feat: Upgrade igraph/C to 0.10

.Rbuildignore

@@ -1,5 +1,3 @@
-src/vendor/cigraph
-
 ^tags$
 ^.github$
 ^cigraph$
@@ -44,5 +42,9 @@ src/vendor/cigraph
 ^CITATION\.cff$
 ^cran$
 ^R/cran\.R$
+^src/build$
+^src/install$
+^src/vendor/cigraph/\..*$
+^rconfigure\.py$
 ^\.ccache$
 ^\.aviator/config\.yml$

.github/workflows/build-and-check.yml

@@ -10,6 +10,10 @@ on:
       - main
       - fix/*
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}-${{ github.head_ref || github.sha }}-${{ github.base_ref || '' }}
+  cancel-in-progress: true
+
 name: R-CMD-check
 
 jobs:
@@ -35,6 +39,7 @@ jobs:
       - name: apt update
         run: |
           sudo apt-get update
+          sudo apt-get install -y libarpack2-dev
         shell: bash
 
       - name: Cache Python virtualenv
@@ -135,6 +140,19 @@ jobs:
           save: false
           restore: false
 
+      - name: apt update
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libarpack2-dev
+        shell: bash
+
+      - name: apt update
+        if: runner.os == 'macOS'
+        run: |
+          brew install glpk
+        shell: bash
+
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
@@ -154,7 +172,7 @@ jobs:
       - name: Check R package
         uses: r-lib/actions/check-r-package@v2
         with:
-          error-on: '"note"'
+          error-on: '"error"'
 
   coverage:
     runs-on: ubuntu-20.04
@@ -173,6 +191,12 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: apt update
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libarpack2-dev
+        shell: bash
+
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
 
@@ -188,7 +212,6 @@ jobs:
       - name: Run coverage
         run: |
           line_exclusions <- fs::dir_ls(c("src/vendor"), type = "file", recurse = TRUE)
-
           cov <- covr::package_coverage(
             type = c("tests", "examples"),
             line_exclusions = as.list(names(line_exclusions)),
@@ -212,6 +235,7 @@ jobs:
       - name: apt update
         run: |
           sudo apt-get update
+          sudo apt-get install -y libarpack2-dev
         shell: bash
 
       - name: run sanitizer
@@ -221,6 +245,7 @@ jobs:
           options: --rm --platform linux/amd64 -v ${{ github.workspace }}:/rigraph
           run: |
             set -e
+            printenv
             cd rigraph
             RDcsan CMD INSTALL . --no-byte-compile
             TESTTHAT_PARALLEL=false CI=true RDcsan -q -e 'testthat::test_local(reporter = c("location", "summary"), load_package = "installed")'

.gitignore

@@ -12,6 +12,7 @@ igraph.Rcheck/
 .vscode/
 .Rproj.user
 /configure~
-/build/
+/src/build/
+/src/install/
 inst/doc
 cran

.gitmodules

@@ -1,4 +0,0 @@
-[submodule "cigraph"]
-	path = cigraph
-	url = https://github.com/igraph/igraph.git
-	branch = cran

Makefile-cigraph

@@ -10,9 +10,7 @@ all: pre_build
 ########################################################
 # Main package
 
-top_srcdir=cigraph
-# FIXME: with the switch to igraph 0.10, change to:
-# vendored_srcdir=src/vendor/cigraph
+top_srcdir=src/vendor/cigraph
 vendored_srcdir=$(top_srcdir)
 VERSION=$(shell tools/getversion.sh)
 
@@ -22,54 +20,23 @@ VERSION=$(shell tools/getversion.sh)
 version_number: force
 	@echo '$(VERSION)' | cmp -s - $@ || echo '$(VERSION)' > $@
 
-# Source files from the C library
-CORESRC := $(shell cd $(top_srcdir) ; git ls-files --full-name src | \
-	      grep -v '\.txt$$' | grep -v "COPYING$$" | grep -v "README" | \
-		  grep -v "src/config.h.in" )
-
-# Vendored dependencies of the C library. We don't need BLAS / LAPACK
-# because they are included in R. We don't need F2C either because we
-# will use the original Fortran sources for ARPACK. We also rely on an
-# external GLPK instead of the one vendored in igraph because the
-# vendored GLPK does not fit well in the build process of the R interface.
-VENDORSRC := $(shell cd $(top_srcdir) ; git ls-files --full-name vendor | \
-	      grep -v "^vendor/lapack/" | grep -v "^vendor/f2c" | \
-	      grep -v "^vendor/glpk/" | \
-	      grep -v '\.txt$$' | grep -v "COPYING$$" | grep -v "README" )
-
-# Include files from the C library
-CINC := $(shell cd $(top_srcdir) ; git ls-files --full-name include)
-CINC := $(patsubst include/%, src/include/%, $(CINC))
-
-# Transform CORESRC and VENDORSRC to their target folders in src/
-CORESRC := $(patsubst src/%, src/core/%, $(CORESRC))
-VENDORSRC := $(patsubst vendor/%, src/vendor/%, $(VENDORSRC))
-
-# Rules that copy the sources from cigraph/ to src/
-$(CORESRC): src/core/%: $(top_srcdir)/src/%
-	mkdir -p $(@D) && cp $< $@
-$(VENDORSRC): src/vendor/%: $(top_srcdir)/vendor/%
-	mkdir -p $(@D) && cp $< $@
-$(CINC): src/include/%: $(top_srcdir)/include/%
-	mkdir -p $(@D) && cp $< $@
-
 # Files generated by flex/bison
 
 PARSER := $(shell cd $(top_srcdir) ; git ls-files --full-name src | \
 	    grep -E '\.(l|y)$$')
-PARSER1 := $(patsubst src/%.l, src/core/%.c, $(PARSER))
-PARSER2 := $(patsubst src/%.y, src/core/%.c, $(PARSER1))
+PARSER1 := $(patsubst src/%.l, src/%.c, $(PARSER))
+PARSER2 := $(patsubst src/%.y, src/%.c, $(PARSER1))
 
 YACC=bison -b yy -d
 LEX=flex
 
 %.c: %.y
 	$(YACC) $<
-	mv -f yy.tab.c $@
-	mv -f yy.tab.h $(@:.c=.h)
+	mv -f yy.tab.c src/vendor/io/$(notdir $@)
+	mv -f yy.tab.h src/vendor/io/parsers/$(basename $(notdir $@)).h
 
 %.c: %.l
-	$(LEX) -o $@ --header-file=$(@:.c=.h) $<
+	$(LEX) -o src/vendor/io/$(notdir $@) --header-file=src/vendor/io/parsers/$(basename $(notdir $@)).h $<
 
 # Create Python virtualenv for Stimulus
 
@@ -83,15 +50,12 @@ $(PYVENV)/stamp: tools/build-requirements.txt
 # Apply possible patches
 
 patches: $(CORESRC) $(VENDORSRC) $(CINC) $(PARSER2)
-	if [ -d "patches" ]; then \
-		find patches -type f -name '*.patch' -print0 | sort -z | xargs -t -0 -n 1 tools/apply-patch.sh; \
-	fi
 	-rm -f src/*.orig
 	tools/fix-lexers.sh
 
 # C files generated by C configure
 
-CGEN = src/include/igraph_export.h src/include/igraph_threading.h src/include/igraph_version.h
+CGEN = src/include/igraph_export.h src/include/igraph_threading.h src/include/igraph_version.h src/sources.mk
 
 src/include/igraph_export.h: tools/stimulus/igraph_export.h
 	mkdir -p src/include
@@ -105,6 +69,11 @@ src/include/igraph_version.h: $(top_srcdir)/include/igraph_version.h.in
 	mkdir -p src/include
 	cp $< $@
 
+# Create sources.mk
+
+src/sources.mk:
+	$(PYTHON) rconfigure.py
+
 # R source and doc files
 
 RSRC := $(shell git ls-files R doc inst demo NEWS cleanup.win configure.win)
@@ -201,8 +170,9 @@ src/Makevars.win src/Makevars.ucrt src/Makevars.in: src/%: tools/stimulus/% \
 	# Can't insert newlines, not all make variants accept them
 	cat object_files >> $@
 
-pre_build: venv patches $(CSRC) $(CINC2) $(PARSER2) $(RSRC) $(RGEN) \
-	$(CGEN) $(RAY2) $(ARPACK2) $(UUID2)
+pre_build: venv patches $(RSRC) \
+	$(CGEN) $(RAY2) $(ARPACK2) $(UUID2) \
+	$(PARSER2)
 
 clean:
 	rm -rf src/core src/vendor src/include src/Makevars.in src/Makevars.ucrt src/Makevars.win src/config.h.in src/rinterface.c R/aaa-auto.R