V0.1 (#7)

* separate core from cli + start doc

* pass lib from .so to .a

* add custom initialiser feature

* check rd perf + clean wrap cereal dep

* start implementing cereal serialization

* Improve post process package + check monod model

* improve way to get particle properties with kokkos_view in post_process and data_exporter

* Refractor kernel into functor + reduce branching in move process + check cstr simulation

* Refractor and add autogenerated compile_time flag + start impl probes

Remove all compile time flag from core and lib to put them into Meson
Generated header + move model selection output dir ("autogenerated").
Working poc implementation of probes to export some events during
simulation using fixed size buffer.

Check RTD for 0D reactor : OK with same stochastic algo

* Fix(simulation) RTD for batch and continuous reactor; Fix(init) gas scalar initialiaser

* Fix(model): mass_transfer + feed support, optimisation(MC), refractor(data_exporter_wip)

MC: use of Kokkos Scatter to limit use of atomic with host space +
change algortihm to remove dead particle

* WIP(Data exporter): new data exporter architecture

* feat: Implement DataExporter and MPI Feed

- Added DataExporter feature to facilitate data export.
- Split DataExporter into two components: main file for host node and partial file for worker nodes.
- Workers now write particle data efficiently.
- Fixed Kokkos/MPI thread count settings for improved performance.
- Updated .dockerfile to ensure proper environment setup.

* feat,fix: add mass calculation function and improve Monod uptake

fix: dataexporter OK
fix: correct weight calculation
feat: start updating postprocess package to handle new export format

* chore, fix(dataexport): refractor, new files

chore: move simulation parameter to core
fix: datexporter file path + integration in to whole algorithm to
correclty export data
fix: post process data with multiple files

* fix: matrix layout (row/column major) between Eigen and Kokkos

* chore + fix rtd

* misc: test sanofi ok

* fix(monod model): fix model to have correct final biomass concentration

* feat: steady_state test

* feat: test model parameters

* Fix Monod and Uptake model, working in steady state

* script steady

* perf: improve flowmap creation and transition performance

* add external hdf5 compressor

* opti: bench and add profiling

* feat: add prng to division model function

* opti,feat: bench try opti + start impl sunya's model

* refractor: model_uptake rename k_pts

* feat(model) fix uptake, implem metabolism

* fix(simulation): fix oxygen transfer and henry constant

* fix(cli): scalar gas-liquid from files, todo find better fix

* fix(main): confirm overriding when using MPI

* chore

* feat,fix,,chore: working 0.0.9 version

* version upgrade

---------

Co-authored-by: Casale Benjamin <casale@insa-toulouse.fr>

.clang-format

@@ -1,4 +1,4 @@
-BasedOnStyle: llvm
+BasedOnStyle: llvm 
 BreakBeforeBraces: Allman
 BraceWrapping:
   AfterFunction: true
@@ -7,3 +7,11 @@ BinPackArguments: false
 BinPackParameters: false
 NamespaceIndentation: All
 IndentPPDirectives: AfterHash
+
+ColumnLimit: 150  # Disables column limit to prevent unwanted line wrapping.
+CommentPragmas: true  # Properly formats comments with pragmas.
+SpaceBeforeParens: ControlStatements  # Space before parentheses for control statements.
+UseTab: Never  # Use spaces for indentation instead of tabs.
+
+
+

.github/workflows/format.yml

@@ -1,13 +1,6 @@
 name: Format
-'on':
-  push:
-    branches:
-      - main
-      - v*/**
-  pull_request:
-    branches:
-      - main
-      - v*/**
+
+on: [push, pull_request]
 permissions:
   contents: read
 jobs:
@@ -30,27 +23,11 @@ jobs:
     name: clang-tidy
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
         with:
-          token: '${{ secrets.PAT_TOKEN }}'
-      - name: Clone GitLab submodule
-        run: >
-          git config --global credential.helper '!f() { echo "username=${{
-          secrets.USER_GITLAB }}"; echo "password=${{ secrets.PAT_GITLAB }}"; };
-          f'
-
-          git submodule update --init --recursive
-      - name: install Python
-        run: >-
-          sudo apt-get install python3 python3-pip python3-setuptools
-          python3-wheel ninja-build
-      - name: install dependencies
-        run: >-
-          sudo apt-get install -y  libomp-dev libopenmpi-dev libeigen3-dev libtbb-dev
-          pkg-config ninja-build
-      - name: Install Meson
-        run: pip3 install meson
+          python-version: "3.11"
       - name: get LLVM clang-tidy/clang-format
         run: |
           sudo sh devutils/clang_config.sh 17
@@ -61,42 +38,3 @@ jobs:
         run: |
           ninja -C builddir clang-tidy 
 
-  clang-format:
-    name: clang-format
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-        with:
-          token: '${{ secrets.PAT_TOKEN }}'
-      - name: Clone GitLab submodule
-        run: >
-          git config --global credential.helper '!f() { echo "username=${{
-          secrets.USER_GITLAB }}"; echo "password=${{ secrets.PAT_GITLAB }}"; };
-          f'
-
-          git submodule update --init --recursive
-      - name: install Python
-        run: >-
-          sudo apt-get install python3 python3-pip python3-setuptools
-          python3-wheel ninja-build
-      - name: install dependencies
-        run: >-
-          sudo apt-get install -y  libomp-dev libopenmpi-dev libeigen3-dev
-          pkg-config ninja-build
-      - name: Install Meson
-        run: pip3 install meson
-      - name: get LLVM clang-tidy/clang-format
-        run: |
-          sudo sh devutils/clang_config.sh 17
-      - name: Configure project
-        run: |
-          meson setup builddir/ --buildtype=release -Dcpp_std=gnu++20
-      - name: Clang-Format
-        run: |
-          ninja -C builddir clang-format-check 
-  
-
-        # which meson
-          # exec=$(which meson)
-          # $exec  --internal clangformat $(pwd) $(pwd)/builddir/debug --check

.gitignore

@@ -35,3 +35,6 @@ __old
 
 ./Documentation/html
 ./Documentation/latex
+
+
+tmp*

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "subprojects/cmtool"]
 	path = subprojects/cmtool
-	url = https://gitlab.com/Bencs/mirror_cma.git
+	url = https://gitlab.com/codes_tim/compartment-modelling-tool.git
 	branch = main

apps/autogenerated/biocma_cst_config.hpp.in

@@ -0,0 +1,65 @@
+#ifndef __BIOMC__AUTOGENERATED_CONFIG_HPP__
+#define __BIOMC__AUTOGENERATED_CONFIG_HPP__
+
+/* ---------------------------------------------------------
+ *                  BIOCMA_MC ST
+ * 
+ * This file has been autogenerated by Meson during project
+ * configuration. 
+ * 
+ * Be careful when modifying values.
+ * ---------------------------------------------------------
+ */
+
+
+#include <cstddef>
+#include <cstdint> 
+#include <string_view>
+
+#mesondefine _BIOMC_VERSION_MAJOR
+#mesondefine _BIOMC_VERSION_MINOR
+#mesondefine _BIOMC_VERSION_DEV
+
+
+namespace AutoGenerated
+{
+
+    constexpr std::string_view cma_data_folder_path = @cma_data_folder_path@; ///<Default folder to find CMA for simulation 
+    constexpr std::string_view result_dir_path = @result_dir_path@; ///<Default folder to store simulation results 
+
+    constexpr std::size_t probe_buffer_size = @probe_buffer_size@; ///<Default size for probes buffer 
+
+
+    constexpr double default_particle_container_allocation_factor = @default_particle_container_allocation_factor@; 
+    constexpr std::size_t MC_MAX_PARTICLE_BUFFER = @MC_MAX_PARTICLE_BUFFER@;
+    constexpr uint64_t debug_MC_RAND_DEFAULT_SEED = @debug_MC_RAND_DEFAULT_SEED@;
+
+    constexpr double dead_particle_ratio_threshold = @_dead_particle_ratio_threshold@;
+
+
+    /**
+    * @namespace FlagCompileTIme
+    * @brief Namespace containing compile-time flags for application configuration.
+    *
+    * This namespace defines compile-time constants that control specific behavior
+    * of the application, such as verbosity and output redirection. These flags are
+    * set based on predefined macros and allow for conditional compilation.
+    */
+    namespace FlagCompileTIme
+    {   
+        constexpr bool __f__redirect__ = @__f__redirect__@; //< Controls whether standard output should be redirected.
+        constexpr bool verbose = @__f_verbose__@; //< Controls whether verbose logging is enabled.
+        constexpr bool dump_particle_state = @dump_particle_state@;
+        constexpr bool use_probe = @use_probe@;
+        constexpr bool const_number_simulation = @const_number_simulation@;
+
+        #ifdef NO_MPI
+        constexpr bool use_mpi = false;
+        #else
+        constexpr bool use_mpi = true;
+        #endif
+    } // namespace FlagCompileTIme
+
+} //namespace AutoGenerated
+
+#endif 

apps/autogenerated/meson.build

@@ -0,0 +1,58 @@
+# Use to generate source/header file before compilation 
+
+version = meson.project_version().split('.')
+assert(version.length()==3)
+
+conf_data = configuration_data(
+    {
+        '_BIOMC_VERSION_MAJOR': version[0],
+        '_BIOMC_VERSION_MINOR': version[1],
+        '_BIOMC_VERSION_DEV':  version[2],
+        'probe_buffer_size': '10e3',
+        '__f__redirect__': 'false',
+        '__f_verbose__': 'true',
+        'dump_particle_state': 'true',
+        'use_probe': 'true',
+        'const_number_simulation': 'false',
+        'default_particle_container_allocation_factor': '2.5',
+        'MC_MAX_PARTICLE_BUFFER': '100e6',
+        'debug_MC_RAND_DEFAULT_SEED': '2024',
+        '_dead_particle_ratio_threshold':'0.01',
+        'result_dir_path':'"./results/"',
+        'cma_data_folder_path':'"cma_data"'
+    },
+)
+
+configure_file(
+    input: 'biocma_cst_config.hpp.in',
+    output: 'biocma_cst_config.hpp',
+    configuration: conf_data,
+)
+
+prog_python = find_program('python3')
+
+model_loader = meson.current_source_dir()+'/model_loader.cxx'
+model_loader_header = meson.current_source_dir()+'/model_loader.hxx'
+variant_model = meson.current_source_dir()+'/variant_model.hxx'
+
+# custom target to generate model_loader.cpp and model_list.hpp
+generated_model_selection = custom_target(
+    'generated_model_selection.[ch]',
+    output: [
+        'wrap_init_model_selector.cpp',
+        'wrap_init_model_selector.hpp',
+        'variant_model.hpp',
+    ],
+    input: f'@root@/devutils/auto_generate/generate_model_loader.py',
+    command: [
+        prog_python,
+        '@INPUT@',
+        f'@root@/apps/libs/biomodels',
+        model_loader,
+        '@OUTPUT0@',
+        model_loader_header,
+        '@OUTPUT1@',
+        variant_model,
+        '@OUTPUT2@',
+    ],
+)

devutils/auto_generate/model_loader.cxx → apps/autogenerated/model_loader.cxx

@@ -1,13 +1,25 @@
+// NOLINTBEGIN
 #include <mc/mcinit.hpp>
 #include <string_view>
 #include <unordered_map>
 
+/* ---------------------------------------------------------
+ *                  BIOCMA_MC ST
+ *
+ * This file has been autogenerated by Meson during project
+ * configuration.
+ *
+ * Be careful when modifying values.
+ * ---------------------------------------------------------
+ */
+
+// clang-format off
 @INCLUDES@
 
-    namespace AutoGenerated
+namespace AutoGenerated
 {
   std::unique_ptr<MC::MonteCarloUnit> wrap_init_model_selector(
-    const int i_model,
+      const int i_model,
       const ExecInfo &info,
       size_t numper_particle,
       std::span<double> liq_volume,
@@ -29,13 +41,13 @@
   int get_model_index_from_name(std::string_view model_name) noexcept
   {
     @MODEL_INDEX_MAP@
-
 
     auto it = map.find(model_name);
-    if (it != map.end()) {
-        return it->second;
+    if (it != map.end())
+    {
+      return it->second;
     }
-    std::cerr<<"Model not found, using DefaultModel instead"<<std::endl;
+    std::cerr << "Model not found, using DefaultModel instead" << std::endl;
     return -1;
   }
 
@@ -44,3 +56,5 @@
     return {};
   }
 } // namespace AutoGenerated
+// clang-format on
+// NOLINTEND

apps/autogenerated/model_loader.hxx

@@ -0,0 +1,34 @@
+#ifndef __GENERATED_MODEL_WRAP__HPP__
+#define __GENERATED_MODEL_WRAP__HPP__
+
+#include <common/execinfo.hpp>
+#include <mc/unit.hpp>
+#include <memory>
+#include <span>
+#include <string_view>
+
+/* ---------------------------------------------------------
+ *                  BIOCMA_MC ST
+ *
+ * This file has been autogenerated by Meson during project
+ * configuration.
+ *
+ * Be careful when modifying values.
+ * ---------------------------------------------------------
+ */
+
+namespace AutoGenerated
+{
+  std::unique_ptr<MC::MonteCarloUnit> wrap_init_model_selector(int i_model,
+                                                               const ExecInfo &info,
+                                                               size_t numper_particle,
+                                                               std::span<double> liq_volume,
+                                                               CmaRead::Neighbors::Neighbors_const_view_t liquid_neighbors,
+                                                               double x0) noexcept;
+
+  int get_model_index_from_name(std::string_view model_name) noexcept;
+
+  std::vector<std::string> get_model_list() noexcept;
+} // namespace AutoGenerated
+
+#endif //__GENERATED_MODEL_WRAP__HPP__

devutils/auto_generate/variant_model.hxx → apps/autogenerated/variant_model.hxx

@@ -1,16 +1,27 @@
 #ifndef __AUTOGENRATED_VARIANT_MODEL_HPP__
 #define __AUTOGENRATED_VARIANT_MODEL_HPP__
 
-#include <mc/particles/particles_container.hpp>
 #include <mc/particles/particle_model.hpp>
+#include <mc/particles/particles_container.hpp>
 #include <variant>
 
+/* ---------------------------------------------------------
+ *                  BIOCMA_MC ST
+ *
+ * This file has been autogenerated by Meson during project
+ * configuration.
+ *
+ * Be careful when modifying values.
+ * ---------------------------------------------------------
+ */
+
+// clang-format off
 @INCLUDES@
 
 namespace AutoGenerated
 {
   using ContainerVariant = std::variant<@VARIANT_TYPE@>;
 } // namespace AutoGenerated
-
+// clang-format on
 
 #endif //__AUTOGENRATED_VARIANT_MODEL_HPP__