merge main after rev-patch

.github/workflows/learn-ci.yml

@@ -0,0 +1,13 @@
+name: learn-github-actions
+run-name: ${{ github.actor }} is learning GitHub Actions
+on: [push]
+jobs:
+  check-bats-version:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '14'
+      - run: npm install -g bats
+      - run: bats -v

.github/workflows/pylint.yml

@@ -0,0 +1,25 @@
+name: Pylint
+run-name: ${{ github.actor }} is linting the code
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        # pylint $(git ls-files '*.py')
+        git ls-files '*.py'

.gitignore

@@ -42,6 +42,8 @@
 **/*.mat*
 **/.DS_Store
 
+build/
+
 # sphinx
 docs/build/
 
@@ -51,4 +53,7 @@ docs/build/
 # branch-specific tests
 build/*
 
-**.egg-info
+**.egg-info
+test_*/
+src/irrevolutions/test/output/*
+**/output/**

.pre-commit-autoflake.yml

@@ -0,0 +1,11 @@
+- id: autoflake
+  name: autoflake
+  entry: autoflake
+  language: python
+  "types": [python]
+  require_serial: true
+  args:
+    - "--in-place"
+    - "--expand-star-imports"
+    - "--remove-duplicate-keys"
+    - "--remove-unused-variables"

.pre-commit-config.yaml

@@ -0,0 +1,47 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 21.12b0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
+  # - repo: https://github.com/PyCQA/pylint
+  #   rev: 2.11.1
+  #   hooks:
+  #     - id: pylint
+  #       args: [src/irrevolutions/*.py]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.2
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+
+  - repo: https://github.com/myint/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+        additional_dependencies: [autoflake==1.8.0]
+        args: [--remove-all-unused-imports, --remove-unused-variables, --in-place, src/irrevolutions/*.py]
+
+  - repo: https://github.com/psf/black
+    rev: 21.12b0
+    hooks:
+      - id: black
+        language_version: python3

CITATION.cff

@@ -0,0 +1,37 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Variational Solvers for Irreversible Evolutionary Systems
+message: >-
+  Three solvers for irreversible evolutionary processes with
+  a general energetic notion of stability.
+type: software
+authors:
+  - given-names: Andrés A
+    family-names: León Baldelli
+    email: [email protected]
+    affiliation: '∂’Alembert Institute, CNRS, Sorbonne Universités'
+    orcid: 'https://orcid.org/0000-0002-3019-602X'
+repository-code: 'https://github.com/kumiori/mec647/'
+url: 'https://irreversible-variational-solvers.readthedocs.io/'
+abstract: >-
+  To study irreversible evolutionary processes with a
+  general energetic notion of stability, three nonlinear
+  variational solvers are modular components that address
+  mathematical problems that are general enough to apply, in
+  principle, to systems with instabilities, jumps, and
+  emergence of patterns which is commonplace in diverse
+  arenas spanning from quantum to continuum mechanics,
+  economy, social sciences, and ecology. Our motivation
+  proceeds from fracture mechanics, with the ultimate goal
+  of deploying a transparent numerical platform for
+  scientific validation and prediction of large scale
+  natural fracture phenomena. 
+keywords:
+  - stability
+  - bifurcation
+  - irreversibility
+  - singular perturbations
+  - fracture
+license: GPL-3.0

README.md

@@ -82,28 +82,6 @@ This code was initially conceived as a support for the teaching course MEC647,
 master programme, joint between École Polytechnique and ENSTA-Paristech throughout 2020-2022. 
 Hence the cryptic repository name.
 
-### Course Schedule
-
-
-- 0 Introduction, motivation, and a simple experiment, in theory.
-- 1 Numerics, from the basics to the solution of a linear variational problem 
-- 2 The notion of stability, stability of a brittle bar. The elasticity problem
-- 3 Energetics link fracture to damage. Project walkthrough 
-- 4 The damage problem: analytics and numerics
-- 5 Calibration (material, numerical) and tests
-- 6 Data analysis and presentation
-- Rest
-- 7 Defence
-
-
-### Authors
-- Cf. commit messages
-
-### Course Instructors/Authors
-
-- V Lazarus, Sorbonne Université.
-- A Leon Baldelli, CR CNRS.
-
 
 ### Acknowledgements
 
@@ -113,22 +91,4 @@ Corrado Maurini, Sorbonne Université.
 
 ### License
 
-MIT License, see `LICENSE` file.
-
-### Tests
-
-test_1d.py
-test_2d.py
-
-test_cone_convergence.py
-test_cone_project.py
-test_elasticity.py
-test_extend.py
-test_rayleigh.py
-test_vector_info.py
-test_vi.py
-test_traction.py
-test_bifurcation.py
-test_logging_mpi.py
-test_scatter.py
-
+See `LICENSE` file.

contributed/DIC_CT_35/export_msh.py

@@ -9,16 +9,15 @@
 
 
 os.system("gmsh -2 " + filename + ".geo -format msh2")
-os.system("dolfin-convert " + filename + ".msh " + filename +".xml")
+os.system("dolfin-convert " + filename + ".msh " + filename + ".xml")
 os.remove(filename + ".msh")
-#xml to h5 (1-3)
+# xml to h5 (1-3)
 mesh = Mesh(filename + ".xml")
 #boundaries = MeshFunction("size_t", mesh, "mesh4_facet_region.xml")
 subdomains = MeshFunction("size_t", mesh, filename + "_physical_region.xml")
 boundaries = MeshFunction("size_t", mesh, filename + "_facet_region.xml")
 
 
-
 hdf = HDF5File(mesh.mpi_comm(), filename + ".h5", "w")
 hdf.write(mesh, "/mesh")
 hdf.write(boundaries, "/boundaries")
@@ -41,5 +40,3 @@
 
 #subdomains = MeshFunction("size_t", mesh,2)
 #hdf.read(subdomains, "/subdomains")
-
-