started clean up in old packages

mohamed-barakat · mohamed-barakat · commit ca44f35a8e13 · 2025-09-20T17:38:53.000+02:00
the category of (co)complexes and the use of ZFunctor needs to be deprecated
diff --git a/CAP/PackageInfo.g b/CAP/PackageInfo.g
@@ -10,7 +10,7 @@ SetPackageInfo( rec(
 
 PackageName := "CAP",
 Subtitle := "Categories, Algorithms, Programming",
-Version := "2025.09-02",
+Version := "2025.09-03",
 Date := (function ( ) if IsBound( GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE ) then return GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE; else return Concatenation( ~.Version{[ 1 .. 4 ]}, "-", ~.Version{[ 6, 7 ]}, "-01" ); fi; end)( ),
 License := "GPL-2.0-or-later",
 
diff --git a/CAP/gap/CategoryObjectsOperations.gi b/CAP/gap/CategoryObjectsOperations.gi
@@ -57,7 +57,7 @@ InstallOtherMethod( IsEqualForObjects,
             
         else
             
-            Error( "Cannot decide whether the object \"", String( object_1 ), "\" and the object \"", String( object_2 ), "\" are equal. You can fix this error by installing `IsEqualForObjects` in <cat> or possibly avoid it by enabling strict caching." );
+            Error( "Cannot decide whether the object \"", String( object_1 ), "\" and the object \"", String( object_2 ), "\" are equal. You can fix this error by installing `IsEqualForObjects` in <cat> or possibly avoid it by enabling strict caching\n" );
             
         fi;
         
diff --git a/ComplexesAndFilteredObjectsForCAP/PackageInfo.g b/ComplexesAndFilteredObjectsForCAP/PackageInfo.g
@@ -10,7 +10,7 @@ SetPackageInfo( rec(
 
 PackageName := "ComplexesAndFilteredObjectsForCAP",
 Subtitle := "Implementation of complexes, cocomplexes and filtered objects for CAP",
-Version := "2025.02-01",
+Version := "2025.09-01",
 Date := (function ( ) if IsBound( GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE ) then return GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE; else return Concatenation( ~.Version{[ 1 .. 4 ]}, "-", ~.Version{[ 6, 7 ]}, "-01" ); fi; end)( ),
 License := "GPL-2.0-or-later",
 
diff --git a/ComplexesAndFilteredObjectsForCAP/gap/CocomplexCategory.gi b/ComplexesAndFilteredObjectsForCAP/gap/CocomplexCategory.gi
@@ -62,12 +62,22 @@ InstallMethod( CocomplexCategory,
     
     cocomplex_category := CreateCapCategory( name : is_computable := false );
     
+    ## TODO: since the following is currently unavoidable deprecate this category constructor
+    DisableInputSanityChecks( cocomplex_category );
+    
     SetUnderlyingCategory( cocomplex_category, category );
     
     SetCocomplexCategory( category, cocomplex_category );
     
     INSTALL_OPERATIONS_FOR_COCOMPLEX_CATEGORY( category );
     
+    AddIsEqualForObjects( cocomplex_category,
+      function( cocomplex_category, C1, C2 )
+        
+        return IsEqualForObjects( UnderlyingZFunctorCell( C1 ), UnderlyingZFunctorCell( C2 ) );
+        
+    end );
+    
     Finalize( cocomplex_category );
     
     return cocomplex_category;
@@ -93,12 +103,22 @@ InstallMethod( ComplexCategory,
     
     complex_category := CreateCapCategory( name : is_computable := false );
     
+    ## TODO: since the following is currently unavoidable deprecate this category constructor
+    DisableInputSanityChecks( complex_category );
+    
     SetUnderlyingCategory( complex_category, category );
     
     SetComplexCategory( category, complex_category );
     
     INSTALL_OPERATIONS_FOR_COMPLEX_CATEGORY( category );
     
+    AddIsEqualForObjects( complex_category,
+      function( complex_category, C1, C2 )
+        
+        return IsEqualForObjects( UnderlyingZFunctorCell( C1 ), UnderlyingZFunctorCell( C2 ) );
+        
+    end );
+    
     Finalize( complex_category );
     
     return complex_category;
diff --git a/ComplexesAndFilteredObjectsForCAP/gap/ZFunctors.gi b/ComplexesAndFilteredObjectsForCAP/gap/ZFunctors.gi
@@ -55,12 +55,23 @@ InstallMethod( ZFunctorCategory,
     
     z_functor_category := CreateCapCategory( name : is_computable := false );
     
+    ## TODO: since the following is currently unavoidable deprecate this category constructor
+    DisableInputSanityChecks( z_functor_category );
+    
     SetUnderlyingCategory( z_functor_category, category );
     
     SetZFunctorCategory( category, z_functor_category );
     
     INSTALL_OPERATIONS_FOR_ZFUNCTOR_CATEGORY( category );
     
+    AddIsEqualForObjects( z_functor_category,
+      function( z_functor_category, ZF1, ZF2 )
+        
+        ## return true;
+        return IsIdenticalObj( ZF1, ZF2 );
+        
+    end );
+    
     Finalize( z_functor_category );
     
     return z_functor_category;
diff --git a/GradedModulePresentationsForCAP/PackageInfo.g b/GradedModulePresentationsForCAP/PackageInfo.g
@@ -10,7 +10,7 @@ SetPackageInfo( rec(
 
 PackageName := "GradedModulePresentationsForCAP",
 Subtitle := "Presentations for graded modules",
-Version := "2025.08-02",
+Version := "2025.09-01",
 Date := (function ( ) if IsBound( GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE ) then return GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE; else return Concatenation( ~.Version{[ 1 .. 4 ]}, "-", ~.Version{[ 6, 7 ]}, "-01" ); fi; end)( ),
 License := "GPL-2.0-or-later",
 
diff --git a/GradedModulePresentationsForCAP/examples/Gabriel_Purity_Paper.g b/GradedModulePresentationsForCAP/examples/Gabriel_Purity_Paper.g
@@ -1,4 +1,4 @@
-LoadPackage( "ModulePresentationsForCAP" );
+LoadPackage( "GradedModulePresentationsForCAP" );
 LoadPackage( "HomologicalAlgebraForCAP" );
 
 SwitchGeneralizedMorphismStandard( "span" );
diff --git a/GradedModulePresentationsForCAP/examples/Purity.g b/GradedModulePresentationsForCAP/examples/Purity.g
@@ -1,5 +1,5 @@
-LoadPackage( "ModulePres" );
-LoadPackage( "Homological" );
+LoadPackage( "GradedModulePresentationsForCAP" );
+LoadPackage( "HomologicalAlgebraForCAP" );
 
 Qxyzt := HomalgFieldOfRationalsInSingular( ) * "x,y,z,t";
 
@@ -24,10 +24,10 @@ SetIsAdditiveCategory( ComplexCategory( CapCategory( S0 ) ), true );
 
 M := AsGradedLeftPresentation( wmat );
 
-res := FreeResolutionComplexOfModule( M );
+res := FreeResolutionComplex( M );
 res := res[ 1 ];
 homres := DualOnComplex( res );
-CE := CartanEilenbergResolution( homres, FreeResolutionCocomplexOfModule );
+CE := CartanEilenbergResolution( homres, FreeResolutionCocomplex );
 homCE := DualOnCocomplexCocomplex( CE );
 trhomCE := TransposeComplexOfComplex( homCE );
 
diff --git a/GradedModulePresentationsForCAP/examples/Resolution.g b/GradedModulePresentationsForCAP/examples/Resolution.g
@@ -1,26 +1,25 @@
-LoadPackage( "ModulePres" );
-LoadPackage( "Homological" );
+LoadPackage( "GradedModulePresentationsForCAP" );
+LoadPackage( "HomologicalAlgebraForCAP" );
+
 Q := HomalgFieldOfRationalsInSingular();
-R := Q*"x,y";
+R := Q["x,y"];
 S := GradedRing( R );
-WeightsOfIndeterminates( S );
-eins := last[1];
-M := HomalgMatrix( "[x^2,xy,y^2]", 3,1, S );
+weights := WeightsOfIndeterminates( S );
+eins := weights[1];
+M := HomalgMatrix( "[x^2,xy,y^2]", 3, 1, S );
 XX := GradedFreeLeftPresentation( 1, S );
 S0 := GradedFreeLeftPresentation( 1, S );
 S1 := GradedFreeLeftPresentation( 3, S, [ 2*eins, 2*eins, 2*eins ] );
 alpha := GradedPresentationMorphism( S1, M, S0 );
 M := CokernelObject( alpha );
-FFhomo := ResolutionFunctorToComplex( GradedLeftPresentations( S ), CoverByFreeModule );
-FF := ResolutionFunctorToCocomplex( GradedLeftPresentations( S ), CoverByFreeModule );
-res := ApplyFunctor( FFhomo, M );
+
 SetIsAdditiveCategory( CocomplexCategory( CapCategory( S0 ) ), true );
 SetIsAdditiveCategory( ComplexCategory( CapCategory( S0 ) ), true );
 
 M := DirectSum( [ M, S0 ] );
 
-res := FreeResolutionComplexOfModule( M );
+res := FreeResolutionComplex( M );
 res := res[ 1 ];
-homres := InternalHomOnComplexWithObject( res, S0 );
-CE := CartanEilenbergResolution( homres, FreeResolutionCocomplexOfModule );
-homCE := InternalHomOnCocomplexCocomplexWithObject( CE, S0 );
+homres := DualOnComplex( res );
+CE := CartanEilenbergResolution( homres, FreeResolutionCocomplex );
+homCE := DualOnCocomplexCocomplex( CE );
diff --git a/GradedModulePresentationsForCAP/examples/SpectralSequenceTest.g b/GradedModulePresentationsForCAP/examples/SpectralSequenceTest.g
@@ -1,5 +1,5 @@
-LoadPackage( "ModulePres" );
-LoadPackage( "Homological" );
+LoadPackage( "GradedModulePresentationsForCAP" );
+LoadPackage( "HomologicalAlgebraForCAP" );
 
 SwitchGeneralizedMorphismStandard( "span" );
 
@@ -26,10 +26,10 @@ SetIsAdditiveCategory( ComplexCategory( CapCategory( S0 ) ), true );
 
 M := AsGradedLeftPresentation( wmat );
 
-res1 := FreeResolutionComplexOfModule( M );
+res1 := FreeResolutionComplex( M );
 res := res1[ 1 ];
 homres := DualOnComplex( res );
-CE := CartanEilenbergResolution( homres, FreeResolutionCocomplexOfModule );
+CE := CartanEilenbergResolution( homres, FreeResolutionCocomplex );
 homCE := DualOnCocomplexCocomplex( CE );
 trhomCE := TransposeComplexOfComplex( homCE );
 
@@ -41,8 +41,8 @@ resolution_len := ResolutionLength( res );
 
 tot := TotalComplexOfBicomplex( homCE, resolution_len );
 
-connection_at_0 := ConnectingMorphismFromCocomplexToCartanEilenbergResolution( homres, 0, FreeResolutionCocomplexOfModule );
-connection_at_1 := ConnectingMorphismFromCocomplexToCartanEilenbergResolution( homres, 1, FreeResolutionCocomplexOfModule );
+connection_at_0 := ConnectingMorphismFromCocomplexToCartanEilenbergResolution( homres, 0, FreeResolutionCocomplex );
+connection_at_1 := ConnectingMorphismFromCocomplexToCartanEilenbergResolution( homres, 1, FreeResolutionCocomplex );
 
 homcon_at_0 := DualOnMorphisms( connection_at_0 );
 homcon_at_1 := DualOnMorphisms( connection_at_1 );
diff --git a/GradedModulePresentationsForCAP/gap/GradedModuleFunctors.gi b/GradedModulePresentationsForCAP/gap/GradedModuleFunctors.gi
@@ -681,17 +681,12 @@ InstallMethod( PurityFiltrationBySpectralSequence,
     
     embedding_list := List( [ 0 .. resolution_len ], i -> GeneralizedEmbeddingOfSpectralSequenceEntry( trhomCE, i, page, homCE, homres, connection_mor ) );
     
-    Print( "Computed embeddings\n" );
-    
     for i in Reversed( [ 1 .. Length( embedding_list ) ] ) do
         if IsZeroForObjects( UnderlyingHonestObject( Source( embedding_list[ i ] ) ) ) then
-            Print( "found a zero\n" );
             Remove( embedding_list, i );
         fi;
     od;
     
-    Print( "Removed irrelevant embeddings" );
-    
     embedding_list := Reversed( embedding_list );
     
     combined_image_embeddings := List( embedding_list, GeneralizedImageEmbedding );
@@ -703,8 +698,6 @@ InstallMethod( PurityFiltrationBySpectralSequence,
         od;
     fi;
     
-    Print( "First functors applied\n" );
-    
     pi_list := List( [ 2 .. Length( embedding_list ) ], i -> PreCompose( AsGeneralizedMorphism( combined_image_embeddings[ i ] ), 
                                                                          PseudoInverse( embedding_list[ i ] ) ) );
     
@@ -716,8 +709,6 @@ InstallMethod( PurityFiltrationBySpectralSequence,
         od;
     fi;
     
-    Print( "second functors applied\n" );
-    
     ## inital_step
     
     for i in [ 2 .. Length( combined_image_embeddings ) ] do
diff --git a/ModulePresentationsForCAP/PackageInfo.g b/ModulePresentationsForCAP/PackageInfo.g
@@ -10,7 +10,7 @@ SetPackageInfo( rec(
 
 PackageName := "ModulePresentationsForCAP",
 Subtitle := "Category R-pres for CAP",
-Version := "2025.08-02",
+Version := "2025.09-01",
 Date := (function ( ) if IsBound( GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE ) then return GAPInfo.SystemEnvironment.GAP_PKG_RELEASE_DATE; else return Concatenation( ~.Version{[ 1 .. 4 ]}, "-", ~.Version{[ 6, 7 ]}, "-01" ); fi; end)( ),
 License := "GPL-2.0-or-later",
 
diff --git a/ModulePresentationsForCAP/examples/Example.g b/ModulePresentationsForCAP/examples/Example.g
@@ -0,0 +1,19 @@
+LoadPackage( "ModulePres" );
+LoadPackage( "Homological" );
+LoadPackage( "Rings" );
+
+R := HomalgFieldOfRationalsInSingular( ) * "x,y,z,t";
+
+wmat := HomalgMatrix( "[ \
+x*y,  y*z,    z*t,        0,           0,          0,\
+x^3*z,x^2*z^2,0,          x*z^2*t,     -z^2*t^2,   0,\
+x^4,  x^3*z,  0,          x^2*z*t,     -x*z*t^2,   0,\
+0,    0,      x*y,        -y^2,        x^2-t^2,    0,\
+0,    0,      x^2*z,      -x*y*z,      y*z*t,      0,\
+0,    0,      x^2*y-x^2*t,-x*y^2+x*y*t,y^2*t-y*t^2,0,\
+0,    0,      0,          0,           -1,         1 \
+]", 7, 6, R );
+
+M := AsLeftPresentation( wmat );
+
+Rmod := CapCategory( M );
diff --git a/ModulePresentationsForCAP/examples/MorphismBetweenDirectSums.g b/ModulePresentationsForCAP/examples/MorphismBetweenDirectSums.g
@@ -1,23 +1,23 @@
 LoadPackage( "ModulePresentationsForCAP" );
 LoadPackage( "RingsForHomalg" );
 
-ZZ := HomalgRingOfIntegersInSingular( );
+zz := HomalgRingOfIntegersInSingular( );
 
-A := FreeLeftPresentation( 2, ZZ );
+A := FreeLeftPresentation( 2, zz );
 
-B := FreeLeftPresentation( 1, ZZ );
+B := FreeLeftPresentation( 1, zz );
 
-C := FreeLeftPresentation( 2, ZZ );
+C := FreeLeftPresentation( 2, zz );
  
-D := AsLeftPresentation( HomalgMatrix( [ [ 1, -1 ] ], ZZ ) );
+D := AsLeftPresentation( HomalgMatrix( [ [ 1, -1 ] ], zz ) );
 
-alpha := PresentationMorphism( A, HomalgMatrix( [ [ 1, -1 ], [ 0, 1 ] ], ZZ ), C );
+alpha := PresentationMorphism( A, HomalgMatrix( [ [ 1, -1 ], [ 0, 1 ] ], zz ), C );
 
-beta := PresentationMorphism( A, HomalgMatrix( [ [ 1, 0 ], [ 0, 1 ] ], ZZ ), D );
+beta := PresentationMorphism( A, HomalgMatrix( [ [ 1, 0 ], [ 0, 1 ] ], zz ), D );
 
-gamma := PresentationMorphism( B, HomalgMatrix( [ [ 1, 0 ] ], ZZ ) , C );
+gamma := PresentationMorphism( B, HomalgMatrix( [ [ 1, 0 ] ], zz ) , C );
 
-delta := PresentationMorphism( B, HomalgMatrix( [ [ 1, -1 ] ], ZZ ), D );
+delta := PresentationMorphism( B, HomalgMatrix( [ [ 1, -1 ] ], zz ), D );
 
 Display( UnderlyingMatrix( MorphismBetweenDirectSums( [ [ alpha, beta ], [ gamma, delta ] ] ) ) );
 
diff --git a/ModulePresentationsForCAP/examples/testfile.g b/ModulePresentationsForCAP/examples/testfile.g
@@ -1,14 +1,14 @@
 LoadPackage( "ModulePresentationsForCAP" );
-ZZ := HOMALG_MATRICES.ZZ;
-LeftPresentations( ZZ );
-RightPresentations( ZZ );
-A := HomalgMatrix( [ [ 1, 2 ], [ 2, 3 ] ], ZZ );
+zz := HOMALG_MATRICES.ZZ;
+LeftPresentations( zz );
+RightPresentations( zz );
+A := HomalgMatrix( [ [ 1, 2 ], [ 2, 3 ] ], zz );
 Aleft := AsLeftPresentation( A );
 Aright := AsRightPresentation( A );
-B := HomalgMatrix( [ [ 1, 2 ] ], ZZ );
+B := HomalgMatrix( [ [ 1, 2 ] ], zz );
 Bleft := AsLeftPresentation( B );
 Bright := AsRightPresentation( B );
-tau := HomalgMatrix( [ [ 1, 0 ], [ 0, 1 ] ], ZZ );
+tau := HomalgMatrix( [ [ 1, 0 ], [ 0, 1 ] ], zz );
 
 
 #########################
@@ -17,15 +17,15 @@ tau := HomalgMatrix( [ [ 1, 0 ], [ 0, 1 ] ], ZZ );
 ##
 #########################
 
-A := AsLeftPresentation( HomalgZeroMatrix( 0, 1, ZZ ) );
-phi := HomalgMatrix( [ [ 4 ] ], ZZ );
+A := AsLeftPresentation( HomalgZeroMatrix( 0, 1, zz ) );
+phi := HomalgMatrix( [ [ 4 ] ], zz );
 
 phi := PresentationMorphism( A, phi, A );
 
 epsilon := CokernelProjection( phi );
 
-tau := HomalgMatrix( [ [ 2 ] ], ZZ );
-B := AsLeftPresentation( HomalgMatrix( [ [ 8 ] ], ZZ ) );
+tau := HomalgMatrix( [ [ 2 ] ], zz );
+B := AsLeftPresentation( HomalgMatrix( [ [ 8 ] ], zz ) );
 tau := PresentationMorphism( A, tau, B );
 
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-LoadPackage( "ModulePresentationsForCAP" );`
	`1`	`+LoadPackage( "GradedModulePresentationsForCAP" );`
`2`	`2`	`LoadPackage( "HomologicalAlgebraForCAP" );`
`3`	`3`
`4`	`4`	`SwitchGeneralizedMorphismStandard( "span" );`