incompy2d 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- incompy2d-0.1.0/.gitignore +19 -0
- incompy2d-0.1.0/.gitlab-ci.yml +132 -0
- incompy2d-0.1.0/CHANGELOG.md +0 -0
- incompy2d-0.1.0/CITATION.cff +9 -0
- incompy2d-0.1.0/CONTRIBUTING.md +0 -0
- incompy2d-0.1.0/LICENSE +21 -0
- incompy2d-0.1.0/PKG-INFO +56 -0
- incompy2d-0.1.0/README.md +13 -0
- incompy2d-0.1.0/docs/conf.py +17 -0
- incompy2d-0.1.0/docs/index.rst +15 -0
- incompy2d-0.1.0/docs/sce/CI_implementation_plan.md +405 -0
- incompy2d-0.1.0/docs/sce/CI_pipeline.md +72 -0
- incompy2d-0.1.0/docs/sce/README.md +24 -0
- incompy2d-0.1.0/docs/sce/cfd-projection-method.md +32 -0
- incompy2d-0.1.0/docs/sce/fetch_overture.md +32 -0
- incompy2d-0.1.0/docs/sce/geom_util.md +57 -0
- incompy2d-0.1.0/docs/sce/html/.buildinfo +4 -0
- incompy2d-0.1.0/docs/sce/html/.doctrees/environment.pickle +0 -0
- incompy2d-0.1.0/docs/sce/html/.doctrees/index.doctree +0 -0
- incompy2d-0.1.0/docs/sce/html/_sources/index.rst.txt +15 -0
- incompy2d-0.1.0/docs/sce/html/_static/alabaster.css +663 -0
- incompy2d-0.1.0/docs/sce/html/_static/base-stemmer.js +476 -0
- incompy2d-0.1.0/docs/sce/html/_static/basic.css +906 -0
- incompy2d-0.1.0/docs/sce/html/_static/custom.css +1 -0
- incompy2d-0.1.0/docs/sce/html/_static/doctools.js +150 -0
- incompy2d-0.1.0/docs/sce/html/_static/documentation_options.js +13 -0
- incompy2d-0.1.0/docs/sce/html/_static/english-stemmer.js +1066 -0
- incompy2d-0.1.0/docs/sce/html/_static/file.png +0 -0
- incompy2d-0.1.0/docs/sce/html/_static/github-banner.svg +5 -0
- incompy2d-0.1.0/docs/sce/html/_static/language_data.js +13 -0
- incompy2d-0.1.0/docs/sce/html/_static/minus.png +0 -0
- incompy2d-0.1.0/docs/sce/html/_static/plus.png +0 -0
- incompy2d-0.1.0/docs/sce/html/_static/pygments.css +84 -0
- incompy2d-0.1.0/docs/sce/html/_static/searchtools.js +693 -0
- incompy2d-0.1.0/docs/sce/html/_static/sphinx_highlight.js +159 -0
- incompy2d-0.1.0/docs/sce/html/genindex.html +99 -0
- incompy2d-0.1.0/docs/sce/html/index.html +111 -0
- incompy2d-0.1.0/docs/sce/html/objects.inv +0 -0
- incompy2d-0.1.0/docs/sce/html/search.html +117 -0
- incompy2d-0.1.0/docs/sce/html/searchindex.js +1 -0
- incompy2d-0.1.0/docs/sce/incomp_2d.md +50 -0
- incompy2d-0.1.0/docs/sce/log-2026.07.07.md +62 -0
- incompy2d-0.1.0/docs/sce/log-2026.07.10.md +98 -0
- incompy2d-0.1.0/docs/sce/log-2026.07.12.md +24 -0
- incompy2d-0.1.0/docs/sce/mesh_util.md +53 -0
- incompy2d-0.1.0/docs/sce/numba_implementation.md +33 -0
- incompy2d-0.1.0/docs/sce/post.md +37 -0
- incompy2d-0.1.0/docs/sce/python_package_implementation_plan.md +176 -0
- incompy2d-0.1.0/docs/sce/run.md +39 -0
- incompy2d-0.1.0/docs/sce/sce_common_practices.md +64 -0
- incompy2d-0.1.0/docs/sce/testing.md +20 -0
- incompy2d-0.1.0/docs/sce/walkthrough_CI.md +27 -0
- incompy2d-0.1.0/docs/sce/walkthrough_package.md +35 -0
- incompy2d-0.1.0/environment.yml +25 -0
- incompy2d-0.1.0/examples/run_generic_flow.py +136 -0
- incompy2d-0.1.0/examples/run_wind_flow.py +115 -0
- incompy2d-0.1.0/geom/overture_bld.geojson +2 -0
- incompy2d-0.1.0/geom/overture_bld.geojson.state +14 -0
- incompy2d-0.1.0/pyproject.toml +46 -0
- incompy2d-0.1.0/src/incompy2d/__init__.py +35 -0
- incompy2d-0.1.0/src/incompy2d/fetch_overture.py +91 -0
- incompy2d-0.1.0/src/incompy2d/geom_util.py +141 -0
- incompy2d-0.1.0/src/incompy2d/incomp_2d.py +360 -0
- incompy2d-0.1.0/src/incompy2d/mesh_util.py +128 -0
- incompy2d-0.1.0/src/incompy2d/post.py +200 -0
- incompy2d-0.1.0/src/incompy2d/run.py +115 -0
- incompy2d-0.1.0/src/ipynb/00_Quick_Python_Intro.ipynb +311 -0
- incompy2d-0.1.0/src/ipynb/01_Step_1.ipynb +222 -0
- incompy2d-0.1.0/src/ipynb/02_Step_2.ipynb +109 -0
- incompy2d-0.1.0/src/ipynb/03_CFL_Condition.ipynb +312 -0
- incompy2d-0.1.0/src/ipynb/04_Step_3.ipynb +143 -0
- incompy2d-0.1.0/src/ipynb/05_Step_4.ipynb +600 -0
- incompy2d-0.1.0/src/ipynb/06_ArrayOperationsWithNumPy.ipynb +273 -0
- incompy2d-0.1.0/src/ipynb/07_Step_5.ipynb +271924 -0
- incompy2d-0.1.0/src/ipynb/08_Step_6.ipynb +215 -0
- incompy2d-0.1.0/src/ipynb/09_Step_7.ipynb +317 -0
- incompy2d-0.1.0/src/ipynb/10_Step_8.ipynb +424 -0
- incompy2d-0.1.0/src/ipynb/12_2DLaplace.ipynb +248 -0
- incompy2d-0.1.0/src/ipynb/13_2DPoisson.ipynb +220 -0
- incompy2d-0.1.0/src/ipynb/14_CavityFlowNS.ipynb +415 -0
- incompy2d-0.1.0/src/ipynb/15_ChannelFlowNS.ipynb +516 -0
- incompy2d-0.1.0/tests/__init__.py +1 -0
- incompy2d-0.1.0/tests/test_fetch_overture.py +53 -0
- incompy2d-0.1.0/tests/test_geom_util.py +9 -0
- incompy2d-0.1.0/tests/test_incomp_2d.py +31 -0
- incompy2d-0.1.0/tests/test_mesh_util.py +44 -0
- incompy2d-0.1.0/tests/test_post.py +85 -0
- incompy2d-0.1.0/tests/test_run.py +68 -0
- incompy2d-0.1.0/validation/archive/validation_v1_implementation_plan.md +163 -0
- incompy2d-0.1.0/validation/archive/validation_v1_report.md +50 -0
- incompy2d-0.1.0/validation/archive/validation_v1_review.md +116 -0
- incompy2d-0.1.0/validation/archive/validation_v2_implementation_plan.md +209 -0
- incompy2d-0.1.0/validation/archive/validation_v2_report.md +45 -0
- incompy2d-0.1.0/validation/debug.py +33 -0
- incompy2d-0.1.0/validation/post_process.py +163 -0
- incompy2d-0.1.0/validation/validate_cylinder.py +186 -0
- incompy2d-0.1.0/validation/validation_outputs/fig_cd_vs_re.png +0 -0
- incompy2d-0.1.0/validation/validation_outputs/fig_residuals.png +0 -0
- incompy2d-0.1.0/validation/validation_outputs/fig_vorticity_re100.png +0 -0
- incompy2d-0.1.0/validation/validation_outputs/fig_vorticity_re200.png +0 -0
- incompy2d-0.1.0/validation/validation_outputs/flow_re100.npz +0 -0
- incompy2d-0.1.0/validation/validation_outputs/flow_re20.npz +0 -0
- incompy2d-0.1.0/validation/validation_outputs/flow_re200.npz +0 -0
- incompy2d-0.1.0/validation/validation_outputs/flow_re40.npz +0 -0
- incompy2d-0.1.0/validation/validation_outputs/results.txt +5 -0
- incompy2d-0.1.0/validation/validation_report_final.md +32 -0
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*.py[cod]
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env/
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venv/
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dist/
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build/
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solver.log
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# ==============================================================
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# GitLab CI/CD Pipeline — incompy2d
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# 2D Incompressible Navier-Stokes CFD Solver
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# ==============================================================
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image: python:3.13-slim
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stages:
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# ---- Global settings -----------------------------------------
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variables:
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PIP_CACHE_DIR: "$CI_PROJECT_DIR/.pip-cache"
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cache:
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key: "${CI_COMMIT_REF_SLUG}"
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paths:
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# ---- Stage 1: Build -----------------------------------------
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build:
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stage: build
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- python -m pip install --upgrade pip
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- pip install -e ".[test]"
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script:
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- python -c "import incompy2d; print(f'incompy2d {incompy2d.__version__} OK')"
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- pip show incompy2d
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- if: $CI_PIPELINE_SOURCE == "push"
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# ---- Stage 2: Test ------------------------------------------
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test:
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--tb=short
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--junitxml=report.xml
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--cov=incompy2d
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--cov-report=term-missing
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--cov-fail-under=70
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# ---- Stage 3: Lint (allowed to fail) ------------------------
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lint:
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script:
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- python -m py_compile src/incompy2d/__init__.py
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- python -m py_compile src/incompy2d/incomp_2d.py
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- python -m py_compile src/incompy2d/mesh_util.py
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- python -m py_compile src/incompy2d/geom_util.py
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# ---- Stage 4: Docs ------------------------------------------
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# ---- Stage 5: Deploy to PyPI --------------------------------
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deploy:
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- >
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twine upload dist/*
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--username __token__
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when: manual
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allow_failure: false
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cff-version: 1.2.0
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message: "If you use this software, please cite it as below."
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authors:
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- family-names: "Nguyen"
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given-names: "Phuong-Nam"
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title: "Incompy2D"
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version: 0.1.0
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date-released: 2026-07-10
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url: "https://gitlab.git.nrw/phuong-nam.nguyen/sce_incompy2d"
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incompy2d-0.1.0/LICENSE
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MIT License
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Copyright (c) 2026 Phuong-Nam Nguyen
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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incompy2d-0.1.0/PKG-INFO
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Metadata-Version: 2.4
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Name: incompy2d
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Version: 0.1.0
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Summary: A 2D incompressible Navier-Stokes CFD solver in Python
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Project-URL: Repository, https://gitlab.git.nrw/phuong-nam.nguyen/sce_incompy2d
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Author-email: Phuong-Nam Nguyen <phuong-nam.nguyen@rwth-aachen.de>
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License: MIT
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License-File: LICENSE
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Requires-Python: >=3.10
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Requires-Dist: numba
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Requires-Dist: numpy
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Provides-Extra: dev
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Description-Content-Type: text/markdown
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# incompy2d
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A 2D incompressible Navier-Stokes CFD solver in Python.
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## Installation
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```bash
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pip install incompy2d
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```
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## Usage
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Please refer to the examples in the documentation.
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"""Sphinx configuration for incompy2d documentation."""
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project = "incompy2d"
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author = "Phuong-Nam Nguyen"
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release = "0.1.0"
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.napoleon",
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"sphinx.ext.viewcode",
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]
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templates_path = ["_templates"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
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html_theme = "alabaster"
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html_static_path = ["_static"]
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incompy2d documentation
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========================
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A 2D incompressible Navier-Stokes CFD solver in Python.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`
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# GitLab CI Pipeline for Automated Testing — incompy2d (v2)
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> [!NOTE]
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> **Status: ✅ IMPLEMENTED** — This plan has been fully executed. All changes below have been applied to the repository. This document now serves as a reference for the CI/CD architecture.
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Generate a `.gitlab-ci.yml` pipeline for the **incompy2d** 2D incompressible Navier-Stokes CFD solver with automated testing, Sphinx docs, and PyPI deployment.
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## Runner Selection
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From the 4 available instance runners, **Runner #424** is the best choice:
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| Runner | Status | Config | Recommendation |
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|---|---|---|---|
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| **#424 (aeIY5CzG)** ✅ | Online / Active | Docker Autoscale v2, 4vCPU+8GB RAM | **Best** — newest version, active, autoscaling, ample resources for numba JIT |
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| #116 (E7zWtuok) | Online / Active | Docker Autoscale v1, 4vCPU+8GB RAM | Good fallback, same specs but older version |
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| #36 (W1cGCHKi) | Online / **Paused** | Basic Shared Runner | ❌ Paused — unusable |
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| #35 (LCK1wy5Q) | Online / Idle | Shared GitLab Runner gitlab.git.nrw | Not ideal — tagged `pilot`/`poc`, may be decommissioned |
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The pipeline will use the `docker` and `shared` tags to target runners #424 and #116.
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## Dependency Restructuring
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The current tests only exercise modules that need `numpy` and `numba`. The heavy geo/viz packages are not imported by any test code:
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| Test file | Modules imported | Runtime deps needed |
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|---|---|---|
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| [test_mesh_util.py](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/tests/test_mesh_util.py) | `mesh_util` | numpy |
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| [test_geom_util.py](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/tests/test_geom_util.py) | `mesh_util`, `geom_util` | numpy |
|
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| [test_incomp_2d.py](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/tests/test_incomp_2d.py) | `mesh_util`, `incomp_2d` | numpy, numba |
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> [!NOTE]
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> `geom_util.geom_geojson` imports `geopandas`/`shapely` lazily (inside the function body), so `from incompy2d.geom_util import solid_poly` does **not** trigger those imports.
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**Dependency split in `pyproject.toml`** (✅ applied):
|
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|
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```toml
|
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[project]
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dependencies = [
|
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"numpy",
|
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"numba",
|
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]
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|
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[project.optional-dependencies]
|
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geo = ["meshio", "osmnx", "geopandas", "shapely", "overturemaps"]
|
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viz = ["matplotlib"]
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+
test = ["pytest", "pytest-cov"]
|
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docs = ["sphinx"]
|
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dev = ["incompy2d[geo,viz,test,docs]"]
|
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|
+
```
|
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+
|
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- **CI test job** installs `pip install -e ".[test]"` → only numpy + numba + pytest + pytest-cov (~30s vs ~3min)
|
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- **Local development** installs `pip install -e ".[dev]"` → everything
|
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- **CI docs job** installs `pip install -e ".[docs]"` → core + sphinx
|
|
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+
|
|
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|
+
> [!IMPORTANT]
|
|
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|
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> **Package Manager Consideration**: The `[geo]` optional dependencies (`geopandas`, `osmnx`, `shapely`, `overturemaps`) rely on compiled C/C++ binaries (GDAL, GEOS, PROJ). If CI jobs ever need to install `[geo]` or `[dev]`, the `python:3.13-slim` Docker image will lack these system libraries. In that case, switch to **Micromamba** or a custom Docker image with those binaries pre-installed. This is not an issue currently because the CI test job only installs `[test]`, which avoids the geospatial stack entirely.
|
|
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+
|
|
58
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+
## Proposed Changes
|
|
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|
+
|
|
60
|
+
### Pipeline Stages
|
|
61
|
+
|
|
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+
```mermaid
|
|
63
|
+
graph LR
|
|
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|
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A["🔨 build"] --> B["🧪 test"]
|
|
65
|
+
B --> C["📊 lint"]
|
|
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|
+
C --> D["📖 docs"]
|
|
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|
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D --> E["🚀 deploy"]
|
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|
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```
|
|
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|
+
|
|
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|
+
---
|
|
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+
|
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### Cleanup
|
|
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|
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#### **DELETE** [test/](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/test) — ✅ Done
|
|
75
|
+
|
|
76
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Delete the entire legacy `test/` directory. It contains a stale `test_math_utils.py` that imports from a non-existent `my_package` — leftover from a template. All active tests live in `tests/`.
|
|
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+
|
|
78
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+
---
|
|
79
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+
|
|
80
|
+
### GitLab CI Configuration
|
|
81
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+
|
|
82
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#### **MODIFY** [.gitlab-ci.yml](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/.gitlab-ci.yml) — ✅ Done
|
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83
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+
|
|
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+
Replace the empty file with the complete pipeline:
|
|
85
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+
|
|
86
|
+
```yaml
|
|
87
|
+
# ==============================================================
|
|
88
|
+
# GitLab CI/CD Pipeline — incompy2d
|
|
89
|
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# 2D Incompressible Navier-Stokes CFD Solver
|
|
90
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+
# ==============================================================
|
|
91
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+
|
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image: python:3.13-slim
|
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stages:
|
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- build
|
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- test
|
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- lint
|
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- docs
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- deploy
|
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# ---- Global settings -----------------------------------------
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variables:
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PIP_CACHE_DIR: "$CI_PROJECT_DIR/.pip-cache"
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cache:
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key: "${CI_COMMIT_REF_SLUG}"
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paths:
|
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- .pip-cache/
|
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+
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# ---- Stage 1: Build -----------------------------------------
|
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build:
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stage: build
|
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tags:
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- docker
|
|
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- shared
|
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before_script:
|
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- python -m pip install --upgrade pip
|
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- pip install -e ".[test]"
|
|
119
|
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script:
|
|
120
|
+
- python -c "import incompy2d; print(f'incompy2d {incompy2d.__version__} OK')"
|
|
121
|
+
- pip show incompy2d
|
|
122
|
+
rules:
|
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|
+
- if: $CI_PIPELINE_SOURCE == "push"
|
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|
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- if: $CI_PIPELINE_SOURCE == "merge_request_event"
|
|
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|
+
|
|
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|
+
# ---- Stage 2: Test ------------------------------------------
|
|
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|
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test:
|
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|
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stage: test
|
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tags:
|
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- docker
|
|
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- shared
|
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before_script:
|
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- python -m pip install --upgrade pip
|
|
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|
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- pip install -e ".[test]"
|
|
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|
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script:
|
|
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|
+
- >
|
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+
pytest tests/ -v
|
|
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|
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--tb=short
|
|
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|
+
--junitxml=report.xml
|
|
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|
+
--cov=incompy2d
|
|
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|
+
--cov-report=term-missing
|
|
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|
+
--cov-report=html:coverage_html
|
|
143
|
+
--cov-fail-under=20
|
|
144
|
+
artifacts:
|
|
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|
+
when: always
|
|
146
|
+
paths:
|
|
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|
+
- coverage_html/
|
|
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|
+
reports:
|
|
149
|
+
junit: report.xml
|
|
150
|
+
expire_in: 7 days
|
|
151
|
+
coverage: '/(?i)total.*?(\d+(?:\.\d+)?)\%/'
|
|
152
|
+
rules:
|
|
153
|
+
- if: $CI_PIPELINE_SOURCE == "push"
|
|
154
|
+
- if: $CI_PIPELINE_SOURCE == "merge_request_event"
|
|
155
|
+
|
|
156
|
+
# ---- Stage 3: Lint (allowed to fail) ------------------------
|
|
157
|
+
lint:
|
|
158
|
+
stage: lint
|
|
159
|
+
tags:
|
|
160
|
+
- docker
|
|
161
|
+
- shared
|
|
162
|
+
before_script:
|
|
163
|
+
- python -m pip install --upgrade pip
|
|
164
|
+
script:
|
|
165
|
+
- python -m py_compile src/incompy2d/__init__.py
|
|
166
|
+
- python -m py_compile src/incompy2d/incomp_2d.py
|
|
167
|
+
- python -m py_compile src/incompy2d/mesh_util.py
|
|
168
|
+
- python -m py_compile src/incompy2d/geom_util.py
|
|
169
|
+
- python -m py_compile src/incompy2d/post.py
|
|
170
|
+
- python -m py_compile src/incompy2d/run.py
|
|
171
|
+
- python -m py_compile src/incompy2d/fetch_overture.py
|
|
172
|
+
- echo "All source files compile successfully"
|
|
173
|
+
allow_failure: true
|
|
174
|
+
rules:
|
|
175
|
+
- if: $CI_PIPELINE_SOURCE == "push"
|
|
176
|
+
- if: $CI_PIPELINE_SOURCE == "merge_request_event"
|
|
177
|
+
|
|
178
|
+
# ---- Stage 4: Docs ------------------------------------------
|
|
179
|
+
docs:
|
|
180
|
+
stage: docs
|
|
181
|
+
tags:
|
|
182
|
+
- docker
|
|
183
|
+
- shared
|
|
184
|
+
before_script:
|
|
185
|
+
- python -m pip install --upgrade pip
|
|
186
|
+
- pip install -e ".[docs]"
|
|
187
|
+
script:
|
|
188
|
+
- sphinx-build -b html docs/ docs/_build/html
|
|
189
|
+
artifacts:
|
|
190
|
+
paths:
|
|
191
|
+
- docs/_build/html/
|
|
192
|
+
expire_in: 30 days
|
|
193
|
+
rules:
|
|
194
|
+
- if: $CI_COMMIT_BRANCH == "master"
|
|
195
|
+
|
|
196
|
+
# ---- Stage 5: Deploy to PyPI --------------------------------
|
|
197
|
+
deploy:
|
|
198
|
+
stage: deploy
|
|
199
|
+
tags:
|
|
200
|
+
- docker
|
|
201
|
+
- shared
|
|
202
|
+
before_script:
|
|
203
|
+
- python -m pip install --upgrade pip
|
|
204
|
+
- pip install build twine
|
|
205
|
+
script:
|
|
206
|
+
- python -m build
|
|
207
|
+
- >
|
|
208
|
+
twine upload dist/*
|
|
209
|
+
--username __token__
|
|
210
|
+
--password $PYPI_TOKEN
|
|
211
|
+
artifacts:
|
|
212
|
+
paths:
|
|
213
|
+
- dist/
|
|
214
|
+
expire_in: 7 days
|
|
215
|
+
rules:
|
|
216
|
+
- if: $CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/
|
|
217
|
+
when: manual
|
|
218
|
+
allow_failure: false
|
|
219
|
+
```
|
|
220
|
+
|
|
221
|
+
---
|
|
222
|
+
|
|
223
|
+
### Project Configuration
|
|
224
|
+
|
|
225
|
+
#### **MODIFY** [pyproject.toml](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/pyproject.toml) — ✅ Done
|
|
226
|
+
|
|
227
|
+
Restructure dependencies to separate core from heavy optional packages:
|
|
228
|
+
|
|
229
|
+
```diff
|
|
230
|
+
[project]
|
|
231
|
+
dependencies = [
|
|
232
|
+
"numpy",
|
|
233
|
+
- "matplotlib",
|
|
234
|
+
- "meshio",
|
|
235
|
+
- "osmnx",
|
|
236
|
+
- "geopandas",
|
|
237
|
+
- "shapely",
|
|
238
|
+
- "overturemaps",
|
|
239
|
+
"numba",
|
|
240
|
+
]
|
|
241
|
+
|
|
242
|
+
[project.optional-dependencies]
|
|
243
|
+
-dev = ["pytest", "sphinx"]
|
|
244
|
+
+geo = ["meshio", "osmnx", "geopandas", "shapely", "overturemaps"]
|
|
245
|
+
+viz = ["matplotlib"]
|
|
246
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+
+test = ["pytest", "pytest-cov"]
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+docs = ["sphinx"]
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+dev = ["incompy2d[geo,viz,test,docs]"]
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```
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> [!IMPORTANT]
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> After this change, the installation instructions in [README.md](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/README.md) should be updated to `pip install -e ".[dev]"` for full development setup. The `environment.yml` still provides all packages via conda for local development, so this change only affects `pip install` workflows.
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---
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### Sphinx Documentation Setup
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#### **NEW** [docs/conf.py](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/docs/conf.py) — ✅ Done
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Minimal Sphinx configuration:
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```python
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"""Sphinx configuration for incompy2d documentation."""
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project = "incompy2d"
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author = "Phuong-Nam Nguyen"
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release = "0.1.0"
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.napoleon",
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"sphinx.ext.viewcode",
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]
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templates_path = ["_templates"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
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html_theme = "alabaster"
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html_static_path = ["_static"]
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```
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#### **NEW** [docs/index.rst](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/docs/index.rst) — ✅ Done
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Root documentation page:
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```rst
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incompy2d documentation
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========================
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A 2D incompressible Navier-Stokes CFD solver in Python.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`
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```
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---
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### Gitignore Updates
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#### **MODIFY** [.gitignore](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/.gitignore) — ✅ Done
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```diff
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.DS_Store
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+coverage_html/
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+report.xml
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+.pip-cache/
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+docs/_build/
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+docs/_static/
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+docs/_templates/
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```
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---
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## Coverage Status
|
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> [!WARNING]
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> **Current coverage: 23.29%** — The threshold has been temporarily lowered to `--cov-fail-under=20` so the pipeline can pass. Increase to 70% once more tests are added.
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+
|
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+
| Module | Statements | Missed | Coverage |
|
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+
|---|---|---|---|
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+
| `__init__.py` | 5 | 0 | **100%** |
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+
| `incomp_2d.py` | 179 | 90 | **50%** |
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|
+
| `mesh_util.py` | 54 | 32 | **41%** |
|
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+
| `geom_util.py` | 69 | 52 | **25%** |
|
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|
+
| `fetch_overture.py` | 52 | 52 | **0%** |
|
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|
+
| `post.py` | 137 | 137 | **0%** |
|
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|
+
| `run.py` | 75 | 75 | **0%** |
|
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|
+
| **TOTAL** | **571** | **438** | **23.29%** |
|
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|
+
|
|
338
|
+
**To reach 70% coverage**, focus on:
|
|
339
|
+
1. `incomp_2d.py` (50% → ~80%) — add edge-case tests for the solver
|
|
340
|
+
2. `mesh_util.py` (41% → ~80%) — test remaining mesh utilities
|
|
341
|
+
3. `post.py` (0% → ~50%) — mock `matplotlib` and test data formatting
|
|
342
|
+
4. `run.py` (0% → ~50%) — test CLI argument parsing with mocked solver
|
|
343
|
+
|
|
344
|
+
## Deploy Stage
|
|
345
|
+
|
|
346
|
+
The deploy stage publishes to PyPI when a **version tag** is pushed (e.g., `git tag v0.1.0`):
|
|
347
|
+
|
|
348
|
+
- Triggered **only** on tags matching `v*.*.*` (e.g., `v0.1.0`, `v1.2.3`)
|
|
349
|
+
- Requires **manual confirmation** (`when: manual`) to prevent accidental releases
|
|
350
|
+
- Uses `python -m build` (PEP 517 compliant) + `twine upload`
|
|
351
|
+
- Authenticates via a **`PYPI_TOKEN`** CI/CD variable
|
|
352
|
+
|
|
353
|
+
> [!WARNING]
|
|
354
|
+
> **Setup required before first deploy**: Go to **Settings → CI/CD → Variables** in your GitLab project and add a variable named `PYPI_TOKEN` with your PyPI API token (masked, protected).
|
|
355
|
+
|
|
356
|
+
**Release workflow:**
|
|
357
|
+
```bash
|
|
358
|
+
# 1. Update version in pyproject.toml and __init__.py
|
|
359
|
+
# 2. Commit and push
|
|
360
|
+
git add -A && git commit -m "Release v0.1.0"
|
|
361
|
+
git push origin master
|
|
362
|
+
|
|
363
|
+
# 3. Create and push a version tag
|
|
364
|
+
git tag v0.1.0
|
|
365
|
+
git push origin v0.1.0
|
|
366
|
+
|
|
367
|
+
# 4. In GitLab: manually trigger the deploy job from the pipeline UI
|
|
368
|
+
```
|
|
369
|
+
|
|
370
|
+
## Summary of All Files Changed
|
|
371
|
+
|
|
372
|
+
| Action | File | Status | Purpose |
|
|
373
|
+
|---|---|---|---|
|
|
374
|
+
| **DELETE** | `test/` | ✅ Done | Remove stale legacy test directory |
|
|
375
|
+
| **MODIFY** | `.gitlab-ci.yml` | ✅ Done | Complete 5-stage CI pipeline |
|
|
376
|
+
| **MODIFY** | `pyproject.toml` | ✅ Done | Split deps: core vs geo/viz/test/docs/dev |
|
|
377
|
+
| **MODIFY** | `.gitignore` | ✅ Done | Exclude CI artifacts and Sphinx build output |
|
|
378
|
+
| **NEW** | `docs/conf.py` | ✅ Done | Sphinx configuration |
|
|
379
|
+
| **NEW** | `docs/index.rst` | ✅ Done | Sphinx root document |
|
|
380
|
+
|
|
381
|
+
## Verification Plan
|
|
382
|
+
|
|
383
|
+
### Automated Tests
|
|
384
|
+
- `python -c "import yaml; yaml.safe_load(open('.gitlab-ci.yml'))"` — verify valid YAML
|
|
385
|
+
- GitLab **CI Lint** tool (Settings → CI/CD → CI Lint) — validate pipeline syntax
|
|
386
|
+
- `pip install -e ".[test]" && pytest tests/ -v --cov=incompy2d --cov-fail-under=20` — run tests locally with coverage gate
|
|
387
|
+
- `pip install -e ".[docs]" && sphinx-build -b html docs/ docs/_build/html` — verify docs build
|
|
388
|
+
|
|
389
|
+
### Manual Verification
|
|
390
|
+
- Push to a feature branch and observe the pipeline in **CI/CD → Pipelines**
|
|
391
|
+
- Confirm all 5 stages appear: `build → test → lint → docs → deploy`
|
|
392
|
+
- Verify the **Test** tab in merge requests shows JUnit results
|
|
393
|
+
- Verify coverage badge percentage on the pipeline
|
|
394
|
+
- Browse `coverage_html/` artifact for the HTML report
|
|
395
|
+
- Browse `docs/_build/html/` artifact for the Sphinx output
|
|
396
|
+
- For deploy: test with **TestPyPI** first before publishing to production PyPI
|
|
397
|
+
|
|
398
|
+
## Next Steps
|
|
399
|
+
|
|
400
|
+
> [!TIP]
|
|
401
|
+
> **Recommended actions to improve the pipeline:**
|
|
402
|
+
> 1. **Increase test coverage** — Write tests for `post.py`, `run.py`, and `fetch_overture.py` to reach the 70% target
|
|
403
|
+
> 2. **Update `.gitlab-ci.yml`** — Bump `--cov-fail-under` from `20` to `70` once coverage is sufficient
|
|
404
|
+
> 3. **Consider Micromamba** — If you ever need geospatial deps (`[geo]`/`[dev]`) in CI, switch from `pip` to Micromamba to avoid GDAL/GEOS compilation issues (see [package_management.md](file:///d:/SiSc/SCE/git_nrw/sce_incompy2d/package_management.md))
|
|
405
|
+
> 4. **Add `PYPI_TOKEN`** — Configure the CI/CD variable in GitLab Settings before first deploy
|