Merge pull request #332 from precice/precice-v3

* Fix whitespace.

* Update action config docs to v3 (#254)

* Update Roadmap

* Update fundamentals-roadmap.md

* Use time step, not timestep. (#259)

* v3: Update documentation w.r.t getMaxTimeStep(). (#258)

* Update documentation w.r.t getMaxTimeStep().
* Implements changes from precice/precice#1623

---------

Co-authored-by: Benjamin Uekermann <[email protected]>

* Minor follow-up for #258.

* Update documentation for initialize (#186)

* Documentation for data initialization changes introduced in v3.0.0.
* Cleanup initializeData.

---------

Co-authored-by: Benjamin Uekermann <[email protected]>
Co-authored-by: Benjamin Uekermann <[email protected]>

* Update profiling section (#266)

* Update profiling section

* Update examples in profiling section

* Apply suggestions from code review

Co-authored-by: Benjamin Uekermann <[email protected]>

* Add motivation for custom tool

* Wording tweaks

* More rewording

* Update event files in output files

---------

Co-authored-by: Benjamin Uekermann <[email protected]>

* Fix typo in profiling

* Update profiling info in guide

* Update CMake variables to new names (#289)

* Clarify some instructions in porting guide (#287)

Co-authored-by: Gerasimos Chourdakis <[email protected]>

* Fix minor issues in tooling/performance-analysis (#272)

* Rename events to profiling

according to precice/precice #1787

* Mention where to find the precice-profiling

* Add hint regarding the event flag in precice-profiling

* Add recommendation for `imvj-restart-mode` in configuration of acceleration (#296)

* Update configuration-acceleration.md

Add recommendation to use restart mode in `IQN-IMVJ` method for large-scale simulations.

* Update pages/docs/configuration/configuration-acceleration.md

Improve descriptive accuracy

Co-authored-by: Benjamin Uekermann <[email protected]>

---------

Co-authored-by: Benjamin Uekermann <[email protected]>

* Apply trivial renaming changes.

* Fix naming.

* Add note.

* Update breaking API changes (#299)

---------

Co-authored-by: Gerasimos Chourdakis <[email protected]>

* Fix token

* Fix arg

* Bump preCICE version

* Update hint on formatting configuration files

* Refer to precice.hpp instead of participant.hpp

* Update version in docs sidebar

* Rewrite mapping docs (#308)

* Add overview figure

* Work in progress

* Fix links

* Transform pdfs to svgs

* Update kernel method section

* Also write about GPU executors

* Language edits by Benjamin and Makis

Co-authored-by: Gerasimos Chourdakis <[email protected]>
Co-authored-by: Benjamin Uekermann <[email protected]>

* Review updates

* Makis language edits

Co-authored-by: Gerasimos Chourdakis <[email protected]>

* Fix typos via aspell

---------

Co-authored-by: Gerasimos Chourdakis <[email protected]>
Co-authored-by: Benjamin Uekermann <[email protected]>

* Fix some outdated solver-interface and dimensions (#314)

* Migrate use-mesh to provide/receive-mesh

* Migrate binprecice to precice-tools

* Update config-visualizer page

* Include instructions to remove .data() in readData function (#313)

* Include instructions to remove .data() in readData function
* Mention span replacing raw pointers
* Remove raw pointers from general porting example

* Cleanup porting guide example

* Update couple your code

* Remove obsolete section regarding IDs

* Apply suggestions from code review

Co-authored-by: Ishaan Desai <[email protected]>

* This PR adds C++ STL linking from Doxygen to cppreference

* Fix WD

* Link to porting guides from the source docs

* Add list of porting guides to overview

* Add new solid solver to Nutils adapter overview page (#325)

* Geometric Multiscale Documentation (#205)

Co-authored-by: Gerasimos Chourdakis <[email protected]>

* Update submodules

* Ignore tooling in images

* Update xmlreference to v3.0.0

* Cleanup porting guide API+Config (#317)

Co-authored-by: Ishaan Desai <[email protected]>
Co-authored-by: Gerasimos Chourdakis <[email protected]>

* Update the rust bindings page

* Fix link

* Make dt in readData mandatory in documentation (#257)

* v3: Make dt mandatory in documentation

* Update read data functions to use relativeReadTime.

* change precice_dt to preciceDt and solver_dt to solverDt to follow
conventions.

* Add missing.

* Shorten a bit.

* Minor follow-up for #258.

* Add figure.

* Remove outdated note.

* Use dt properly.

* Remove unnecessary pdf.

* Partial update of documentation w.r.t breaking changes.

* Redice diff.

* Redice diff.

* Reduce diff.

* Fix some more breaking changes.

* Add how dt is computed. See #257.

* Apply suggestions from code review

Co-authored-by: Gerasimos Chourdakis <[email protected]>

* Remove unneeded.

* Add pointer to interpolation section.

* Fix format.

* Add advice on precice/precice#1866.

* Apply suggestions from code review

* Update some minor, obviously outdated points.

* Update png.

* Update pages/docs/couple-your-code/couple-your-code-mesh-and-data-access.md

Co-authored-by: Frédéric Simonis <[email protected]>

* Update heading.

* Moved changes to #326.

* Update pages/docs/couple-your-code/couple-your-code-mesh-and-data-access.md

* Update pages/docs/couple-your-code/couple-your-code-waveform.md

---------

Co-authored-by: Gerasimos Chourdakis <[email protected]>
Co-authored-by: Frédéric Simonis <[email protected]>
Co-authored-by: Benjamin Uekermann <[email protected]>

* Update submodules

* Remove v3 tip from roadmap

* Add rust bindings to installation overview

* Update libprecice2 to libprecice3 on Ubuntu packages page

* Update header names in installation-linking

* Update porting information on configuration overview page

* Update several things on configuration basics page

* Update configuration communication page

* Revert tweaks in configuration basics page

Previously, I changed from precice to participant as name for the preCICE handle and I used "Force" instead of "Forces" to be consistent with the tutorial guidelines. But both changes would also need updates on many other pages. Thus, I left them for the moment for consistency.

* Refer to QN default values on acceleration configuration

* Update porting info and mention Rust on couple your code start

* Change global dim to mesh dim in step 3

* Remove dim handling from step 6

* Fix getDataDim arguments in step 3

* Fix dim handling in step 9

* Fix dim in direct access

* Fix and tweak porting guide

* Make linter happy

* Make linter happier

* Add missing tutorials in the sidebar and overview (#334)

* Add partitioned-pipe-two-phase to sidebar and overview

* Add oscillator overlap in sidebar and overview

* Add partitioned-heat-conduction-overlap to the sidebar and overview

* Add volume-coupled-flow to sidebar and overview

* Add two-scale-heat-conduction to sidebar and overview

* Update pages/tutorials/tutorials.md

Co-authored-by: Ishaan Desai <[email protected]>

* Update pages/tutorials/tutorials.md

---------

Co-authored-by: Benjamin Uekermann <[email protected]>
Co-authored-by: Ishaan Desai <[email protected]>

* Update bindings overview picture (#333)

* Update bindings overview picture

* Move arrow of Python bindings to precice.hpp

* Add Rust bindings

---------

Co-authored-by: Benjamin Rodenberg <[email protected]>
Co-authored-by: Gerasimos Chourdakis <[email protected]>
Co-authored-by: Benjamin Rodenberg <[email protected]>
Co-authored-by: Frédéric Simonis <[email protected]>
Co-authored-by: David Schneider <[email protected]>
Co-authored-by: carme-hp <[email protected]>
Co-authored-by: June <[email protected]>
Co-authored-by: homspons <ge35joj>
Co-authored-by: Ishaan Desai <[email protected]>
Co-authored-by: Elia Zonta <[email protected]>
Co-authored-by: precice-bot <[email protected]>
Co-authored-by: Ishaan Desai <[email protected]>

Author: 10 people

.github/workflows/deploy.yml

@@ -30,6 +30,10 @@ jobs:
           ref: main
           path: main
 
+      - name: Patch doxyfiles
+        working-directory: website
+        run: doxygen/patch.sh
+
       - name: Install dependencies
         run: |
           sudo apt-get -yyq update

.github/workflows/testing.yml

@@ -30,6 +30,10 @@ jobs:
           ref: main
           path: main
 
+      - name: Patch doxyfiles
+        working-directory: website
+        run: doxygen/patch.sh
+
       - name: Install dependencies
         run: |
           sudo apt-get -yyq update
@@ -71,7 +75,7 @@ jobs:
       - name: Deploy to testing
         uses: peaceiris/actions-gh-pages@v3
         with:
-          github_token: ${{ secrets.JEKYLL_PAT }}
+          personal_token: ${{ secrets.WEB_TESTING_TOKEN }}
           publish_dir: ./public
           external_repository: precice/website-testing
           publish_branch: main

_config.yml

@@ -38,6 +38,7 @@ exclude:
   - pdf/
   - createtag
   - pdf-docs.sh
+  - doxygen/
 # these are the files and directories that jekyll will exclude from the build
 
 feedback_subject_line: XXX
@@ -229,16 +230,21 @@ subprojects:
   - imported/tutorials/partitioned-heat-conduction
   - imported/tutorials/partitioned-heat-conduction-complex
   - imported/tutorials/partitioned-heat-conduction-direct
+  - imported/tutorials/partitioned-heat-conduction-overlap
   - imported/tutorials/oscillator
+  - imported/tutorials/oscillator-overlap
   - imported/tutorials/perpendicular-flap
   - imported/tutorials/turek-hron-fsi3
   - imported/tutorials/partitioned-pipe
+  - imported/tutorials/partitioned-pipe-two-phase
   - imported/tutorials/partitioned-backwards-facing-step
   - imported/tutorials/flow-over-heated-plate-partitioned-flow
   - imported/tutorials/volume-coupled-diffusion
+  - imported/tutorials/volume-coupled-flow
   - imported/tutorials/channel-transport
   - imported/tutorials/channel-transport-reaction
   - imported/tutorials/aste-turbine
+  - imported/tutorials/two-scale-heat-conduction
   - imported/tutorials/tools/tests
   - imported/openfoam-adapter/docs
   - imported/micro-manager/docs
@@ -248,7 +254,7 @@ subprojects:
 # We use these versions to centrally update links
 # and other version-specific information.
 # Note that Jekyll cuts off trailing zeros: https://stackoverflow.com/questions/37862167/trailing-zeros-in-jekyll-liquid
-precice_version: 2.5.0
+precice_version: 3.0.0
 calculix_version: "2.20"
 calculix_adapter_version: "2.20.0"
 

_data/sidebars/docs_sidebar.yml

@@ -3,7 +3,7 @@
 entries:
 - title: sidebar
   product: Docs
-  version: v2.5.0
+  version: v3.0.0
   folders:
 
   - title:

_data/sidebars/tutorial_sidebar.yml

@@ -70,6 +70,10 @@ entries:
       url: /tutorials-partitioned-heat-conduction-direct.html
       output: web
 
+    - title: Partitioned heat conduction overlap
+      url: /tutorials-partitioned-heat-conduction-overlap.html
+      output: web
+
     - title: Partitioned elastic beam
       url: /tutorials-partitioned-elastic-beam.html
       output: web
@@ -78,6 +82,10 @@ entries:
       url: /tutorials-partitioned-pipe.html
       output: web
 
+    - title: Partitioned pipe two-phase
+      url: /tutorials-partitioned-pipe-two-phase.html
+      output: web
+
     - title: Partitioned flow over a step
       url: /tutorials-partitioned-backwards-facing-step.html
       output: web
@@ -90,6 +98,10 @@ entries:
       url: /tutorials-oscillator.html
       output: web
 
+    - title: Oscillator overlap
+      url: /tutorials-oscillator-overlap.html
+      output: web
+
     - title: ASTE turbine
       url: /tutorials-aste-turbine.html
       output: web
@@ -98,10 +110,18 @@ entries:
       url: /tutorials-volume-coupled-diffusion.html
       output: web
 
+    - title: Volume-coupled flow 
+      url: /tutorials-volume-coupled-flow.html
+      output: web
+
     - title: Channel transport
       url: /tutorials-channel-transport.html
       output: web
 
     - title: Channel transport reaction
       url: /tutorials-channel-transport-reaction.html
       output: web
+
+    - title: Two-scale heat conduction
+      url: /tutorials-two-scale-heat-conduction.html
+      output: web