apply PackageJanitor

Author: kamalsaleh

.github/workflows/Tests.yml

@@ -22,10 +22,12 @@ 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/
+      - uses: actions/checkout@v3
+        with:
+          # the persisted token interferes with the subsplit token used below
+          persist-credentials: false
+          fetch-depth: 0
+      - run: cp -a $GITHUB_WORKSPACE /home/gap/.gap/pkg/
       - run: |
           export HOME="/home/gap"
           cd /home/gap/.gap/pkg/
@@ -52,15 +54,15 @@ jobs:
           [ -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 HigherHomologicalAlgebra -j $(nproc) --output-sync ci-test
-          cp ./HigherHomologicalAlgebra/.codecov.yml ./
-          (cd HigherHomologicalAlgebra && LANG=C.UTF-8 python3 process_coverage.py)
-          [ "$GITHUB_EVENT_NAME" != "schedule" ] && [ "${{ matrix.image }}" = "ghcr.io/homalg-project/gap-docker-master:latest" ] && ./HigherHomologicalAlgebra/upload_codecov.sh
+          make -C HigherHomologicalAlgebra -j $(nproc) --output-sync ci-test
+          cd HigherHomologicalAlgebra
+          LANG=C.UTF-8 python3 process_coverage.py
+          [ "$GITHUB_EVENT_NAME" != "schedule" ] && [ "${{ matrix.image }}" = "ghcr.io/homalg-project/gap-docker-master:latest" ] && ./upload_codecov.sh
           git config --global user.name "Bot"
           git config --global user.email "empty"
-          cd HigherHomologicalAlgebra
           CUR_SHA=$(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 }}"; \

BBGG/PackageInfo.g

@@ -74,7 +74,7 @@ PackageDoc := rec(
 ),
 
 Dependencies := rec(
-  GAP := ">= 4.11.1",
+  GAP := ">= 4.12.1",
   NeededOtherPackages := [
                       [ "GAPDoc", ">= 1.5" ],
 			                [ "GradedModulePresentationsForCAP", ">= 0.1" ],

BBGG/makefile

@@ -17,10 +17,10 @@ test: doc
 	gap tst/testall.g
 
 test-basic-spacing:
-	grep -RPl "\t" examples/ gap/ && echo "Tabs found" && exit 1 || exit 0
-	grep -RPl "\r" examples/ gap/ && echo "Windows line-endings found" && exit 1 || exit 0
-	# the second grep is a hack to fix the exit code with -L for grep <= 3.1
-	grep -RPzL "\n\z" examples/ gap/ | grep "" && echo "File with no newline at end of file found" && exit 1 || exit 0
+	# exit code 1 means no match, which is what we want here (exit code 2 signals an error)
+	grep -RPl "\t" examples/ gap/; test $$? -eq 1 || (echo "Tabs found" && exit 1)
+	grep -RPl "\r" examples/ gap/; test $$? -eq 1 || (echo "Windows line-endings found" && exit 1)
+	grep -RPzL "\n\z" examples/ gap/ | grep ""; test $$? -eq 1 || (echo "File with no newline at end of file found" && exit 1)
 
 test-doc: doc
 	cp -aT doc/ doc_tmp/
@@ -32,12 +32,12 @@ test-with-coverage: doc
 	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 '[^ ] +$$' gap/* && echo "Trailing whitespace found" && exit 1 || exit 0
+	# exit code 1 means no match, which is what we want here (exit code 2 signals an error)
+	grep -R "[^ [\"]  " gap/*.gi; test $$? -eq 1 || (echo "Duplicate spaces found" && exit 1)
+	grep -RE '[^ ] +$$' gap/*; test $$? -eq 1 || (echo "Trailing whitespace found" && exit 1)
 	for filename in gap/*; do \
 		echo $$filename; \
 		gap --quitonbreak --norepl --banner -c "LoadPackage(\"BBGG\"); SizeScreen([4096]); func := ReadAsFunction(\"$$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. \
 		cat "gap_spacing" | tail -n +2 | head -n -2 | sed 's/\[  \]/[ ]/g' | sed 's/(  )/( )/g' | sed 's/(  :/( :/g' | sed 's/ *$$//' | sed 's/^ *//' | grep -v "^$$" | tr "\n" " " | sed 's/;/;\n/g' > modified_gap_spacing; \

BBGG/tst/100_LoadPackage.tst

@@ -3,20 +3,22 @@
 #
 # This file tests if the package can be loaded without errors or warnings.
 #
+# do not load suggested dependencies automatically
+gap> PushOptions( rec( OnlyNeeded := true ) );
 gap> package_loading_info_level := InfoLevel( InfoPackageLoading );;
 gap> SetInfoLevel( InfoPackageLoading, PACKAGE_ERROR );;
-gap> LoadPackage( "BBGG", false );
-true
 gap> LoadPackage( "IO_ForHomalg", false );
 true
 gap> LoadPackage( "FreydCategoriesForCAP", false );
 true
-gap> SetInfoLevel( InfoPackageLoading, PACKAGE_INFO );;
-gap> LoadPackage( "BBGG" );
+gap> LoadPackage( "BBGG", false );
 true
+gap> SetInfoLevel( InfoPackageLoading, PACKAGE_INFO );;
 gap> LoadPackage( "IO_ForHomalg" );
 true
 gap> LoadPackage( "FreydCategoriesForCAP" );
 true
+gap> LoadPackage( "BBGG" );
+true
 gap> SetInfoLevel( InfoPackageLoading, package_loading_info_level );;
 gap> HOMALG_IO.show_banners := false;;

Bicomplexes/PackageInfo.g

@@ -82,7 +82,7 @@ PackageDoc := rec(
 ),
 
 Dependencies := rec(
-  GAP := ">= 4.11.1",
+  GAP := ">= 4.12.1",
   NeededOtherPackages := [ [ "GAPDoc", ">= 1.5" ],
                    [ "CAP", ">= 2021.05-02" ],
                    [ "ComplexesCategories", ">= 2020.03.12" ] ],

Bicomplexes/makefile

@@ -17,10 +17,10 @@ test: doc
 	gap tst/testall.g
 
 test-basic-spacing:
-	grep -RPl "\t" examples/ gap/ && echo "Tabs found" && exit 1 || exit 0
-	grep -RPl "\r" examples/ gap/ && echo "Windows line-endings found" && exit 1 || exit 0
-	# the second grep is a hack to fix the exit code with -L for grep <= 3.1
-	grep -RPzL "\n\z" examples/ gap/ | grep "" && echo "File with no newline at end of file found" && exit 1 || exit 0
+	# exit code 1 means no match, which is what we want here (exit code 2 signals an error)
+	grep -RPl "\t" examples/ gap/; test $$? -eq 1 || (echo "Tabs found" && exit 1)
+	grep -RPl "\r" examples/ gap/; test $$? -eq 1 || (echo "Windows line-endings found" && exit 1)
+	grep -RPzL "\n\z" examples/ gap/ | grep ""; test $$? -eq 1 || (echo "File with no newline at end of file found" && exit 1)
 
 test-doc: doc
 	cp -aT doc/ doc_tmp/
@@ -32,12 +32,12 @@ test-with-coverage: doc
 	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 '[^ ] +$$' gap/* && echo "Trailing whitespace found" && exit 1 || exit 0
+	# exit code 1 means no match, which is what we want here (exit code 2 signals an error)
+	grep -R "[^ [\"]  " gap/*.gi; test $$? -eq 1 || (echo "Duplicate spaces found" && exit 1)
+	grep -RE '[^ ] +$$' gap/*; test $$? -eq 1 || (echo "Trailing whitespace found" && exit 1)
 	for filename in gap/*; do \
 		echo $$filename; \
 		gap --quitonbreak --norepl --banner -c "LoadPackage(\"Bicomplexes\"); SizeScreen([4096]); func := ReadAsFunction(\"$$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. \
 		cat "gap_spacing" | tail -n +2 | head -n -2 | sed 's/\[  \]/[ ]/g' | sed 's/(  )/( )/g' | sed 's/(  :/( :/g' | sed 's/ *$$//' | sed 's/^ *//' | grep -v "^$$" | tr "\n" " " | sed 's/;/;\n/g' > modified_gap_spacing; \

Bicomplexes/tst/100_LoadPackage.tst

@@ -3,15 +3,17 @@
 #
 # This file tests if the package can be loaded without errors or warnings.
 #
+# do not load suggested dependencies automatically
+gap> PushOptions( rec( OnlyNeeded := true ) );
 gap> package_loading_info_level := InfoLevel( InfoPackageLoading );;
 gap> SetInfoLevel( InfoPackageLoading, PACKAGE_ERROR );;
-gap> LoadPackage( "Bicomplexes", false );
-true
 gap> LoadPackage( "ModulePresentations", false );
 true
-gap> SetInfoLevel( InfoPackageLoading, PACKAGE_INFO );;
-gap> LoadPackage( "Bicomplexes" );
+gap> LoadPackage( "Bicomplexes", false );
 true
+gap> SetInfoLevel( InfoPackageLoading, PACKAGE_INFO );;
 gap> LoadPackage( "ModulePresentations" );
 true
+gap> LoadPackage( "Bicomplexes" );
+true
 gap> SetInfoLevel( InfoPackageLoading, package_loading_info_level );;

ComplexesCategories/PackageInfo.g

@@ -72,7 +72,7 @@ PackageDoc := rec(
 ),
 
 Dependencies := rec(
-  GAP := ">= 4.11.1",
+  GAP := ">= 4.12.1",
   NeededOtherPackages := [
                             [ "AutoDoc", ">= 2019.09.04" ],
                             [ "CAP", ">= 2022.09-02" ],

ComplexesCategories/makefile

@@ -17,10 +17,10 @@ test: doc
 	gap tst/testall.g
 
 test-basic-spacing:
-	grep -RPl "\t" examples/ gap/ && echo "Tabs found" && exit 1 || exit 0
-	grep -RPl "\r" examples/ gap/ && echo "Windows line-endings found" && exit 1 || exit 0
-	# the second grep is a hack to fix the exit code with -L for grep <= 3.1
-	grep -RPzL "\n\z" examples/ gap/ | grep "" && echo "File with no newline at end of file found" && exit 1 || exit 0
+	# exit code 1 means no match, which is what we want here (exit code 2 signals an error)
+	grep -RPl "\t" examples/ gap/; test $$? -eq 1 || (echo "Tabs found" && exit 1)
+	grep -RPl "\r" examples/ gap/; test $$? -eq 1 || (echo "Windows line-endings found" && exit 1)
+	grep -RPzL "\n\z" examples/ gap/ | grep ""; test $$? -eq 1 || (echo "File with no newline at end of file found" && exit 1)
 
 test-doc: doc
 	cp -aT doc/ doc_tmp/
@@ -32,12 +32,12 @@ test-with-coverage: doc
 	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 '[^ ] +$$' gap/* && echo "Trailing whitespace found" && exit 1 || exit 0
+	# exit code 1 means no match, which is what we want here (exit code 2 signals an error)
+	grep -R "[^ [\"]  " gap/*.gi; test $$? -eq 1 || (echo "Duplicate spaces found" && exit 1)
+	grep -RE '[^ ] +$$' gap/*; test $$? -eq 1 || (echo "Trailing whitespace found" && exit 1)
 	for filename in gap/*; do \
 		echo $$filename; \
 		gap --quitonbreak --norepl --banner -c "LoadPackage(\"ComplexesCategories\"); SizeScreen([4096]); func := ReadAsFunction(\"$$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. \
 		cat "gap_spacing" | tail -n +2 | head -n -2 | sed 's/\[  \]/[ ]/g' | sed 's/(  )/( )/g' | sed 's/(  :/( :/g' | sed 's/ *$$//' | sed 's/^ *//' | grep -v "^$$" | tr "\n" " " | sed 's/;/;\n/g' > modified_gap_spacing; \

ComplexesCategories/tst/100_LoadPackage.tst

@@ -3,28 +3,26 @@
 #
 # This file tests if the package can be loaded without errors or warnings.
 #
+# do not load suggested dependencies automatically
+gap> PushOptions( rec( OnlyNeeded := true ) );
 gap> package_loading_info_level := InfoLevel( InfoPackageLoading );;
 gap> SetInfoLevel( InfoPackageLoading, PACKAGE_ERROR );;
-gap> LoadPackage( "ComplexesCategories", false );
-true
 gap> LoadPackage( "IO_ForHomalg", false );
 true
 gap> LoadPackage( "ModulePresentations", false );
 true
 gap> LoadPackage( "FreydCategoriesForCAP", false );
 true
-gap> LoadPackage( "LinearAlgebraForCAP", false );
+gap> LoadPackage( "ComplexesCategories", false );
 true
 gap> SetInfoLevel( InfoPackageLoading, PACKAGE_INFO );;
-gap> LoadPackage( "ComplexesCategories" );
-true
 gap> LoadPackage( "IO_ForHomalg" );
 true
 gap> LoadPackage( "ModulePresentations" );
 true
 gap> LoadPackage( "FreydCategoriesForCAP" );
 true
-gap> LoadPackage( "LinearAlgebraForCAP" );
+gap> LoadPackage( "ComplexesCategories" );
 true
 gap> SetInfoLevel( InfoPackageLoading, package_loading_info_level );;
 gap> HOMALG_IO.show_banners := false;;