Packaging and numpy>=2

.github/workflows/manual_tests_CPU.yml

@@ -25,18 +25,18 @@ jobs:
       with:
         miniforge-version: latest
         python-version: "3.10"
-    - name: pip install
-      run:  |
-        pip install wakis['notebook']
-        pip uninstall vtk -y
-        pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
-
     - name: Print versions
       run: conda list
     - name: Checkout wakis
       uses: actions/checkout@v4
       with:
         path: wakis
+    - name: pip install
+      run:  |
+        cd wakis
+        pip install .[notebook,tests]
+        pip uninstall vtk -y
+        pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
     - name: Run pytest
       run:  |
         cd wakis

.github/workflows/manual_tests_MPI.yml

@@ -29,16 +29,16 @@ jobs:
       run: |
         conda install -c conda-forge openmpi
         conda install -c conda-forge mpi4py
-    - name: pip install
-      run:  |
-        pip install wakis['notebook']
-
     - name: Print versions
       run: conda list
     - name: Checkout wakis
       uses: actions/checkout@v4
       with:
         path: wakis
+    - name: pip install
+      run:  |
+        cd wakis
+        pip install .[notebook,tests]
     - name: Run pytest
       run:  |
         cd wakis

.github/workflows/nightly_codecov_CPU.yml

@@ -24,16 +24,16 @@ jobs:
       with:
         miniforge-version: latest
         python-version: "3.10"
-    - name: pip install
-      run:  |
-        pip install wakis['notebook']
-        pip install pytest pytest-cov
     - name: Print versions
       run: conda list
     - name: Checkout wakis
       uses: actions/checkout@v4
       with:
         path: wakis
+    - name: pip install
+      run:  |
+        cd wakis
+        pip install .[notebook,tests]
     - name: Run pytest
       run:  |
         cd wakis

.github/workflows/nightly_tests_CPU.yml

@@ -25,17 +25,18 @@ jobs:
       with:
         miniforge-version: latest
         python-version: "3.10"
-    - name: pip install
-      run:  |
-        pip install wakis['notebook']
-        pip uninstall vtk -y
-        pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
     - name: Print versions
       run: conda list
     - name: Checkout wakis
       uses: actions/checkout@v4
       with:
         path: wakis
+    - name: pip install
+      run:  |
+        cd wakis
+        pip install .[notebook,tests]
+        pip uninstall vtk -y
+        pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
     - name: Run pytest
       run:  |
         cd wakis

.github/workflows/pull_request_CPU.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Install wakis
         run: |
           cd wakis
-          pip install .['notebook']
+          pip install .[notebook,tests]
           pip uninstall vtk -y
           pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
 

.github/workflows/pull_request_MPI.yml

@@ -24,26 +24,25 @@ jobs:
 
     # 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
+      - 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 mpi4py
+      - name: pip install
+        run: |
+          cd wakis
+          pip install .[notebook,tests]
+      - 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

.gitignore

@@ -21,4 +21,16 @@ ECT_*
 *.PNG
 _build/
 dist/
-wakis.egg-info/
+wakis.egg-info/
+.venv
+.coverage
+coverage.xml
+*.pyc
+*.pyo
+*.pyd
+*.so
+.Python
+*.ipynb_checkpoints
+htmlcov/
+uv.lock
+build

MANIFEST.in

@@ -4,7 +4,4 @@ include pyproject.toml
 include *.md
 
 # Include the license file
-include LICENSE.txt
-
-# Include requirements
-include requirements.txt
+include LICENSE

Makefile

@@ -0,0 +1,52 @@
+# wakis Makefile
+
+
+# Colors for output
+RED := \033[0;31m
+GREEN := \033[0;32m
+YELLOW := \033[1;33m
+NC := \033[0m # No Color
+
+.PHONY: help install install-gpu clean docs
+
+# Based on https://gist.github.com/prwhite/8168133?permalink_comment_id=4718682#gistcomment-4718682
+
+## (Default) Print listing of key targets with their descriptions
+help:
+	@printf "\n\033[1;33mwakis Makefile\033[0m\n"
+	@printf "\n\033[1;34mUsage:\033[0m \033[1;33mmake <target>\033[0m\n\n"
+	@awk '\
+		/^## / { \
+			desc = substr($$0, 4); \
+			getline nextline; \
+			if (match(nextline, /^([a-zA-Z0-9._-]+):/)) { \
+				target = substr(nextline, RSTART, RLENGTH-1); \
+				printf "  \033[34m%-20s\033[0m %s\n", target, desc; \
+			} \
+		} \
+	' $(MAKEFILE_LIST)
+
+## Install Python dependencies
+install:
+	@echo -e "Installing Python dependencies..."
+	@pip install -e  .[full]
+
+## Install Python dependencies
+install-gpu:
+	@echo -e "Installing Python dependencies with GPU support..."
+	@pip install -e  .[full-gpu]
+
+## Remove temporary and generated files
+clean:
+	@echo -e "Cleaning up directory..."
+	@rm -rf __pycache__ .ruff_cache .pytest_cache *.egg-info .html *.html coverage.xml .coverage .mypy_cache results
+	@ cd docs && make -s clean
+
+
+## Run Python tests
+test:
+	pytest -s
+
+## Build documentation
+docs:
+	cd docs && make html

README.md

@@ -99,8 +99,7 @@ Create a dedicated **conda environment** and install dependencies:
 cd wakis/
 conda create --name wakis-env python=3.11
 conda activate wakis-env
-pip install -r requirements.txt
-pip install -e .  # install wakis in editable mode
+pip install -e .[notebook, tests, docs]  # install wakis in editable mode
 pip install neffint iddefix bihc  # Optional tools
 ```
 🛠️ **Want to contribute?**  To merge your changes into `main`, create a **Pull Request (PR)** following our [PR template](https://github.com/ImpedanCEI/wakis/blob/main/.github/pull_request_template.md).