install $(cat ./base-requirements-dev.txt | grep mypy)
-                  python -m pip install $(cat ./base-requirements-dev.txt | grep gt4py)
-                  python -m pip install $(cat ./requirements-dev.txt | grep '\-e')
-            - name: Run checks
+                  python -m pip install -r ./requirements-dev.txt
+
+            - name: Install icon4py-common
+              working-directory: model/common
+              run: |
+                  python -m pip install --upgrade pip setuptools wheel
+                  python -m pip install -r ./requirements-dev.txt
+            - name: Run checks icon4py-model
               run: |
                   python -m pip list
-                  pre-commit run --config .pre-commit-config.yaml --all-files
+                  pre-commit run --config model/.pre-commit-config.yaml --all-files

.github/workflows/icon4py-tox.yml

@@ -43,15 +43,9 @@ jobs:
               run: |
                   python -m pip install --upgrade pip setuptools wheel
 
-            - name: Test with tox
+            - name: Test icon4py-model with tox
               run: |
                   pyversion_no_dot="${{ matrix.python-version }}"
                   pyversion_no_dot="${pyversion_no_dot/./}"
                   pip install tox clang-format
-                  tox -r -e py${pyversion_no_dot}
-
-            - name: Archive code coverage results
-              uses: actions/upload-artifact@v2
-              with:
-                  name: code-coverage-report
-                  path: _reports/coverage_html/
+                  tox -r -e py${pyversion_no_dot} -c model/

.github/workflows/icon4pytools-qa.yml

@@ -36,6 +36,7 @@ jobs:
               with:
                   python-version: "3.10"
             - name: Install dependencies
+              working-directory: tools
               run: |
                   python -m pip install --upgrade pip setuptools wheel
                   python -m pip install -r ./requirements-dev.txt

.github/workflows/icon4pytools-tox.yml

@@ -32,9 +32,6 @@ jobs:
         strategy:
             matrix:
                 python-version: ["3.10"]
-        defaults:
-            run:
-                working-directory: tools
 
         steps:
             - uses: actions/checkout@v2
@@ -58,10 +55,4 @@ jobs:
                   pyversion_no_dot="${{ matrix.python-version }}"
                   pyversion_no_dot="${pyversion_no_dot/./}"
                   pip install tox clang-format
-                  tox -r -e py${pyversion_no_dot}
-
-            - name: Archive code coverage results
-              uses: actions/upload-artifact@v2
-              with:
-                  name: code-coverage-report
-                  path: _reports/coverage_html/
+                  tox -r -e py${pyversion_no_dot} -c tools/

README.md

@@ -2,13 +2,11 @@
 
 # ICON4Py
 
-## Description
+ICON4Py hosts Python implementations of various components from the ICON climate and weather model. Additionally, it includes icon4pytools, a collection of command-line interfaces (CLIs), and utilities required for the integration of ICON4Py code into the ICON Fortran model. ICON4Py leverages [GT4Py](https://github.com/GridTools/gt4py) to ensure efficient and performance portable implementations of these components.
 
-ICON4Py contains Python (GT4Py) implementations of ICON (inspired) components for weather and climate models as well as `icon4pytools`, a package containing CLIs and utilties needed for the integration of ICON4Py code into the ICON Fortran model.
+## Project Structure
 
-## Project structure
-
-Each directory contains Python packages of ICON components or utility packages that are deployable on their own. As these packages are not available from a package repository (yet), location of dependencies within this repository have to be provided explicitly, e.g. by installing the dependencies first. See [Installation instructions](#installation-instructions).
+The repository is organized into directories, each containing independent Python namespace packages for different ICON components or utility packages. These packages can be installed independently. Since these packages are not available from a package repository (yet), you need to specify the location of dependencies within this repository. This can be done by installing the required dependencies first. Refer to the [Installation instructions](#installation-instructions) below.
 
 ## Installation instructions
 
@@ -49,7 +47,7 @@ pip install --src _external_src -r requirements-dev.txt
 pytest -v
 ```
 
-The `--src _external_src` option tells `pip` to use a specific folder as base path for checked out sources, which is very convenient for development tasks involving changes in external dependencies like `gt4py`. For convenience, `./_external_src` has been already added to the repository `.gitignore`.
+The `--src _external_src` option tells `pip` to use a specific folder as the base path for checked out sources, which is very convenient for development tasks involving changes in external dependencies like `gt4py`. For convenience, `./_external_src` has been already added to the repository `.gitignore`.
 
 ### Installation of specific subpackages
 
@@ -70,7 +68,7 @@ source .venv/bin/activate
 pip install --upgrade wheel
 
 # Install a specific ICON4Py subpackage and its dependencies
-cd _SUBPACKAGE_  # where _SUBPACKAGE_ in atm_dyn_iconam | tools | ...
+cd _SUBPACKAGE_  # where _SUBPACKAGE_ in model/atmosphere/dycore | tools | ...
 pip install -r requirements-dev.txt
 
 # or in the case of there being a pyproject.toml file
@@ -83,24 +81,14 @@ After following the installation instructions above using the development requir
 
 ### Code quality checks
 
-[pre-commit](https://pre-commit.com/) is used to run several linting and checking tools. It should always be executed locally before opening a pull request. `pre-commit` can also be installed as a _git hook_ to automatically check the staged changes before committing:
+[pre-commit](https://pre-commit.com/) is used to run several linting and checking tools. It should always be executed locally before opening a pull request. When executing pre-commit locally you can either run it for the `model` or `tools` folder:
 
-```bash
-# Install pre-commit as a git hook and set up all the tools
-pre-commit install --install-hooks
-```
-
-Or it can be executed on demand from the command line:
+For example to run code checks on all components in `icon4py.model` you can do:
 
 ```bash
-# Check only the staged changes
-pre-commit run
-
-# Check all the files in the repository
-pre-commit run -a
-
-# Run only some of the tools (e.g. mypy)
-pre-commit run -a mypy
+# running precommit for all components in model
+cd model/
+pre-commit run --all-files
 ```
 
 ### Testing
@@ -126,3 +114,11 @@ tox -e py310
 ```
 
 The default `tox` environment is configured to generate HTML test coverage reports in `_reports/coverage_html/`.
+
+### Benchmarking
+
+We use [`pytest-benchmark`](https://pytest-benchmark.readthedocs.io/en/latest/) to benchmark the execution time of stencils in icon4py. To disable benchmarking during testing you can use `--benchmark-disable` when invoking `pytest`.
+
+### More Information
+
+For more information please consult the package specific READMEs found in the `model` and `tools` folders.