Capture package examples by default

.github/workflows/test_build.yml

@@ -142,8 +142,13 @@ jobs:
       - name: Build Macaulay2 using Ninja
         if: matrix.build-system == 'cmake'
         run: |
-          cmake --build . --target M2-core M2-emacs install-packages
-          if [[ "${{ runner.os }}" == "Linux" ]] && [[ "${{ matrix.build-system }}" == "cmake" ]]; then
+          cmake --build . --target M2-core M2-emacs
+
+      - name: Install packages using Ninja
+        if: matrix.build-system == 'cmake'
+        run: |
+          cmake --build . --target install-packages
+          if [[ "${{ runner.os }}" == "Linux" ]]; then
               sudo apt-get install -y -q --no-install-recommends dpkg-dev
               echo "GIT_COMMIT=`git describe --dirty --always --match HEAD`" >> $GITHUB_ENV
               cpack -G DEB
@@ -168,6 +173,11 @@ jobs:
           ../../configure --with-system-gc --with-fplll
 
       - name: Build Macaulay2 using Make
+        if: matrix.build-system == 'autotools'
+        run: |
+          make -j$(nproc 2>/dev/null || sysctl -n hw.logicalcpu) PACKAGES=
+
+      - name: Install packages using Make
         if: matrix.build-system == 'autotools'
         run: |
           make -j$(nproc 2>/dev/null || sysctl -n hw.logicalcpu)

M2/Macaulay2/m2/examples.m2

@@ -124,27 +124,25 @@ capture String := opts -> s -> if opts.UserMode then capture' s else (
 protect symbol capture
 
 -- returns false if the inputs or the package are not known to behave well with capture
--- this is also used in testing.m2, where isTest is set to true.
-isCapturable = (inputs, pkg, isTest) -> (
+-- this is also used in testing.m2
+isCapturable = (inputs, pkg) -> (
     -- argumentMode is mainly used by ctest to select M2 subprocess arguments,
     -- or whether capture should be avoided; see packages/CMakeLists.txt
     -- alternatively, no-capture-flag can be used with an example or test
     if argumentMode & NoCapture =!= 0 or match("no-capture-flag", inputs) then return false;
     -- strip commented segments first
     inputs = replace("--.*$", "",            inputs);
     inputs = replace("-\\*(.|\n)*?\\*-", "", inputs);
-    -- TODO: remove this when the effects of capture on other packages is reviewed
-    (isTest or match({"FirstPackage", "Macaulay2Doc"},            pkg#"pkgname"))
-    and not match({
-	    "FastMinors", "TerraciniLoci",
+    not match({
+	    "FastMinors", "TerraciniLoci", "OldPolyhedra", "Normaliz",
 	    "MultiprojectiveVarieties", "SpecialFanoFourfolds",
 	    "EngineTests", "ThreadedGB", "RunExternalM2"}, pkg#"pkgname")
     and not (match({"Cremona"}, pkg#"pkgname") and version#"pointer size" == 4)
     -- FIXME: these are workarounds to prevent bugs, in order of priority for being fixed:
     and not match("(gbTrace|NAGtrace)",                       inputs) -- cerr/cout directly from engine isn't captured
     and not match("(notify|stopIfError|debuggingMode)",       inputs) -- stopIfError and debuggingMode may be fixable
     and not match("(alarm|exec|exit|quit|restart|run)\\b",    inputs) -- these commands interrupt the interpreter
-    and not match("(capture|read|input|load|needs)\\b",       inputs) -- these commands hide undesirable functions
+    and not match("(capture|read|input|load|needs|check)\\b", inputs) -- these commands hide undesirable functions
     and not match("([Cc]ommand|fork|schedule|thread|Task)",   inputs) -- remove when threads work more predictably
     and not match("(temporaryFileName)",                      inputs) -- this is sometimes bug prone
     and not match("(addHook|export|newPackage)",              inputs) -- these commands have permanent effects
@@ -242,7 +240,7 @@ storeExampleOutput = (pkg, fkey, outf, verboseLog) -> (
 captureExampleOutput = (desc, inputs, pkg, inf, outf, errf, data, inputhash, changeFunc, usermode) -> (
     stdio << flush; -- just in case previous timing information hasn't been flushed yet
     -- try capturing in the same process
-    if isCapturable(inputs, pkg, false) then (
+    if isCapturable(inputs, pkg) then (
 	desc = concatenate(desc, 62 - #desc);
 	stderr << commentize pad("capturing " | desc, 72) << flush; -- the timing info will appear at the end
 	(err, output) := capture(inputs, UserMode => false);

M2/Macaulay2/m2/testing.m2

@@ -53,7 +53,7 @@ captureTestResult := (desc, teststring, pkg, usermode) -> (
     -- TODO: remove this when capture uses ArgQ
     if usermode === not noinitfile then
     -- try capturing in the same process
-    if isCapturable(teststring, pkg, true) then (
+    if isCapturable(teststring, pkg) then (
 	checkmsg("capturing", desc);
 	-- TODO: adjust and pass argumentMode, instead. This can be done earlier, too.
 	-- Note: UserMode option of capture is not related to UserMode option of check

M2/Macaulay2/packages/GroebnerWalk.m2

@@ -552,7 +552,7 @@ Description
   Text
     while running at Level 2 gives some conversion information.
   Example
-    setWalkTrace 2;
+    setWalkTrace 2; -* no-capture-flag *-
     groebnerWalk(gb I1, R2)
 SeeAlso
   groebnerWalk
@@ -596,7 +596,7 @@ Description
     down the computation, and is not recommended except for testing.
   Example
     getWalkTrace()
-    setWalkTrace 2;
+    setWalkTrace 2; -* no-capture-flag *-
     getWalkTrace()
 SeeAlso
   groebnerWalk

M2/Macaulay2/packages/LatticePolytopes.m2

@@ -211,7 +211,7 @@ toricBlowUp(Polyhedron,Polyhedron,ZZ) := (P,F,k) -> (
             and contains(e,(facesAsPolyhedra((dim F),F))_0)
         ));
     pt := k * matrix{(vertices Edges_i)_0+(vertices Edges_i)_1-2*(vertices F)_0}*(1/(#latticePoints(Edges_i)-1))+matrix((vertices F)_0);
-    return intersection(A||E,b||(E*pt)));
+    polyhedronFromHData(A||E,b||(E*pt)));
 
 
 
@@ -685,9 +685,9 @@ iskCayleykEdges(Polyhedron):=P->(
 	 if length(L)==2 then(
 	     k:=(L_1-L_0)/gcd(flatten entries(A^{i}));
 	     if k==minLen then(
-		 H0:=intersection(A^{i}||-A^{i},matrix{{L_0},{-L_0}});
+		 H0:=polyhedronFromHData(A^{i}||-A^{i},matrix{{L_0},{-L_0}});
 		 P0=intersection(P,H0);
-		 H1:=intersection(A^{i}||-A^{i},matrix{{L_1},{-L_1}});
+		 H1:=polyhedronFromHData(A^{i}||-A^{i},matrix{{L_1},{-L_1}});
 		 P1=intersection(P,H1);
 		 boolean=false;
 	     );

M2/Macaulay2/packages/Macaulay2Doc/functions/check-doc.m2

@@ -87,7 +87,7 @@ Node
 
       For example, to run the tests for the @TO "FirstPackage::FirstPackage"@ package, use:
     Example
-      needsPackage "FirstPackage" -* no-capture-flag *-
+      needsPackage "FirstPackage"
       check_1 FirstPackage
       check FirstPackage
     Text

M2/Macaulay2/packages/Msolve.m2

@@ -305,7 +305,7 @@ Node
 	  Example
 	      R = QQ[x,y,z]
 	      I = ideal(x, y, z)
-	      msolveGB(I, Verbosity => 2, Threads => 6)
+	      msolveGB(I, Verbosity => 2, Threads => 6) -* no-capture-flag *-
     References
       [1] The msolve library: @HREF {"https://msolve.lip6.fr"}@;
 

M2/Macaulay2/packages/NumericalSchubertCalculus/doc.m2

@@ -430,7 +430,7 @@ document{
        "setVerboseLevel 0;",
        "S = solveSchubertProblem(SchPblm,2,4)",
        "assert all(S,s->checkIncidenceSolution(s,SchPblm))",
-       "setVerboseLevel 1;",
+       "setVerboseLevel 1; -* no-capture-flag *-",
        "S = solveSchubertProblem(SchPblm,2,4)",
        "assert all(S,s->checkIncidenceSolution(s,SchPblm))"
        },

M2/Macaulay2/packages/Python/doc.m2

@@ -612,7 +612,7 @@ doc ///
       @TO "toPython"@.
     Example
       math = import "math"
-      setattr(math, "pi", 22/7)
+      setattr(math, "pi", 22/7) -* no-capture-flag *-
       math@@pi
     Text
       As with @TO "getattr"@, when using the shortcut @TT "\@\@"@, @TT "y"@

M2/Macaulay2/packages/RandomMonomialIdeals.m2

@@ -1704,7 +1704,7 @@ doc ///
       using the function writeSample. 
       This shows how to retrieve that stored sample and have it loaded as an object of type Sample: 
     Example 
-      writeSample(sample(ER(2,3,0.1),5), "testDirectory")
+      writeSample(sample(ER(2,3,0.1),5), "testDirectory") -* no-capture-flag *-
       mySample = sample("testDirectory")
       peek mySample 
   SeeAlso
@@ -1846,7 +1846,7 @@ doc ///
       about the model used to generate the sample, and another text file contains the 
       information about the sample itself. 
     Example
-      writeSample(sample(ER(2,3,0.1),5), "testDirectory")
+      writeSample(sample(ER(2,3,0.1),5), "testDirectory") -* no-capture-flag *-
       mySample = sample("testDirectory")
       peek mySample 
   SeeAlso

M2/Macaulay2/packages/Tableaux/documentation.m2

@@ -112,7 +112,7 @@ Description
     The inner shape may be drawn by calling drawInnerShape.
   Example
     T'' = skewTableau(new Partition from {5,4,-1}, new Partition from {2,4,-3})
-    drawInnerShape true
+    drawInnerShape true -* no-capture-flag *-
     T''
     drawInnerShape false
     T''
@@ -420,7 +420,7 @@ Description
   Text
     The number of rows is the same as largest part in its shape, minus the smallest part in the shape.
   Example
-    drawInnerShape true
+    drawInnerShape true -* no-capture-flag *-
     T = skewTableau(new Partition from {4,3,1}, new Partition from {1,1,1})
     numColumns T
   Text

M2/Macaulay2/packages/XML.m2

@@ -558,7 +558,7 @@ Node
  Description
   Example
    xmlNewRoot "foo"
-   xmlDocDump oo
+   xmlDocDump oo -* no-capture-flag *-
  SeeAlso
   xmlDocDump
 Node
@@ -613,7 +613,7 @@ Node
    xmlAddElement(n,"key")
    xmlAddText(oo,"frobble 你好")
    n
-   xmlDocDump n   
+   xmlDocDump n -* no-capture-flag *-
  SeeAlso
   xmlNewRoot
 Node