Rework of the CLI argument parser and add the option to define inputs…

… through a JSON file (#93) * Add first parser attempt * Use argparser * Convert all execs to use new argparser * Add json option and example files for all parameters * Include json in dependencies * Add json to readme * Bump version * Bump version * Fix missing json check and add install to workflows * Run ubuntu on 22.04 * Add unit tests and documentation for parser * Fix unit test * Use template function to convert value in types * Fix windows uint problem and get catch2 through conan * Unify spelling * Unify spelling of arguments * Update cpp-linter.yml * Update cpp-linter.yml * apply cmake-format * Automated commit of cmake-format changes. * logger docu * Apply suggestions from code review Co-authored-by: Lisa Biermann <[email protected]> * Remove duplicate cmakedefs * Fix missing install on mac * Only print help output once * Update CMakeLists.txt Co-authored-by: Lisa Biermann <[email protected]> * Fix openmp missing on * opt openmp * link to openmp target Co-authored-by: phbasler <[email protected]> Co-authored-by: Lisa Biermann <[email protected]>
phbasler · Nov 5, 2022 · f24ba97 · f24ba97
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diff --git a/.github/workflows/build-mac.yml b/.github/workflows/build-mac.yml
@@ -18,7 +18,7 @@ jobs:
       with:
           persist-credentials: false
     - name: installPackages
-      run: brew install eigen && brew install gsl && brew install nlopt && brew install boost && brew install libomp
+      run: brew install eigen && brew install gsl && brew install nlopt && brew install boost && brew install libomp && brew install nlohmann-json
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,15 +10,15 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
 
     steps:
     - uses: actions/checkout@v3
       with:
           persist-credentials: false
     - name : installPackages
-      run : sudo apt-get install --no-install-recommends --yes libgsl-dev libeigen3-dev libnlopt-dev libnlopt-cxx-dev libboost-all-dev
+      run : sudo apt-get install --no-install-recommends --yes libgsl-dev libeigen3-dev libnlopt-dev libnlopt-cxx-dev libboost-all-dev nlohmann-json3-dev
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores

diff --git a/.github/workflows/cpp-linter.yml b/.github/workflows/cpp-linter.yml
@@ -14,8 +14,9 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          style: file
+          style: "file"
           tidy-checks: '-*'
+          version: '14'
 
       - name: Fail fast?!
         if: steps.linter.outputs.checks-failed > 0

diff --git a/.github/workflows/test-mac.yml b/.github/workflows/test-mac.yml
@@ -22,7 +22,7 @@ jobs:
       with:
           persist-credentials: false
     - name : installPackages
-      run : brew install eigen gsl nlopt boost libomp
+      run : brew install eigen gsl nlopt boost libomp nlohmann-json
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores
@@ -42,7 +42,7 @@ jobs:
       with:
           persist-credentials: false
     - name : installPackages
-      run : brew install eigen gsl boost libomp
+      run : brew install eigen gsl boost libomp nlohmann-json
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,7 +6,7 @@
 cmake_minimum_required(VERSION 3.13)
 project(
   BSMPT
-  VERSION 2.4.0
+  VERSION 2.5.0
   LANGUAGES C CXX
   DESCRIPTION
     "BSMPT - Beyond the Standard Model Phase Transitions : A C++ package for the computation of the EWPT in BSM models"
@@ -37,6 +37,10 @@ if(EnableCoverage)
   set(BSMPT_USE_VECTORIZATION OFF)
 endif()
 
+if(BSMPT_IS_TOPLEVEL)
+  include(CTest)
+endif()
+
 # -------------------------------- setup cmake --------------------------------
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW) # use <packagename>_ROOT as search path
@@ -62,6 +66,7 @@ find_package(PkgConfig)
 find_package(Eigen3 3.3.0 REQUIRED)
 find_package(Boost 1.66)
 find_package(GSL 2.1 REQUIRED)
+find_package(nlohmann_json 3.7.3)
 
 find_package(Threads REQUIRED)
 
@@ -83,6 +88,11 @@ if(Boost_FOUND)
   endif()
 endif()
 
+if(nlohmann_json_FOUND)
+  set(CodeCoverageExcludesFromOtherPkgs ${CodeCoverageExcludesFromOtherPkgs}
+                                        "${nlohmann_json}/*")
+endif()
+
 set(EXPORT_CMAES FALSE)
 include(FetchContent)
 if(UseLibCMAES AND NOT WIN32)
@@ -211,9 +221,6 @@ endif(BSMPT_IS_TOPLEVEL)
 
 # -------------------- Testing
 # ---------------------------------------------------
-if(BSMPT_IS_TOPLEVEL)
-  include(CTest)
-endif()
 
 if(BSMPT_IS_TOPLEVEL AND BUILD_TESTING)
   add_subdirectory(tests)

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ SPDX-FileCopyrightText: 2021 Philipp Basler, Margarete Mühlleitner and Jonas M
 SPDX-License-Identifier: GPL-3.0-or-later
 -->
 
-Program: BSMPT version 2.4.0
+Program: BSMPT version 2.5.0
 
 Released by: Philipp Basler and Lisa Biermann and Margarete Mühlleitner and Jonas Müller
 
@@ -137,6 +137,9 @@ Also contact us if you have a custom model for BSMPT v1.x and you have trouble c
 
 ## Executables
 BSMPT provides multiple executables. Here we give a quick overview of them. For every executable you can call them with the `--help` option to get an overview of possible input parameters.
+
+Additionally, every executable has the option to set the `--json=/path/to/your/file.json` which contains a json string with the parameters you can set through the CLI. This can be useful if you want to store the parameters you used for a given call. Please beware that all relative paths in the json file are considered relative to the current working directory and not to the location of the json file. Examples can be found in `example/JSON`. If you want to be sure to have the correct output file we recommend using absolute paths.
+
 For the following examples the C2HDM with the example/C2HDM_Input.dat file is used.
 
 ### BSMPT

diff --git a/example/JSON/BSMPT.json b/example/JSON/BSMPT.json
@@ -0,0 +1,17 @@
+{
+    "firstLine": "2",
+    "lastLine": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "useMultiThreading": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/CalcCT.json b/example/JSON/CalcCT.json
@@ -0,0 +1,13 @@
+{
+    "firstLine": "2",
+    "lastLine": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/CalculateEWBG.json b/example/JSON/CalculateEWBG.json
@@ -0,0 +1,19 @@
+{
+    "firstLine": "2",
+    "lastLine": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "config": "../example/EWBG_config.txt",
+
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "useMultiThreading": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/NLOVEV.json b/example/JSON/NLOVEV.json
@@ -0,0 +1,17 @@
+{
+    "firstLine": "2",
+    "lastLine": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "useMultiThreading": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/PlotEWBG_nL.json b/example/JSON/PlotEWBG_nL.json
@@ -0,0 +1,19 @@
+{
+    "line": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "config": "../example/EWBG_config.txt",
+    "vw": "0.1",
+
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "useMultiThreading": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/PlotEWBG_vw.json b/example/JSON/PlotEWBG_vw.json
@@ -0,0 +1,21 @@
+{
+    "line": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "config": "../example/EWBG_config.txt",
+    "vw_min": "0.1",
+    "vw_max": "0.2",
+    "vw_stepsize": "0.05",
+
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "useMultiThreading": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/Test.json b/example/JSON/Test.json
@@ -0,0 +1,14 @@
+{
+    "line": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "model": "c2hdm",
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/TripleHiggsCouplingsNLO.json b/example/JSON/TripleHiggsCouplingsNLO.json
@@ -0,0 +1,13 @@
+{
+    "firstLine": "2",
+    "lastLine": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/example/JSON/VEVEVO.json b/example/JSON/VEVEVO.json
@@ -0,0 +1,20 @@
+{
+    "line": "2",
+    "input": "../example/C2HDM_Input.dat",
+    "output": "test.tsv",
+    "model": "c2hdm",
+    "temperatureStart": "0",
+    "temperatureEnd": "100",
+    "temperatureStep": "5",
+
+    "useNLopt": "true",
+    "useCMAES": "true",
+    "useGSL": "true",
+    "useMultiThreading": "true",
+    "logginglevel::default": "true",
+    "logginglevel::minimizerdetailed": "false",
+    "logginglevel::ewbgdetailed": "false",
+    "logginglevel::debug": "false",
+    "logginglevel::progdetailed": "false",
+    "logginglevel::disabled_comment": "remove _comment from key to disable logger"
+}
diff --git a/include/BSMPT/config.h.in b/include/BSMPT/config.h.in
@@ -3,3 +3,4 @@
 #cmakedefine libcmaes_FOUND
 #cmakedefine NLopt_FOUND
 #cmakedefine Boost_FOUND
+#cmakedefine nlohmann_json_FOUND
diff --git a/include/BSMPT/utility/Logger.h b/include/BSMPT/utility/Logger.h
@@ -18,8 +18,10 @@ namespace BSMPT
 {
 
 class Logger;
+class parser;
 
 void ShowLoggerHelp();
+void SetLogger(const parser &argparser);
 void SetLogger(const std::vector<std::string> &args);
 
 enum class LoggingLevel
@@ -32,18 +34,29 @@ enum class LoggingLevel
   Debug
 };
 
+/**
+ * @brief The BSMPTLogger class
+ */
 class BSMPTLogger
 {
 public:
   friend Logger;
   BSMPTLogger(std::ostream &os) : mOstream{os.rdbuf()} {}
-  BSMPTLogger(const BSMPTLogger &) = delete;
-  BSMPTLogger(BSMPTLogger &&)      = delete;
+  BSMPTLogger(const BSMPTLogger &)            = delete;
+  BSMPTLogger(BSMPTLogger &&)                 = delete;
   BSMPTLogger &operator=(const BSMPTLogger &) = delete;
-  BSMPTLogger &operator=(BSMPTLogger &&) = delete;
+  BSMPTLogger &operator=(BSMPTLogger &&)      = delete;
 
 private:
+  /**
+   * @brief SetOStream sets the output of the logger to a certain ostream
+   * @param Ostream
+   */
   void SetOStream(std::ostream &Ostream);
+  /**
+   * @brief SetOStream writes the output of the logger to a file
+   * @param file
+   */
   void SetOStream(const std::string &file);
   template <typename T>
   void
@@ -81,10 +94,10 @@ class BSMPTLogger
 class Logger
 {
 public:
-  Logger(const Logger &) = delete;
-  Logger(Logger &&)      = delete;
+  Logger(const Logger &)            = delete;
+  Logger(Logger &&)                 = delete;
   Logger &operator=(const Logger &) = delete;
-  Logger &operator=(Logger &&) = delete;
+  Logger &operator=(Logger &&)      = delete;
 
   static void SetLevel(const std::map<LoggingLevel, bool> &Setup)
   {