feat: Bump igraph format version to 1.5.0

R/versions.R

@@ -22,7 +22,7 @@
 ##
 ## ----------------------------------------------------------------------
 
-pkg_graph_version <- "0.8.0"
+pkg_graph_version <- "1.5.0"
 
 pkg_graph_version_obj <- as.package_version(pkg_graph_version)
 
@@ -96,7 +96,20 @@ upgrade_graph <- function(graph) {
   if (g_ver == "0.4.0") {
     .Call(R_igraph_add_env, graph)
   } else if (g_ver == "0.7.999") {
+    # Not observed in the wild
+    .Call(R_igraph_add_myid_to_env, graph)
     .Call(R_igraph_add_version_to_env, graph)
+  } else if (g_ver == "0.8.0") {
+    .Call(R_igraph_add_version_to_env, graph)
+    graph <- unclass(graph)
+    graph[igraph_t_idx_oi:igraph_t_idx_is] <- list(NULL)
+    class(graph) <- "igraph"
+
+    # Calling for side effect: error if R_SEXP_to_igraph() fails, create native igraph,
+    # update "me" element of environment
+    V(graph)
+
+    graph
   } else {
     stop("Don't know how to upgrade graph from ", g_ver, " to ", p_ver)
   }
@@ -122,6 +135,17 @@ warn_version <- function(graph) {
       "  Call upgrade_graph() on it to use with the current igraph version\n",
       "  For now we convert it on the fly..."
     )
+
+    # In-place upgrade:
+    # - The igraph element in the igraph_t_idx_env component will be added
+    #   transparently because it's missing.
+    # - The components igraph_t_idx_oi, igraph_t_idx_ii, igraph_t_idx_os,
+    #   igraph_t_idx_is are ignored, but we can't do much about the contents.
+    #   Users will have to call upgrade_graph(), but this is what the message
+    #   is about.
+    if (pkg_graph_version <= "1.5.0") {
+      .Call(R_igraph_add_version_to_env, graph)
+    }
     return(TRUE)
   }
 
@@ -149,3 +173,9 @@ oldsamples <- function() {
     "0.1.1" = oldsample_0_1_1()
   )
 }
+
+clear_native_ptr <- function(g) {
+  gx <- unclass(g)
+  gx[[igraph_t_idx_env]]$igraph <- NULL
+  g
+}

src/cpp11.cpp

@@ -17,6 +17,7 @@ extern "C" {
 /* .Call calls */
 extern SEXP R_igraph_add_edges(SEXP, SEXP);
 extern SEXP R_igraph_add_env(SEXP);
+extern SEXP R_igraph_add_myid_to_env(SEXP);
 extern SEXP R_igraph_add_version_to_env(SEXP);
 extern SEXP R_igraph_add_vertices(SEXP, SEXP);
 extern SEXP R_igraph_address(SEXP);
@@ -398,6 +399,7 @@ extern SEXP promise_expr_(SEXP);
 static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_add_edges",                                  (DL_FUNC) &R_igraph_add_edges,                                   2},
     {"R_igraph_add_env",                                    (DL_FUNC) &R_igraph_add_env,                                     1},
+    {"R_igraph_add_myid_to_env",                            (DL_FUNC) &R_igraph_add_myid_to_env,                             1},
     {"R_igraph_add_version_to_env",                         (DL_FUNC) &R_igraph_add_version_to_env,                          1},
     {"R_igraph_add_vertices",                               (DL_FUNC) &R_igraph_add_vertices,                                2},
     {"R_igraph_address",                                    (DL_FUNC) &R_igraph_address,                                     1},

src/rinterface.h

@@ -25,7 +25,7 @@
 
 #include "uuid/uuid.h"
 
-#define R_IGRAPH_TYPE_VERSION "0.8.0"
+#define R_IGRAPH_TYPE_VERSION "1.5.0"
 #define R_IGRAPH_VERSION_VAR ".__igraph_version__."
 
 SEXP R_igraph_add_env(SEXP graph);

src/rinterface_extra.c

@@ -2986,6 +2986,9 @@ void R_igraph_restore_pointer(SEXP graph) {
 
 igraph_t *R_igraph_get_pointer(SEXP graph) {
   if (GET_LENGTH(graph) != igraph_t_idx_max || !Rf_isEnvironment(R_igraph_graph_env(graph))) {
+    if (GET_LENGTH(graph) == 11) {
+      Rf_error("This graph was created by igraph < 0.2.\n  Upgrading this format is not supported, sorry.");
+    }
     Rf_error("This graph was created by a now unsupported old igraph version.\n  Call upgrade_version() before using igraph functions on that object.");
   }
 
@@ -9945,7 +9948,9 @@ SEXP R_igraph_identical_graphs(SEXP g1, SEXP g2, SEXP attrs) {
 }
 
 SEXP R_igraph_graph_version(SEXP graph) {
-  if (GET_LENGTH(graph) == igraph_t_idx_max && Rf_isEnvironment(R_igraph_graph_env(graph))) {
+  if (GET_LENGTH(graph) == 11) {
+    return Rf_mkString("0.1.1");
+  } else if (GET_LENGTH(graph) == igraph_t_idx_max && Rf_isEnvironment(R_igraph_graph_env(graph))) {
     SEXP ver = Rf_findVar(Rf_install(R_IGRAPH_VERSION_VAR), R_igraph_graph_env(graph));
     if (ver != R_UnboundValue) {
       return ver;
@@ -9957,24 +9962,26 @@ SEXP R_igraph_graph_version(SEXP graph) {
   }
 }
 
-SEXP R_igraph_add_version_to_env(SEXP graph) {
+SEXP R_igraph_add_myid_to_env(SEXP graph) {
   uuid_t my_id;
   char my_id_chr[40];
 
-  PROTECT(graph = Rf_duplicate(graph));
-
   uuid_generate(my_id);
   uuid_unparse_lower(my_id, my_id_chr);
   SEXP l1 = PROTECT(Rf_install("myid"));
   SEXP l2 = PROTECT(Rf_mkString(my_id_chr));
   Rf_defineVar(l1, l2, R_igraph_graph_env(graph));
   UNPROTECT(2);
-  l1 = PROTECT(Rf_install(R_IGRAPH_VERSION_VAR));
-  l2 = PROTECT(Rf_mkString(R_IGRAPH_TYPE_VERSION));
+
+  return graph;
+}
+
+SEXP R_igraph_add_version_to_env(SEXP graph) {
+  SEXP l1 = PROTECT(Rf_install(R_IGRAPH_VERSION_VAR));
+  SEXP l2 = PROTECT(Rf_mkString(R_IGRAPH_TYPE_VERSION));
   Rf_defineVar(l1, l2, R_igraph_graph_env(graph));
   UNPROTECT(2);
 
-  UNPROTECT(1);
   return graph;
 }
 

tests/testthat/_snaps/versions.md

@@ -1,11 +1,73 @@
-# reading of old igraph formats
+# we can't upgrade from 0.1.1 to 1.5.0, on the fly
 
     Code
-      s[["0.1.1"]]
+      oldsample_0_1_1()
+    Error <simpleError>
+      This graph was created by igraph < 0.2.
+        Upgrading this format is not supported, sorry.
+
+# we can't upgrade from 0.1.1 to 1.5.0, explicitly
+
+    Code
+      upgrade_graph(g)
+    Error <simpleError>
+      Don't know how to upgrade graph from 0.1.1 to 1.5.0
+
+# we can't upgrade from 0.2 to 1.5.0, on the fly
+
+    Code
+      oldsample_0_2()
     Error <simpleError>
       This graph was created by a now unsupported old igraph version.
         Call upgrade_version() before using igraph functions on that object.
 
+# we can't upgrade from 0.5 to 1.5.0, on the fly
+
+    Code
+      oldsample_0_5()
+    Error <simpleError>
+      This graph was created by a now unsupported old igraph version.
+        Call upgrade_version() before using igraph functions on that object.
+
+# we can't upgrade from 0.6 to 1.5.0, on the fly
+
+    Code
+      oldsample_0_6()
+    Error <simpleError>
+      This graph was created by a now unsupported old igraph version.
+        Call upgrade_version() before using igraph functions on that object.
+
+# we can upgrade from 1.0.0 to 1.5.0, on the fly
+
+    Code
+      g <- oldsample_1_0_0()
+      graph_version(g)
+    Output
+      [1] '0.8.0'
+    Code
+      g
+    Message <simpleMessage>
+      This graph was created by an old(er) igraph version.
+        Call upgrade_graph() on it to use with the current igraph version
+        For now we convert it on the fly...
+    Output
+      IGRAPH D--- 3 3 -- Ring graph
+      + attr: name (g/c), mutual (g/l), circular (g/l), bar (v/c), foo (e/c)
+      + edges:
+      [1] 1->2 2->3 3->1
+    Code
+      graph_version(g)
+    Output
+      [1] '1.5.0'
+
+# reading of old igraph formats
+
+    Code
+      s[["0.1.1"]]
+    Error <simpleError>
+      This graph was created by igraph < 0.2.
+        Upgrading this format is not supported, sorry.
+
 ---
 
     Code
@@ -34,6 +96,10 @@
 
     Code
       s[["1.0.0"]]
+    Message <simpleMessage>
+      This graph was created by an old(er) igraph version.
+        Call upgrade_graph() on it to use with the current igraph version
+        For now we convert it on the fly...
     Output
       IGRAPH D--- 3 3 -- Ring graph
       + attr: name (g/c), mutual (g/l), circular (g/l), bar (v/c), foo (e/c)
@@ -44,6 +110,9 @@
 
     Code
       s[["1.5.0"]]
-    Error <simpleError>
-      This graph was created by a new(er) igraph version. Please install the latest version of igraph and try again.
+    Output
+      IGRAPH D--- 3 3 -- Ring graph
+      + attr: name (g/c), mutual (g/l), circular (g/l), bar (v/c), foo (e/c)
+      + edges:
+      [1] 1->2 2->3 3->1
 

tests/testthat/test-versions.R

@@ -5,16 +5,90 @@ test_that("we create graphs of the current version", {
   expect_equal(v1, v2)
 })
 
-test_that("we can upgrade from 0.4.0 to 0.8.0", {
-  g <- make_ring(10)
-  g <- unclass(g)
-  g[[10]] <- NULL
-  class(g) <- "igraph"
+test_that("we can't upgrade from 0.1.1 to 1.5.0, on the fly", {
+  expect_snapshot(error = TRUE, {
+    oldsample_0_1_1()
+  })
+})
+
+test_that("we can't upgrade from 0.1.1 to 1.5.0, explicitly", {
+  g <- oldsample_0_1_1()
+
+  expect_equal(graph_version(g), as.package_version("0.1.1"))
+
+  expect_snapshot(error = TRUE, {
+    upgrade_graph(g)
+  })
+})
+
+test_that("we can't upgrade from 0.2 to 1.5.0, on the fly", {
+  expect_snapshot(error = TRUE, {
+    oldsample_0_2()
+  })
+})
+
+test_that("we can upgrade from 0.2 to 1.5.0, explicitly", {
+  g <- oldsample_0_2()
+
+  expect_equal(graph_version(g), as.package_version("0.4.0"))
+
+  g2 <- upgrade_graph(g)
+  expect_equal(graph_version(g2), as.package_version("1.5.0"))
+})
+
+test_that("we can't upgrade from 0.5 to 1.5.0, on the fly", {
+  expect_snapshot(error = TRUE, {
+    oldsample_0_5()
+  })
+})
+
+test_that("we can upgrade from 0.5 to 1.5.0, explicitly", {
+  g <- oldsample_0_5()
+
+  expect_equal(graph_version(g), as.package_version("0.4.0"))
+
+  g2 <- upgrade_graph(g)
+  expect_equal(graph_version(g2), as.package_version("1.5.0"))
+})
+
+test_that("we can't upgrade from 0.6 to 1.5.0, on the fly", {
+  expect_snapshot(error = TRUE, {
+    oldsample_0_6()
+  })
+})
+
+test_that("we can upgrade from 0.6 to 1.5.0, explicitly", {
+  g <- oldsample_0_6()
 
   expect_equal(graph_version(g), as.package_version("0.4.0"))
 
   g2 <- upgrade_graph(g)
-  expect_equal(graph_version(g2), as.package_version("0.8.0"))
+  expect_equal(graph_version(g2), as.package_version("1.5.0"))
+})
+
+test_that("we can upgrade from 1.0.0 to 1.5.0, on the fly", {
+  local_igraph_options(print.id = FALSE)
+
+  expect_snapshot({
+    g <- oldsample_1_0_0()
+    graph_version(g)
+    g
+    graph_version(g)
+  })
+})
+
+test_that("we can upgrade from 1.0.0 to 1.5.0, explicitly", {
+  g <- oldsample_1_0_0()
+  graph_version(g)
+  g2 <- upgrade_graph(g)
+  graph_version(g2)
+
+  g3 <- oldsample_1_5_0()
+
+  expect_identical(
+    unclass(clear_native_ptr(g2)),
+    unclass(clear_native_ptr(g3))
+  )
 })
 
 test_that("reading of old igraph formats", {
@@ -36,7 +110,7 @@ test_that("reading of old igraph formats", {
   expect_snapshot({
     s[["1.0.0"]]
   })
-  expect_snapshot(error = TRUE, {
+  expect_snapshot({
     s[["1.5.0"]]
   })
 })