Iss36 tmp dir

CONTRIBUTING.md

@@ -8,7 +8,7 @@ bug reports, and code reviews.
 * Before you report an issue, or wish to add functionality, please try
   and check to see if there are existing issues or pull requests. We
   do not want you wasting your time duplicating somebody else's work.
-	
+
 * For substantial changes it is also advisable to contact us before
   you start work to discuss your ideas.
 
@@ -20,10 +20,10 @@ bug reports, and code reviews.
 * To help increase the chance of your pull request being accepted:
 
   - Run the tests.
-  
+
   - Update the documentation, tests, examples, guides, and whatever
     else is affected by your contribution.
-	
+
   - Use appropriate code formatting for your code.
 
 * Try to follow *the Campsite Rule:* leave the codebase in better

PackageInfo.g

@@ -16,8 +16,8 @@ SetPackageInfo(
         rec( 
              PackageName := "QDistRnd",             
              Subtitle := "Calculate the distance of a q-ary quantum stabilizer code",
-             Version := "0.9.1",
-             Date := "12/01/2024",  
+             Version := "0.9.2",
+             Date := "19/01/2024",  
              License := "GPL-2.0-or-later",
              PackageWWWHome := "https://QEC-pages.github.io/QDistRnd", 
              SourceRepository :=

doc/body.autodoc

@@ -436,7 +436,7 @@ storage options for elements of an extension field can in be used.
   $a_0+a_1x+a_2x^2+\ldots +a_{m-1}x^{m-1}$ as
   digits of a $p$-ary integer $(a_{m-1}a_{m-2}\ldots a_2a_1)_p$. 
   (**this is currently not implemented**)
-	
+        
 @Subsection Matrix storage format
 
 There are two recommended storage formats.
@@ -593,7 +593,7 @@ i     j     element[i,j]
 @EndCode
 @InsertCode MMXFormatLineB
 
-* `type=complex`:	
+* `type=complex`:       
 @BeginCode  MMXFormatLineC
 i     j     a[i,j]     b[i,j]
 @EndCode
@@ -649,7 +649,7 @@ is specified explicitly, this matrix would work with any
 prime field.
 
 @BeginCode SampleFileA
-%%MatrixMarket matrix coordinate integer general		
+%%MatrixMarket matrix coordinate integer general                
 % Field: GF(7)
 % 5-qubit code generator matrix / normal storage with intercalated cols
 5 10 20
@@ -679,7 +679,7 @@ prime field.
 This same matrix is stored in the file `matrices/n5k1A.mtx`.  This is
 how the matrix can be read and distance calculated:
 @BeginExample
-	filedir:=DirectoriesPackageLibrary("QDistRnd","matrices");;
+        filedir:=DirectoriesPackageLibrary("QDistRnd","matrices");;
     lis:=ReadMTXE(Filename(filedir,"n5k1A.mtx" ));;
     Print("field ",lis[1],"\n");
 #! field GF(7)

examples/examples.g

@@ -1,12 +1,14 @@
 #! @Chapter Examples
 #! @Section The 5-qubit code
 
-#! Generate the matrix of the 5-qubit code over GF(3) with the stabilizer group
+#! In this example, we generate the matrix of the 5-qubit code over GF(3) with 
+#! the stabilizer group
 #! generated by cyclic shifts of the operator $X_0Z_1 \bar Z_2 \bar
 #! X_3$ which corresponds to the polynomial $h(x)=1+x^3-x^5-x^6$
 #! (a factor $X_i^a$ corresponds to a monomial $a x^{2i}$, and a
 #! factor $Z_i^b$ to a monomial $b x^{2i+1}$),  
-#! calculate the distance, and save into the file.
+#! calculate the distance, save into a file using the function `WriteMTXE()`, and read the file back in 
+#! using the function `ReadMTXE()`. 
 #! @BeginExample
 q:=3;; F:=GF(q);; 
 x:=Indeterminate(F,"x");; poly:=One(F)*(1+x^3-x^5-x^6);;
@@ -19,14 +21,39 @@ Display(mat);
 #!  . 2 2 . . . 1 . . 1
 d:=DistRandStab(mat,100,1,0 : field:=F,maxav:=20/n);
 #! 3
-WriteMTXE("matrices/n5_q3_complex.mtx",3,mat,
+tmp_file_name:=Filename(DirectoryTemporary(),"n5_q3_complex.mtx");;
+WriteMTXE(tmp_file_name,3,mat,
         "% The 5-qubit code [[5,1,3]]_3",
         "% Generated from h(x)=1+x^3-x^5-x^6",
-        "% Example from the QDistRnd GAP package"   : field:=F);
-#! File matrices/n5_q3_complex.mtx was created
+        "% Example from the QDistRnd GAP package"   : field:=F);;
+lis:=ReadMTXE(tmp_file_name);;  # Filename(filedir,"n5_q3_complex.mtx")
+lis[1]; # the field 
+#! GF(3)
+lis[2]; # converted to `pair=1`
+#! 1
+Display(lis[3]);
+#!  1 . . 1 . 2 2 . . .
+#!  . . 1 . . 1 . 2 2 .
+#!  2 . . . 1 . . 1 . 2
+#!  . 2 2 . . . 1 . . 1
 #! @EndExample
-
-#! Here is the contents of the resulting file which also illustrates
+#! The function `WriteMTXE()` takes several arguments which specify the details of the output file format
+#! and the optional comments, see Section <Ref Sect="Section_IOFunctions"/> for the details.
+#! These ensure that all information about the code is written into the file, so that for 
+#! reading with the function `ReadMTXE()` only the file name is needed.
+#! Output is a list: `[field,pair,matrix,(list of comments)]`, where the `pair` parameter describes 
+#! the ordering of columns in the matrix, see  <Ref Chap="Chapter_FileFormat"/>.  
+#! Notice that a `pair=2` or `pair=3` matrix is always converted to `pair=1`, i.e., with $2n$
+#! intercalated columns $(a_1,b_1,a_2,b_2,\ldots)$. 
+#! The remaining portion is the list of comments.  Notice that the 1st
+#! and the last comment lines have been added automatically.
+#! @BeginLog
+#! gap> lis[4];
+#! [ "% Field: GF(3)", "% The 5-qubit code [[5,1,3]]_3",
+#!   "% Generated from h(x)=1+x^3-x^5-x^6",
+#!   "% Example from the QDistRnd GAP package", "% Values Z(3) are given" ]
+#! @EndLog
+#! Here is the contents of the created file which illustrates
 #! the `coordinate complex` data format.  Here a pair $(a_{i,j},b_{i,j})$
 #! in row $i$ and column $j$ is written as a row of 4 integers, "$i$ $j$ $a_{i,j}$
 #! $b_{i,j}$", e.g., "1 2 0 1" 
@@ -58,33 +85,6 @@ WriteMTXE("matrices/n5_q3_complex.mtx",3,mat,
 #! 4 5 0 1
 #! @EndLog
 
-#! And now let us read the matrix back from the file using the function `ReadMTXE`.   In the simplest
-#! case, only the file name is needed.
-#! Output is a list: `[field,pair,matrix,(list of comments)]`, where the `pair` parameter describes 
-#! the ordering of columns in the matrix, see  <Ref Chap="Chapter_FileFormat"/>.  
-#! Notice that a `pair=2` or `pair=3` matrix is always converted to `pair=1`, i.e., with $2n$
-#! intercalated columns $(a_1,b_1,a_2,b_2,\ldots)$. 
-#! @BeginExample
-lis:=ReadMTXE("matrices/n5_q3_complex.mtx");;  
-lis[1]; # the field 
-#! GF(3)
-lis[2]; # converted to `pair=1`
-#! 1
-Display(lis[3]);
-#!  1 . . 1 . 2 2 . . .
-#!  . . 1 . . 1 . 2 2 .
-#!  2 . . . 1 . . 1 . 2
-#!  . 2 2 . . . 1 . . 1
-#! @EndExample
-#! The remaining portion is the list of comments.  Notice that the 1st
-#! and the last comment lines have been added automatically.
-#! @BeginLog
-#! gap> lis[4];
-#! [ "% Field: GF(3)", "% The 5-qubit code [[5,1,3]]_3",
-#!   "% Generated from h(x)=1+x^3-x^5-x^6",
-#!   "% Example from the QDistRnd GAP package", "% Values Z(3) are given" ]
-#! @EndLog
-
 #! @Section Hyperbolic codes from a file
 
 #! Here we read two CSS matrices from two different files which