From c19f3573aeda15f5e016183cc3ef2aa628d7f592 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Fri, 11 Oct 2024 18:35:35 +0200
Subject: [PATCH 1/3] STY: add missing `#include` directives reported by
 cpplint 2.0.0

---
 src/dataBlock/dataBlock.cpp     | 2 ++
 src/dataBlock/dataBlock.hpp     | 1 +
 src/dataBlock/dataBlockHost.cpp | 1 +
 src/dataBlock/dumpToFile.cpp    | 2 ++
 src/fluid/boundary/axis.cpp     | 1 +
 src/fluid/checkNan.hpp          | 1 +
 src/global.cpp                  | 1 +
 src/global.hpp                  | 1 +
 src/idefix.hpp                  | 1 +
 src/macros.hpp                  | 1 +
 src/main.cpp                    | 1 +
 src/mpi.cpp                     | 1 +
 src/output/dump.cpp             | 2 ++
 src/output/output.cpp           | 1 +
 src/output/slice.cpp            | 1 +
 src/output/vtk.cpp              | 1 +
 src/output/vtk.hpp              | 1 +
 src/utils/dumpImage.cpp         | 2 ++
 src/utils/npy.hpp               | 1 +
 19 files changed, 23 insertions(+)

diff --git a/src/dataBlock/dataBlock.cpp b/src/dataBlock/dataBlock.cpp
index c0648f92..81874cef 100644
--- a/src/dataBlock/dataBlock.cpp
+++ b/src/dataBlock/dataBlock.cpp
@@ -6,6 +6,8 @@
 // ***********************************************************************************
 
 #include <algorithm>
+#include <memory>
+#include <string>
 #include "idefix.hpp"
 #include "dataBlock.hpp"
 #include "fluid.hpp"
diff --git a/src/dataBlock/dataBlock.hpp b/src/dataBlock/dataBlock.hpp
index 12f0847e..89b745fa 100644
--- a/src/dataBlock/dataBlock.hpp
+++ b/src/dataBlock/dataBlock.hpp
@@ -12,6 +12,7 @@
 #include <string>
 #include <map>
 #include <memory>
+#include <cstdio>
 
 #include "idefix.hpp"
 #include "grid.hpp"
diff --git a/src/dataBlock/dataBlockHost.cpp b/src/dataBlock/dataBlockHost.cpp
index ca26e5cb..b5dff915 100644
--- a/src/dataBlock/dataBlockHost.cpp
+++ b/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"
diff --git a/src/dataBlock/dumpToFile.cpp b/src/dataBlock/dumpToFile.cpp
index 9980d09c..98b4a474 100644
--- a/src/dataBlock/dumpToFile.cpp
+++ b/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"
diff --git a/src/fluid/boundary/axis.cpp b/src/fluid/boundary/axis.cpp
index ead51f4f..b77fe3b5 100644
--- a/src/fluid/boundary/axis.cpp
+++ b/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"
 
diff --git a/src/fluid/checkNan.hpp b/src/fluid/checkNan.hpp
index 71911c58..88e206e5 100644
--- a/src/fluid/checkNan.hpp
+++ b/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"
diff --git a/src/global.cpp b/src/global.cpp
index 1e9c11ee..4d9499d9 100644
--- a/src/global.cpp
+++ b/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"
diff --git a/src/global.hpp b/src/global.hpp
index 47fca42e..8651f974 100644
--- a/src/global.hpp
+++ b/src/global.hpp
@@ -7,6 +7,7 @@
 
 #ifndef GLOBAL_HPP_
 #define GLOBAL_HPP_
+#include <iostream>
 #include <string>
 #include <vector>
 #include "arrays.hpp"
diff --git a/src/idefix.hpp b/src/idefix.hpp
index a44bf4c2..f547c5d7 100644
--- a/src/idefix.hpp
+++ b/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
diff --git a/src/macros.hpp b/src/macros.hpp
index 9a484c3d..2c7bda12 100644
--- a/src/macros.hpp
+++ b/src/macros.hpp
@@ -10,6 +10,7 @@
 #ifndef MACROS_HPP_
 #define MACROS_HPP_
 
+#include <cstdio>
 
 #if COMPONENTS == 1
   #define EXPAND(a,b,c) a
diff --git a/src/main.cpp b/src/main.cpp
index 5a7f6f73..c242ccef 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -23,6 +23,7 @@
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
+#include <string>
 
 #include <Kokkos_Core.hpp>
 
diff --git a/src/mpi.cpp b/src/mpi.cpp
index ee2fdb5c..d25056fa 100644
--- a/src/mpi.cpp
+++ b/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"
 
diff --git a/src/output/dump.cpp b/src/output/dump.cpp
index 5a27ecc2..7aa853d6 100644
--- a/src/output/dump.cpp
+++ b/src/output/dump.cpp
@@ -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"
diff --git a/src/output/output.cpp b/src/output/output.cpp
index 30a85039..658e1cdd 100644
--- a/src/output/output.cpp
+++ b/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"
diff --git a/src/output/slice.cpp b/src/output/slice.cpp
index 3f971932..98caa5c2 100644
--- a/src/output/slice.cpp
+++ b/src/output/slice.cpp
@@ -7,6 +7,7 @@
 
 #include <string>
 #include <map>
+#include <memory>
 #include "slice.hpp"
 #include "input.hpp"
 #include "physics.hpp"
diff --git a/src/output/vtk.cpp b/src/output/vtk.cpp
index 559f00c8..6db50255 100644
--- a/src/output/vtk.cpp
+++ b/src/output/vtk.cpp
@@ -8,6 +8,7 @@
 #include "vtk.hpp"
 #include <limits.h>
 #include <string>
+#include <cstdio>
 #include <sstream>
 #include <iomanip>
 #if __has_include(<filesystem>)
diff --git a/src/output/vtk.hpp b/src/output/vtk.hpp
index 4857f19d..7438678c 100644
--- a/src/output/vtk.hpp
+++ b/src/output/vtk.hpp
@@ -18,6 +18,7 @@
 #else
   error "Missing the <filesystem> header."
 #endif
+#include <cstdio>
 #include "idefix.hpp"
 #include "input.hpp"
 #include "dataBlock.hpp"
diff --git a/src/utils/dumpImage.cpp b/src/utils/dumpImage.cpp
index 03a456e1..04f413a7 100644
--- a/src/utils/dumpImage.cpp
+++ b/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"
diff --git a/src/utils/npy.hpp b/src/utils/npy.hpp
index 34b7c724..edae82ee 100644
--- a/src/utils/npy.hpp
+++ b/src/utils/npy.hpp
@@ -34,6 +34,7 @@
 #include <sstream>
 #include <cstdint>
 #include <cstring>
+#include <cstdio>
 #include <array>
 #include <vector>
 #include <stdexcept>

From 3ba6b71edacc30f7990b69615889df99d3a128dc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Fri, 11 Oct 2024 18:36:14 +0200
Subject: [PATCH 2/3] STY: ignore whitespace linting rule violations (new in
 cpplint 2.0.0)

---
 CPPLINT.cfg | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CPPLINT.cfg b/CPPLINT.cfg
index 4f3e42cb..b02d056c 100644
--- a/CPPLINT.cfg
+++ b/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

From 6a4f395a134cd5501ff3ac596fe7c932ea0c61dd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Robert?= <cr52@protonmail.com>
Date: Fri, 11 Oct 2024 18:39:21 +0200
Subject: [PATCH 3/3] RFC: fix rogue `#include <filesystem>` and locally
 disable linting around it

---
 src/output/dump.cpp |  2 +-
 src/output/dump.hpp |  2 +-
 src/output/vtk.cpp  |  2 +-
 src/output/vtk.hpp  |  2 +-
 src/output/xdmf.hpp | 10 +++++++++-
 5 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/output/dump.cpp b/src/output/dump.cpp
index 7aa853d6..77a8d88d 100644
--- a/src/output/dump.cpp
+++ b/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>
diff --git a/src/output/dump.hpp b/src/output/dump.hpp
index a9a52554..d823ddca 100644
--- a/src/output/dump.hpp
+++ b/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>
diff --git a/src/output/vtk.cpp b/src/output/vtk.cpp
index 6db50255..56562109 100644
--- a/src/output/vtk.cpp
+++ b/src/output/vtk.cpp
@@ -12,7 +12,7 @@
 #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>
diff --git a/src/output/vtk.hpp b/src/output/vtk.hpp
index 7438678c..31557320 100644
--- a/src/output/vtk.hpp
+++ b/src/output/vtk.hpp
@@ -10,7 +10,7 @@
 #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>
diff --git a/src/output/xdmf.hpp b/src/output/xdmf.hpp
index b2fb6628..6c6fc15c 100644
--- a/src/output/xdmf.hpp
+++ b/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"