Merge pull request #42 from zickgraf/master

Apply PackageJanitor and adjust to homalg-project/CAP_project#1073

.codecov.yml

@@ -1,7 +1,3 @@
 codecov:
   disable_default_path_fixes: true
   require_ci_to_pass: false
-fixes:
-  - "/home/gap/.gap/pkg/FinGSetsForCAP/::"
-ignore:
-  - "home/"

.github/workflows/Tests.yml

@@ -22,10 +22,11 @@ jobs:
     steps:
       # keep workflow active even if repository has no activity for 60 days (do not execute for pull requests)
       - run: '[ "$GITHUB_EVENT_NAME" = "pull_request" ] || curl --fail -X PUT -H "Accept: application/vnd.github.v3+json" -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/repos/$GITHUB_REPOSITORY/actions/workflows/Tests.yml/enable'
-      - uses: actions/checkout@v1
-      - run: mkdir -p /home/gap/.gap/pkg/
-      - run: sudo cp -a $GITHUB_WORKSPACE /home/gap/.gap/pkg/
-      - run: sudo chown -R gap:gap /home/gap/.gap/pkg/
+      # checkout needs access to temporary directory
+      - run: sudo chmod 1777 $RUNNER_TEMP
+      - run: sudo chown gap:gap $GITHUB_WORKSPACE
+      - uses: actions/checkout@v3
+      - run: cp -a $GITHUB_WORKSPACE /home/gap/.gap/pkg/
       - run: |
           export HOME="/home/gap"
           cd /home/gap/.gap/pkg/
@@ -40,21 +41,23 @@ jobs:
           # build documentation of packages which we might want to reference, keep this in sync with `release-gap-package`
           [ -d "CAP_project/CAP" ] && make -C "CAP_project/CAP" doc
           [ -d "CAP_project/CompilerForCAP" ] && make -C "CAP_project/CompilerForCAP" doc
-          [ -d "CAP_project/FreydCategoriesForCAP" ] && make -C "CAP_project/FreydCategoriesForCAP" doc
           [ -d "CAP_project/MonoidalCategories" ] && make -C "CAP_project/MonoidalCategories" doc
+          [ -d "CAP_project/CartesianCategories" ] && make -C "CAP_project/CartesianCategories" doc
+          [ -d "CAP_project/FreydCategoriesForCAP" ] && make -C "CAP_project/FreydCategoriesForCAP" doc
           [ -d "HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra" ] && make -C "HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra" doc
           [ -d "homalg_project/homalg" ] && make -C "homalg_project/homalg" doc
           [ -d "homalg_project/Modules" ] && make -C "homalg_project/Modules" doc
           [ -d "Toposes" ] && make -C "Toposes" doc
           TERM=dumb make -C FinGSetsForCAP -j $(nproc) --output-sync ci-test
           cp ./FinGSetsForCAP/.codecov.yml ./
-          (cd FinGSetsForCAP && LANG=C.UTF-8 python3 process_coverage_ignored_lines.py)
+          (cd FinGSetsForCAP && LANG=C.UTF-8 python3 process_coverage.py)
           [ "$GITHUB_EVENT_NAME" != "schedule" ] && [ "${{ matrix.image }}" = "ghcr.io/homalg-project/gap-docker-master:latest" ] && ./FinGSetsForCAP/upload_codecov.sh
           git config --global user.name "Bot"
           git config --global user.email "empty"
           cd FinGSetsForCAP
           CUR_SHA=$(git rev-parse --verify HEAD)
           if [ "${{ matrix.image }}" = "ghcr.io/homalg-project/gap-docker:latest" ] && [ "$CUR_SHA" = "$(git rev-parse origin/master)" ] && [ $(dirname "$GITHUB_REPOSITORY") = "homalg-project" ]; then \
+            git fetch origin gh-pages; \
             git worktree add gh-pages/ gh-pages || (echo "There was an error. Make sure there is a branch named 'gh-pages'. See https://github.com/homalg-project/PackageJanitor#error-there-was-an-error-make-sure-there-is-a-branch-named-gh-pages"; exit 1); \
             git checkout master; \
             LANG=C.UTF-8 ./make_dist.sh --token "${{ secrets.GITHUB_TOKEN }}"; \

PackageInfo.g

@@ -10,7 +10,7 @@ SetPackageInfo( rec(
 
 PackageName := "FinGSetsForCAP",
 Subtitle := "The elementary topos of (skeletal) finite G-sets",
-Version := "2021.05-02",
+Version := "2022.09-01",
 
 Date := Concatenation( "01/", ~.Version{[ 6, 7 ]}, "/", ~.Version{[ 1 .. 4 ]} ),
 License := "GPL-2.0-or-later",
@@ -99,7 +99,7 @@ Dependencies := rec(
   GAP := ">= 4.11.1",
   NeededOtherPackages := [
                    [ "GAPDoc", ">= 1.5" ],
-                   [ "CAP", ">= 2021.05-02" ],
+                   [ "CAP", ">= 2022.09-23" ],
                    [ "Toposes", ">= 2021.03-01" ],
                    ],
   SuggestedOtherPackages := [

README.md

@@ -35,8 +35,8 @@ To obtain current versions of all dependencies, `git clone` (or `git pull` to up
 [date-img]: https://img.shields.io/endpoint?url=https://homalg-project.github.io/FinGSetsForCAP/badge_date.json&label=🔗%20released%20on&color=yellow
 [date-url]: https://homalg-project.github.io/FinGSetsForCAP/view_release.html
 
-[tests-img]: https://github.com/homalg-project/FinGSetsForCAP/workflows/Tests/badge.svg?branch=master
-[tests-url]: https://github.com/homalg-project/FinGSetsForCAP/actions?query=workflow%3ATests+branch%3Amaster
+[tests-img]: https://github.com/homalg-project/FinGSetsForCAP/actions/workflows/Tests.yml/badge.svg?branch=master
+[tests-url]: https://github.com/homalg-project/FinGSetsForCAP/actions/workflows/Tests.yml?query=branch%3Amaster
 
 [codecov-img]: https://codecov.io/gh/homalg-project/FinGSetsForCAP/branch/master/graph/badge.svg
 [codecov-url]: https://codecov.io/gh/homalg-project/FinGSetsForCAP

gap/EndAsEqualizer.gi

@@ -138,7 +138,7 @@ InstallGlobalFunction( EndAsEqualizer, function ( C, HomC, ForgetfulFunctor, Ind
     LambdaComponents := Concatenation( List( [ 1 .. Size( IndexSet ) ], c_1 -> List( [ 1 .. Size( IndexSet ) ], c_2 -> GetLambdaComponent( IndexSet, Projections, c_1, c_2 ) ) ) );
     Lambda := UniversalMorphismIntoDirectProduct( LambdaComponents );
 
-    iota := EmbeddingOfEqualizer( [ Rho, Lambda ] );
+    iota := EmbeddingOfEqualizer( S, [ Rho, Lambda ] );
     EndSkeletal := Source( iota );
 
     # each element x in EndSkeletal corresponds to a tuple of integers by taking all projections of the image of x under the embedding iota

gap/SkeletalFinGSetsForCAP.gi

@@ -751,13 +751,11 @@ InstallMethod( SkeletalFinGSets,
 
     ##
     AddEmbeddingOfEqualizer( SkeletalFinGSets,
-      function ( cat, D )
-        local phi_1, S, positions;
+      function ( cat, S, D )
+        local phi_1, positions;
 
         phi_1 := D[1];
 
-        S := Source( phi_1 );
-
         D := D{[ 2 .. Length( D ) ]};
 
         positions := Filtered( Positions( S ), p -> ForAll( D, phi -> Component( phi_1, p ) = Component( phi, p ) ) );
@@ -956,12 +954,11 @@ InstallMethod( SkeletalFinGSets,
 
     ##
     AddProjectionOntoCoequalizer( SkeletalFinGSets,
-      function ( cat, D )
-        local S, T, M, N, Cq, rangePositions, imgs, j, r, previousImagePositions, preimagePositions, imagePositions, iota, preimageEmbedding, imageEmbedding, projection, imageEmbeddings, projections, tau, alpha, pi;
+      function ( cat, T, D )
+        local S, M, N, Cq, rangePositions, imgs, j, r, previousImagePositions, preimagePositions, imagePositions, iota, preimageEmbedding, imageEmbedding, projection, imageEmbeddings, projections, tau, alpha, pi;
 
         S := Source( D[1] );
-        T := Range( D[1] );
-
+
         M := AsList( S );
         N := AsList( T );
 

makefile

@@ -29,14 +29,14 @@ test-doc: doc
 
 test-with-coverage: doc
 	gap --quitonbreak --cover stats tst/testall.g
-	echo 'LoadPackage("profiling"); OutputJsonCoverage("stats", "coverage.json");' | gap --quitonbreak
+	gap --quitonbreak --norepl -c 'LoadPackage("profiling"); OutputJsonCoverage("stats", "coverage.json");'
 
 test-spacing:
 	grep -R "[^ [\"]  " gap/*.gi && echo "Duplicate spaces found" && exit 1 || exit 0
 	grep -RE '[^ ] +$$' gap/* && echo "Trailing whitespace found" && exit 1 || exit 0
 	for filename in gap/*; do \
 		echo $$filename; \
-		echo "LoadPackage(\"FinGSetsForCAP\"); SizeScreen([4096]); func := ReadAsFunction(\"$$filename\"); FileString(\"gap_spacing\", DisplayString(func));" | gap --quitonbreak --banner; \
+		gap --quitonbreak --norepl --banner -c "LoadPackage(\"FinGSetsForCAP\"); SizeScreen([4096]); func := ReadAsFunction(\"$$filename\"); FileString(\"gap_spacing\", DisplayString(func));"; \
 		echo -e "\033[0m"; \
 		# In a perfect world, the DisplayString of a function would exactly match our code. However, our line breaks and indentation might differ from the GAP ones, \
 		# so we remove all indentation, line breaks, and empty lines, and afterwards insert line breaks at semicolons again for better readability. \

process_coverage_ignored_lines.py → process_coverage.py

@@ -7,6 +7,12 @@
 # c) calls of `TryNextMethod` leading to external code.
 #######################################################
 
+# This script applies three rules to all coverage*.json files below the current working directory:
+# a) Remove all coverage information of files not below the current working directory
+#    (this technically includes "tst/testall.g" because it is not referenced by an absolute path).
+# b) Strip the current working directory from the paths of files below the current working directory.
+# c) Ignore lines with one of the "COVERAGE_IGNORE_..." annotations (see below).
+
 import json
 import re
 import os
@@ -17,14 +23,18 @@
 regex_next_line = re.compile("^\s*# COVERAGE_IGNORE_NEXT_LINE$")
 regex_return_void = re.compile("^\s*return;$")
 
-for coverage_filename in Path(".").glob("**/coverage*.json"):
+for coverage_filename in Path("../").glob("**/coverage*.json"):
     print("processing coverage file " + str(coverage_filename))
+    new_data = {}
+    new_data["coverage"] = {}
     with open(coverage_filename) as json_file:
         data = json.load(json_file)
         files = data["coverage"]
         for filename, lines_covered in files.items():
-            if filename.startswith(os.getcwd()):
+            if filename.startswith(os.getcwd() + "/"):
                 print(" processing code file " + filename)
+                # ignored lines will be delete from lines_covered in-place
+                new_data["coverage"][filename.replace(os.getcwd() + "/", "", 1)] = lines_covered
                 line_number = 0
                 ignoring = False
                 ignored_lines = []
@@ -77,4 +87,4 @@
                         del lines_covered[str(line_number)]
 
     with open(coverage_filename, "w") as outfile:
-        json.dump(data, outfile, indent=0)
+        json.dump(new_data, outfile, indent=0)

release-gap-package

@@ -461,7 +461,7 @@ fi
 chmod -R a+r .
 
 # replace links to packages which are possibly referenced in the documentation, keep this in sync with `Tests.yml.j2`
-for package in CAP_project/CAP CAP_project/CompilerForCAP CAP_project/FreydCategoriesForCAP CAP_project/MonoidalCategories HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra homalg_project/homalg homalg_project/Modules Toposes; do
+for package in CAP_project/CAP CAP_project/CompilerForCAP CAP_project/MonoidalCategories CAP_project/CartesianCategories CAP_project/FreydCategoriesForCAP HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra homalg_project/homalg homalg_project/Modules Toposes; do
 
     # adjust links to other manuals
     # Note that we cannot use sed's `-i` option for in-place editing, as

tst/testall.g

@@ -11,6 +11,25 @@ options := rec(
     ),
 );
 
+# reverse RecNames 50% of the time to detect code relying on the order of RecNames
+if Random( RandomSource( IsMersenneTwister, NanosecondsSinceEpoch( ) ), [ false, true ] ) then
+
+    Display( "Executing with reversed RecNames" );
+
+    MakeReadWriteGlobal( "RecNames" );
+
+    old_RecNames := RecNames;
+
+    RecNames := record -> Reversed( old_RecNames( record ) );
+
+    MakeReadOnlyGlobal( "RecNames" );
+
+else
+
+    Display( "Executing with non-reversed RecNames" );
+
+fi;
+
 TestDirectory( DirectoriesPackageLibrary( "FinGSetsForCAP", "tst" ), options );
 
 FORCE_QUIT_GAP( 1 ); # if we ever get here, there was an error