Allow saving and loading the 3D grid to and from an HDF5 file (#38)

* build: include static images

* build: bump scipy and numpy version in requirements

* style: apply ruff suggestions + improve verbose prints

* style: apply Ruffs code quality suggestions

* Potential fix for pull request finding 'Except block handles 'BaseException''

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* feature: add load_from_h5 and save_to_h5 functions

* Potential fix for pull request finding 'Unnecessary pass'

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

* fix: MPI test failing fix: re-compute z with the final subdomain samples

* fix: wakis install failed

* fix: mpi tests_007 passing, fixed typo Nz->NZ

* style: apply RUFFs style suggestions

* fix: put 3D plot flag back to false

* style: fix Ruffs warnings

* style: add RUFFs suggestions + remove the `if False` at the end of the file

* test: add workflow to run MPI tests on pull request update

* style: minor improvements and Ruff fixes

* style: improve notebook 006 to match CST result, clear outputs

* tests: include test functions for load and save grid

* style: add Ruffs suggestions + improve load_results to update self.folder and/or take folder from class constructor. Ez_file is now None, and default value is result_folder+Ez.h5

* refact: move verbosity in __init__ to `load_from_h5` and improved information

* fix: add logger lines, wrongly skipped during merge + fix MPI workflow action

* reafact+test: fix logger updates and included them in load_from_h5.Included domain boundaries in logger and updated test_007 to compare dict with tolerances

* test: update static dict with use_mpi for MPI tests

---------

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Author: elenafuengar

.github/workflows/pull_request_MPI.yml

@@ -0,0 +1,49 @@
+# This is a basic workflow that is manually triggered
+
+name: pull_request_tests_MPI_python10
+
+# Controls when the action will run. Workflow runs when manually triggered using the UI
+# or API.
+on:
+  # Run tests for every pull request targeting main
+  pull_request:
+    branches:
+      - main
+    types: [opened, synchronize, reopened]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  run_tests:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Make the default shell a login shell, so that conda is initialised properly
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        path: wakis
+    - name: Setup Miniforge
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniforge-version: latest
+        python-version: "3.11"
+    - name: mpi install
+      run: |
+        conda install -c conda-forge openmpi
+        conda install -c conda-forge mpi4py
+    - name: pip install
+      run:  |
+        cd wakis
+        pip install .['notebook']
+    - name: Print versions
+      run: conda list
+    - name: Run pytest
+      run:  |
+        cd wakis
+        mpiexec -n 2 python -m pytest --color=yes -v -s tests/test_007_mpi_lossy_cavity.py