Merge branch 'master' into core-updates-frozen

 Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/chez.scm
	gnu/packages/docbook.scm
	gnu/packages/ebook.scm
	gnu/packages/gnome.scm
	gnu/packages/linux.scm
	gnu/packages/networking.scm
	gnu/packages/python-web.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tex.scm
	gnu/packages/version-control.scm
	gnu/packages/xml.scm
	guix/build-system/dune.scm
	guix/build-system/go.scm
	guix/build-system/linux-module.scm
	guix/packages.scm

1 files changed, 261 insertions, 5 deletions

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index a69e38249f..e9cf75bd7d 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -458,7 +458,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.14)
     (name "go")
-    (version "1.16.7")
+    (version "1.16.8")
     (source
      (origin
        (method git-fetch)
@@ -468,7 +468,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1id6nsavf7gm78bmzsvym135pi2xa0v75ny51xrw93j70clz9w0h"))))
+         "00zv65v09kr2cljxxqypk980r4b4aqjijhbw4ikppn8km68h831n"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.14)
        ((#:tests? _) #t)
@@ -613,6 +613,188 @@ in the style of communicating sequential processes (@dfn{CSP}).")
              (alist-replace "go" (list gccgo-10) (package-native-inputs go-1.14))
              (package-native-inputs go-1.14))))))
 
+(define-public go-1.17
+  (package
+    (inherit go-1.16)
+    (name "go")
+    (version "1.17.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/golang/go")
+             (commit (string-append "go" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0wk99lwpzp4qwrksl932lm9vb70nyf4vgb5lxwh7gzjcbhlqj992"))))
+    (outputs '("out" "tests")) ; 'tests' contains distribution tests.
+    (arguments
+     `(#:modules ((ice-9 match)
+                  (guix build gnu-build-system)
+                  (guix build utils))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((output (assoc-ref outputs "out"))
+                   (loader (string-append (assoc-ref inputs "libc")
+                                          ,(glibc-dynamic-linker))))
+               (setenv "GOOS" "linux")
+               (setenv "GO_LDSO" loader)
+               (setenv "GOROOT" (getcwd))
+               (setenv "GOROOT_FINAL" (string-append output "/lib/go"))
+               (setenv "GOGC" "400")
+               (setenv "GOCACHE" "/tmp/go-cache"))))
+         (add-after 'unpack 'patch-source
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((net-base (assoc-ref inputs "net-base"))
+                    (tzdata-path (string-append (assoc-ref inputs "tzdata")
+                                                "/share/zoneinfo")))
+               ;; XXX: Remove when #49729 is merged?
+               (for-each make-file-writable (find-files "src"))
+
+               ;; Having the patch in the 'patches' field of <origin> breaks
+               ;; the 'TestServeContent' test due to the fact that
+               ;; timestamps are reset.  Thus, apply it from here.
+               (invoke "patch" "-p1" "--force" "-i"
+                       (assoc-ref inputs "go-skip-gc-test.patch"))
+               (invoke "patch" "-p1" "--force" "-i"
+                       (assoc-ref inputs "go-fix-script-tests.patch"))
+
+               (substitute* "src/os/os_test.go"
+                 (("/usr/bin") (getcwd))
+                 (("/bin/sh") (which "sh")))
+
+               (substitute* "src/cmd/go/testdata/script/cgo_path_space.txt"
+                 (("/bin/sh") (which "sh")))
+
+               ;; fix shebang for testar script
+               ;; note the target script is generated at build time.
+               (substitute* "misc/cgo/testcarchive/carchive_test.go"
+                 (("/usr/bin/env bash") (which "bash")))
+
+               (substitute* "src/net/lookup_unix.go"
+                 (("/etc/protocols")
+                  (string-append net-base "/etc/protocols")))
+               (substitute* "src/net/port_unix.go"
+                 (("/etc/services")
+                  (string-append net-base "/etc/services")))
+               (substitute* "src/time/zoneinfo_unix.go"
+                 (("/usr/share/zoneinfo/") tzdata-path)))))
+         (add-after 'patch-source 'disable-failing-tests
+           (lambda _
+             ;; Disable failing tests: these tests attempt to access
+             ;; commands or network resources which are neither available
+             ;; nor necessary for the build to succeed.
+             (for-each
+              (match-lambda
+                ((file test)
+                 (let ((regex (string-append "^(func\\s+)(" test "\\()")))
+                   (substitute* file
+                     ((regex all before test_name)
+                      (string-append before "Disabled" test_name))))))
+              '(("src/net/cgo_unix_test.go" "TestCgoLookupPort")
+                ("src/net/cgo_unix_test.go" "TestCgoLookupPortWithCancel")
+                ;; 127.0.0.1 doesn't exist
+                ("src/net/cgo_unix_test.go" "TestCgoLookupPTR")
+                ("src/net/cgo_unix_test.go" "TestCgoLookupPTRWithCancel")
+                ;; /etc/services doesn't exist
+                ("src/net/parse_test.go" "TestReadLine")
+                ;; The user's directory doesn't exist
+                ("src/os/os_test.go" "TestUserHomeDir")))
+
+             ;; These tests fail on aarch64-linux
+             (substitute* "src/cmd/dist/test.go"
+               (("t.registerHostTest\\(\"testsanitizers/msan.*") ""))))
+         (add-after 'patch-source 'enable-external-linking
+           (lambda _
+             ;; Invoke GCC to link any archives created with GCC (that is, any
+             ;; packages built using 'cgo'), because Go doesn't know how to
+             ;; handle the runpaths but GCC does.  Use substitute* rather than
+             ;; a patch since these files are liable to change often.
+             ;;
+             ;; XXX: Replace with GO_EXTLINK_ENABLED=1 or similar when
+             ;; <https://github.com/golang/go/issues/31544> and/or
+             ;; <https://github.com/golang/go/issues/43525> are resolved.
+             (substitute* "src/cmd/link/internal/ld/config.go"
+               (("iscgo && externalobj") "iscgo"))
+             (substitute* '("src/cmd/nm/nm_cgo_test.go"
+                            "src/cmd/dist/test.go")
+               (("^func.*?nternalLink\\(\\).*" all)
+                (string-append all "\n\treturn false\n")))))
+         (replace 'build
+           (lambda* (#:key (parallel-build? #t) #:allow-other-keys)
+             (let* ((njobs (if parallel-build? (parallel-job-count) 1)))
+               (with-directory-excursion "src"
+                 (setenv "GOMAXPROCS" (number->string njobs))
+                 (invoke "sh" "make.bash" "--no-banner")))))
+         (replace 'check
+           (lambda* (#:key target (tests? (not target)) (parallel-tests? #t)
+                     #:allow-other-keys)
+             (let* ((njobs (if parallel-tests? (parallel-job-count) 1)))
+               (when tests?
+                 (with-directory-excursion "src"
+                   (setenv "GOMAXPROCS" (number->string njobs))
+                   (invoke "sh" "run.bash" "--no-rebuild"))))))
+         (add-before 'install 'unpatch-perl-shebangs
+           (lambda _
+             ;; Avoid inclusion of perl in closure by rewriting references
+             ;; to perl input in sourcecode generators and test scripts
+             (substitute* (cons "src/net/http/cgi/testdata/test.cgi"
+                                (find-files "src" "\\.pl$"))
+               (("^#!.*") "#!/usr/bin/env perl\n"))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Notably, we do not install archives (180M), which Go will
+             ;; happily recompile quickly (and cache) if needed, almost
+             ;; surely faster than they could be substituted.
+             ;;
+             ;; The main motivation for pre-compiled archives is to use
+             ;; libc-linked `net' or `os' packages without a C compiler,
+             ;; but on Guix a C compiler is necessary to properly link the
+             ;; final binaries anyway.  Many build flags also invalidate
+             ;; these pre-compiled archives, so in practice Go often
+             ;; recompiles them anyway.
+             ;;
+             ;; Upstream is also planning to no longer install these
+             ;; archives: <https://github.com/golang/go/issues/47257>
+             ;;
+             ;; When necessary, a custom pre-compiled library package can
+             ;; be created with `#:import-path "std"' and used with
+             ;; `-pkgdir'.
+             (let* ((out (assoc-ref outputs "out"))
+                    (tests (assoc-ref outputs "tests")))
+               (for-each
+                (lambda (file)
+                  (copy-recursively file (string-append out "/lib/go/" file)))
+                '("lib" "VERSION" "pkg/include" "pkg/tool"))
+
+               (for-each
+                (match-lambda
+                  ((file dest output)
+                   ;; Copy to output/dest and symlink from output/lib/go/file.
+                   (let ((file* (string-append output "/lib/go/" file))
+                         (dest* (string-append output "/" dest)))
+                     (copy-recursively file dest*)
+                     (mkdir-p (dirname file*))
+                     (symlink (string-append "../../" dest) file*))))
+                `(("bin"          "bin"                 ,out)
+                  ("src"          "share/go/src"        ,out)
+                  ("misc"         "share/go/misc"       ,out)
+                  ("doc"          "share/doc/go/doc"    ,out)
+                  ("api"          "share/go/api"        ,tests)
+                  ("test"         "share/go/test"       ,tests))))))
+         (add-after 'install 'install-doc-files
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each
+                (lambda (file)
+                  (install-file file (string-append out "/share/doc/go")))
+                '("AUTHORS" "CONTRIBUTORS" "CONTRIBUTING.md" "PATENTS"
+                  "README.md" "SECURITY.md"))))))))
+    (inputs (alist-delete "gcc:lib" (package-inputs go-1.16)))))
+
 (define-public go go-1.14)
 
 (define-public go-0xacab-org-leap-shapeshifter
@@ -1381,6 +1563,12 @@ Go.")
          (url "https://github.com/sevlyar/go-daemon")
          (commit (string-append "v" version))))
        (file-name (git-file-name name version))
+       (modules '((guix build utils)))
+       (snippet
+        ;; XXX: Remove when updating
+        '(begin
+           (substitute* "compilation_test.go"
+             ((".*\"darwin/386\".*") ""))))
        (sha256
         (base32 "1y3gnxaifykcjcbzx91lz9bc93b95w3xj4rjxjbii26pm3j7gqyk"))))
     (build-system go-build-system)
@@ -1420,7 +1608,9 @@ Go.")
                  (("/bin/sleep" command)
                   (string-append
                    (assoc-ref (or native-inputs inputs) "coreutils")
-                   command))))))))
+                   command)))
+               (substitute* "src/github.com/keybase/go-ps/process_openbsd.go"
+                 (("^// \\+build ignore") "")))))))
       (native-inputs
        `(("coreutils" ,coreutils)
          ("go-github-com-stretchr-testify"
@@ -2759,6 +2949,68 @@ developers to use @code{http} methods explicitly and in a way that's consistent
 with the HTTP protocol definition.")
     (license license:expat)))
 
+(define-public go-cloud-google-com-go-compute-metadata
+  (package
+    (name "go-cloud-google-com-go-compute-metadata")
+    (version "0.81.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/googleapis/google-cloud-go")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "15jgynqb5pbxqbj3a7ii970yn4srsw1dbxzxnhpkfkmplalpgyh3"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:unpack-path "cloud.google.com/go"
+       #:import-path "cloud.google.com/go/compute/metadata"))
+    (home-page
+     "https://pkg.go.dev/cloud.google.com/go/compute/metadata")
+    (synopsis
+     "Go wrapper for Google Compute Engine metadata service")
+    (description
+     "This package provides access to Google Compute Engine (GCE) metadata and
+API service accounts for Go.")
+    (license license:asl2.0)))
+
+(define-public go-github-com-google-gmail-oauth2-tools-go-sendgmail
+  (let ((commit "e3229155a4037267ce40f1a3a681f53221aa4d8d")
+        (revision "0"))
+    (package
+      (name "go-github-com-google-gmail-oauth2-tools-go-sendgmail")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/google/gmail-oauth2-tools")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1cxpkiaajhq1gjsg47r2b5xgck0r63pvkyrkm7af8c8dw7fyn64f"))))
+      (propagated-inputs
+       `(("go-golang-org-x-oauth2" ,go-golang-org-x-oauth2)
+         ("go-cloud-google-com-go-compute-metadata"
+          ,go-cloud-google-com-go-compute-metadata)))
+      (build-system go-build-system)
+      (arguments
+       '(#:unpack-path "github.com/google/gmail-oauth2-tools"
+         #:import-path "github.com/google/gmail-oauth2-tools/go/sendgmail"))
+      (home-page
+       "https://github.com/google/gmail-oauth2-tools/tree/master/go/sendgmail")
+      (synopsis
+       "Sendmail-compatible tool for using Gmail with @code{git send-email}")
+      (description
+       "The @command{sendgmail} command provides a minimal sendmail-compatible
+front-end that connects to Gmail using OAuth2.  It is specifically designed
+for use with @code{git send-email}.  The command needs a Gmail API key to
+function.")
+      (license license:asl2.0))))
+
 (define-public go-github-com-google-cadvisor
   (let ((commit "2ed7198f77395ee9a172878a0a7ab92ab59a2cfd")
         (revision "0"))
@@ -4791,7 +5043,8 @@ as conversion to and from @command{net.Addr}.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "10mcnvi5qmn00vpyk6si8gjka7p654wr9hac4zc9w5h3ickhvbdc"))))
+         "10mcnvi5qmn00vpyk6si8gjka7p654wr9hac4zc9w5h3ickhvbdc"))
+       (patches (search-patches "go-github-com-urfave-cli-fix-tests.patch"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/urfave/cli"))
@@ -4817,7 +5070,10 @@ fast and distributable command line applications in an expressive way.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "08pvn7gyfznni72xrxfh2x6xxa8ykr7l1ka278js8g8qkh71bj8l"))))
+        (base32 "08pvn7gyfznni72xrxfh2x6xxa8ykr7l1ka278js8g8qkh71bj8l"))
+       ;; XXX: Remove patch when updating.
+       (patches
+        (search-patches "go-github-com-urfave-cli-v2-fix-tests.patch"))))
     (arguments
      '(#:import-path "github.com/urfave/cli/v2"))))