comply with AutoDoc v2025.12.19

Author: mohamed-barakat

.github/workflows/Tests.yml

@@ -56,6 +56,7 @@ jobs:
           if [ -d "CAP_project/CompilerForCAP" ]; then make -C "CAP_project/CompilerForCAP" doc; fi
           if [ -d "CAP_project/MonoidalCategories" ]; then make -C "CAP_project/MonoidalCategories" doc; fi
           if [ -d "CAP_project/CartesianCategories" ]; then make -C "CAP_project/CartesianCategories" doc; fi
+          if [ -d "CAP_project/AdditiveClosuresForCAP" ]; then make -C "CAP_project/AdditiveClosuresForCAP" doc; fi
           if [ -d "CAP_project/FreydCategoriesForCAP" ]; then make -C "CAP_project/FreydCategoriesForCAP" doc; fi
           if [ -d "HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra" ]; then make -C "HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra" doc; fi
           if [ -d "homalg_project/homalg" ]; then make -C "homalg_project/homalg" doc; fi
@@ -81,7 +82,9 @@ jobs:
             TOKEN="${{ secrets.GITHUB_TOKEN }}" ./dev/simulate_dist.sh; \
           fi
       - name: Upload code coverage
-        if: github.event_name != 'schedule' && matrix.image == 'ghcr.io/homalg-project/gap-docker-master:latest'
+        if: github.event_name != 'schedule' && matrix.image == 'ghcr.io/homalg-project/gap-docker:latest'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         run: |
           cd LoopIntegrals
           ./dev/upload_codecov.sh

PackageInfo.g

@@ -10,7 +10,7 @@ SetPackageInfo( rec(
 
 PackageName := "LoopIntegrals",
 Subtitle := "Compute master integrals using commutative and noncommutative methods from computational algebraic geometry",
-Version := "2025.11-01",
+Version := "2025.12-01",
 
 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)( ),
 

dev/.release

@@ -14,7 +14,7 @@ sed "s;Date := .*;Date := \"$(date -I)\",;" PackageInfo.g > PackageInfo.g.bak
 mv PackageInfo.g.bak PackageInfo.g
 
 # 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/MonoidalCategories CAP_project/CartesianCategories CAP_project/FreydCategoriesForCAP HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra homalg_project/homalg homalg_project/Modules CategoricalTowers/ToolsForCategoricalTowers CategoricalTowers/Toposes; do
+for package in CAP_project/CAP CAP_project/CompilerForCAP CAP_project/MonoidalCategories CAP_project/CartesianCategories CAP_project/AdditiveClosuresForCAP CAP_project/FreydCategoriesForCAP HigherHomologicalAlgebra/ToolsForHigherHomologicalAlgebra homalg_project/homalg homalg_project/Modules CategoricalTowers/ToolsForCategoricalTowers CategoricalTowers/Toposes; do
 
     # adjust links to other manuals
     # Note that we cannot use sed's `-i` option for in-place editing, as

dev/upload_codecov.sh

@@ -21,9 +21,16 @@ curl -O https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
 gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
 shasum -a 256 -c codecov.SHA256SUM
 
+# read the token
+if [ -z "$CODECOV_TOKEN" ]; then
+  echo -e "\033[0;33mCODECOV_TOKEN is not set. Proceeding without token.\033[0m"
+else
+  echo -e "\033[0;32mUsing CODECOV_TOKEN from environment variable.\033[0m"
+fi
+
 # execute
 chmod +x codecov
-while ! ./codecov -Z -v -s ../; do
+while ! ./codecov -Z -v -s ../ -t $CODECOV_TOKEN; do
     echo "Codecov upload failed, retrying in 60s"
     sleep 60
 done

examples/notebooks/1LoopBox.ipynb

@@ -1035,7 +1035,7 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.12.1"
+   "version": "1.12.3"
   }
  },
  "nbformat": 4,

makedoc.g

@@ -3,9 +3,9 @@
 #
 # This file is a script which compiles the package manual.
 #
-if fail = LoadPackage( "AutoDoc", "2019.05.20" ) then
+if fail = LoadPackage( "AutoDoc", "2025.12.19" ) then
 
-    Error( "AutoDoc version 2019.05.20 or newer is required." );
+    Error( "AutoDoc version 2025.12.19 or newer is required." );
 
 fi;
 
@@ -25,7 +25,7 @@ AutoDoc( rec(
         ),
     ),
     scaffold := rec(
-        entities := [ "homalg", "CAP" ],
+        entities := rec( homalg := "homalg", CAP := "CAP" ),
     ),
 ) );
 

makedoc_with_overfull_hbox_warnings.g

@@ -3,9 +3,9 @@
 #
 # This file is a script which compiles the package manual and prints overfull hbox warnings.
 #
-if fail = LoadPackage( "AutoDoc", "2019.05.20" ) then
+if fail = LoadPackage( "AutoDoc", "2025.12.19" ) then
 
-    Error( "AutoDoc version 2019.05.20 or newer is required." );
+    Error( "AutoDoc version 2025.12.19 or newer is required." );
 
 fi;
 
@@ -36,7 +36,7 @@ AutoDoc( rec(
         ),
     ),
     scaffold := rec(
-        entities := [ "homalg", "CAP" ],
+        entities := rec( homalg := "homalg", CAP := "CAP" ),
     ),
 ) );