Merge branch 'main' into pbrubeck/trace

Author: pbrubeck

.github/actions/install/action.yml

@@ -124,6 +124,9 @@ runs:
         python3 -m venv venv
         . venv/bin/activate
 
+        echo 'Cython!=3.2.6' > constraints.txt
+        export PIP_CONSTRAINT=constraints.txt
+
         : # Empty the pip cache to ensure that everything is compiled from scratch
         pip cache purge
 

.github/workflows/core.yml

@@ -536,7 +536,8 @@ jobs:
       - name: Install system dependencies
         run: |
           apt-get update
-          apt-get -y install inkscape texlive-full
+          # pandoc is required by nbsphinx to render the tutorial notebooks
+          apt-get -y install inkscape texlive-full pandoc
 
       - uses: actions/checkout@v5
         with:
@@ -577,7 +578,7 @@ jobs:
         with:
           name: github-pages
           path: firedrake-repo/docs/build/html
-          retention-days: 1
+          retention-days: 5
 
       # Some files are automatically generated when we install or build the
       # docs (e.g. AUTHORS.rst). These files are committed to the repository

.github/workflows/push.yml

@@ -40,7 +40,7 @@ jobs:
           python-version: '3.13'
 
       - name: Install dependencies
-        run: pip install nbformat
+        run: pip install nbformat jupytext
 
       - name: Checkout Firedrake
         uses: actions/checkout@v5
@@ -55,8 +55,15 @@ jobs:
           path: notebooks
           token: ${{ secrets.NOTEBOOKS_REPO_TOKEN }}
 
+      - name: Convert notebooks to .ipynb
+        run: jupytext --to ipynb firedrake/docs/notebooks/*.py
+
       - name: Copy notebooks
-        run: cp -r firedrake/docs/notebooks/* notebooks/
+        # Ship the generated notebooks and all their data files, but not the
+        # jupytext .py sources or config.
+        run: |
+          rsync -a --exclude='*.py' --exclude='jupytext.toml' \
+            firedrake/docs/notebooks/ notebooks/
 
       - name: Prepare notebooks for Colab
         working-directory: notebooks

.gitignore

@@ -27,6 +27,7 @@ __pycache__/
 /docs/source/teamgrid.rst
 /docs/source/teaminactive.rst
 /docs/source/demos
+/docs/source/notebooks
 /firedrake/cython/*.c
 /firedrake.egg-info
 /firedrake/_check/Makefile

AGENTS.md

@@ -1,3 +1,79 @@
+@Article{Farrell:2019,
+  author  = {Farrell, Patrick E. and Mitchell, Lawrence and Wechsung, Florian},
+  title   = {{An augmented Lagrangian preconditioner for the 3D stationary incompressible Navier--Stokes equations at High Reynolds Number}},
+  journal = {SIAM Journal on Scientific Computing},
+  year    = {2019},
+  volume  = {41},
+  number  = {5},
+  pages   = {A3073--A3096},
+  doi     = {10.1137/18M1219370},
+}
+
+@book{Fortin:1983,
+  author    = {Fortin, Michel and Glowinski, Roland},
+  title     = {{Augmented Lagrangian Methods: Applications to the Numerical Solution of Boundary-Value Problems}},
+  publisher = {North-Holland},
+  year      = {1983},
+}
+
+@phdthesis{Schoberl:1999,
+  author  = {Sch\"{o}berl, Joachim},
+  title   = {{Robust multigrid methods for parameter dependent problems}},
+  school = {Johannes Kepler Universit\"{a}t Linz},
+  year    = {1999},
+}
+
+@Article{Silvester:1994,
+  author  = {Silvester, David and Wathen, Andrew J.},
+  title   = {{Fast iterative solution of stabilised {S}tokes systems. {Part II}: {U}sing general block preconditioners}},
+  journal = {SIAM Journal on Numerical Analysis},
+  year    = {1994},
+  volume  = {31},
+  number  = {5},
+  pages   = {1352--1367},
+  doi     = {10.1137/0731070},
+}
+
+@Article{Farrell:2021b,
+  author  = {Farrell, Patrick E. and Mitchell, Lawrence and Scott, L. Ridgway and Wechsung, Florian},
+  title   = {{A Reynolds-robust preconditioner for the Scott--Vogelius discretization of the stationary incompressible Navier--Stokes equations}},
+  journal = {SMAI Journal of Computational Mathematics},
+  year    = {2021},
+  volume  = {7},
+  pages   = {75--96},
+  doi     = {10.5802/smai-jcm.72},
+}
+
+@Article{Farrell:2021,
+  author  = {Farrell, Patrick E. and Mitchell, Lawrence and Scott, L. Ridgway and Wechsung, Florian},
+  title   = {{Robust multigrid for nearly incompressible elasticity using macro elements}},
+  journal = {IMA Journal on Numerical Analysis},
+  year    = {2021},
+  doi     = {10.1093/imanum/drab083},
+}
+
+@Article{Benzi:2006,
+  author  = {Benzi, Michele and Olshanskii, Maxim A.},
+  title   = {{An augmented {L}agrangian-based approach to the {O}seen problem}},
+  journal = {{SIAM} Journal on Scientific Computing},
+  year    = {2006},
+  volume  = {28},
+  number  = {6},
+  pages   = {2095--2113},
+  doi     = {10.1137/050646421},
+}
+
+@Article{Hong:2015,
+  author  = {Hong, Qingguo and Kraus, Johannes and Xu, Jinchao and Zikatanov, Ludmil},
+  title   = {{A robust multigrid method for discontinuous {G}alerkin discretizations of {S}tokes and linear elasticity equations}},
+  journal = {Numerische Mathematik},
+  year    = {2015},
+  volume  = {132},
+  number  = {1},
+  pages   = {23--49},
+  doi     = {10.1007/s00211-015-0712-y},
+}
+
 @Article{Egger:2018,
   author  = {Egger, Herbert and Fellner, Klemens and Pietschmann, Jan-Frederik and Tang, Bao Quoc},
   title   = {{Analysis and numerical solution of coupled volume-surface reaction-diffusion systems with application to cell biology}},
@@ -416,3 +492,26 @@ @article{brune2015composing
   publisher={SIAM},
   doi={10.1137/130936725}
 }
+
+@article{Mardal:2002,
+	doi = {10.1137/s0036142901383910},
+	year = 2002,
+	volume = {40},
+	number = {5},
+	pages = {1605--1631},
+	author = {Kent-Andre Mardal and Xue-Cheng Tai and Ragnar Winther},
+	title = {A robust finite element method for {Darcy--Stokes} flow},
+	journal = {{SIAM} Journal on Numerical Analysis}
+}
+
+@article{John:2017,
+	doi = {10.1137/15m1047696},
+	year = 2017,
+	volume = {59},
+	number = {3},
+	pages = {492--544},
+	author = {Volker John and Alexander Linke and Christian Merdon and Michael Neilan and Leo G. Rebholz},
+	title = {On the divergence constraint in mixed finite element methods for incompressible flows},
+	journal = {{SIAM} Review}
+}
+