Issue #40/increase warning level on build (#51)

* make releases as draft, to be manually published

* fix tnt

* fix RbtAtom warnings

* fix RbtError.h reorder warnings

* Fix reorder warnings in RbtBaseFileSource

* fix reorder warnings in RbtBaseGrid

* fix reorder warning in RbtBaseMolecularFileSink

* fix reorder warining in RbtCellTokenIter

* fix reorder warnings in RbtFFTGrid

* fix RbtRealGrid reorder warnings

* fix issues with virtual destructors (possible performance hit)

* fix reorder warnings in RbtStringTokenIter

* fix reorder warnings in RbtToken

* fix reorder warnings in RbtVble

* fix tnt array2d utils for braces

* lint

.github/workflows/build_matrix.yml

@@ -62,3 +62,5 @@ jobs:
       with:
         tag: v${{ steps.set_version.outputs.RELEASE_VERSION }}
         artifacts: artifacts/*/*.tar.gz
+        draft: true
+

import/tnt/include/tnt_array2d_utils.h

@@ -59,12 +59,12 @@ std::istream& operator>>(std::istream &s, Array2D<T> &A)
 
 	Array2D<T> B(M,N);
 
-    for (int i=0; i<M; i++)
+    for (int i=0; i<M; i++) {
         for (int j=0; j<N; j++)
         {
             s >>  B[i][j];
         }
-
+	}
 	A = B;
     return s;
 }

import/tnt/include/tnt_array3d_utils.h

@@ -44,11 +44,13 @@ std::istream& operator>>(std::istream &s, Array3D<T> &A)
 
 	Array3D<T> B(M,N,K);
 
-    for (int i=0; i<M; i++)
-        for (int j=0; j<N; j++)
-			for (int k=0; k<K; k++)
+    for (int i=0; i<M; i++) {
+        for (int j=0; j<N; j++) {
+			for (int k=0; k<K; k++) {
             	s >>  B[i][j][k];
-
+			}
+		}
+	}
 	A = B;
     return s;
 }

import/tnt/include/tnt_fortran_array2d_utils.h

@@ -58,12 +58,11 @@ std::istream& operator>>(std::istream &s, Fortran_Array2D<T> &A)
 
 	Fortran_Array2D<T> B(M,N);
 
-    for (int i=1; i<=M; i++)
-        for (int j=1; j<=N; j++)
-        {
+    for (int i=1; i<=M; i++) {
+        for (int j=1; j<=N; j++) {
             s >>  B(i,j);
         }
-
+	}
 	A = B;
     return s;
 }

import/tnt/include/tnt_fortran_array3d_utils.h

@@ -62,11 +62,13 @@ std::istream& operator>>(std::istream &s, Fortran_Array3D<T> &A)
 
 	Fortran_Array3D<T> B(M,N,K);
 
-    for (int i=1; i<=M; i++)
-        for (int j=1; j<=N; j++)
-			for (int k=1; k<=K; k++)
-            	s >>  B(i,j,k);
-
+    for (int i=1; i<=M; i++) {
+        for (int j=1; j<=N; j++) {
+            for (int k=1; k<=K; k++) {
+                s >>  B(i,j,k);
+            }
+        }
+    }
 	A = B;
     return s;
 }

include/RbtAtom.h

@@ -752,37 +752,37 @@ class isAtomLipophilic: public std::unary_function<RbtAtom*, RbtBool> {
 // Other constructors check atomic number, force field type and hybridisation state coordination numbers
 class isCoordinationNumber_eq: public std::unary_function<RbtAtom*, RbtBool> {
     enum { TOTAL, ATNO, FFTYPE, HYBRID } eCNType;  // Type of coordination number to check
-    RbtInt n;                                      // Coordination number value to check
+    RbtUInt n;                                     // Coordination number value to check
     RbtInt atNo;
     RbtString ffType;
     RbtAtom::eHybridState hybrid;
 
  public:
     // Total coordination number
-    explicit isCoordinationNumber_eq(RbtInt nn):
-        n(nn),
+    explicit isCoordinationNumber_eq(RbtUInt nn):
         eCNType(TOTAL),
+        n(nn),
         atNo(0),
         ffType(""),
         hybrid(RbtAtom::UNDEFINED) {}
     // Atomic number coordination number
-    explicit isCoordinationNumber_eq(RbtInt nn, RbtInt nAt):
-        n(nn),
+    explicit isCoordinationNumber_eq(RbtUInt nn, RbtUInt nAt):
         eCNType(ATNO),
+        n(nn),
         atNo(nAt),
         ffType(""),
         hybrid(RbtAtom::UNDEFINED) {}
     // Force field type coordination number
-    explicit isCoordinationNumber_eq(RbtInt nn, const RbtString& strType):
-        n(nn),
+    explicit isCoordinationNumber_eq(RbtUInt nn, const RbtString& strType):
         eCNType(FFTYPE),
+        n(nn),
         atNo(0),
         ffType(strType),
         hybrid(RbtAtom::UNDEFINED) {}
     // Hybridisation state coordination number
-    explicit isCoordinationNumber_eq(RbtInt nn, RbtAtom::eHybridState eState):
-        n(nn),
+    explicit isCoordinationNumber_eq(RbtUInt nn, RbtAtom::eHybridState eState):
         eCNType(HYBRID),
+        n(nn),
         atNo(0),
         ffType(""),
         hybrid(eState) {}

include/RbtCavity.h

@@ -38,7 +38,7 @@ class RbtCavity {
     RbtCavity(istream& istr) { Read(istr); }
 
     // Destructor
-    ~RbtCavity(){};
+    virtual ~RbtCavity(){};
 
     ///////////////////////////////////////////////
     // Stream functions

include/RbtDockingSite.h

@@ -51,7 +51,7 @@ class RbtDockingSite {
     RbtDockingSite(istream& istr);
 
     // Destructor
-    ~RbtDockingSite();
+    virtual ~RbtDockingSite();
 
     // Insertion operator
     friend ostream& operator<<(ostream& s, const RbtDockingSite& site);

include/RbtError.h

@@ -63,15 +63,15 @@ class RbtError {
     // Default constructor
     // Use to create an "error" with status=OK, no line, no file, no message
     // All other constructors set the OK flag to false
-    RbtError(): m_strName(IDS_OK), m_strFile(""), m_nLine(0), m_strMessage(""), m_bOK(true) {}
+    RbtError(): m_strName(IDS_OK), m_strFile(""), m_strMessage(""), m_nLine(0), m_bOK(true) {}
 
     // Parameterised constructor
     // Use to create unspecified Rbt Errors
     RbtError(const RbtString& strFile, RbtInt nLine, const RbtString& strMessage = ""):
         m_strName(IDS_ERROR),
         m_strFile(strFile),
-        m_nLine(nLine),
         m_strMessage(strMessage),
+        m_nLine(nLine),
         m_bOK(false) {}
 
     // Default destructor
@@ -102,8 +102,8 @@ class RbtError {
     RbtError(const RbtString& strName, const RbtString& strFile, RbtInt nLine, const RbtString& strMessage = ""):
         m_strName(strName),
         m_strFile(strFile),
-        m_nLine(nLine),
         m_strMessage(strMessage),
+        m_nLine(nLine),
         m_bOK(false) {}
 
     ///////////////////////

include/RbtFFTGrid.h

@@ -22,7 +22,7 @@
 class RbtFFTPeak {
  public:
     // Constructor
-    RbtFFTPeak(): index(0), coord(0.0, 0.0, 0.0), volume(0), height(0.0) {}
+    RbtFFTPeak(): index(0), coord(0.0, 0.0, 0.0), height(0.0), volume(0) {}
 
     // Data attributes - public to avoid need for accessor functions
     RbtUInt index;      // Location of peak maximum - iXYZ index into grid

include/RbtVble.h

@@ -24,7 +24,7 @@ class RbtVble {
  public:
     static RbtString _CT;
     enum VbleType { CTE, LIG, SCORE, SITE };
-    RbtVble(): value(0.0), vt(CTE), name("") { _RBTOBJECTCOUNTER_CONSTR_(_CT); };  // default const.
+    RbtVble(): vt(CTE), value(0.0), name("") { _RBTOBJECTCOUNTER_CONSTR_(_CT); };  // default const.
     RbtVble(RbtString s, RbtReturnType val = 0.0): value(val), name(s) {
         if (s.find("LIG_") == 0)
             vt = LIG;
@@ -36,7 +36,7 @@ class RbtVble {
             vt = CTE;
         _RBTOBJECTCOUNTER_CONSTR_(_CT);
     }
-    RbtVble(const RbtVble& v): value(v.value), vt(v.vt), name(v.name) { _RBTOBJECTCOUNTER_COPYCONSTR_(_CT); }
+    RbtVble(const RbtVble& v): vt(v.vt), value(v.value), name(v.name) { _RBTOBJECTCOUNTER_COPYCONSTR_(_CT); }
     void SetValue(RbtReturnType val) {
         value = val;
         if (name == "") {

src/lib/RbtAtom.cxx

@@ -27,29 +27,29 @@ using std::ptr_fun;
 // Initialise 2-D attributes to suitable defaults
 // Initialise 3-D attributes to zero/null
 RbtAtom::RbtAtom():
-    m_nAtomId(0),
     m_nAtomicNo(6),
+    m_nAtomId(0),
     m_strAtomName("C"),
     m_strSubunitId("1"),
     m_strSubunitName("RES"),
     m_strSegmentName("SEG1"),
     m_eState(UNDEFINED),  // DM 8 Dec 1998 Changed from SP3 to UNDEFINED
     m_nHydrogens(0),
     m_nFormalCharge(0),
-    m_coord(0.0, 0.0, 0.0),
-    m_dPartialCharge(0.0),
-    m_dGroupCharge(0.0),
-    m_dAtomicMass(0.0),
-    m_dVdwRadius(0.0),
-    m_strFFType(""),
     m_pModel(NULL),
     m_bCyclic(false),
     m_bSelected(false),
     m_bUser1(false),
     m_dUser1(1.0),  // DM 27 Jul 2000 - initialise user values to 1 as they are commonly used as weightings
     m_dUser2(1.0),
     m_nPMFType(PMF_UNDEFINED),
-    m_triposType(RbtTriposAtomType::UNDEFINED) {
+    m_triposType(RbtTriposAtomType::UNDEFINED),
+    m_coord(0.0, 0.0, 0.0),
+    m_dPartialCharge(0.0),
+    m_dGroupCharge(0.0),
+    m_dAtomicMass(0.0),
+    m_dVdwRadius(0.0),
+    m_strFFType("") {
     _RBTOBJECTCOUNTER_CONSTR_("RbtAtom");
 }
 
@@ -66,29 +66,29 @@ RbtAtom::RbtAtom(
     RbtUInt nHydrogens /*= 0*/,
     RbtInt nFormalCharge /*= 0.0*/
 ):
-    m_nAtomId(nAtomId),
     m_nAtomicNo(nAtomicNo),
+    m_nAtomId(nAtomId),
     m_strAtomName(strAtomName),
     m_strSubunitId(strSubunitId),
     m_strSubunitName(strSubunitName),
     m_strSegmentName(strSegmentName),
     m_eState(eState),
     m_nHydrogens(nHydrogens),
     m_nFormalCharge(nFormalCharge),
-    m_coord(0.0, 0.0, 0.0),
-    m_dPartialCharge(0.0),
-    m_dGroupCharge(0.0),
-    m_dAtomicMass(0.0),
-    m_dVdwRadius(0.0),
-    m_strFFType(""),
     m_pModel(NULL),
     m_bCyclic(false),
     m_bSelected(false),
     m_bUser1(false),
     m_dUser1(1.0),  // DM 27 Jul 2000 - initialise user values to 1 as they are commonly used as weightings
     m_dUser2(1.0),
     m_nPMFType(PMF_UNDEFINED),
-    m_triposType(RbtTriposAtomType::UNDEFINED) {
+    m_triposType(RbtTriposAtomType::UNDEFINED),
+    m_coord(0.0, 0.0, 0.0),
+    m_dPartialCharge(0.0),
+    m_dGroupCharge(0.0),
+    m_dAtomicMass(0.0),
+    m_dVdwRadius(0.0),
+    m_strFFType("") {
     _RBTOBJECTCOUNTER_CONSTR_("RbtAtom");
 }
 
@@ -97,8 +97,8 @@ RbtAtom::~RbtAtom() { _RBTOBJECTCOUNTER_DESTR_("RbtAtom"); }
 
 // Copy constructor
 RbtAtom::RbtAtom(const RbtAtom& atom) {
-    m_nAtomId = atom.m_nAtomId;
     m_nAtomicNo = atom.m_nAtomicNo;
+    m_nAtomId = atom.m_nAtomId;
     m_strAtomName = atom.m_strAtomName;
     m_strSubunitId = atom.m_strSubunitId;
     m_strSubunitName = atom.m_strSubunitName;

src/lib/RbtBaseFileSource.cxx

@@ -24,7 +24,7 @@
 //   _RBTOBJECTCOUNTER_CONSTR_("RbtBaseFileSource");
 // }
 
-RbtBaseFileSource::RbtBaseFileSource(const RbtString& fileName): m_bMultiRec(false), m_bFileOpen(false) {
+RbtBaseFileSource::RbtBaseFileSource(const RbtString& fileName): m_bFileOpen(false), m_bMultiRec(false) {
     m_strFileName = fileName;
     m_szBuf = new char[MAXLINELENGTH + 1];  // DM 24 Mar - allocate line buffer
     ClearCache();
@@ -33,9 +33,9 @@ RbtBaseFileSource::RbtBaseFileSource(const RbtString& fileName): m_bMultiRec(fal
 
 // Multi-record constructor
 RbtBaseFileSource::RbtBaseFileSource(const RbtString& fileName, const RbtString& strRecDelim):
+    m_bFileOpen(false),
     m_bMultiRec(true),
-    m_strRecDelim(strRecDelim),
-    m_bFileOpen(false) {
+    m_strRecDelim(strRecDelim) {
     m_strFileName = fileName;
     m_szBuf = new char[MAXLINELENGTH + 1];  // DM 24 Mar - allocate line buffer
     ClearCache();

src/lib/RbtBaseGrid.cxx

@@ -27,14 +27,14 @@ RbtString RbtBaseGrid::_CT("RbtBaseGrid");
 RbtBaseGrid::RbtBaseGrid(
     const RbtCoord& gridMin, const RbtCoord& gridStep, RbtUInt NX, RbtUInt NY, RbtUInt NZ, RbtUInt NPad
 ):
-    m_step(gridStep),
     m_NX(NX),
     m_NY(NY),
     m_NZ(NZ),
     m_N(NX * NY * NZ),
     m_SX(NY * NZ),
     m_SY(NZ),
     m_SZ(1),
+    m_step(gridStep),
     m_NPad(NPad) {
     // Set the logical (real-world) dimensions of the grid
     SetGridMin(gridMin);

src/lib/RbtBaseMolecularFileSink.cxx

@@ -29,9 +29,9 @@ RbtBaseMolecularFileSink::RbtBaseMolecularFileSink(
     const RbtString& fileName, RbtModelPtr spModel, RbtBool bUseModelSegmentNames
 ):
     RbtBaseFileSink(fileName),
+    m_bUseModelSegmentNames(bUseModelSegmentNames),
     m_spModel(spModel),
-    m_bMultiConf(false),
-    m_bUseModelSegmentNames(bUseModelSegmentNames) {
+    m_bMultiConf(false) {
     Reset();
     _RBTOBJECTCOUNTER_CONSTR_("RbtBaseMolecularFileSink");
 }

src/lib/RbtCellTokenIter.cxx

@@ -36,7 +36,7 @@ RbtCellTokenIter::RbtCellTokenIter(const RbtGPChromosomePtr c, RbtContextPtr con
     _RBTOBJECTCOUNTER_CONSTR_(_CT);
 }
 
-RbtCellTokenIter::RbtCellTokenIter(const RbtCellTokenIter& ti): chrom(ti.chrom), cells(ti.cells), current(ti.current) {
+RbtCellTokenIter::RbtCellTokenIter(const RbtCellTokenIter& ti): chrom(ti.chrom), current(ti.current), cells(ti.cells) {
     _RBTOBJECTCOUNTER_COPYCONSTR_(_CT);
 }
 

src/lib/RbtRealGrid.cxx

@@ -28,9 +28,9 @@ RbtRealGrid::RbtRealGrid(
     const RbtCoord& gridMin, const RbtCoord& gridStep, RbtUInt NX, RbtUInt NY, RbtUInt NZ, RbtUInt NPad
 ):
     RbtBaseGrid(gridMin, gridStep, NX, NY, NZ, NPad),
-    m_tol(0.001),
     m_grid(NULL),
-    m_data(NULL) {
+    m_data(NULL),
+    m_tol(0.001) {
     CreateArrays();
     // Initialise the grid to zero
     SetAllValues(0.0);

src/lib/RbtStringTokenIter.cxx

@@ -29,8 +29,8 @@ RbtStringTokenIter::RbtStringTokenIter(const istreamPtr fn, RbtContextPtr co): f
 }
 
 RbtStringTokenIter::RbtStringTokenIter(const RbtStringTokenIter& ti):
-    current(ti.current),
     filep(ti.filep),
+    current(ti.current),
     strtok(ti.strtok),
     contextp(ti.contextp) {
     _RBTOBJECTCOUNTER_COPYCONSTR_(_CT);

src/lib/RbtToken.cxx

@@ -24,13 +24,13 @@ RbtString RbtToken::_CT("RbtToken");
 ///////////////////
 // Constructors
 ///////////////////
-RbtToken::RbtToken(const RbtVble& v): isvble(true), vble(v), comm(-1) { _RBTOBJECTCOUNTER_CONSTR_(_CT); }
+RbtToken::RbtToken(const RbtVble& v): comm(-1), vble(v), isvble(true) { _RBTOBJECTCOUNTER_CONSTR_(_CT); }
 
-RbtToken::RbtToken(RbtCommands c): isvble(false), comm(c), vble(RBT::defaultConstRbtVble) {
+RbtToken::RbtToken(RbtCommands c): comm(c), vble(RBT::defaultConstRbtVble), isvble(false) {
     _RBTOBJECTCOUNTER_CONSTR_(_CT);
 }
 
-RbtToken::RbtToken(const RbtToken& t): isvble(t.isvble), comm(t.comm), vble(t.vble) {
+RbtToken::RbtToken(const RbtToken& t): comm(t.comm), vble(t.vble), isvble(t.isvble) {
     _RBTOBJECTCOUNTER_COPYCONSTR_(_CT);
 }