feat: rename solver into ponio (#47)

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<!-- Please check the following before submitting your PR -->
- [x] I have installed [pre-commit](https://pre-commit.com/) locally and
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- [x] The PR title follows the [conventional
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Available tags: 'build', 'chore', 'ci', 'docs', 'feat', 'fix', 'perf',
'refactor', 'revert', 'style', 'test'
- [x] This new PR is tested.

## Description
<!-- A clear and concise description of what you have done in this PR.
-->
Rename `solver` directories into `ponio`.

## Code of Conduct
By submitting this PR, you agree to follow our [Code of
Conduct](https://github.com/hpc-maths/ponio/blob/master/solver/doc/CODE_OF_CONDUCT.md)
- [x] I agree to follow this project's Code of Conduct

.cppcheck

@@ -4,11 +4,11 @@ missingIncludeSystem
 preprocessorErrorDirective
 checkersReport
 # suppress unusedFunction in butcher_methods.hpp
-unusedFunction:solver/include/solver/runge_kutta/butcher_methods.hpp
+unusedFunction:ponio/include/ponio/runge_kutta/butcher_methods.hpp
 # possible false positive
-unusedFunction:solver/include/solver/detail.hpp:82
-unusedFunction:solver/include/solver/detail.hpp:91
-unusedFunction:solver/include/solver/problem.hpp:114
-unusedFunction:solver/include/solver/problem.hpp:153
-unusedFunction:solver/include/solver/runge_kutta/exprk.hpp:27
-unusedFunction:solver/include/solver/runge_kutta/exprk.hpp:42
+unusedFunction:ponio/include/ponio/detail.hpp:82
+unusedFunction:ponio/include/ponio/detail.hpp:91
+unusedFunction:ponio/include/ponio/problem.hpp:114
+unusedFunction:ponio/include/ponio/problem.hpp:153
+unusedFunction:ponio/include/ponio/runge_kutta/exprk.hpp:27
+unusedFunction:ponio/include/ponio/runge_kutta/exprk.hpp:42

.github/pull_request_template.md

@@ -18,5 +18,5 @@
 <!-- Give the list of files used to test this new implementation. -->
 
 ## Code of Conduct
-By submitting this PR, you agree to follow our [Code of Conduct](https://github.com/hpc-maths/ponio/blob/master/solver/doc/CODE_OF_CONDUCT.md)
+By submitting this PR, you agree to follow our [Code of Conduct](https://github.com/hpc-maths/ponio/blob/master/ponio/doc/CODE_OF_CONDUCT.md)
 - [ ] I agree to follow this project's Code of Conduct

.github/workflows/conan.yml

@@ -54,7 +54,7 @@ jobs:
       - name: Unix test
         if: runner.os != 'Windows'
         run: |
-          ./build/solver/test/Release/ponio_tests
+          ./build/ponio/test/Release/ponio_tests
       - name: Windows test
         if: runner.os == 'Windows'
         run: |

.pre-commit-config.yaml

@@ -23,4 +23,4 @@ repos:
     rev: v15.0.7
     hooks:
       - id: clang-format
-        files: solver/.*\.[hc]pp$
+        files: ponio/.*\.[hc]pp$

.readthedocs.yml

@@ -5,8 +5,8 @@ build:
         python: "mambaforge-latest"
     jobs:
         pre_install:
-            - bash ./solver/doc/scripts/pre_install.sh
+            - bash ./ponio/doc/scripts/pre_install.sh
 sphinx:
-    configuration: solver/doc/source/conf.py
+    configuration: ponio/doc/source/conf.py
 conda:
-    environment: solver/doc/environment.yml
+    environment: ponio/doc/environment.yml

CMakeLists.txt

@@ -74,11 +74,11 @@ project_options(
 )
 
 # includes
-set(INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/solver/include)
+set(INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ponio/include)
 
 # generate butcher_methods.hpp
 find_package(Python COMPONENTS Interpreter REQUIRED)
-set(BUTCHER_METHODS "${INCLUDE_DIR}/solver/runge_kutta/butcher_methods.hpp")
+set(BUTCHER_METHODS "${INCLUDE_DIR}/ponio/runge_kutta/butcher_methods.hpp")
 
 set(Ndigit 36)
 
@@ -87,7 +87,7 @@ file(GLOB json_files
 
 add_custom_command(
     OUTPUT ${BUTCHER_METHODS}
-    COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/solver/code_generator.py ${json_files}
+    COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/ponio/code_generator.py ${json_files}
                 -o ${BUTCHER_METHODS}
                 --Ndigit=${Ndigit}
     COMMENT "Generating code..."
@@ -118,19 +118,19 @@ foreach(DEPENDENCY ${DEPENDENCIES_CONFIGURED})
   find_package(${DEPENDENCY} CONFIG REQUIRED)
 endforeach()
 
-set(PONIO_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/solver/include)
+set(PONIO_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/ponio/include)
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
 option(BUILD_TESTS "build the tests" OFF)
 option(BUILD_DEMOS "build the demos" OFF)
 option(BUILD_SAMURAI_DEMOS "build demos working with samurai" OFF)
 
 if (BUILD_TESTS)
-    add_subdirectory(solver/test)
+    add_subdirectory(ponio/test)
 endif()
 
 if (BUILD_DEMOS)
-  add_subdirectory(solver/demos)
+  add_subdirectory(ponio/demos)
 endif()
 
 # package the project

README.md

@@ -100,8 +100,8 @@ Now you are ready to solve your problem with an explicit Runge-Kutta method, see
 
 * [Documentation](https://ponio.readthedocs.io/en/latest/index.html)
 * [Github repository](https://github.com/hpc-maths/ponio)
-* [Demos](https://github.com/hpc-maths/ponio/tree/main/solver/demos)
-* [Notebooks examples](https://github.com/hpc-maths/ponio/tree/main/solver/notebooks)
+* [Demos](https://github.com/hpc-maths/ponio/tree/main/ponio/demos)
+* [Notebooks examples](https://github.com/hpc-maths/ponio/tree/main/ponio/notebooks)
 * [List of methods and their analysis](http://jmassot.perso.math.cnrs.fr/ponio/) (personal webpage of main developer)
 
 ## How to contribute

pixi.toml

@@ -25,10 +25,10 @@ build = { depends_on = ["configure", "build_ninja"] }
 build_test = { depends_on = ["configure_test", "build_ninja"] }
 build_test_samurai = { depends_on = ["configure_test_samurai", "build_ninja"] }
 build_debug = { cmd = "ninja -C build ponio", depends_on = ["configure_debug"] }
-test = { cmd = "./build/solver/test/Release/ponio_tests", depends_on = [
+test = { cmd = "./build/ponio/test/Release/ponio_tests", depends_on = [
   "build_test",
 ] }
-nbval = { cmd = "pytest --nbval --nbval-current-env -p no:warnings", cwd = "./solver/notebooks", depends_on = [
+nbval = { cmd = "pytest --nbval --nbval-current-env -p no:warnings", cwd = "./ponio/notebooks", depends_on = [
   "build",
 ] }
 cppcheck = { cmd = "cppcheck --enable=all -q --project=./build/compile_commands.json --suppressions-list=.cppcheck --inline-suppr 2> cppcheck_err.txt", depends_on = [

solver/demos/CMakeLists.txt → ponio/demos/CMakeLists.txt

@@ -43,6 +43,6 @@ foreach(demo IN LISTS demos)
 endforeach()
 
 foreach(demo IN LISTS demos)
-    add_custom_target(visu_${demo} python ${CMAKE_SOURCE_DIR}/solver/demos/${demo}.py)
+    add_custom_target(visu_${demo} python ${CMAKE_SOURCE_DIR}/ponio/demos/${demo}.py)
     add_custom_target(${demo}_visu make visu_${demo})
 endforeach()

solver/demos/arenstorf.cpp → ponio/demos/arenstorf.cpp

@@ -7,10 +7,10 @@
 #include <numeric>
 #include <valarray>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
 
 /*
 solve Arenstorf orbit problem

solver/demos/brownian.cpp → ponio/demos/brownian.cpp

@@ -11,10 +11,10 @@
 #include <string>
 #include <valarray>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
 
 #include <CLI/CLI.hpp>
 

solver/demos/brusselator.cpp → ponio/demos/brusselator.cpp

@@ -5,11 +5,11 @@
 #include <iostream>
 #include <valarray>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 // Brusselator
 

solver/demos/brusselator_dirk.cpp → ponio/demos/brusselator_dirk.cpp

@@ -7,12 +7,12 @@
 
 #include <Eigen/Dense>
 
-#include <solver/eigen_linear_algebra.hpp>
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/eigen_linear_algebra.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 struct lin_alg_2_2
 {

solver/demos/curtiss_hirschfelder.cpp → ponio/demos/curtiss_hirschfelder.cpp

@@ -7,10 +7,10 @@
 #include <numbers>
 #include <numeric>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
 
 /*
 solve Curtiss and Hirschfelder problem:

solver/demos/curtiss_hirschfelder_exprk.cpp → ponio/demos/curtiss_hirschfelder_exprk.cpp

@@ -7,10 +7,10 @@
 #include <numbers>
 #include <numeric>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
 
 /*
 solve Curtiss and Hirschfelder problem:

solver/demos/exp.cpp → ponio/demos/exp.cpp

@@ -6,16 +6,16 @@
 #include <iostream>
 #include <tuple>
 
-#include <solver/observer.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
 
 // solve $\dot{u} = u$ with $u(t=0) = 1$, and $t\in[0,2]$.
 
 int
 main( int, char** )
 {
-    const std::string dirname = "exp_data";
+    std::string const dirname = "exp_data";
     auto filename             = std::filesystem::path( dirname ) / "exp.dat";
     observer::file_observer fobs( filename );
 

solver/demos/heat.cpp → ponio/demos/heat.cpp

@@ -12,10 +12,10 @@
 #include <numbers>
 #include <sstream>
 
-#include <solver/observer.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 // Heat
 class heat_model

solver/demos/heat_rock.cpp → ponio/demos/heat_rock.cpp

@@ -12,10 +12,10 @@
 #include <numbers>
 #include <sstream>
 
-#include <solver/observer.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 // Heat
 class heat_model

solver/demos/heat_samurai.cpp → ponio/demos/heat_samurai.cpp

@@ -8,11 +8,11 @@
 #include <samurai/mr/mesh.hpp>
 #include <samurai/schemes/fv.hpp>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/samurai_linear_algebra.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/samurai_linear_algebra.hpp>
+#include <ponio/solver.hpp>
 
 #include <filesystem>
 

solver/demos/lorenz.cpp → ponio/demos/lorenz.cpp

@@ -7,10 +7,10 @@
 #include <numeric>
 #include <valarray>
 
-#include <solver/observer.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 int
 main( int, char** )

solver/demos/lorenz_tuto.cpp → ponio/demos/lorenz_tuto.cpp

@@ -8,12 +8,12 @@
 #include <Eigen/Dense>
 #include <unsupported/Eigen/MatrixFunctions>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/splitting.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/splitting.hpp>
+#include <ponio/time_span.hpp>
 
 // Lorenz
 /*

solver/demos/lotka_volterra.cpp → ponio/demos/lotka_volterra.cpp

@@ -8,11 +8,11 @@
 #include <string>
 #include <valarray>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 #include <CLI/CLI.hpp>
 

solver/demos/nagumo.cpp → ponio/demos/nagumo.cpp

@@ -12,10 +12,10 @@
 #include <numbers>
 #include <sstream>
 
-#include <solver/observer.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
-#include <solver/time_span.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
+#include <ponio/time_span.hpp>
 
 struct nagumo
 {

solver/demos/pendulum.cpp → ponio/demos/pendulum.cpp

@@ -8,10 +8,10 @@
 #include <numeric>
 #include <valarray>
 
-#include <solver/observer.hpp>
-#include <solver/problem.hpp>
-#include <solver/runge_kutta.hpp>
-#include <solver/solver.hpp>
+#include <ponio/observer.hpp>
+#include <ponio/problem.hpp>
+#include <ponio/runge_kutta.hpp>
+#include <ponio/solver.hpp>
 
 /*
 solve pendulum problem :

solver/doc/scripts/pre_install.sh → ponio/doc/scripts/pre_install.sh

@@ -2,7 +2,7 @@
 
 cmake . -B ./build -G "Ninja Multi-Config"
 cmake --build ./build --config Release
-pushd solver/doc
+pushd ponio/doc
 doxygen
 ls
 ls xml