adding lightweight precommit

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+default_language_version:
+    python: python3
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit hooks
+    autofix_prs: true
+    autoupdate_branch: 'pre-commit-autoupdate'
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: [no-commit-to-branch]
+    submodules: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+        exclude: 'meta.yaml'
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Prevent Commit to Main Branch
+        args: ["--branch", "main"]
+        stages: [pre-commit]

CHANGELOG.md

@@ -3,13 +3,13 @@
 ## Version 2024.1.1,  - 2024-02-06
 
 ### Added
-- Make sure Molecule::BuildConnectivityTable() always list all atoms, 
+- Make sure Molecule::BuildConnectivityTable() always list all atoms,
   even if their connectivity list is empty (pathological case)
 
 ## Version 2022.1.4,  - 2022-12-03
 
 ### Added
-- Add UnitCell::ChangeSpaceGroup(), which updates lattice parameter symmetry constraints. 
+- Add UnitCell::ChangeSpaceGroup(), which updates lattice parameter symmetry constraints.
 
 ### Changed
 - Take into account spacegroup clock in UnitCell::GetLatticePar and InitMatrices
@@ -20,8 +20,8 @@
 
 ### Changed
 
-- the list of HKL reflections will now be automatically be re-generated 
-  for a PowderPatternDiffraction when the Crystal's spacegroup changes,  
+- the list of HKL reflections will now be automatically be re-generated
+  for a PowderPatternDiffraction when the Crystal's spacegroup changes,
   or the lattice parameters are modified by more than 0.5%
 - Fixed the powder pattern indexing test
 
@@ -44,7 +44,7 @@
 
 ### Changed
 
-- Add relative_length_tolerance and absolute_angle_tolerance_degree to 
+- Add relative_length_tolerance and absolute_angle_tolerance_degree to
   SpaceGroupExplorer::Run() and RunAll()
 - Crystal::XMLInput(): add a hook to re-use atomic scattering power when
   mDeleteSubObjInDestructor is False
@@ -72,13 +72,13 @@
 ### Added
 - Move SpaceGroupExplorer in a separate class for non-GUI access.
   Allow keeping or not the tested spacegroup, or the best solution.
-  Sort solutions by the GoF multiplied by the ratio of the number 
+  Sort solutions by the GoF multiplied by the ratio of the number
   of non-extinct reflections in the spacegoup relative to P1.
 - MonteCarloObj: add public access to AutoLSQ option
 - OptimizationObj: add access to Options by number or name
 - RefinableObj: provide access to options by name
 - Add STL-type methods (begin, end, size) for ObjRegistry and Molecule objects
-- Add Crystal.GetFormula(). Use formula to automatically name Crystal and 
+- Add Crystal.GetFormula(). Use formula to automatically name Crystal and
   DiffractionDataSingleCrystal when imported from CIF and no name is given
 
 ### Changed

src/ObjCryst/ObjCryst/CIF.cpp

@@ -1008,7 +1008,7 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
    (*fpObjCrystInformUser)("CIF: Opening CIF");
    Chronometer chrono;
    chrono.start();
-   
+
    // If oneScatteringPowerPerElement==true, we hold this to compute the average Biso per element
    std::map<ScatteringPower*,std::pair<REAL,unsigned int> > vElementBiso;
 
@@ -1184,7 +1184,7 @@ Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsX
          // Try to set name from CIF. If that fails, the computed formula will be used at the end
          if(pos->second.mName!="") pCryst->SetName(pos->second.mName);
          else if(pos->second.mFormula!="") pCryst->SetName(pos->second.mFormula);
-         
+
          const float t1=chrono.seconds();
          (*fpObjCrystInformUser)((boost::format("CIF: Create Crystal:%s(%s)(dt=%6.3fs)")%pCryst->GetName() % pCryst->GetSpaceGroup().GetName() % t1).str());
 

src/ObjCryst/ObjCryst/Crystal.h

@@ -189,7 +189,7 @@ class Crystal:public UnitCell
       /// \todo one function to print on one line and a PrintLong() function
       /// \param os the stream to which the information is outputed (default=cout)
       void Print(ostream &os=cout) const;
-   
+
       /// Formula with atoms in alphabetic order
       std::string GetFormula() const;
       /// Weight for the crystal formula, in atomic units (g/mol). This should be

src/ObjCryst/ObjCryst/Molecule.cpp

@@ -7962,7 +7962,7 @@ Molecule *ZScatterer2Molecule(ZScatterer *scatt)
       z0+=z;
       mol->AddAtom(x,y,z,scatt->GetZAtomRegistry().GetObj(i).GetScatteringPower(),
                    scatt->GetZAtomRegistry().GetObj(i).GetName());
-      
+
       #if 0
       if(i>0)
       {
@@ -8014,7 +8014,7 @@ Molecule *ZScatterer2Molecule(ZScatterer *scatt)
       #endif
       mol->GetAtom(i).SetOccupancy(scatt->GetZAtomRegistry().GetObj(i).GetOccupancy());
    }
-   
+
    CrystVector_REAL x(nb),y(nb),z(nb),radius(nb);
    vector<pair<const ScatteringPowerAtom *,long> > scattpow(nb);
    for(unsigned int i=0;i<nb;++i)

src/ObjCryst/ObjCryst/PowderPattern.cpp

@@ -2118,7 +2118,7 @@ void PowderPatternDiffraction::CalcIntensityCorr()const
    }
    mpCorr[4]=&(mCorrTextureEllipsoid.GetCorr());
    if(mClockIntensityCorr<mCorrTextureEllipsoid.GetClockCorr()) needRecalc=true;
-   
+
    if(needRecalc==false) return;
 
    TAU_PROFILE("PowderPatternDiffraction::CalcIntensityCorr()","void ()",TAU_DEFAULT);
@@ -2615,13 +2615,13 @@ void PowderPattern::RemovePowderPatternComponent(PowderPatternComponent &comp)
       this->RemovePar(&this->GetPar(mScaleFactor.data()+mPowderPatternComponentRegistry.GetNb()-1));
       this->Print();
    }
-   
+
    this->RemoveSubRefObj(comp);
    comp.DeRegisterClient(*this);
    mClockPowderPatternCalc.Reset();
    mClockIntegratedFactorsPrep.Reset();
    mPowderPatternComponentRegistry.DeRegister(comp);
-   
+
    // Shift scale factors
    unsigned int i=0;
    for(unsigned int i=0;i<this->GetNbPowderPatternComponent();i++)
@@ -6968,7 +6968,7 @@ SPGScore SpaceGroupExplorer::Run(const cctbx::sgtbx::space_group &spg, const boo
    lsq.PrepareRefParList(true);
    const unsigned int saved_par = lsq.GetCompiledRefinedObj().CreateParamSet("SpaceGroupExplorer saved parameters");
    lsq.GetCompiledRefinedObj().SaveParamSet(saved_par);
-   
+
    Chronometer chrono;
    for(unsigned int j=0;j<nbcycle;j++)
    {
@@ -7039,7 +7039,7 @@ SPGScore SpaceGroupExplorer::Run(const cctbx::sgtbx::space_group &spg, const boo
    for(unsigned int i=6;i<fgp.size();++i) nbextinct446+=(unsigned int)(fgp[i]);
    const unsigned int nbrefl = mpDiff->GetNbReflBelowMaxSinThetaOvLambda();
    if(verbose>0) cout << boost::format(" Rwp= %5.2f%%  GoF=%9.2f  nGoF =%9.2f (%3u reflections, %3u extinct)") % rw % gof % ngof % nbrefl % nbextinct446<<endl;
-   
+
    if(restore_orig)
    {
       mpDiff->GetCrystal().Init(a,b,c,d,e,f,spghm,name);
@@ -7059,7 +7059,7 @@ void SpaceGroupExplorer::RunAll(const bool fitprofile_all, const bool verbose, c
                                 const REAL relative_length_tolerance, const REAL absolute_angle_tolerance_degree)
 {
    Crystal *pCrystal=&(mpDiff->GetCrystal());
-   
+
    // Initial lattice parameters & spg
    const REAL a=pCrystal->GetLatticePar(0),
    b=pCrystal->GetLatticePar(1),
@@ -7086,7 +7086,7 @@ void SpaceGroupExplorer::RunAll(const bool fitprofile_all, const bool verbose, c
 
    mvSPG.clear();
    mvSPGExtinctionFingerprint.clear();
-   
+
    // Nb refl below max sin(theta/lambda) for p1, to compute nGoF
    unsigned int nb_refl_p1=1;
 
@@ -7170,7 +7170,7 @@ REAL SpaceGroupExplorer::GetP1IntegratedGoF()
       //     <<FormatVertVectorHKLFloats<REAL>(mP1IntegratedProfileMin, mP1IntegratedProfileMax,mP1IntegratedProfileMax)<<endl;
    }
    else if (mP1IntegratedProfileMin.size()==0) return 0;
-   
+
    //cout<<FormatVertVectorHKLFloats<REAL>(mpDiff->GetH(), mpDiff->GetK(), mpDiff->GetL(), mpDiff->GetFhklCalcSq());
    REAL integratedChi2=0.;
    REAL integratedChi2LikeNorm=0.;
@@ -7199,5 +7199,5 @@ REAL SpaceGroupExplorer::GetP1IntegratedGoF()
    }
    return chi2 / nbpoint;
 }
-   
+
 }//namespace ObjCryst

src/ObjCryst/ObjCryst/PowderPattern.h

@@ -1097,7 +1097,7 @@ class PowderPattern : public RefinableObj
          /// This is mutable because generally we use the 'best' scale factor, but
          /// it should not be...
          mutable CrystVector_REAL mScaleFactor;
-   
+
       /// Mu*R parameter for cylinder absorption correction
       REAL mMuR;
 
@@ -1189,7 +1189,7 @@ struct SPGScore
    string hm;
    /// Rw factor, from PowderPattern::GetRw()
    REAL rw;
-   /// Goodness-of-fit, from PowderPattern::GetChi2() normalised by 
+   /// Goodness-of-fit, from PowderPattern::GetChi2() normalised by
    REAL gof;
    /// Normalised & integrated goodness-of-fit =  iGoF * (nb_refl) / (nb_refl in P1),
    /// where iGoF is the integrated goodness-of-fit, computed using the integration
@@ -1289,7 +1289,7 @@ class SpaceGroupExplorer
    /// Map extinction fingerprint
    std::map<std::vector<bool>,SPGScore> mvSPGExtinctionFingerprint;
 };
-   
+
 
 }//namespace ObjCryst
 #endif // _OBJCRYST_POWDERPATTERN_H_

src/ObjCryst/RefinableObj/GlobalOptimObj.cpp

@@ -2299,16 +2299,16 @@ void MonteCarloObj::InitLSQ(const bool useFullPowderPatternProfile)
    }
    // Only refine structural parameters (excepting parameters already fixed) and scale factor
    mLSQ.PrepareRefParList(true);
-   
+
    // Intensity corrections can be refined
    std::list<RefinablePar*> vIntCorrPar;
    for(int i=0; i<mLSQ.GetCompiledRefinedObj().GetNbPar();i++)
       if(mLSQ.GetCompiledRefinedObj().GetPar(i).GetType()->IsDescendantFromOrSameAs(gpRefParTypeScattDataCorrInt) && mLSQ.GetCompiledRefinedObj().GetPar(i).IsFixed()==false)
          vIntCorrPar.push_back(&mLSQ.GetCompiledRefinedObj().GetPar(i));
-   
+
    mLSQ.SetParIsFixed(gpRefParTypeScattData,true);
    mLSQ.SetParIsFixed(gpRefParTypeScattDataScale,false);
-   
+
    for(std::list<RefinablePar*>::iterator pos=vIntCorrPar.begin();pos!=vIntCorrPar.end();pos++)
       (*pos)->SetIsFixed(false);
    mLSQ.SetParIsFixed(gpRefParTypeUnitCell,true);

src/ObjCryst/RefinableObj/RefinableObj.cpp

@@ -931,10 +931,10 @@ template<class T> void ObjRegistry<T>::DeRegister(T &obj)
    if(0!=mpWXRegistry) mpWXRegistry->Remove(obj.WXGet());
    #endif
    mvpRegistry.erase(pos);
-   
+
    typename list<T*>::iterator pos2=find(mvpRegistryList.begin(),mvpRegistryList.end(),&obj);
    mvpRegistryList.erase(pos2);
-   
+
    mListClock.Click();
    VFN_DEBUG_EXIT("ObjRegistry("<<mName<<")::Deregister(&obj)",2)
 }

src/cctbx/include/scitbx/array_family/small_reductions.h

@@ -152,4 +152,3 @@ namespace scitbx { namespace af {
 #endif // DOXYGEN_SHOULD_SKIP_THIS
 
 #endif // SCITBX_ARRAY_FAMILY_SMALL_REDUCTIONS_H
-

src/cctbx/include/scitbx/array_family/tiny_reductions.h

@@ -152,4 +152,3 @@ namespace scitbx { namespace af {
 #endif // DOXYGEN_SHOULD_SKIP_THIS
 
 #endif // SCITBX_ARRAY_FAMILY_TINY_REDUCTIONS_H
-

src/newmat/Makefile.in

@@ -113,4 +113,3 @@ submat.o:     $(newmatxx) $(srcdir)/newmatrc.h $(srcdir)/controlw.h $(srcdir)/su
 
 svd.o:        $(newmatxx) $(srcdir)/newmatrm.h $(srcdir)/precisio.h $(srcdir)/svd.cpp
 	$(CXX) $(CXXFLAGS) $(OPT++DEFINES) $(OPT++INCLUDES) $(srcdir)/svd.cpp
-

src/newmat/_newmat.dox

@@ -22,8 +22,3 @@
 ///rather inefficient.
 
 ///@}
-
-
-
-
-

src/newmat/_rbd_com.dox

@@ -19,8 +19,3 @@
 
 
 ///@}
-
-
-
-
-

src/newmat/bandmat.cpp

@@ -284,8 +284,8 @@ GeneralMatrix* BandLUMatrix::Evaluate(MatrixType mt)
 // could we use SetParameters instead of this
 void BandLUMatrix::get_aux(BandLUMatrix& X)
 {
-   X.d = d; X.sing = sing; X.storage2 = storage2; X.m1 = m1; X.m2 = m2;   
-   if (tag_val == 0 || tag_val == 1) // reuse the array 
+   X.d = d; X.sing = sing; X.storage2 = storage2; X.m1 = m1; X.m2 = m2;
+   if (tag_val == 0 || tag_val == 1) // reuse the array
    {
       REPORT
       X.indx = indx; indx = 0;
@@ -333,7 +333,7 @@ void BandLUMatrix::operator=(const BandLUMatrix& gm)
    ((BandLUMatrix&)gm).get_aux(*this);
    Eq(gm);
 }
-   
+
 
 
 
@@ -714,5 +714,3 @@ Real SymmetricBandMatrix::sum() const
 #endif
 
 ///@}
-
-

src/newmat/cholesky.cpp

@@ -104,7 +104,7 @@ void update_Cholesky(UpperTriangularMatrix &chol, RowVector x)
    int nc = chol.Nrows();
    ColumnVector cGivens(nc); cGivens = 0.0;
    ColumnVector sGivens(nc); sGivens = 0.0;
-	
+
    for(int j = 1; j <= nc; ++j) // process the jth column of chol
    {
       // apply the previous Givens rotations k = 1,...,j-1 to column j
@@ -129,12 +129,12 @@ void update_Cholesky(UpperTriangularMatrix &chol, RowVector x)
 void downdate_Cholesky(UpperTriangularMatrix &chol, RowVector x)
 {
    int nRC = chol.Nrows();
-	
+
    // solve R^T a = x
    LowerTriangularMatrix L = chol.t();
    ColumnVector a(nRC); a = 0.0;
    int i, j;
-	
+
    for (i = 1; i <= nRC; ++i)
    {
       // accumulate subtr sum
@@ -177,7 +177,7 @@ void right_circular_update_Cholesky(UpperTriangularMatrix &chol, int k, int l)
 {
    int nRC = chol.Nrows();
    int i, j;
-	
+
    // I. compute shift of column l to the kth position
    Matrix cholCopy = chol;
    // a. grab column l
@@ -202,7 +202,7 @@ void right_circular_update_Cholesky(UpperTriangularMatrix &chol, int k, int l)
    }
    // the kth entry of columnL is the new diagonal element in column k of cholCopy
    cholCopy(k,k) = columnL(k);
-	
+
    // III. apply these Given's rotations to subsequent columns
    // for columns k+1,...,l-1 we only need to apply the last nGivens-(j-k) rotations
    for(j = k+1; j <= nRC; ++j)
@@ -276,7 +276,7 @@ void left_circular_update_Cholesky(UpperTriangularMatrix &chol, int k, int l)
    }
 
    chol << cholCopy;
-	
+
 }
 
 

src/newmat/controlw.h

@@ -53,4 +53,3 @@ class ControlWord
 #endif
 
 ///@}
-