Merge branch 'hotfix/0.24.1'

CHANGELOG.md

@@ -7,6 +7,13 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.24.1] - 2021-04-06
+### Fixed
+- Periodic halo for HEALPix mesh
+- General warnings and suggestions by DeepCode bot
+- Compilation problems with clang 3.8
+
+
 ## [0.24.0] - 2021-03-19
 ### Fixed
 - Fixed hang in band distribution for L160000x8000 grid
@@ -273,6 +280,7 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 ## 0.13.0 - 2018-02-16
 
 [Unreleased]: https://github.com/ecmwf/atlas/compare/master...develop
+[0.24.1]: https://github.com/ecmwf/atlas/compare/0.24.0...0.24.1
 [0.24.0]: https://github.com/ecmwf/atlas/compare/0.23.0...0.24.0
 [0.23.0]: https://github.com/ecmwf/atlas/compare/0.22.1...0.23.0
 [0.22.1]: https://github.com/ecmwf/atlas/compare/0.22.0...0.22.1

README.md

@@ -5,6 +5,7 @@ Atlas
 [![travis master](https://img.shields.io/travis/ecmwf/atlas/master.svg?label=master&logo=travis)](http://travis-ci.org/ecmwf/atlas "master")
 [![travis develop](https://img.shields.io/travis/ecmwf/atlas/develop.svg?label=develop&logo=travis)](http://travis-ci.org/ecmwf/atlas "develop")
 [![codecov](https://codecov.io/gh/ecmwf/atlas/branch/develop/graph/badge.svg)](https://codecov.io/gh/ecmwf/atlas)
+[![deepcode](https://www.deepcode.ai/api/gh/badge?key=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJwbGF0Zm9ybTEiOiJnaCIsIm93bmVyMSI6ImVjbXdmIiwicmVwbzEiOiJhdGxhcyIsImluY2x1ZGVMaW50IjpmYWxzZSwiYXV0aG9ySWQiOjI4NzA4LCJpYXQiOjE2MTc3MDk0NjR9.dzPznp_XHjk1qD3h--C0wFBJg0EA_dYYtFQWPS69p8k)](https://www.deepcode.ai/app/gh/ecmwf/atlas/_/dashboard?utm_content=gh%2Fecmwf%2Fatlas)
 
 Project home: https://confluence.ecmwf.int/display/ATLAS  
 Contact: Willem Deconinck ([email protected])  

VERSION

@@ -1 +1 @@
-0.24.0
+0.24.1

src/apps/atlas-meshgen.cc

@@ -274,7 +274,7 @@ int Meshgen2Gmsh::execute( const Args& args ) {
     catch ( eckit::Exception& e ) {
         Log::error() << e.what() << std::endl;
         Log::error() << e.callStack() << std::endl;
-        throw e;
+        throw;
     }
 
     if ( grid.projection().units() == "degrees" ) {

src/atlas/domain/detail/Domain.cc

@@ -46,18 +46,18 @@ const Domain* atlas__Domain__ctor_config( const eckit::Parametrisation* config )
 void atlas__Domain__type( const Domain* This, char*& type, int& size ) {
     ATLAS_ASSERT( This != nullptr, "Cannot access uninitialised atlas_Domain" );
     std::string s = This->type();
-    size          = static_cast<int>( s.size() + 1 );
-    type          = new char[size];
-    strcpy( type, s.c_str() );
+    size          = static_cast<int>( s.size() );
+    type          = new char[size + 1];
+    std::strncpy( type, s.c_str(), size + 1 );
 }
 void atlas__Domain__hash( const Domain* This, char*& hash, int& size ) {
     ATLAS_ASSERT( This != nullptr, "Cannot access uninitialised atlas_Domain" );
     eckit::MD5 md5;
     This->hash( md5 );
     std::string s = md5.digest();
-    size          = static_cast<int>( s.size() + 1 );
-    hash          = new char[size];
-    strcpy( hash, s.c_str() );
+    size          = static_cast<int>( s.size() );
+    hash          = new char[size + 1 ];
+    std::strncpy( hash, s.c_str(), size + 1 );
 }
 Domain::Spec* atlas__Domain__spec( const Domain* This ) {
     ATLAS_ASSERT( This != nullptr, "Cannot access uninitialised atlas_Domain" );

src/atlas/domain/detail/RectangularDomain.h

@@ -52,7 +52,10 @@ class RectangularDomain : public Domain {
     virtual bool global() const override { return global_; }
     bool zonal_band() const { return is_zonal_band( {xmin_, xmax_}, units_ ); }
 
-    virtual bool empty() const override { return ( xmin_ == xmax_ ) or ( ymin_ == ymax_ ); }
+    virtual bool empty() const override {
+        //  deepcode ignore FloatingPointEquals: We want exact comparison
+        return ( xmin_ == xmax_ ) or ( ymin_ == ymax_ );
+    }
 
     virtual Spec spec() const override;
 

src/atlas/field/FieldCreator.cc

@@ -8,6 +8,8 @@
  * nor does it submit to any jurisdiction.
  */
 
+// file deepcode ignore CppMemoryLeak: static pointers for global registry are OK and will be cleaned up at end
+
 #include "atlas/field/FieldCreator.h"
 
 #include <map>

src/atlas/field/State.cc

@@ -8,6 +8,8 @@
  * nor does it submit to any jurisdiction.
  */
 
+// file deepcode ignore CppMemoryLeak: static pointers for global registry are OK and will be cleaned up at end
+
 #include "atlas/field/State.h"
 
 #include <iomanip>

src/atlas/field/detail/FieldInterface.cc

@@ -104,9 +104,9 @@ const char* atlas__Field__name( FieldImpl* This ) {
 void atlas__Field__datatype( FieldImpl* This, char*& datatype, int& size, int& allocated ) {
     ATLAS_ASSERT( This != nullptr, "Cannot access datatype of uninitialised atlas_Field" );
     std::string s = This->datatype().str();
-    size          = s.size() + 1;
-    datatype      = new char[size];
-    strcpy( datatype, s.c_str() );
+    size          = static_cast<int>( s.size() );
+    datatype      = new char[size + 1];
+    std::strncpy( datatype, s.c_str(), size + 1 );
     allocated = true;
 }
 

src/atlas/functionspace/CellColumns.cc

@@ -741,10 +741,10 @@ void atlas__fs__CellColumns__checksum_fieldset( const CellColumns* This, const f
     ATLAS_ASSERT( This );
     ATLAS_ASSERT( fieldset );
     std::string checksum_str( This->checksum( fieldset ) );
-    size      = checksum_str.size();
+    size      = static_cast<int>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 
 // -----------------------------------------------------------------------------------
@@ -754,10 +754,10 @@ void atlas__fs__CellColumns__checksum_field( const CellColumns* This, const fiel
     ATLAS_ASSERT( This );
     ATLAS_ASSERT( field );
     std::string checksum_str( This->checksum( field ) );
-    size      = checksum_str.size();
+    size      = static_cast<int>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 }
 

src/atlas/functionspace/EdgeColumns.cc

@@ -740,10 +740,10 @@ void atlas__fs__EdgeColumns__checksum_fieldset( const EdgeColumns* This, const f
     ATLAS_ASSERT( This );
     ATLAS_ASSERT( fieldset );
     std::string checksum_str( This->checksum( fieldset ) );
-    size      = checksum_str.size();
+    size      = static_cast<int>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 
 // -----------------------------------------------------------------------------------
@@ -753,10 +753,10 @@ void atlas__fs__EdgeColumns__checksum_field( const EdgeColumns* This, const fiel
     ATLAS_ASSERT( This );
     ATLAS_ASSERT( field );
     std::string checksum_str( This->checksum( field ) );
-    size      = checksum_str.size();
+    size      = static_cast<int>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 }
 

src/atlas/functionspace/detail/FunctionSpaceInterface.cc

@@ -36,9 +36,9 @@ void atlas__FunctionSpace__delete( FunctionSpaceImpl* This ) {
 void atlas__FunctionSpace__name( const FunctionSpaceImpl* This, char*& name, int& size ) {
     ATLAS_ASSERT( This != nullptr, "Cannot access uninitialised atlas_FunctionSpace" );
     std::string s = This->type();
-    size          = static_cast<int>( s.size() + 1 );
-    name          = new char[size];
-    strcpy( name, s.c_str() );
+    size          = static_cast<int>( s.size() );
+    name          = new char[size + 1];
+    std::strncpy( name, s.c_str(), size + 1 );
 }
 
 field::FieldImpl* atlas__FunctionSpace__create_field( const FunctionSpaceImpl* This,

src/atlas/functionspace/detail/NodeColumnsInterface.cc

@@ -131,21 +131,21 @@ void atlas__NodesFunctionSpace__checksum_fieldset( const NodeColumns* This, cons
     ATLAS_ASSERT( This != nullptr, "Cannot access uninitialised atlas_functionspace_NodeColumns" );
     ATLAS_ASSERT( fieldset != nullptr, "Cannot access uninitialised atlas_FieldSet" );
     std::string checksum_str( This->checksum( fieldset ) );
-    size      = checksum_str.size();
+    size      = static_cast<int>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 
 void atlas__NodesFunctionSpace__checksum_field( const NodeColumns* This, const field::FieldImpl* field, char*& checksum,
                                                 int& size, int& allocated ) {
     ATLAS_ASSERT( This != nullptr, "Cannot access uninitialised atlas_functionspace_NodeColumns" );
     ATLAS_ASSERT( field != nullptr, "Cannot access uninitialised atlas_Field" );
     std::string checksum_str( This->checksum( field ) );
-    size      = checksum_str.size();
+    size      = static_cast<int>(checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 
 void atlas__NodesFunctionSpace__sum_double( const NodeColumns* This, const field::FieldImpl* field, double& sum,

src/atlas/functionspace/detail/StructuredColumnsInterface.cc

@@ -120,7 +120,7 @@ void atlas__fs__StructuredColumns__checksum_fieldset( const detail::StructuredCo
     size      = static_cast<idx_t>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1);
 }
 
 void atlas__fs__StructuredColumns__checksum_field( const detail::StructuredColumns* This, const field::FieldImpl* field,
@@ -131,7 +131,7 @@ void atlas__fs__StructuredColumns__checksum_field( const detail::StructuredColum
     size      = static_cast<idx_t>( checksum_str.size() );
     checksum  = new char[size + 1];
     allocated = true;
-    strcpy( checksum, checksum_str.c_str() );
+    std::strncpy( checksum, checksum_str.c_str(), size + 1 );
 }
 
 void atlas__fs__StructuredColumns__index_host( const detail::StructuredColumns* This, idx_t*& data, idx_t& i_min,

src/atlas/grid/StructuredPartitionPolygon.cc

@@ -8,6 +8,8 @@
  * nor does it submit to any jurisdiction.
  */
 
+// file deepcode ignore MissingOpenCheckOnFile: False positive
+
 #include "atlas/grid/StructuredPartitionPolygon.h"
 
 #include <fstream>
@@ -339,7 +341,7 @@ void StructuredPartitionPolygon::outputPythonScript( const eckit::PathName& file
         // clang-format off
         if ( mpi_rank == r ) {
             std::ofstream f( filepath.asString().c_str(), mpi_rank == 0 ? std::ios::trunc : std::ios::app );
-
+            ATLAS_ASSERT( f.is_open() );
             if ( mpi_rank == 0 ) {
                 f << "\n" "import sys"
                      "\n"

src/atlas/grid/detail/grid/Grid.cc

@@ -162,9 +162,9 @@ void atlas__grid__Grid__uid( const Grid* This, char*& uid, int& size ) {
     eckit::MD5 md5;
     This->hash( md5 );
     std::string s = This->uid();
-    size          = static_cast<int>( s.size() + 1 );
-    uid           = new char[size];
-    strcpy( uid, s.c_str() );
+    size          = static_cast<int>( s.size() );
+    uid           = new char[size + 1];
+    std::strncpy( uid, s.c_str(), size + 1 );
 }
 
 Grid::Domain::Implementation* atlas__grid__Grid__lonlat_bounding_box( const Grid* This ) {

src/atlas/grid/detail/grid/GridBuilder.cc

@@ -8,6 +8,8 @@
  * nor does it submit to any jurisdiction.
  */
 
+// file deepcode ignore CppMemoryLeak: static pointers for global registry are OK and will be cleaned up at end
+
 #include "GridBuilder.h"
 
 #include <regex.h>

src/atlas/grid/detail/partitioner/Partitioner.cc

@@ -8,6 +8,8 @@
  * nor does it submit to any jurisdiction.
  */
 
+// file deepcode ignore CppMemoryLeak: static pointers for global registry are OK and will be cleaned up at end
+
 #include "atlas/grid/detail/partitioner/Partitioner.h"
 
 #include <map>

src/atlas/grid/detail/spacing/LinearSpacing.cc

@@ -85,6 +85,7 @@ void LinearSpacing::setup( double start, double end, long N, bool endpoint ) {
 
     double step;
     volatile double _N = N;  // volatile keyword prevents agressive optimization by Cray compiler
+    //  deepcode ignore FloatingPointEquals: Expect possible bit-identical start and end
     if ( start == end ) {
         step = 0.;
     }

src/atlas/io/Exceptions.cc

@@ -80,12 +80,12 @@ NotDecodable::NotDecodable( const std::string& type_name ) :
 
 //---------------------------------------------------------------------------------------------------------------------
 
-Exception::~Exception() {}
-NotEncodable::~NotEncodable() {}
-NotDecodable::~NotDecodable() {}
-InvalidRecord::~InvalidRecord() {}
-DataCorruption::~DataCorruption() {}
-WriteError::~WriteError() {}
+Exception::~Exception() = default;
+NotEncodable::~NotEncodable() = default;
+NotDecodable::~NotDecodable() = default;
+InvalidRecord::~InvalidRecord() = default;
+DataCorruption::~DataCorruption() = default;
+WriteError::~WriteError() = default;
 
 //---------------------------------------------------------------------------------------------------------------------
 

src/atlas/io/Record.cc

@@ -73,7 +73,7 @@ std::string Record::URI::str() const {
 
 Record::Record() : record_( new ParsedRecord() ) {}
 
-Record::Record( const Record& other ) : record_( other.record_ ) {}
+Record::Record( const Record& other ) = default;
 
 //---------------------------------------------------------------------------------------------------------------------
 

src/atlas/io/Stream.cc

@@ -25,7 +25,7 @@ Stream::Stream( eckit::DataHandle* datahandle ) : shared_( datahandle ), ptr_( s
 
 Stream::Stream( std::shared_ptr<eckit::DataHandle> datahandle ) : shared_( datahandle ), ptr_( shared_.get() ) {}
 
-Stream::Stream( const Stream& other ) : shared_( other.shared_ ), ptr_( other.ptr_ ) {}
+Stream::Stream( const Stream& other ) = default;
 
 eckit::DataHandle& Stream::datahandle() {
     ATLAS_ASSERT( ptr_ != nullptr );

src/atlas/io/detail/Base64.cc

@@ -48,8 +48,9 @@ std::string Base64::encode( const void* data, size_t len ) {
 
     size_t out_len = 4 * ( ( len + 2 ) / 3 ); /* 3-byte blocks to 4-byte */
 
-    if ( out_len < len )
+    if ( out_len < len ) {
         return std::string(); /* integer overflow */
+    }
 
     std::string str;
     str.resize( out_len );

src/atlas/io/detail/StaticAssert.h

@@ -9,7 +9,18 @@
  */
 
 #pragma once
-#ifndef __clang_analyzer__
+
+#ifndef ATLAS_IO_STATIC_ASSERT
+#if defined(__clang_analyzer__)
+#define ATLAS_IO_STATIC_ASSERT 0
+#elif defined(__clang__) && (__clang_major__ < 4)
+#define ATLAS_IO_STATIC_ASSERT 0
+#else
+#define ATLAS_IO_STATIC_ASSERT 1
+#endif
+#endif
+
+#if ATLAS_IO_STATIC_ASSERT
 
 #include <cstdlib>
 #include "atlas/io/detail/TypeTraits.h"

src/atlas/io/detail/Time.cc

@@ -35,8 +35,8 @@ inline _put_time<CharT> put_time( const std::tm* time, const CharT* fmt ) {
 
 template <typename CharT, typename Traits>
 std::basic_ostream<CharT, Traits>& operator<<( std::basic_ostream<CharT, Traits>& os, _put_time<CharT> f ) {
-    typedef typename std::ostreambuf_iterator<CharT, Traits> Iter;
-    typedef std::time_put<CharT, Iter> TimePut;
+    using Iter    = typename std::ostreambuf_iterator<CharT, Traits>;
+    using TimePut = std::time_put<CharT, Iter>;
 
     const CharT* const fmt_end = f.fmt + Traits::length( f.fmt );
     const TimePut& mp          = std::use_facet<TimePut>( os.getloc() );

src/atlas/mesh/Connectivity.h

@@ -213,7 +213,7 @@ class IrregularConnectivityImpl {
 
     /// @brief Rename this Connectivity
     void rename( const std::string& name ) {
-        strncpy( name_, name.c_str(), std::max( name.size(), MAX_STRING_SIZE() ) );
+        std::strncpy( name_, name.c_str(), std::max( name.size(), MAX_STRING_SIZE() ) );
     }
 
     /// @brief Number of rows in the connectivity table

src/atlas/mesh/Nodes.cc

@@ -249,7 +249,7 @@ void atlas__mesh__Nodes__str( Nodes* This, char*& str, int& size ) {
     std::string s = ss.str();
     size          = static_cast<int>( s.size() );
     str           = new char[size + 1];
-    strcpy( str, s.c_str() );
+    std::strncpy( str, s.c_str(), size + 1 );
 }
 
 IrregularConnectivity* atlas__mesh__Nodes__edge_connectivity( Nodes* This ) {

src/atlas/mesh/PartitionPolygon.cc

@@ -11,6 +11,8 @@
 #include <fstream>
 #include <sstream>
 
+#include "eckit/exception/Exceptions.h"
+
 #include "atlas/array/MakeView.h"
 #include "atlas/field/Field.h"
 #include "atlas/mesh.h"
@@ -112,6 +114,9 @@ void PartitionPolygon::outputPythonScript( const eckit::PathName& filepath, cons
     for ( int r = 0; r < mpi_size; ++r ) {
         if ( mpi_rank == r ) {
             std::ofstream f( filepath.asString().c_str(), mpi_rank == 0 ? std::ios::trunc : std::ios::app );
+            if( !f.is_open() ) {
+                throw eckit::CantOpenFile(filepath);
+            }
             //clang-format off
             if ( mpi_rank == 0 ) {
                 f << "\n"