From 158f0044ca84261e9537cb9356856d7ace18c96e Mon Sep 17 00:00:00 2001 From: ggutierrez-sunbright <94693768+ggutierrez-sunbright@users.noreply.github.com> Date: Sat, 9 Dec 2023 14:28:45 +0100 Subject: [PATCH] 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 | 2 ++ import/tnt/include/tnt_array2d_utils.h | 4 +-- import/tnt/include/tnt_array3d_utils.h | 10 +++--- .../tnt/include/tnt_fortran_array2d_utils.h | 7 ++-- .../tnt/include/tnt_fortran_array3d_utils.h | 12 ++++--- include/RbtAtom.h | 18 +++++----- include/RbtCavity.h | 2 +- include/RbtDockingSite.h | 2 +- include/RbtError.h | 6 ++-- include/RbtFFTGrid.h | 2 +- include/RbtVble.h | 4 +-- src/lib/RbtAtom.cxx | 34 +++++++++---------- src/lib/RbtBaseFileSource.cxx | 6 ++-- src/lib/RbtBaseGrid.cxx | 2 +- src/lib/RbtBaseMolecularFileSink.cxx | 4 +-- src/lib/RbtCellTokenIter.cxx | 2 +- src/lib/RbtRealGrid.cxx | 4 +-- src/lib/RbtStringTokenIter.cxx | 2 +- src/lib/RbtToken.cxx | 6 ++-- 19 files changed, 67 insertions(+), 62 deletions(-) diff --git a/.github/workflows/build_matrix.yml b/.github/workflows/build_matrix.yml index 632e8ce4..89b70361 100644 --- a/.github/workflows/build_matrix.yml +++ b/.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 + diff --git a/import/tnt/include/tnt_array2d_utils.h b/import/tnt/include/tnt_array2d_utils.h index 7041ed37..d63eb913 100644 --- a/import/tnt/include/tnt_array2d_utils.h +++ b/import/tnt/include/tnt_array2d_utils.h @@ -59,12 +59,12 @@ std::istream& operator>>(std::istream &s, Array2D &A) Array2D B(M,N); - for (int i=0; i> B[i][j]; } - + } A = B; return s; } diff --git a/import/tnt/include/tnt_array3d_utils.h b/import/tnt/include/tnt_array3d_utils.h index 5acdc1d5..b4d5ea97 100644 --- a/import/tnt/include/tnt_array3d_utils.h +++ b/import/tnt/include/tnt_array3d_utils.h @@ -44,11 +44,13 @@ std::istream& operator>>(std::istream &s, Array3D &A) Array3D B(M,N,K); - for (int i=0; i> B[i][j][k]; - + } + } + } A = B; return s; } diff --git a/import/tnt/include/tnt_fortran_array2d_utils.h b/import/tnt/include/tnt_fortran_array2d_utils.h index bb686736..96775c2f 100644 --- a/import/tnt/include/tnt_fortran_array2d_utils.h +++ b/import/tnt/include/tnt_fortran_array2d_utils.h @@ -58,12 +58,11 @@ std::istream& operator>>(std::istream &s, Fortran_Array2D &A) Fortran_Array2D 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; } diff --git a/import/tnt/include/tnt_fortran_array3d_utils.h b/import/tnt/include/tnt_fortran_array3d_utils.h index a13a275d..07202033 100644 --- a/import/tnt/include/tnt_fortran_array3d_utils.h +++ b/import/tnt/include/tnt_fortran_array3d_utils.h @@ -62,11 +62,13 @@ std::istream& operator>>(std::istream &s, Fortran_Array3D &A) Fortran_Array3D 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; } diff --git a/include/RbtAtom.h b/include/RbtAtom.h index 5f43bf6e..855a8d8f 100644 --- a/include/RbtAtom.h +++ b/include/RbtAtom.h @@ -752,37 +752,37 @@ class isAtomLipophilic: public std::unary_function { // Other constructors check atomic number, force field type and hybridisation state coordination numbers class isCoordinationNumber_eq: public std::unary_function { 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) {} diff --git a/include/RbtCavity.h b/include/RbtCavity.h index df6ca8cd..c9ad13aa 100644 --- a/include/RbtCavity.h +++ b/include/RbtCavity.h @@ -38,7 +38,7 @@ class RbtCavity { RbtCavity(istream& istr) { Read(istr); } // Destructor - ~RbtCavity(){}; + virtual ~RbtCavity(){}; /////////////////////////////////////////////// // Stream functions diff --git a/include/RbtDockingSite.h b/include/RbtDockingSite.h index 7f9e660d..538dc15c 100644 --- a/include/RbtDockingSite.h +++ b/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); diff --git a/include/RbtError.h b/include/RbtError.h index cf6e172b..7ec5f6bb 100644 --- a/include/RbtError.h +++ b/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) {} /////////////////////// diff --git a/include/RbtFFTGrid.h b/include/RbtFFTGrid.h index da466a4c..af990d8a 100644 --- a/include/RbtFFTGrid.h +++ b/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 diff --git a/include/RbtVble.h b/include/RbtVble.h index 24a5de4a..37e96cb9 100644 --- a/include/RbtVble.h +++ b/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 == "") { diff --git a/src/lib/RbtAtom.cxx b/src/lib/RbtAtom.cxx index b24dd43e..308a5caa 100644 --- a/src/lib/RbtAtom.cxx +++ b/src/lib/RbtAtom.cxx @@ -27,8 +27,8 @@ 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"), @@ -36,12 +36,6 @@ RbtAtom::RbtAtom(): 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), @@ -49,7 +43,13 @@ RbtAtom::RbtAtom(): 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"); } @@ -66,8 +66,8 @@ 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), @@ -75,12 +75,6 @@ RbtAtom::RbtAtom( 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), @@ -88,7 +82,13 @@ RbtAtom::RbtAtom( 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; diff --git a/src/lib/RbtBaseFileSource.cxx b/src/lib/RbtBaseFileSource.cxx index c3cb08e2..1cd37328 100644 --- a/src/lib/RbtBaseFileSource.cxx +++ b/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(); diff --git a/src/lib/RbtBaseGrid.cxx b/src/lib/RbtBaseGrid.cxx index d07774cc..c00cd136 100644 --- a/src/lib/RbtBaseGrid.cxx +++ b/src/lib/RbtBaseGrid.cxx @@ -27,7 +27,6 @@ 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), @@ -35,6 +34,7 @@ RbtBaseGrid::RbtBaseGrid( 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); diff --git a/src/lib/RbtBaseMolecularFileSink.cxx b/src/lib/RbtBaseMolecularFileSink.cxx index 8493469f..d34ffdbc 100644 --- a/src/lib/RbtBaseMolecularFileSink.cxx +++ b/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"); } diff --git a/src/lib/RbtCellTokenIter.cxx b/src/lib/RbtCellTokenIter.cxx index 8f0f5d9b..c588e263 100644 --- a/src/lib/RbtCellTokenIter.cxx +++ b/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); } diff --git a/src/lib/RbtRealGrid.cxx b/src/lib/RbtRealGrid.cxx index 3e975dba..41281356 100644 --- a/src/lib/RbtRealGrid.cxx +++ b/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); diff --git a/src/lib/RbtStringTokenIter.cxx b/src/lib/RbtStringTokenIter.cxx index beb7d451..ffe25015 100644 --- a/src/lib/RbtStringTokenIter.cxx +++ b/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); diff --git a/src/lib/RbtToken.cxx b/src/lib/RbtToken.cxx index df95e562..b14276bf 100644 --- a/src/lib/RbtToken.cxx +++ b/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); }