profiles: Do not repeat entries in 'manifest' file.

Fixes <https://issues.guix.gnu.org/55499>.
Reported by Ricardo Wurmus <rekado@elephly.net>.

With this change, the manifest file created for:

  guix install r r-seurat r-cistopic r-monocle3 r-cicero-monocle3 r-assertthat

goes from 5.7M to 176K.  Likewise, on this profile, wall-clock time of:

  GUIX_PROFILING=gc guix package -I

goes from 0.7s to 0.1s, with heap usage going from 55M to 9M.

* guix/profiles.scm (manifest->gexp)[optional]: New procedure.
[entry->gexp]: Turn into a monadic procedure.  Return a 'repeated' sexp
if ENTRY was already visited before.
Adjust caller accordingly.  Bump manifest version.
(sexp->manifest)[sexp->manifest-entry]: Turn into a monadic procedure.
Add case for 'repeated' nodes.  Add each entry to the current state
vhash.
Add clause for version 4 manifests.
[sexp->manifest-entry/v3]: New procedure, with former
'sexp->manifest-entry' code.
* tests/profiles.scm ("deduplication of repeated entries"): New test.
* guix/build/profiles.scm (manifest-sexp->inputs+search-paths)[let-fields]:
New macro.
Use it.  Expect version 4.  Add clause for 'repeated' nodes.

guix/build/profiles.scm

@@ -149,19 +149,33 @@ instead make DIRECTORY a \"real\" directory containing symlinks."
   "Parse MANIFEST, an sexp as produced by 'manifest->gexp', and return two
 values: the list of store items of its manifest entries, and the list of
 search path specifications."
+  (define-syntax let-fields
+    (syntax-rules ()
+      ;; Bind the fields NAME of LST to same-named variables in the lexical
+      ;; scope of BODY.
+      ((_ lst (name rest ...) body ...)
+       (let ((name (match (assq 'name lst)
+                     ((_ value) value)
+                     (#f '()))))
+         (let-fields lst (rest ...) body ...)))
+      ((_ lst () body ...)
+       (begin body ...))))
+
   (match manifest                            ;this must match 'manifest->gexp'
-    (('manifest ('version 3)
+    (('manifest ('version 4)
                 ('packages (entries ...)))
      (let loop ((entries entries)
                 (inputs '())
                 (search-paths '()))
        (match entries
-         (((name version output item
-                 ('propagated-inputs deps)
-                 ('search-paths paths) _ ...) . rest)
-          (loop (append rest deps)                ;breadth-first traversal
-                (cons item inputs)
-                (append paths search-paths)))
+         (((name version output item fields ...) . rest)
+          (let ((paths search-paths))
+            (let-fields fields (propagated-inputs search-paths properties)
+              (loop (append rest propagated-inputs) ;breadth-first traversal
+                    (cons item inputs)
+                    (append search-paths paths)))))
+         ((('repeated name version item) . rest)
+          (loop rest inputs search-paths))
          (()
           (values (reverse inputs)
                   (delete-duplicates
@@ -212,4 +226,8 @@ search paths of MANIFEST's entries."
     ;; Write 'OUTPUT/etc/profile'.
     (build-etc/profile output search-paths)))
 
+;;; Local Variables:
+;;; eval: (put 'let-fields 'scheme-indent-function 2)
+;;; End:
+
 ;;; profile.scm ends here

guix/profiles.scm

@@ -454,32 +454,58 @@ denoting a specific output of a package."
 
 (define (manifest->gexp manifest)
   "Return a representation of MANIFEST as a gexp."
+  (define (optional name value)
+    (if (null? value)
+        #~()
+        #~((#$name #$value))))
+
   (define (entry->gexp entry)
-    (match entry
-      (($ <manifest-entry> name version output (? string? path)
-                           (deps ...) (search-paths ...) _ (properties ...))
-       #~(#$name #$version #$output #$path
-                 (propagated-inputs #$(map entry->gexp deps))
-                 (search-paths #$(map search-path-specification->sexp
-                                      search-paths))
-                 #$@(if (null? properties)
-                        #~()
-                        #~((properties . #$properties)))))
-      (($ <manifest-entry> name version output package
-                           (deps ...) (search-paths ...) _ (properties ...))
-       #~(#$name #$version #$output
-                 (ungexp package (or output "out"))
-                 (propagated-inputs #$(map entry->gexp deps))
-                 (search-paths #$(map search-path-specification->sexp
-                                      search-paths))
-                 #$@(if (null? properties)
-                        #~()
-                        #~((properties . #$properties)))))))
+    ;; Maintain in state monad a vhash of visited entries, indexed by their
+    ;; item, usually package objects (we cannot use the entry itself as an
+    ;; index since identical entries are usually not 'eq?').  Use that vhash
+    ;; to avoid repeating duplicate entries.  This is particularly useful in
+    ;; the presence of propagated inputs, where we could otherwise end up
+    ;; repeating large trees.
+    (mlet %state-monad ((visited (current-state)))
+      (if (match (vhash-assq (manifest-entry-item entry) visited)
+            ((_ . previous-entry)
+             (manifest-entry=? previous-entry entry))
+            (#f #f))
+          (return #~(repeated #$(manifest-entry-name entry)
+                              #$(manifest-entry-version entry)
+                              (ungexp (manifest-entry-item entry)
+                                      (manifest-entry-output entry))))
+          (mbegin %state-monad
+            (set-current-state (vhash-consq (manifest-entry-item entry)
+                                            entry visited))
+            (mlet %state-monad ((deps (mapm %state-monad entry->gexp
+                                            (manifest-entry-dependencies entry))))
+              (return
+               (match entry
+                 (($ <manifest-entry> name version output (? string? path)
+                                      (_ ...) (search-paths ...) _ (properties ...))
+                  #~(#$name #$version #$output #$path
+                            #$@(optional 'propagated-inputs deps)
+                            #$@(optional 'search-paths
+                                         (map search-path-specification->sexp
+                                              search-paths))
+                            #$@(optional 'properties properties)))
+                 (($ <manifest-entry> name version output package
+                                      (_deps ...) (search-paths ...) _ (properties ...))
+                  #~(#$name #$version #$output
+                            (ungexp package (or output "out"))
+                            #$@(optional 'propagated-inputs deps)
+                            #$@(optional 'search-paths
+                                         (map search-path-specification->sexp
+                                              search-paths))
+                            #$@(optional 'properties properties))))))))))
 
   (match manifest
     (($ <manifest> (entries ...))
-     #~(manifest (version 3)
-                 (packages #$(map entry->gexp entries))))))
+     #~(manifest (version 4)
+                 (packages #$(run-with-state
+                                 (mapm %state-monad entry->gexp entries)
+                               vlist-null))))))
 
 (define (find-package name version)
   "Return a package from the distro matching NAME and possibly VERSION.  This
@@ -520,14 +546,15 @@ procedure is here for backward-compatibility and will eventually vanish."
         (item item)
         (parent parent))))
 
-  (define* (sexp->manifest-entry sexp #:optional (parent (delay #f)))
+  (define* (sexp->manifest-entry/v3 sexp #:optional (parent (delay #f)))
+    ;; Read SEXP as a version 3 manifest entry.
     (match sexp
       ((name version output path
              ('propagated-inputs deps)
              ('search-paths search-paths)
              extra-stuff ...)
        ;; For each of DEPS, keep a promise pointing to ENTRY.
-       (letrec* ((deps* (map (cut sexp->manifest-entry <> (delay entry))
+       (letrec* ((deps* (map (cut sexp->manifest-entry/v3 <> (delay entry))
                              deps))
                  (entry (manifest-entry
                           (name name)
@@ -542,6 +569,56 @@ procedure is here for backward-compatibility and will eventually vanish."
                                           '())))))
          entry))))
 
+  (define-syntax let-fields
+    (syntax-rules ()
+      ;; Bind the fields NAME of LST to same-named variables in the lexical
+      ;; scope of BODY.
+      ((_ lst (name rest ...) body ...)
+       (let ((name (match (assq 'name lst)
+                     ((_ value) value)
+                     (#f '()))))
+         (let-fields lst (rest ...) body ...)))
+      ((_ lst () body ...)
+       (begin body ...))))
+
+  (define* (sexp->manifest-entry sexp #:optional (parent (delay #f)))
+    (match sexp
+      (('repeated name version path)
+       ;; This entry is the same as another one encountered earlier; look it
+       ;; up and return it.
+       (mlet %state-monad ((visited (current-state))
+                           (key -> (list name version path)))
+         (match (vhash-assoc key visited)
+           (#f
+            (raise (formatted-message
+                    (G_ "invalid repeated entry in profile: ~s")
+                    sexp)))
+           ((_ . entry)
+            (return entry)))))
+      ((name version output path fields ...)
+       (let-fields fields (propagated-inputs search-paths properties)
+         (mlet* %state-monad
+             ((entry -> #f)
+              (deps     (mapm %state-monad
+                              (cut sexp->manifest-entry <> (delay entry))
+                              propagated-inputs))
+              (visited  (current-state))
+              (key ->   (list name version path)))
+           (set! entry                             ;XXX: emulate 'letrec*'
+                 (manifest-entry
+                   (name name)
+                   (version version)
+                   (output output)
+                   (item path)
+                   (dependencies deps)
+                   (search-paths (map sexp->search-path-specification
+                                      search-paths))
+                   (parent parent)
+                   (properties properties)))
+           (mbegin %state-monad
+             (set-current-state (vhash-cons key entry visited))
+             (return entry)))))))
+
   (match sexp
     (('manifest ('version 0)
                 ('packages ((name version output path) ...)))
@@ -608,7 +685,15 @@ procedure is here for backward-compatibility and will eventually vanish."
     ;; Version 3 represents DEPS as full-blown manifest entries.
     (('manifest ('version 3 minor-version ...)
                 ('packages (entries ...)))
-     (manifest (map sexp->manifest-entry entries)))
+     (manifest (map sexp->manifest-entry/v3 entries)))
+
+    ;; Version 4 deduplicates repeated entries and makes manifest entry fields
+    ;; such as 'propagated-inputs' and 'search-paths' optional.
+    (('manifest ('version 4 minor-version ...)
+                ('packages (entries ...)))
+     (manifest (run-with-state
+                   (mapm %state-monad sexp->manifest-entry entries)
+                 vlist-null)))
     (_
      (raise (condition
              (&message (message "unsupported manifest format")))))))
@@ -2317,4 +2402,8 @@ PROFILE refers to, directly or indirectly, or PROFILE."
             %known-shorthand-profiles)
       profile))
 
+;;; Local Variables:
+;;; eval: (put 'let-fields 'scheme-indent-function 2)
+;;; End:
+
 ;;; profiles.scm ends here

tests/profiles.scm

@@ -586,6 +586,48 @@
                                                     #:locales? #f)))
         (return #f)))))
 
+(test-assertm "deduplication of repeated entries"
+  ;; Make sure the 'manifest' file does not duplicate identical entries.
+  ;; See <https://issues.guix.gnu.org/55499>.
+  (mlet* %store-monad ((p0 -> (dummy-package "p0"
+                                (build-system trivial-build-system)
+                                (arguments
+                                 `(#:guile ,%bootstrap-guile
+                                   #:builder (mkdir (assoc-ref %outputs "out"))))
+                                (propagated-inputs
+                                 `(("guile" ,%bootstrap-guile)))))
+                       (p1 -> (package
+                                (inherit p0)
+                                (name "p1")))
+                       (drv (profile-derivation (packages->manifest
+                                                 (list p0 p1))
+                                                #:hooks '()
+                                                #:locales? #f)))
+    (mbegin %store-monad
+      (built-derivations (list drv))
+      (let ((file     (string-append (derivation->output-path drv)
+                                     "/manifest"))
+            (manifest (profile-manifest (derivation->output-path drv))))
+        (define (contains-repeated? sexp)
+          (match sexp
+            (('repeated _ ...) #t)
+            ((lst ...) (any contains-repeated? sexp))
+            (_ #f)))
+
+        (return (and (contains-repeated? (call-with-input-file file read))
+
+                     ;; MANIFEST has two entries for %BOOTSTRAP-GUILE since
+                     ;; it's propagated both from P0 and from P1.  When
+                     ;; reading a 'repeated' node, 'read-manifest' should
+                     ;; reuse the previously-read entry so the two
+                     ;; %BOOTSTRAP-GUILE entries must be 'eq?'.
+                     (match (manifest-entries manifest)
+                       (((= manifest-entry-dependencies (dep0))
+                         (= manifest-entry-dependencies (dep1)))
+                        (and (string=? (manifest-entry-name dep0)
+                                       (package-name %bootstrap-guile))
+                             (eq? dep0 dep1))))))))))
+
 (test-assertm "no collision"
   ;; Here we have an entry that is "lowered" (its 'item' field is a store file
   ;; name) and another entry (its 'item' field is a package) that is