MNT: fix linting with cpplint 2.0.0

CPPLINT.cfg

@@ -16,6 +16,8 @@ filter=-whitespace/comma  # 6027 errors
 filter=-whitespace/comments  # 881 errors
 filter=-whitespace/operators  # 5240 errors
 filter=-whitespace/parens  # 413 error
+filter=-whitespace/newline
+filter=-whitespace/indent_namespace
 filter=-readability/multiline_string
 filter=-build/include_subdir  # 296 errors
 #filter=-whitespace/end_of_line

src/dataBlock/dataBlock.cpp

@@ -6,6 +6,8 @@
 // ***********************************************************************************
 
 #include <algorithm>
+#include <memory>
+#include <string>
 #include "idefix.hpp"
 #include "dataBlock.hpp"
 #include "fluid.hpp"

src/dataBlock/dataBlock.hpp

@@ -12,6 +12,7 @@
 #include <string>
 #include <map>
 #include <memory>
+#include <cstdio>
 
 #include "idefix.hpp"
 #include "grid.hpp"

src/dataBlock/dataBlockHost.cpp

@@ -5,6 +5,7 @@
 // Licensed under CeCILL 2.1 License, see COPYING for more information
 // ***********************************************************************************
 
+#include <vector>
 #include "idefix.hpp"
 #include "dataBlockHost.hpp"
 #include "fluid.hpp"

src/dataBlock/dumpToFile.cpp

@@ -5,6 +5,8 @@
 // Licensed under CeCILL 2.1 License, see COPYING for more information
 // ***********************************************************************************
 
+#include <string>
+#include <cstdio>
 #include "../idefix.hpp"
 #include "dataBlock.hpp"
 #include "version.hpp"

src/fluid/boundary/axis.cpp

@@ -5,6 +5,7 @@
 // Licensed under CeCILL 2.1 License, see COPYING for more information
 // ***********************************************************************************
 
+#include <vector>
 #include "axis.hpp"
 #include "boundary.hpp"
 

src/fluid/checkNan.hpp

@@ -7,6 +7,7 @@
 
 #ifndef FLUID_CHECKNAN_HPP_
 #define FLUID_CHECKNAN_HPP_
+#include <iostream>
 #include "dataBlock.hpp"
 #include "dataBlockHost.hpp"
 #include "fluid.hpp"

src/global.cpp

@@ -5,6 +5,7 @@
 // Licensed under CeCILL 2.1 License, see COPYING for more information
 // ***********************************************************************************
 
+#include <iostream>
 #include <string>
 #include <sstream>
 #include "idefix.hpp"

src/global.hpp

@@ -7,6 +7,7 @@
 
 #ifndef GLOBAL_HPP_
 #define GLOBAL_HPP_
+#include <iostream>
 #include <string>
 #include <vector>
 #include "arrays.hpp"

src/idefix.hpp

@@ -9,6 +9,7 @@
 #define IDEFIX_HPP_
 #include <fstream>
 #include <iostream>
+#include <cstdio>
 #include <Kokkos_Core.hpp>
 // #include <Kokkos_DualView.hpp> // do we still need this?
 #ifdef WITH_MPI

src/macros.hpp

@@ -10,6 +10,7 @@
 #ifndef MACROS_HPP_
 #define MACROS_HPP_
 
+#include <cstdio>
 
 #if COMPONENTS == 1
   #define EXPAND(a,b,c) a

src/main.cpp

@@ -23,6 +23,7 @@
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
+#include <string>
 
 #include <Kokkos_Core.hpp>
 

src/mpi.cpp

@@ -12,6 +12,7 @@
 #include <chrono>   // NOLINT [build/c++11]
 #include <thread>  // NOLINT [build/c++11]
 #include <utility>
+#include <vector>
 #include "idefix.hpp"
 #include "dataBlock.hpp"
 

src/output/dump.cpp

@@ -8,7 +8,7 @@
 #include <algorithm>
 #include <unordered_set>
 #if __has_include(<filesystem>)
-  #include <filesystem>
+  #include <filesystem> // NOLINT [build/c++17]
   namespace fs = std::filesystem;
 #elif __has_include(<experimental/filesystem>)
   #include <experimental/filesystem>
@@ -17,6 +17,8 @@
   #error "Missing the <filesystem> header."
 #endif
 #include <iomanip>
+#include <string>
+#include <cstdio>
 #include "dump.hpp"
 #include "version.hpp"
 #include "dataBlockHost.hpp"

src/output/dump.hpp

@@ -11,7 +11,7 @@
 #include <map>
 #include <array>
 #if __has_include(<filesystem>)
-  #include <filesystem>
+  #include <filesystem> // NOLINT [build/c++17]
   namespace fs = std::filesystem;
 #elif __has_include(<experimental/filesystem>)
   #include <experimental/filesystem>

src/output/output.cpp

@@ -5,6 +5,7 @@
 // Licensed under CeCILL 2.1 License, see COPYING for more information
 // ***********************************************************************************
 
+#include <string>
 #include "output.hpp"
 #include "dataBlock.hpp"
 #include "fluid.hpp"

src/output/slice.cpp

@@ -7,6 +7,7 @@
 
 #include <string>
 #include <map>
+#include <memory>
 #include "slice.hpp"
 #include "input.hpp"
 #include "physics.hpp"

src/output/vtk.cpp

@@ -8,10 +8,11 @@
 #include "vtk.hpp"
 #include <limits.h>
 #include <string>
+#include <cstdio>
 #include <sstream>
 #include <iomanip>
 #if __has_include(<filesystem>)
-  #include <filesystem>
+  #include <filesystem> // NOLINT [build/c++17]
   namespace fs = std::filesystem;
 #elif __has_include(<experimental/filesystem>)
   #include <experimental/filesystem>

src/output/vtk.hpp

@@ -10,14 +10,15 @@
 #include <string>
 #include <map>
 #if __has_include(<filesystem>)
-  #include <filesystem>
+  #include <filesystem> // NOLINT [build/c++17]
   namespace fs = std::filesystem;
 #elif __has_include(<experimental/filesystem>)
   #include <experimental/filesystem>
   namespace fs = std::experimental::filesystem;
 #else
   error "Missing the <filesystem> header."
 #endif
+#include <cstdio>
 #include "idefix.hpp"
 #include "input.hpp"
 #include "dataBlock.hpp"

src/output/xdmf.hpp

@@ -8,7 +8,15 @@
 #ifndef OUTPUT_XDMF_HPP_
 #define OUTPUT_XDMF_HPP_
 #include <string>
-#include <filesystem>
+#if __has_include(<filesystem>)
+  #include <filesystem> // NOLINT [build/c++17]
+  namespace fs = std::filesystem;
+#elif __has_include(<experimental/filesystem>)
+  #include <experimental/filesystem>
+  namespace fs = std::experimental::filesystem;
+#else
+  error "Missing the <filesystem> header."
+#endif
 #include <map>
 #include "idefix.hpp"
 #include "input.hpp"

src/utils/dumpImage.cpp

@@ -5,6 +5,8 @@
 // Licensed under CeCILL 2.1 License, see COPYING for more information
 // ***********************************************************************************
 
+#include <string>
+#include <cstdio>
 #include "dumpImage.hpp"
 #include "dataBlock.hpp"
 #include "idefix.hpp"

src/utils/npy.hpp

@@ -34,6 +34,7 @@
 #include <sstream>
 #include <cstdint>
 #include <cstring>
+#include <cstdio>
 #include <array>
 #include <vector>
 #include <stdexcept>