Refactored main and restructured code

.coveragerc

@@ -0,0 +1,20 @@
+[run]
+source = src
+omit = 
+    src/data_assimilation/*
+    src/inputs/*
+    src/utils/debug_helpers.py
+    */tests/*
+    */test_*
+    setup.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise AssertionError
+    raise NotImplementedError
+    if __name__ == .__main__.:
+
+[html]
+directory = htmlcov

.github/workflows/deploy.yml

@@ -0,0 +1,94 @@
+name: deploy
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  integration-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # Skip setup-python if running under act
+      - name: Set up Python (GitHub only)
+        if: ${{ !env.ACT }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      # Show system Python version when running under act
+      - name: Use system Python (act)
+        if: ${{ env.ACT }}
+        run: |
+          echo "Using system Python"
+          which python
+          python --version
+
+      - name: Install dependencies
+        run: |
+          pip install -r dev-requirements.txt
+          pip install .
+
+      - name: Run tests without coverage
+        run: |
+          # pytest --cov=src --cov-report=xml --cov-report=html --cov-report=term
+          pytest ./test_scripts/test_blending.py
+          pytest ./test_scripts/test_flow_solver.py
+
+      # - name: Upload coverage HTML report
+      #   if: ${{ !env.ACT }}
+      #   uses: actions/upload-artifact@v4
+      #   with:
+      #     name: coverage-html
+      #     path: htmlcov/
+
+      - name: Upload test plots and logs
+        if: ${{ !env.ACT }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-outputs
+          path: |
+            outputs/**/*.png
+            logs/**/*.log
+            !outputs/**/*.dat
+            !outputs/**/*.h5
+
+  # docs:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+
+  #     - uses: ConorMacBride/install-package@v1
+  #       with:
+  #         apt: graphviz
+
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: '3.10'
+
+  #     - uses: actions/cache@v4
+  #       with:
+  #         path: ~/.cache/pip
+  #         key: ${{ runner.os }}-pip-${{ hashFiles('**/dev-requirements.txt') }}
+  #         restore-keys: |
+  #           ${{ runner.os }}-pip-
+
+  #     - name: Install dependencies
+  #       run: |
+  #         pip install -r dev-requirements.txt
+  #         pip install .
+
+  #     - name: Sphinx build
+  #       run: |
+  #         sphinx-build docs/source _build
+
+  #     - name: Deploy to GitHub Pages
+  #       uses: peaceiris/actions-gh-pages@v4
+  #       if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+  #       with:
+  #         publish_branch: gh-pages
+  #         github_token: ${{ secrets.GITHUB_TOKEN }}
+  #         publish_dir: _build/
+  #         force_orphan: true

.gitignore

@@ -4,9 +4,19 @@
 **dask-worker-space*
 *.ipynb_checkpoints*
 *.egg-info*
+*.coverage*
+profile.html
+profile.json
+
+# Ignore everything under outputs/
+outputs/**
+
+# Do not ignore directories (so unignore rules can match their contents)
+!outputs/
+!outputs/**/
+!outputs/**/*_stripped.h5
 
 # Ignore local development and output subdirectories
-**outputs*
 **build*
 **changelog.d*
 

CHANGELOG.rst

@@ -1,3 +1,21 @@
+0.60.0 (2024-12-23)
+-------------------
+
+Changed
+^^^^^^^
+
+- Restructured outermost looping in main() (23a7817db225fe2188bcf3045cfdc863435b6888)
+
+
+0.50.6 (2024-12-10)
+-------------------
+
+Changed
+^^^^^^^
+
+- Cleaned __main__ with restructuring of code (61e48c2c60e32aa8ac7699979a9836c8d17ded64)
+
+
 0.50.5 (2024-03-24)
 -------------------
 

README.md

@@ -74,7 +74,13 @@ A simple test can be found in [`run_scripts.test_dycore`](https://github.com/ray
 pytest ./run_scripts/test_dycore.py -v
 ```
 
-However, the codebase is structured such that the user can easily assemble a run script to define their own experiments. Refer to the documentation for the [available APIs](https://ray-chew.github.io/pyBELLA/apis.html).
+To run a simulation:
+```console
+pybella -ic rb -N 1
+```
+Note that only the rising bubble initial condition is implemented for now with ensemble size of 1. 
+
+The codebase is structured such that the user can easily assemble a run script to define their own experiments. Refer to the documentation for the [available APIs](https://ray-chew.github.io/pyBELLA/apis.html).
 
 ## License
 
@@ -86,3 +92,14 @@ Refer to the [open issues](https://github.com/ray-chew/pyBELLA/issues), in parti
 
 Any changes, improvements, or bug fixes can be submitted from your remote to upstream via a pull request.
 
+## To be tidied up
+
+### Profiler 
+```bash
+$ PYTHONPATH=src scalene -m pybella -ic test_lamb_wave -N 1
+```
+
+### Coverage
+```bash
+$ pytest --cov test_scripts/ --cov-report=html 
+```

dev-requirements.txt

@@ -1,17 +1,15 @@
-dask==2022.7.0
-dask[distributed]==2022.7.0
-dill==0.3.6
-h5py==3.7.0
-matplotlib==3.5.1
-numba==0.56.4
-numpy==1.22.1
-pyemd==1.0.0
-pytest==8.1.1
-PyYAML==6.0
-scipy==1.7.3
-termcolor==2.4.0
+dill
+h5py
+matplotlib
+numba
+numpy
+pytest
+scipy
+dask
+pytest
+pytest-cov
 # dependencies for documentation
-sphinx==7.2.6
-sphinx_changelog==1.5.0
-sphinx-math-dollar==1.2.1
-furo==2024.1.29
+sphinx
+sphinx_changelog
+sphinx-math-dollar
+furo