Merge pull request #53 from scientificcomputing/dokken/updates

jorgensd · web-flow · commit 6f552abcd05a · 2024-05-08T20:54:51.000+02:00
Suggested updates to scientific computing.
diff --git a/.cspell_dict.txt b/.cspell_dict.txt
@@ -4,6 +4,7 @@ Bippe
 brainpulse
 budisa
 CauseMann
+checkpointing
 cibuildwheel
 conda
 Cookiecutter
@@ -30,6 +31,7 @@ Jørgen
 jorgensd
 Jupyterbook
 jupytext
+Laughlin
 Meep
 minrk
 Multiphysics
diff --git a/.gitignore b/.gitignore
@@ -1 +1,3 @@
 docs/_build
+sc_webpage_env
+*.egg-info
diff --git a/README.md b/README.md
@@ -1,4 +1,43 @@
 ![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)
+
 # scientificcomputing.github.io
 
 The resources for generating <https://scientificcomputing.github.io/>.
+
+## How to add a paper with repository?
+
+Please fill in [https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-repo&projects=&template=repository.yml&title=%5BAdd+repo%5D%3A+](https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-repo&projects=&template=repository.yml&title=%5BAdd+repo%5D%3A+)
+
+## How to add a paper relating to a software?
+
+Please fill in [https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-package&projects=&template=package.yml&title=%5BAdd+package%5D%3A+](https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-package&projects=&template=package.yml&title=%5BAdd+package%5D%3A+)
+
+# Contribute to the webpage
+
+To contribute, please make a fork of the repository and clone it to your local system, then make a new branch with
+
+```bash
+git checkout -b name_of_author/describe_feature
+```
+
+Then add the relevant text.
+Next ensure that the webpage builds, this can be done with
+
+```bash
+python3 -m venv sc_webpage_env
+source sc_webpage_env/bin/activate
+python3 -m pip install .
+python3 -m jupyter book build -W ./docs
+```
+
+Inspect the webpage locally by opening `./docs/_build/html/index.html` and navigating to the appropriate page.
+
+Before you push the changes, ensure that the text is properly formatted, run
+
+```bash
+pre-commit
+```
+
+Then, make corrections and commit any changes before re-running pre-commit.
+
+Push the branch to your fork, and then make a pull request through the github web-interface.
diff --git a/docs/packages.md b/docs/packages.md
@@ -1,5 +1,9 @@
 # Software
-A list scientific software (and corresponding publication) developed in the Scientific Computing Department.
+
+A list scientific software (and corresponding publication) developed by personnel in the Scientific Computing Department.
+
+- ADIOS4DOLFINx: A framework for checkpointing in FEniCS [ADIOS4DOLFINx](https://github.com/jorgensd/adios4dolfinx/) {cite}`Dokken2024adios`
+- SMART: Spatial Modeling Algorithms for Reactions and Transport [smart](https://github.com/RangamaniLabUCSD/smart) {cite}`Laughlin2023smart`
 - Surface Volume Meshing ToolKit: [SVMTK](https://github.com/SVMTK/SVMTK) {cite}`Valnes2022`
 - Intracranial Pulsation: [brainpulse](https://github.com/MariusCausemann/intracranialPulsation) {cite}`Causemann2022`
 - Software Components for Multiphysics Problems: [HAZniCS](https://github.com/HAZmathTeam/hazmath) {cite}`budisa2022`
@@ -10,8 +14,6 @@ A list scientific software (and corresponding publication) developed in the Scie
 
 If you package is missing from the list, go to [Add new package](https://github.com/scientificcomputing/scientificcomputing.github.io/issues/new?assignees=&labels=new-package&template=package.yml&title=%5BAdd+package%5D%3A+)
 
-
-
 ## References
 
 ```{bibliography}
diff --git a/docs/references.bib b/docs/references.bib
@@ -1,107 +1,133 @@
 
 @unpublished{poulain2022,
-  TITLE = {{Multi-compartmental model of glymphatic clearance of solutes in brain tissue}},
-  AUTHOR = {Poulain, Alexandre and Riseth, J{{\o}}rgen and Vinje, Vegard},
-  URL = {https://hal.archives-ouvertes.fr/hal-03789563},
-  NOTE = {working paper or preprint},
-  YEAR = {2022},
-  MONTH = Sep,
-  PDF = {https://hal.archives-ouvertes.fr/hal-03789563/file/multicompartment-glymphatics.pdf},
-  HAL_ID = {hal-03789563},
-  HAL_VERSION = {v1},
+  title       = {{Multi-compartmental model of glymphatic clearance of solutes in brain tissue}},
+  author      = {Poulain, Alexandre and Riseth, J{{\o}}rgen and Vinje, Vegard},
+  url         = {https://hal.archives-ouvertes.fr/hal-03789563},
+  note        = {working paper or preprint},
+  year        = {2022},
+  month       = Sep,
+  pdf         = {https://hal.archives-ouvertes.fr/hal-03789563/file/multicompartment-glymphatics.pdf},
+  hal_id      = {hal-03789563},
+  hal_version = {v1}
 }
 
 
-@article {Causemann2022,
-	author = {Causemann, Marius and Vinje, Vegard and Rognes, Marie E.},
-	title = {Human intracranial pulsatility during the cardiac cycle: a computational modelling framework},
-	elocation-id = {2022.05.19.492650},
-	year = {2022},
-	doi = {10.1101/2022.05.19.492650},
-	publisher = {Cold Spring Harbor Laboratory},
-	journal = {bioRxiv}
+@article{Causemann2022,
+  author       = {Causemann, Marius and Vinje, Vegard and Rognes, Marie E.},
+  title        = {Human intracranial pulsatility during the cardiac cycle: a computational modelling framework},
+  elocation-id = {2022.05.19.492650},
+  year         = {2022},
+  doi          = {10.1101/2022.05.19.492650},
+  publisher    = {Cold Spring Harbor Laboratory},
+  journal      = {bioRxiv}
 }
 
 
-@Inbook{Valnes2022,
-author="Mardal, Kent-Andr{\'e}
-and Rognes, Marie E.
-and Thompson, Travis B.
-and Valnes, Lars Magnus",
-title={{Getting started: from T1 images to simulation}},
-bookTitle={{Mathematical Modeling of the Human Brain: From Magnetic Resonance Images to Finite Element Simulation}},
-year="2022",
-publisher={{Springer International Publishing}},
-address="Cham",
-pages="23--46",
-isbn="978-3-030-95136-8",
-doi="10.1007/978-3-030-95136-8_3"
+@inbook{Valnes2022,
+  author    = {Mardal, Kent-Andr{\'e}
+               and Rognes, Marie E.
+               and Thompson, Travis B.
+               and Valnes, Lars Magnus},
+  title     = {{Getting started: from T1 images to simulation}},
+  booktitle = {{Mathematical Modeling of the Human Brain: From Magnetic Resonance Images to Finite Element Simulation}},
+  year      = {2022},
+  publisher = {{Springer International Publishing}},
+  address   = {Cham},
+  pages     = {23--46},
+  isbn      = {978-3-030-95136-8},
+  doi       = {10.1007/978-3-030-95136-8_3}
 }
 
 
-@ARTICLE{Daversin2022,
-AUTHOR={Daversin-Catty, Cécile and Gjerde, Ingeborg G. and Rognes, Marie E.},
-TITLE={{Geometrically Reduced Modelling of Pulsatile Flow in Perivascular Networks}},
-JOURNAL={Frontiers in Physics},
-VOLUME={10},
-YEAR={2022},
-DOI={10.3389/fphy.2022.882260},
-ISSN={2296-424X}
+@article{Daversin2022,
+  author  = {Daversin-Catty, Cécile and Gjerde, Ingeborg G. and Rognes, Marie E.},
+  title   = {{Geometrically Reduced Modelling of Pulsatile Flow in Perivascular Networks}},
+  journal = {Frontiers in Physics},
+  volume  = {10},
+  year    = {2022},
+  doi     = {10.3389/fphy.2022.882260},
+  issn    = {2296-424X}
 }
 
 
 @article{Gjerde2022,
-  title={Nitsche's method for Navier--Stokes equations with slip boundary conditions},
-  author={Gjerde, Ingeborg and Scott, L},
-  journal={Mathematics of Computation},
-  volume={91},
-  number={334},
-  pages={597--622},
-  year={2022},
-  doi={10.1090/mcom/3682}
+  title   = {Nitsche's method for Navier--Stokes equations with slip boundary conditions},
+  author  = {Gjerde, Ingeborg and Scott, L},
+  journal = {Mathematics of Computation},
+  volume  = {91},
+  number  = {334},
+  pages   = {597--622},
+  year    = {2022},
+  doi     = {10.1090/mcom/3682}
 }
 
 
 @article{Haubner2021,
-author = {Haubner, Johannes and Neumann, Franziska and Ulbrich, Michael},
-title = {{A Novel Density Based Approach for Topology Optimization of Stokes Flow}},
-journal = {SIAM Journal on Scientific Computing},
-volume = {45},
-number = {2},
-pages = {A338-A368},
-year = {2023},
-doi = {10.1137/21M143114X}
+  author  = {Haubner, Johannes and Neumann, Franziska and Ulbrich, Michael},
+  title   = {{A Novel Density Based Approach for Topology Optimization of Stokes Flow}},
+  journal = {SIAM Journal on Scientific Computing},
+  volume  = {45},
+  number  = {2},
+  pages   = {A338-A368},
+  year    = {2023},
+  doi     = {10.1137/21M143114X}
 }
 
 @article{saetra2021,
-    doi = {10.1371/journal.pcbi.1008143},
-    author = {Sætra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir},
-    journal = {PLOS Computational Biology},
-    publisher = {Public Library of Science},
-    title = {An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain},
-    year = {2021},
-    month = {07},
-    volume = {17},
-    pages = {1-45},
-    number = {7}
+  doi       = {10.1371/journal.pcbi.1008143},
+  author    = {Sætra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir},
+  journal   = {PLOS Computational Biology},
+  publisher = {Public Library of Science},
+  title     = {An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain},
+  year      = {2021},
+  month     = {07},
+  volume    = {17},
+  pages     = {1-45},
+  number    = {7}
 }
 
 @misc{budisa2022,
-  doi = {10.48550/ARXIV.2210.13274},
-  url = {https://arxiv.org/abs/2210.13274},
-  author = {Budisa, Ana and Hu, Xiaozhe and Kuchta, Miroslav and Mardal, Kent-Andre and Zikatanov, Ludmil},
-  keywords = {Numerical Analysis (math.NA), FOS: Mathematics, FOS: Mathematics, G.1.8; G.4, 65-04, 65N55, 65F08, 65H10},
-  title = {{HAZniCS -- Software Components for Multiphysics Problems}},
+  doi       = {10.48550/ARXIV.2210.13274},
+  url       = {https://arxiv.org/abs/2210.13274},
+  author    = {Budisa, Ana and Hu, Xiaozhe and Kuchta, Miroslav and Mardal, Kent-Andre and Zikatanov, Ludmil},
+  keywords  = {Numerical Analysis (math.NA), FOS: Mathematics, FOS: Mathematics, G.1.8; G.4, 65-04, 65N55, 65F08, 65H10},
+  title     = {{HAZniCS -- Software Components for Multiphysics Problems}},
   publisher = {arXiv},
-  year = {2022},
+  year      = {2022},
   copyright = {arXiv.org perpetual, non-exclusive license}
 }
 
 @misc{zapf2023medical,
-      title={Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization},
-      author={Bastian Zapf and Johannes Haubner and Lukas Baumgärtner and Stephan Schmidt},
-      year={2023},
-      eprint={2305.03020},
-      archivePrefix={arXiv},
-      primaryClass={math.NA}
+  title         = {Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization},
+  author        = {Bastian Zapf and Johannes Haubner and Lukas Baumgärtner and Stephan Schmidt},
+  year          = {2023},
+  eprint        = {2305.03020},
+  archiveprefix = {arXiv},
+  primaryclass  = {math.NA}
+}
+
+
+@article{Dokken2024adios,
+  doi       = {10.21105/joss.06451},
+  year      = {2024},
+  publisher = {The Open Journal},
+  volume    = {9},
+  number    = {96},
+  pages     = {6451},
+  author    = {Jørgen Schartum Dokken},
+  title     = {{ADIOS4DOLFINx: A framework for checkpointing in FEniCS}},
+  journal   = {Journal of Open Source Software}
+}
+
+
+@article{Laughlin2023smart,
+  doi       = {10.21105/joss.05580},
+  year      = {2023},
+  publisher = {The Open Journal},
+  volume    = {8},
+  number    = {90},
+  pages     = {5580},
+  author    = {Justin G. Laughlin and Jørgen S. Dokken and Henrik N.t. Finsberg and Emmet A. Francis and Christopher T. Lee and Marie E. Rognes and Padmini Rangamani},
+  title     = {{SMART: Spatial Modeling Algorithms for Reactions and Transport}},
+  journal   = {Journal of Open Source Software}
 }
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,11 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "Scientific_Computing_Webpage"
+version = "1.0.0"
+dynamic = ["dependencies"]
+
+[tool.setuptools.dynamic]
+dependencies = { file = ["requirements.txt"] }
diff --git a/requirements.txt b/requirements.txt
@@ -1 +1,2 @@
 jupyter-book>=0.13.2
+pre-commit

Original file line number	Diff line number	Diff line change
`@@ -1 +1,3 @@`
`1`	`1`	`docs/_build`
	`2`	`+sc_webpage_env`
	`3`	`+*.egg-info`