Updating boost process rebased

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: unconfirmed bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - OpenFLUID version [e.g. 2.1.11]
+
+**Additional context**
+Add any other context about the problem here.

.github/workflows/CI-macos.yaml

@@ -23,20 +23,14 @@ jobs:
           gnuplot
       - name: Installation of pandoc
         uses: r-lib/actions/setup-pandoc@v2
-      - name: Installation of latex
-        uses: teatimeguest/setup-texlive-action@v3
-        with:
-          packages: |
-            scheme-full
-            bibtex
       - name: Checkout of source code
         uses: actions/checkout@v3
       - name: Preparation
         run: |
           echo "$(brew --prefix qt6)/bin" >> $GITHUB_PATH
           mkdir ./_build
       - name: Configuration
-        run: cmake .. -DCMAKE_PREFIX_PATH=$(brew --prefix qt6)/lib/cmake
+        run: cmake .. -DCMAKE_PREFIX_PATH=$(brew --prefix qt6)/lib/cmake -DOFBUILD_ENABLE_DOCS=OFF
         working-directory: ./_build
       - name: Build
         run: make -j 2

.github/workflows/CI-windows.yaml

@@ -10,7 +10,7 @@ jobs:
 
 
   ci-windows-debug:
-    runs-on: windows-2019
+    runs-on: windows-2025
 
     defaults:
       run:
@@ -25,7 +25,7 @@ jobs:
           release: false
           install: >-
             mingw-w64-x86_64-toolchain mingw-w64-x86_64-gcc mingw-w64-x86_64-gcc-fortran
-            mingw-w64-x86_64-cmake mingw-w64-x86_64-doxygen
+            mingw-w64-x86_64-cmake mingw-w64-x86_64-doxygen make
             mingw-w64-x86_64-boost mingw-w64-x86_64-gdal mingw-w64-x86_64-curl-winssl
             mingw-w64-x86_64-qt5 mingw-w64-x86_64-openssl
             git p7zip mingw-w64-x86_64-gnuplot mingw-w64-x86_64-graphviz

CMake.in.cmake

@@ -1,7 +1,8 @@
 #
 # Configuration file for CMakeLists.txt files
 #
-# Author : Jean-Christophe FABRE <jean-christophe.fabre@inra.fr>
+# Authors : Jean-Christophe FABRE <jean-christophe.fabre@inra.fr>
+#           Armel THÖNI <armel.thoni@inrae.fr>
 #
 # This file is included by the main CMakeLists.txt file, and defines variables
 # to configure the build and install
@@ -22,8 +23,8 @@ SET(OFBUILD_CUSTOM_CMAKE_VERSION "${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.
 
 SET(OPENFLUID_VERSION_MAJOR 2)
 SET(OPENFLUID_VERSION_MINOR 2)
-SET(OPENFLUID_VERSION_PATCH 0)
-SET(OPENFLUID_VERSION_STATUS "") # example: SET(OPENFLUID_VERSION_STATUS "rc1")
+SET(OPENFLUID_VERSION_PATCH 1)
+SET(OPENFLUID_VERSION_STATUS "alpha6") # example: SET(OPENFLUID_VERSION_STATUS "rc1")
 
 SET(OPENFLUID_VERSION_FULL "${OPENFLUID_VERSION_MAJOR}.${OPENFLUID_VERSION_MINOR}.${OPENFLUID_VERSION_PATCH}")
 

cmake/OpenFLUIDTestScript.cmake

@@ -54,6 +54,13 @@ FUNCTION(EXECUTE_COMMAND CMD)
     ENDIF()
     FILE(REMOVE_RECURSE ${TMPDIR})
 
+  ELSEIF(${CMD} STREQUAL "CHECK_FILE_CONTAINS")
+    FILE(READ ${TMPDIR}/${ARGV1} TMPTXT)
+    STRING(FIND "${TMPTXT}" "${ARGV2}" ISMATCH)
+    IF(${ISMATCH} EQUAL -1)
+      MESSAGE(FATAL_ERROR "CHECK_FILE_CONTAINS: file ${ARGV1} does not contain string ${ARGV2}")
+    ENDIF()
+
   ELSEIF(${CMD} STREQUAL "CHECK_FILE_IDENTICAL")
     # generates consistent eol between files (can be replaced by option ignore_eol in cmake 3.14)
     CONFIGURE_FILE(${ARGV1}${ARGV3} ${ARGV1}${ARGV3}_UNIX_EOL NEWLINE_STYLE UNIX)
@@ -73,6 +80,8 @@ FUNCTION(EXECUTE_COMMAND CMD)
     IF(IS_DIRECTORY ${ARGV1})
       MESSAGE(FATAL_ERROR "CHECK_DIRECTORY_NOT_EXISTING: directory ${ARGV1} found")
     ENDIF()
+  ELSEIF(${CMD} STREQUAL "CREATE_DIRECTORY")
+    FILE(MAKE_DIRECTORY ${ARGV1})
   ELSEIF(${CMD} STREQUAL "REMOVE_FILE")
     IF(EXISTS ${ARGV1})
       FILE(REMOVE ${ARGV1})
@@ -116,6 +125,7 @@ FUNCTION(PARSE_COMMANDS)
     IF(${CMD_EXPECTED})
       IF(${ELEM} STREQUAL "CHECK_FILE_EXIST" OR
          ${ELEM} STREQUAL "CHECK_FILE_EXIST_IN_ARCHIVE" OR
+         ${ELEM} STREQUAL "CHECK_FILE_CONTAINS" OR
          ${ELEM} STREQUAL "CHECK_FILE_IDENTICAL" OR
          ${ELEM} STREQUAL "CHECK_DIRECTORY_EXIST" OR
          ${ELEM} STREQUAL "CHECK_DIRECTORY_NOT_EXISTING" OR
@@ -125,7 +135,7 @@ FUNCTION(PARSE_COMMANDS)
          ${ELEM} STREQUAL "COPY_DIRECTORY" OR
          ${ELEM} STREQUAL "EMPTY_DIRECTORY" OR
          ${ELEM} STREQUAL "CREATE_FILE" OR
-         ${ELEM} STREQUAL "CREATE_DIR" OR
+         ${ELEM} STREQUAL "CREATE_DIRECTORY" OR
          ${ELEM} STREQUAL "COMPARE_FILES" OR
          ${ELEM} STREQUAL "COMPARE_DIRECTORIES")
         SET(CURRENT_CMD "${ELEM}")
@@ -141,6 +151,7 @@ FUNCTION(PARSE_COMMANDS)
     ELSE()
       IF(${CURRENT_CMD} STREQUAL "COMPARE_FILES" OR
          ${CURRENT_CMD} STREQUAL "CHECK_FILE_EXIST_IN_ARCHIVE" OR
+         ${CURRENT_CMD} STREQUAL "CHECK_FILE_CONTAINS" OR
          ${CURRENT_CMD} STREQUAL "COMPARE_DIRECTORIES" OR
          ${CURRENT_CMD} STREQUAL "COPY_FILE" OR
          ${CURRENT_CMD} STREQUAL "COPY_DIRECTORY")
@@ -208,7 +219,7 @@ MESSAGE("TEST command: ${CMD}")
 EXECUTE_PROCESS(COMMAND ${CMD}
                 RESULT_VARIABLE CMD_RESULT)
 IF(CMD_RESULT)
-  MESSAGE(FATAL_ERROR "Test error")
+  MESSAGE(FATAL_ERROR "Test error: ${CMD_RESULT}")
 ENDIF()
 
 

doc/contents/dev_signature.md

@@ -130,9 +130,7 @@ Simulator parameters, variables and attributes are declared in the "simulator" p
 ### Simulator parameters {#dev_signature_data_simparams}
 
 Simulator parameters are values provided to each simulator, 
-and are declared using the @if DocIsLaTeX **DECLARE_REQUIRED_PARAMETER** or **DECLARE_USED_PARAMETER**
-@else DECLARE_REQUIRED_PARAMETER or DECLARE_USED_PARAMETER @endif
- instructions.
+and are declared in three blocks: "required", "used" or "produced".
 These instructions takes 3 arguments
 
 * the name of the parameter

resources/CMakeLists.txt

@@ -111,6 +111,15 @@ IF(PYTHON3_EXECUTABLE)
           "${CMAKE_SOURCE_DIR}"
   )
 
+  # import ref wares from repositories
+  ADD_CUSTOM_TARGET(importwares
+                    COMMENT "Copying reference wares from their remote repository"
+                    COMMAND "${PYTHON3_EXECUTABLE}"
+                            "${CMAKE_CURRENT_SOURCE_DIR}/tools/ofsrc-importwares.py"
+                            "${CMAKE_CURRENT_SOURCE_DIR}/tools/wares-to-import.txt"
+                            "${CMAKE_SOURCE_DIR}"
+                    )
+
 ENDIF()
 
 

resources/tests/miscdata/SignatureSerializer/ref_sim.json

@@ -93,6 +93,18 @@
             "description": "coefficient",
             "siunit": "",
             "type": ""
+          },
+          {
+            "name": "coeff 2",
+            "description": "coefficient with a space",
+            "siunit": "",
+            "type": ""
+          },
+          {
+            "name": "coeff&3",
+            "description": "coefficient with weïrd char",
+            "siunit": "",
+            "type": ""
           }
         ]
       },

resources/tests/miscdata/SignatureSerializer/ref_sim_unordered.json

@@ -93,6 +93,18 @@
             "description": "coefficient",
             "siunit": "",
             "type": ""
+          },
+          {
+            "name": "coeff 2",
+            "description": "coefficient with a space",
+            "siunit": "",
+            "type": ""
+          },
+          {
+            "name": "coeff&3",
+            "description": "coefficient with weïrd char",
+            "siunit": "",
+            "type": ""
           }
         ]
       },

resources/tests/miscdata/SignatureSerializer/ref_sim_unordered_array.json

@@ -93,6 +93,18 @@
             "description": "coefficient",
             "siunit": "",
             "type": ""
+          },
+          {
+            "name": "coeff 2",
+            "description": "coefficient with a space",
+            "siunit": "",
+            "type": ""
+          },
+          {
+            "name": "coeff&3",
+            "description": "coefficient with weïrd char",
+            "siunit": "",
+            "type": ""
           }
         ]
       },

resources/tests/miscsrc/wares-dev-201xx/sim/tests.cmdline.sim-migration/CMakeLists.txt

@@ -5,4 +5,8 @@ INCLUDE(CMake.in.config)
 
 FIND_PACKAGE(OpenFLUIDHelpers REQUIRED)
 
+SET(CUSTOM_VAR foo)
+
 OPENFLUID_ADD_SIMULATOR(SIM)
+
+MESSAGE(STATUS "custom message")

resources/tools/importsim.py → resources/tools/ofsrc-importwares.py

@@ -32,13 +32,16 @@
 #  This scripts imports simulators in a destination folder by specifying the git url and branch.
 #  It will then remove all git related files in simualors and potential fragments
 #
-#  Usage: importsim.py /path/to/sims_text_file /path/to/destination_folder
+#  Usage: importwares.py /path/to/sims_text_file /path/to/destination_folder
 #
 #  - sims_text_file: Text file where we specify the simulators to import on each lines of the file.
 #                    A line must be written as follows : 
 #                    GitURL#branch_name clone_folder_name
 #  - /path/to/destination_folder: The destination folder path where all simulators are cloned
 #
+#  When in openfluid root dir: 
+#     `python3 resources/tools/ofsrc-importwares.py resources/tools/wares-to-import.txt .`
+
 ############################################################################
 
 
@@ -82,8 +85,10 @@ def clone_and_clean_repo(file_line, destination_path):
   repo_name = file_line_split[1]
   giturl_split = giturl_branch.split("#")
 
+  print("Processing "+repo_name.split("/")[-1]+"...")
+
   if(len(giturl_split) != 2):
-    print("[ERROR] Wrong file format")
+    print("  [ERROR] Wrong file format")
     return
 
   git_url, git_branch = giturl_split
@@ -92,7 +97,7 @@ def clone_and_clean_repo(file_line, destination_path):
   repo_path = os.path.join(destination_path, repo_name)
 
   if(delete_folder(repo_path)):
-    print(repo_path + " deleted")
+    print("  " + repo_path + " deleted")
 
 
   # Clone repo
@@ -103,10 +108,10 @@ def clone_and_clean_repo(file_line, destination_path):
                   text=True)
 
   if clone_process.returncode != 0:
-    print("[ERROR] Could not clone git repo " + git_url)
+    print("  [ERROR] Could not clone git repo " + git_url)
     return
 
-  print(repo_path + " successfullly cloned")
+  print("  " + repo_path + " successfully cloned")
 
 
   # Checkout branch
@@ -117,10 +122,10 @@ def clone_and_clean_repo(file_line, destination_path):
                    text=True)
 
   if branch_process.returncode != 0:
-    print("[ERROR] Could not checkout branch " + git_branch)
+    print("  [ERROR] Could not checkout branch " + git_branch)
     return
 
-  print(git_branch + " successfullly checkout")
+  print("  " + git_branch + " successfully checkout")
 
   # Update potential submodules
   subprocess.run(["git", "submodule", "update", "--init", "--recursive"],
@@ -131,28 +136,28 @@ def clone_and_clean_repo(file_line, destination_path):
   # Delete versionning files
   git_folder = os.path.join(repo_path, ".git")
   if(delete_folder(git_folder)):
-    print(git_folder + " deleted")
+    print("  " + git_folder + " deleted")
 
   gitignore_file = os.path.join(repo_path, ".gitignore")
   if(delete_file(gitignore_file)):
-    print(gitignore_file + " deleted")
+    print("  " + gitignore_file + " deleted")
 
   # Check for submodules
   git_submodules_file = os.path.join(repo_path, ".gitmodules")
   if(delete_file(git_submodules_file)):
-    print(git_submodules_file + " deleted")
+    print("  " + git_submodules_file + " deleted")
 
     # Loop through fragments
     fragments_path = os.path.join(repo_path, "src", "fragments")
     if(os.path.exists(fragments_path) and os.path.isdir(fragments_path)):
       for fragment in os.listdir(fragments_path):
         fragment_git_file = os.path.join(fragments_path, fragment, ".git")
         if(delete_file(fragment_git_file)):
-          print(fragment_git_file + " deleted")
+          print("  " + fragment_git_file + " deleted")
 
         fragment_gitignore_file = os.path.join(fragments_path, fragment, ".gitignore")
         if(delete_file(fragment_gitignore_file)):
-          print(fragment_gitignore_file + " deleted")
+          print("  " + fragment_gitignore_file + " deleted")
 
 
 # ===========================================================

resources/tools/ofsrc-stylecheck.py

@@ -382,15 +382,16 @@ def checkHeaderGuard(self, Filename, Content):
 
                     ExpectedGuardName = '__OPENFLUID_'+MiddlePart+LastPart+'__'
 
-
         if ExpectedGuardName:
-            Result = re.search( r'#ifndef '+re.escape(ExpectedGuardName)+'\s*\n#define '+re.escape(ExpectedGuardName), Content)
-            if not Result:
-                self.addProblem('HGRD',Filename,1,'missing or malformed header guard definition (expected',ExpectedGuardName+')')
-
-            Result = re.search( r'#endif /\* '+re.escape(ExpectedGuardName)+ r' \*/\s*\n', Content)
-            if not Result:
-                self.addProblem('HGRD',Filename,1,'missing or malformed header guard closing')
+            ResultPragma = re.search( r'#pragma once', Content)
+            if not ResultPragma:
+                Result = re.search( r'#ifndef '+re.escape(ExpectedGuardName)+'\s*\n#define '+re.escape(ExpectedGuardName), Content)
+                if not Result:
+                    self.addProblem('HGRD',Filename,1,'missing or malformed header guard definition (expected',ExpectedGuardName+')')
+
+                Result = re.search( r'#endif /\* '+re.escape(ExpectedGuardName)+ r' \*/\s*\n', Content)
+                if not Result:
+                    self.addProblem('HGRD',Filename,1,'missing or malformed header guard closing')
 
 
 

resources/tools/wares-to-import.txt

@@ -0,0 +1,8 @@
+https://hub.openfluid-project.org/git-service/wares/simulators/water.surf.transfer-su.hayami#openfluid-2.2 examples/wares-dev/simulators/water.surf.transfer-su.hayami
+https://hub.openfluid-project.org/git-service/wares/simulators/water.surf.transfer-rs.hayami#openfluid-2.2 examples/wares-dev/simulators/water.surf.transfer-rs.hayami
+https://hub.openfluid-project.org/git-service/wares/simulators/water.atm-surf.rain-su.files#openfluid-2.2 examples/wares-dev/simulators/water.atm-surf.rain-su.files
+https://hub.openfluid-project.org/git-service/wares/simulators/water.surf-uz.runoff-infiltration.mseytoux#openfluid-2.2 examples/wares-dev/simulators/water.surf-uz.runoff-infiltration.mseytoux
+https://hub.openfluid-project.org/git-service/wares/observers/export.vars.files.csv#openfluid-2.2 src/observers/export.vars.files.csv
+https://hub.openfluid-project.org/git-service/wares/observers/export.vars.files.csv-multicols#openfluid-2.2 src/observers/export.vars.files.csv-multicols
+https://hub.openfluid-project.org/git-service/wares/observers/export.vars.files.kml-plot#openfluid-2.2 src/observers/export.vars.files.kml-plot
+https://hub.openfluid-project.org/git-service/wares/observers/export.vars.files.kml-anim#openfluid-2.2 src/observers/export.vars.files.kml-anim

share/openfluid/waresdev/cmake.syntaxhl.ofdev.xml

@@ -483,7 +483,7 @@
           <pattern value="\'[^\']*\'" />
         </rule>
 
-        <rule name="comment" style="comment">
+        <rule name="comment-singleline" style="comment">
           <pattern value="#.*$" />
         </rule>