[bug#32260] [PATCH 00/21] Python updates

[bug#32260] [PATCH 00/21] Python updates

[Marius Bakke]

This series updates Python to 3.7 and bumps many of the python-*
packages to the latest upstream releases.

Also, Python 3.7 is now reproducible on my system.  As well as most of
the library packages.  Woohoo!  :-)

Do we have time for a 'python-updates' round before core-updates?
Relatedly, can the existing 'python-updates' branch be deleted?

Marius Bakke (21):
  gnu: python: Remove outdated comment and phases.
  gnu: python: Update to 3.7.0.
  gnu: python: Rebuild bytecode after removing tests.
  gnu: python: Build reproducibly.
  gnu: python-py: Add missing dependency on setuptools-scm.
  gnu: python-py: Update to 1.5.4.
  gnu: python-py: Update home page.
  gnu: python-pyflakes: Update to 2.0.0.
  gnu: python-more-itertools: Update to 4.2.0.
  gnu: python-pycodestyle: Update to 2.4.0.
  gnu: python-setuptools: Update to 40.0.0.
  gnu: python-pytest-runner: Update to 4.2.
  gnu: python-flake8: Update to 3.5.0.
  gnu: python-hypothesis: Update to 3.66.6.
  gnu: python-pytest-cov: Update to 2.5.1.
  gnu: Add python-invoke.
  gnu: python-pytest: Update to 3.6.3.
  gnu: python-pytest-mock: Update to 1.10.0.
  gnu: docbook-xsl: Delete bundled jars.
  gnu: gdb: Fix build with Python >= 3.7.
  gnu: python-fonttools: Update to 3.28.0.

 gnu/local.mk                              |   1 +
 gnu/packages/check.scm                    |  35 ++---
 gnu/packages/docbook.scm                  |  10 +-
 gnu/packages/gdb.scm                      |   1 +
 gnu/packages/patches/gdb-python-3.7.patch |  52 +++++++
 gnu/packages/python.scm                   | 178 ++++++++--------------
 guix/build/python-build-system.scm        |   2 -
 7 files changed, 140 insertions(+), 139 deletions(-)
 create mode 100644 gnu/packages/patches/gdb-python-3.7.patch

-- 
2.18.0

[bug#32260] [PATCH 00/21] Python updates

[Marius Bakke]

This series updates Python to 3.7 and bumps many of the python-*
packages to the latest upstream releases.

Also, Python 3.7 is now reproducible on my system.  As well as most of
the library packages.  Woohoo!  :-)

Do we have time for a 'python-updates' round before core-updates?
Relatedly, can the existing 'python-updates' branch be deleted?

Marius Bakke (21):
  gnu: python: Remove outdated comment and phases.
  gnu: python: Update to 3.7.0.
  gnu: python: Rebuild bytecode after removing tests.
  gnu: python: Build reproducibly.
  gnu: python-py: Add missing dependency on setuptools-scm.
  gnu: python-py: Update to 1.5.4.
  gnu: python-py: Update home page.
  gnu: python-pyflakes: Update to 2.0.0.
  gnu: python-more-itertools: Update to 4.2.0.
  gnu: python-pycodestyle: Update to 2.4.0.
  gnu: python-setuptools: Update to 40.0.0.
  gnu: python-pytest-runner: Update to 4.2.
  gnu: python-flake8: Update to 3.5.0.
  gnu: python-hypothesis: Update to 3.66.6.
  gnu: python-pytest-cov: Update to 2.5.1.
  gnu: Add python-invoke.
  gnu: python-pytest: Update to 3.6.3.
  gnu: python-pytest-mock: Update to 1.10.0.
  gnu: docbook-xsl: Delete bundled jars.
  gnu: gdb: Fix build with Python >= 3.7.
  gnu: python-fonttools: Update to 3.28.0.

 gnu/local.mk                              |   1 +
 gnu/packages/check.scm                    |  35 ++---
 gnu/packages/docbook.scm                  |  10 +-
 gnu/packages/gdb.scm                      |   1 +
 gnu/packages/patches/gdb-python-3.7.patch |  52 +++++++
 gnu/packages/python.scm                   | 178 ++++++++--------------
 guix/build/python-build-system.scm        |   2 -
 7 files changed, 140 insertions(+), 139 deletions(-)
 create mode 100644 gnu/packages/patches/gdb-python-3.7.patch

-- 
2.18.0

[bug#32260] [PATCH 01/21] gnu: python: Remove outdated comment and phases.

[Marius Bakke]

* gnu/packages/python.scm (python-2.7)[arguments]: Don't set SOURCE_DATE_EPOCH
or make libraries writable, since those are handled by gnu-build-system.
(python-3.6): Don't override :#tests?.
---
 gnu/packages/python.scm | 33 +--------------------------------
 1 file changed, 1 insertion(+), 32 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index fc1ef3eb2..d173bbe61 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -178,23 +178,7 @@
                "tk"))                     ;tkinter; adds 50 MiB to the closure
     (build-system gnu-build-system)
     (arguments
-     `(;; 356 tests OK.
-       ;; 6 tests failed:
-       ;;     test_compileall test_distutils test_import test_shutil test_socket
-       ;;     test_subprocess
-       ;; 39 tests skipped:
-       ;;     test_aepack test_al test_applesingle test_bsddb test_bsddb185
-       ;;     test_bsddb3 test_cd test_cl test_codecmaps_cn test_codecmaps_hk
-       ;;     test_codecmaps_jp test_codecmaps_kr test_codecmaps_tw test_curses
-       ;;     test_dl test_gdb test_gl test_imageop test_imgfile test_ioctl
-       ;;     test_kqueue test_linuxaudiodev test_macos test_macostools
-       ;;     test_msilib test_ossaudiodev test_scriptpackages test_smtpnet
-       ;;     test_socketserver test_startfile test_sunaudiodev test_timeout
-       ;;     test_tk test_ttk_guionly test_urllib2net test_urllibnet
-       ;;     test_winreg test_winsound test_zipfile64
-       ;; 4 skips unexpected on linux2:
-       ;;     test_bsddb test_bsddb3 test_gdb test_ioctl
-       #:test-target "test"
+     `(#:test-target "test"
        #:configure-flags
        (list "--enable-shared"                    ;allow embedding
              "--with-system-ffi"                  ;build ctypes
@@ -219,11 +203,6 @@
                                     "Lib/test/support/__init__.py"
                                     "Lib/test/test_subprocess.py"))
                (("/bin/sh") (which "sh")))
-
-             ;; Use zero as the timestamp in .pyc files so that builds are
-             ;; deterministic.  TODO: Remove it when this variable is set in
-             ;; gnu-build-system.scm.
-             (setenv "SOURCE_DATE_EPOCH" "1")
              #t))
           (add-before 'configure 'do-not-record-configure-flags
             (lambda* (#:key configure-flags #:allow-other-keys)
@@ -281,15 +260,6 @@
                                                               file))))))
                        (call-with-output-file "__init__.py" (const #t))
                        #t)))))))
-          (add-before 'strip 'make-libraries-writable
-            (lambda* (#:key outputs #:allow-other-keys)
-              ;; Make .so files writable so they can be stripped.
-              (let ((out (assoc-ref outputs "out")))
-                (for-each (lambda (file)
-                            (chmod file #o755))
-                          (find-files (string-append out "/lib")
-                                      "\\.so"))
-                #t)))
           (add-after 'install 'move-tk-inter
             (lambda* (#:key outputs #:allow-other-keys)
               ;; When Tkinter support is built move it to a separate output so
@@ -377,7 +347,6 @@ data types.")
                   #t))))
     (arguments
      (substitute-keyword-arguments (package-arguments python-2)
-       ((#:tests? _) #t)
        ((#:phases phases)
         `(modify-phases ,phases
            (add-after 'unpack 'patch-timestamp-for-pyc-files
-- 
2.18.0

[bug#32260] [PATCH 02/21] gnu: python: Update to 3.7.0.

[Marius Bakke]

* gnu/packages/python.scm (python-3.6): Rename to ...
(python-3.7): ... this.  Update to 3.7.0.
[arguments]: Remove phase 'patch-timestamp-for-pyc-files' and related code.
Add phases to unset SOURCE_DATE_EPOCH during the check phase.
(python-3): Is now PYTHON-3.7.
* guix/build/python-build-system.scm (enable-bytecode-determinism): Don't set
DETERMINISTIC_BUILD.
---
 gnu/packages/python.scm            | 61 +++++++-----------------------
 guix/build/python-build-system.scm |  2 -
 2 files changed, 13 insertions(+), 50 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index d173bbe61..dcc8f0921 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -321,10 +321,10 @@ data types.")
     (name "python")
     (properties `((superseded . ,python-2)))))
 
-(define-public python-3.6
+(define-public python-3.7
   (package (inherit python-2)
     (name "python")
-    (version "3.6.5")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.python.org/ftp/python/"
@@ -337,7 +337,7 @@ data types.")
               (patch-flags '("-p0"))
               (sha256
                (base32
-                "19l7inxm056jjw33zz97z0m02hsi7jnnx5kyb76abj5ml4xhad7l"))
+                "0j9mic5c9lbd2b20wka7hily7szz740wy9ilfrczxap63rnrk0h3"))
               (snippet
                '(begin
                   (for-each delete-file
@@ -348,53 +348,18 @@ data types.")
     (arguments
      (substitute-keyword-arguments (package-arguments python-2)
        ((#:phases phases)
-        `(modify-phases ,phases
-           (add-after 'unpack 'patch-timestamp-for-pyc-files
-             (lambda _
-               ;; We set DETERMINISTIC_BUILD to only override the mtime when
-               ;; building with Guix, lest we break auto-compilation in
-               ;; environments.
-               (setenv "DETERMINISTIC_BUILD" "1")
-               (substitute* "Lib/py_compile.py"
-                 (("source_stats\\['mtime'\\]")
-                  "(1 if 'DETERMINISTIC_BUILD' in os.environ else source_stats['mtime'])"))
-
-               ;; Use deterministic hashes for strings, bytes, and datetime
-               ;; objects.
-               (setenv "PYTHONHASHSEED" "0")
-
-               ;; Reset mtime when validating bytecode header.
-               (substitute* "Lib/importlib/_bootstrap_external.py"
-                 (("source_mtime = int\\(source_stats\\['mtime'\\]\\)")
-                  "source_mtime = 1"))
-               #t))
-           ;; These tests fail because of our change to the bytecode
-           ;; validation.  They fail because expected exceptions do not get
-           ;; thrown.  This seems to be no problem.
-           (add-after 'unpack 'disable-broken-bytecode-tests
-             (lambda _
-               (substitute* "Lib/test/test_importlib/source/test_file_loader.py"
-                 (("test_bad_marshal")
-                  "disable_test_bad_marshal")
-                 (("test_no_marshal")
-                  "disable_test_no_marshal")
-                 (("test_non_code_marshal")
-                  "disable_test_non_code_marshal"))
-               #t))
-           ;; Unset DETERMINISTIC_BUILD to allow for tests that check that
-           ;; stale pyc files are rebuilt.
-           (add-before 'check 'allow-non-deterministic-compilation
-             (lambda _ (unsetenv "DETERMINISTIC_BUILD") #t))
-           ;; We need to rebuild all pyc files for three different
-           ;; optimization levels to replace all files that were not built
-           ;; deterministically.
-
-           ;; FIXME: Without this phase we have close to 2000 files that
+       `(modify-phases ,phases
+          ;; Unset SOURCE_DATE_EPOCH while running the test-suite and set it
+          ;; again afterwards.  See <https://bugs.python.org/issue34022>.
+          (add-before 'check 'unset-SOURCE_DATE_EPOCH
+            (lambda _ (unsetenv "SOURCE_DATE_EPOCH") #t))
+          (add-after 'check 'reset-SOURCE_DATE_EPOCH
+            (lambda _ (setenv "SOURCE_DATE_EPOCH" "1") #t))
+           ;; FIXME: Without this phase we have close to 400 files that
            ;; differ across different builds of this package.  With this phase
-           ;; there are about 500 files left that differ.
+           ;; there are 44 files left that differ.
            (add-after 'install 'rebuild-bytecode
              (lambda* (#:key outputs #:allow-other-keys)
-               (setenv "DETERMINISTIC_BUILD" "1")
                (let ((out (assoc-ref outputs "out")))
                  (for-each
                   (lambda (opt)
@@ -421,7 +386,7 @@ data types.")
                                         "/site-packages"))))))))
 
 ;; Current 3.x version.
-(define-public python-3 python-3.6)
+(define-public python-3 python-3.7)
 
 ;; Current major version.
 (define-public python python-3)
diff --git a/guix/build/python-build-system.scm b/guix/build/python-build-system.scm
index 376ea81f1..5bb0ba49d 100644
--- a/guix/build/python-build-system.scm
+++ b/guix/build/python-build-system.scm
@@ -246,8 +246,6 @@ installed with setuptools."
 
 (define* (enable-bytecode-determinism #:rest _)
   "Improve determinism of pyc files."
-  ;; Set DETERMINISTIC_BUILD to override the embedded mtime in pyc files.
-  (setenv "DETERMINISTIC_BUILD" "1")
   ;; Use deterministic hashes for strings, bytes, and datetime objects.
   (setenv "PYTHONHASHSEED" "0")
   #t)
-- 
2.18.0

[bug#32260] [PATCH 03/21] gnu: python: Rebuild bytecode after removing tests.

[Marius Bakke]

* gnu/packages/python.scm (python-3.7)[arguments]: Run 'rebuild-bytecode'
after 'remove-tests' to save CPU cycles.  Adjust exclude regex.
---
 gnu/packages/python.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index dcc8f0921..395258aa9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -358,7 +358,7 @@ data types.")
            ;; FIXME: Without this phase we have close to 400 files that
            ;; differ across different builds of this package.  With this phase
            ;; there are 44 files left that differ.
-           (add-after 'install 'rebuild-bytecode
+           (add-after 'remove-tests 'rebuild-bytecode
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))
                  (for-each
@@ -372,8 +372,7 @@ data types.")
                                          "-m" "compileall"
                                          "-f" ; force rebuild
                                          ;; Don't build lib2to3, because it's Python 2 code.
-                                         ;; Also don't build obviously broken test code.
-                                         "-x" "(lib2to3|test/bad.*)"
+                                         "-x" "lib2to3.*"
                                          ,file)))
                               (find-files out "\\.py$")))
                   (list '() '("-O") '("-OO")))
-- 
2.18.0

[bug#32260] [PATCH 04/21] gnu: python: Build reproducibly.

[Marius Bakke]

\o/

* gnu/packages/python.scm (python-3.7)[arguments]: Set PYTHONHASHSEED before
rebuilding all bytecode.  Adjust regex so that lib2to3_ex.py gets compiled.
---
 gnu/packages/python.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 395258aa9..7a42d9bc5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -361,6 +361,9 @@ data types.")
            (add-after 'remove-tests 'rebuild-bytecode
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))
+                 ;; Disable hash randomization to ensure the generated .pycs
+                 ;; are reproducible.
+                 (setenv "PYTHONHASHSEED" "0")
                  (for-each
                   (lambda (opt)
                     (format #t "Compiling with optimization level: ~a\n"
@@ -372,7 +375,7 @@ data types.")
                                          "-m" "compileall"
                                          "-f" ; force rebuild
                                          ;; Don't build lib2to3, because it's Python 2 code.
-                                         "-x" "lib2to3.*"
+                                         "-x" "lib2to3/.*"
                                          ,file)))
                               (find-files out "\\.py$")))
                   (list '() '("-O") '("-OO")))
-- 
2.18.0

[bug#32260] [PATCH 05/21] gnu: python-py: Add missing dependency on setuptools-scm.

[Marius Bakke]

* gnu/packages/python.scm (python-py)[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
---
 gnu/packages/python.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7a42d9bc5..5f3642e49 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1725,6 +1725,8 @@ matching them against a list of media-ranges.")
      ;; Expected '/tmp/guix-build-python-py-1.4.31.drv-0/py-1.4.31/py'.
      ;; Is this module globally installed?"
      '(#:tests? #f))
+    (native-inputs
+     `(("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "http://pylib.readthedocs.io/")
     (synopsis "Python library for parsing, I/O, instrospection, and logging")
     (description
-- 
2.18.0

[bug#32260] [PATCH 06/21] gnu: python-py: Update to 1.5.4.

[Marius Bakke]

* gnu/packages/python.scm (python-py): Update to 1.5.4.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5f3642e49..aa128a13c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1710,14 +1710,14 @@ matching them against a list of media-ranges.")
 (define-public python-py
   (package
     (name "python-py")
-    (version "1.5.3")
+    (version "1.5.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "py" version))
        (sha256
         (base32
-         "10gq2lckvgwlk9w6yzijhzkarx44hsaknd0ypa08wlnpjnsgmj99"))))
+         "1xxvwfn82457djf55f5n2c94699rfqnk43br8fif2r2q8gvrmm9z"))))
     (build-system python-build-system)
     (arguments
      ;; FIXME: "ImportError: 'test' module incorrectly imported from
-- 
2.18.0

[bug#32260] [PATCH 07/21] gnu: python-py: Update home page.

[Marius Bakke]

* gnu/packages/python.scm (python-py)[home-page]: Change to repository URL.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index aa128a13c..5acb700fe 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1727,7 +1727,7 @@ matching them against a list of media-ranges.")
      '(#:tests? #f))
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm)))
-    (home-page "http://pylib.readthedocs.io/")
+    (home-page "https://github.com/pytest-dev/py")
     (synopsis "Python library for parsing, I/O, instrospection, and logging")
     (description
      "Py is a Python library for file name parsing, .ini file parsing, I/O,
-- 
2.18.0

[bug#32260] [PATCH 08/21] gnu: python-pyflakes: Update to 2.0.0.

[Marius Bakke]

* gnu/packages/python.scm (python-pyflakes): Update to 2.0.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5acb700fe..37274f055 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5512,14 +5512,14 @@ PEP 8.")
 (define-public python-pyflakes
   (package
     (name "python-pyflakes")
-    (version "1.5.0")
+    (version "2.0.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pyflakes" version))
         (sha256
           (base32
-            "1x1pcca4a24k4pw8x1c77sgi58cg1wl2k38mp8a25k608pzls3da"))))
+            "0jba28czyvimdc72llms3f17swp3i8jdcabf5w0j00adfbn64xls"))))
     (build-system python-build-system)
     (home-page
       "https://github.com/pyflakes/pyflakes")
-- 
2.18.0

[bug#32260] [PATCH 09/21] gnu: python-more-itertools: Update to 4.2.0.

[Marius Bakke]

* gnu/packages/python.scm (python-more-itertools): Update to 4.2.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 37274f055..26fd20f0c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -13299,14 +13299,14 @@ file system events on Linux.")
 (define-public python-more-itertools
   (package
     (name "python-more-itertools")
-    (version "4.1.0")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "more-itertools" version))
        (sha256
         (base32
-         "0i3ch700g5fyjp692gprlnzbysl8w0sa2vijbp3s40drvk67xkn9"))))
+         "1s6qhl7a7jy8gqw8p545rxfp7rwz1hmjr9p6prk93zbv6f9rhsrb"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-six" ,python-six-bootstrap)))
-- 
2.18.0

[bug#32260] [PATCH 10/21] gnu: python-pycodestyle: Update to 2.4.0.

[Marius Bakke]

* gnu/packages/python.scm (python-pycodestyle): Update to 2.4.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 26fd20f0c..a3083bd76 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3806,14 +3806,14 @@ as the original project seems to have been abandoned circa 2007.")
 (define-public python-pycodestyle
   (package
     (name "python-pycodestyle")
-    (version "2.3.1")
+    (version "2.4.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pycodestyle" version))
         (sha256
           (base32
-            "0rk78b66p57ala26mdldl9lafr48blv5s659sah9q50qnfjmc8k8"))))
+            "0fhy4vnlgpjq4qd1wdnl6pvdw7rah0ypmn8c9mkhz8clsndskz6b"))))
     (build-system python-build-system)
     (home-page "https://pycodestyle.readthedocs.io/")
     (synopsis "Python style guide checker")
-- 
2.18.0

[bug#32260] [PATCH 11/21] gnu: python-setuptools: Update to 40.0.0.

[Marius Bakke]

* gnu/packages/python.scm (python-setuptools): Update to 40.0.0.
[source](uri): Adjust to zipball archive.
---
 gnu/packages/python.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index a3083bd76..ed0935b74 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -844,14 +844,14 @@ API for locking files.")
 (define-public python-setuptools
   (package
     (name "python-setuptools")
-    (version "31.0.0")
+    (version "40.0.0")
     (source
      (origin
       (method url-fetch)
-      (uri (pypi-uri "setuptools" version))
+      (uri (pypi-uri "setuptools" version ".zip"))
       (sha256
        (base32
-        "0ypybh4hx3bv4vhg2dc74xpj1g56ggnaffm87k4abhwjwq6wq608"))
+        "0pq116lr14gnc62v76nk0npkm6krb2mpp7p9ab369zgv4n7dnah1"))
       (modules '((guix build utils)))
       (snippet
        '(begin
-- 
2.18.0

[bug#32260] [PATCH 12/21] gnu: python-pytest-runner: Update to 4.2.

[Marius Bakke]

* gnu/packages/check.scm (python-pytest-runner): Update to 4.2.
[arguments]: Remove.
---
 gnu/packages/check.scm | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 42b90bc2b..3239bf895 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -729,26 +729,15 @@ supports coverage of subprocesses.")
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
-    (version "2.11.1")
+    (version "4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-runner" version))
        (sha256
         (base32
-         "1cw978kqqcq916b9gfns1qjqvg33c5ail5jhw9054dsynkm32flq"))))
+         "1gkpyphawxz38ni1gdq1fmwyqcg02m7ypzqvv46z06crwdxi2gyj"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; The fancy way of setting the version with setuptools_scm does not
-         ;; seem to work here.
-         (add-after 'unpack 'set-version
-          (lambda _
-            (substitute* "docs/conf.py"
-              (("version = setuptools_scm\\.get_version\\(root='\\.\\.')")
-               (string-append "version = \"" ,version "\"")))
-            #t)))))
     (native-inputs
      `(("python-pytest" ,python-pytest-bootstrap)
        ("python-setuptools-scm" ,python-setuptools-scm)))
-- 
2.18.0

[bug#32260] [PATCH 13/21] gnu: python-flake8: Update to 3.5.0.

[Marius Bakke]

* gnu/packages/python.scm (python-flake8): Update to 3.5.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ed0935b74..36b519faf 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5617,14 +5617,14 @@ complexity of Python source code.")
 (define-public python-flake8
   (package
     (name "python-flake8")
-    (version "3.4.1")
+    (version "3.5.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "flake8" version))
         (sha256
           (base32
-            "1n0i38592vy3q0x2a9bf8z6rhhn04i30wsn5i5zzcj7qkxvl8062"))))
+            "184b33grvvjmiwlv9kyd7yng9qv5ld24154j70z332xxg9gjclvj"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.18.0

[bug#32260] [PATCH 14/21] gnu: python-hypothesis: Update to 3.66.6.

[Marius Bakke]

* gnu/packages/check.scm (python-hypothesis): Update to 3.66.6.
---
 gnu/packages/check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 3239bf895..8ee7d9773 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1386,13 +1386,13 @@ normally the case.")
 (define-public python-hypothesis
   (package
     (name "python-hypothesis")
-    (version "3.52.0")
+    (version "3.66.6")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "hypothesis" version))
               (sha256
                (base32
-                "0g54cypfi5qj6cgxfr7l1nb41r1cqhhngx4qxn4ga9h720rcsbr8"))))
+                "0jlcbnirj5ndv4gvb3rmydligljn1alim9d4dk377188y09iwl5k"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-flake8" ,python-flake8)
-- 
2.18.0

[bug#32260] [PATCH 15/21] gnu: python-pytest-cov: Update to 2.5.1.

[Marius Bakke]

* gnu/packages/check.scm (python-pytest-cov): Update to 2.5.1.
---
 gnu/packages/check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 8ee7d9773..b2a0ecce4 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -693,14 +693,14 @@ and many external plugins.")
 (define-public python-pytest-cov
   (package
     (name "python-pytest-cov")
-    (version "2.4.0")
+    (version "2.5.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pytest-cov" version))
         (sha256
          (base32
-          "03c2qc42r4bczyw93gd7n0qi1h1jfhw7fnbhi33c3vp1hs81gm2k"))))
+          "0bbfpwdh9k3636bxc88vz9fa7vf4akchgn513ql1vd0xy4n7bah3"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.18.0

[bug#32260] [PATCH 16/21] gnu: Add python-invoke.

[Marius Bakke]

* gnu/packages/python.scm (python-invoke, python2-invoke): New public variables.
---
 gnu/packages/python.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 36b519faf..d0df96f7d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10767,6 +10767,32 @@ projects.")
 (define-public python2-incremental
   (package-with-python2 python-incremental))
 
+(define-public python-invoke
+  (package
+    (name "python-invoke")
+    (home-page "http://www.pyinvoke.org/")
+    (version "1.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "invoke" version))
+              (sha256
+               (base32
+                "0aiy1xvk1f91246zxd1zqrm679vdvd10h843a2na41cqr3cflpi6"))))
+    (build-system python-build-system)
+    (arguments
+     ;; XXX: Requires many dependencies that are not yet in Guix.
+     `(#:tests? #f))
+    (synopsis "Pythonic task execution")
+    (description
+     "Invoke is a Python task execution tool and library, drawing inspiration
+from various sources to arrive at a powerful and clean feature set.  It is
+evolved from the Fabric project, but focuses on local and abstract concerns
+instead of servers and network commands.")
+    (license license:bsd-3)))
+
+(define-public python2-invoke
+  (package-with-python2 python-invoke))
+
 (define-public python-automat
   (package
     (name "python-automat")
-- 
2.18.0

[bug#32260] [PATCH 17/21] gnu: python-pytest: Update to 3.6.3.

[Marius Bakke]

* gnu/packages/check.scm (python-pytest): Update to 3.6.3.
[propagated-inputs]: Add PYTHON-ATOMICWRITES.
[native-inputs]: Add PYTHON-INVOKE.
---
 gnu/packages/check.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index b2a0ecce4..134e64034 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -619,14 +619,14 @@ standard library.")
 (define-public python-pytest
   (package
     (name "python-pytest")
-    (version "3.5.0")
+    (version "3.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest" version))
        (sha256
         (base32
-         "1q832zd07zak2lyxbycxjydh0jp7y3hvawjqzlvra6aghz8r3r7s"))))
+         "0lnppwpz5i06sdhzv5b2j4x2f42mil38nx1l0kmnzvibdikwhlq4"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -644,7 +644,8 @@ standard library.")
                                line)))
              #t)))))
     (propagated-inputs
-     `(("python-attrs" ,python-attrs-bootstrap)
+     `(("python-atomicwrites" ,python-atomicwrites)
+       ("python-attrs" ,python-attrs-bootstrap)
        ("python-more-itertools" ,python-more-itertools)
        ("python-pluggy" ,python-pluggy)
        ("python-py" ,python-py)
@@ -653,6 +654,7 @@ standard library.")
      `(;; Tests need the "regular" bash since 'bash-final' lacks `compgen`.
        ("bash" ,bash)
        ("python-hypothesis" ,python-hypothesis)
+       ("python-invoke" ,python-invoke)   ;XXX: not needed for >3.6.3
        ("python-nose" ,python-nose)
        ("python-mock" ,python-mock)
        ("python-setuptools-scm" ,python-setuptools-scm)))
-- 
2.18.0

[bug#32260] [PATCH 18/21] gnu: python-pytest-mock: Update to 1.10.0.

[Marius Bakke]

* gnu/packages/check.scm (python-pytest-mock): Update to 1.10.1.
---
 gnu/packages/check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 134e64034..9a53a7eb7 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -756,14 +756,14 @@ supports coverage of subprocesses.")
 (define-public python-pytest-mock
   (package
     (name "python-pytest-mock")
-    (version "1.6.3")
+    (version "1.10.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "pytest-mock" version))
         (sha256
          (base32
-          "075v7b2wm5f839r1a30n21wfk5rfqp3d05q7zb9jlb2wmxki23cj"))))
+          "1h6lgpmsvs9s8j2s80v06f9f3iaw1n1rc51mbrxk1f12sw4q56nq"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm)))
-- 
2.18.0

[bug#32260] [PATCH 19/21] gnu: docbook-xsl: Delete bundled jars.

[Marius Bakke]

* gnu/packages/docbook.scm (docbook-xsl)[source](modules, snippet): New fields.
---
 gnu/packages/docbook.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/docbook.scm b/gnu/packages/docbook.scm
index 1c00e56d6..1e5379b02 100644
--- a/gnu/packages/docbook.scm
+++ b/gnu/packages/docbook.scm
@@ -138,11 +138,15 @@ by no means limited to these applications.)  This package provides XML DTDs.")
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/docbook/docbook-xsl/"
                                   version "/docbook-xsl-" version ".tar.bz2"))
-              ;; Note: If removing all patches, the XZ dependency is no longer needed.
               (patches (search-patches "docbook-xsl-nonrecursive-string-subst.patch"))
               (sha256
                (base32
-                "0s59lihif2fr7rznckxr2kfyrvkirv76r1zvidp9b5mj28p4apvj"))))
+                "0s59lihif2fr7rznckxr2kfyrvkirv76r1zvidp9b5mj28p4apvj"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (for-each delete-file (find-files "." "\\.jar$"))
+                  #t))))
     (build-system trivial-build-system)
     (arguments
      `(#:builder (let ((name-version (string-append ,name "-" ,version)))
@@ -168,7 +172,7 @@ by no means limited to these applications.)  This package provides XML DTDs.")
                      #t))
        #:modules ((guix build utils))))
     (native-inputs `(("bzip2" ,bzip2)
-                     ("xz" ,xz)
+                     ("xz" ,xz)         ;needed for repacked tarballs
                      ("tar" ,tar)))
     (home-page "http://docbook.org")
     (synopsis "DocBook XSL style sheets for document authoring")
-- 
2.18.0

[bug#32260] [PATCH 20/21] gnu: gdb: Fix build with Python >= 3.7.

[Marius Bakke]

* gnu/packages/patches/gdb-python-3.7.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/gdb.scm (gdb)[source](patches): New field.
---
 gnu/local.mk                              |  1 +
 gnu/packages/gdb.scm                      |  1 +
 gnu/packages/patches/gdb-python-3.7.patch | 52 +++++++++++++++++++++++
 3 files changed, 54 insertions(+)
 create mode 100644 gnu/packages/patches/gdb-python-3.7.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 16521e8e0..eb3764410 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -711,6 +711,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-CVE-2018-5711.patch			\
   %D%/packages/patches/gd-fix-tests-on-i686.patch		\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
+  %D%/packages/patches/gdb-python-3.7.patch			\
   %D%/packages/patches/gemma-intel-compat.patch			\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
diff --git a/gnu/packages/gdb.scm b/gnu/packages/gdb.scm
index 36ccb79d6..4c47cc585 100644
--- a/gnu/packages/gdb.scm
+++ b/gnu/packages/gdb.scm
@@ -42,6 +42,7 @@
              (method url-fetch)
              (uri (string-append "mirror://gnu/gdb/gdb-"
                                  version ".tar.xz"))
+             (patches (search-patches "gdb-python-3.7.patch"))
              (sha256
               (base32
                "0d2bpqk58fqlx21rbnk8mbcjlggzc9kb5sjirrfrrrjq70ka0qdg"))))
diff --git a/gnu/packages/patches/gdb-python-3.7.patch b/gnu/packages/patches/gdb-python-3.7.patch
new file mode 100644
index 000000000..c51442c8b
--- /dev/null
+++ b/gnu/packages/patches/gdb-python-3.7.patch
@@ -0,0 +1,52 @@
+Fix build failure with Python 3.7 and newer.
+
+Taken from this upstream commit, sans ChangeLog update:
+
+https://sourceware.org/git/gitweb.cgi?p=binutils-gdb.git;a=commitdiff;h=aeab512851bf6ed623d1c6c4305b6ce05e51a10c
+
+diff --git a/gdb/python/python.c b/gdb/python/python.c
+index 1805c90..20fc674 100644
+--- a/gdb/python/python.c
++++ b/gdb/python/python.c
+@@ -1667,6 +1667,17 @@ finalize_python (void *ignore)
+   restore_active_ext_lang (previous_active);
+ }
+ 
++#ifdef IS_PY3K
++/* This is called via the PyImport_AppendInittab mechanism called
++   during initialization, to make the built-in _gdb module known to
++   Python.  */
++PyMODINIT_FUNC
++init__gdb_module (void)
++{
++  return PyModule_Create (&python_GdbModuleDef);
++}
++#endif
++
+ static bool
+ do_start_initialization ()
+ {
+@@ -1707,6 +1718,9 @@ do_start_initialization ()
+      remain alive for the duration of the program's execution, so
+      it is not freed after this call.  */
+   Py_SetProgramName (progname_copy);
++
++  /* Define _gdb as a built-in module.  */
++  PyImport_AppendInittab ("_gdb", init__gdb_module);
+ #else
+   Py_SetProgramName (progname.release ());
+ #endif
+@@ -1716,9 +1730,7 @@ do_start_initialization ()
+   PyEval_InitThreads ();
+ 
+ #ifdef IS_PY3K
+-  gdb_module = PyModule_Create (&python_GdbModuleDef);
+-  /* Add _gdb module to the list of known built-in modules.  */
+-  _PyImport_FixupBuiltin (gdb_module, "_gdb");
++  gdb_module = PyImport_ImportModule ("_gdb");
+ #else
+   gdb_module = Py_InitModule ("_gdb", python_GdbMethods);
+ #endif
+-- 
+2.9.3
+
-- 
2.18.0

[bug#32260] [PATCH 21/21] gnu: python-fonttools: Update to 3.28.0.

[Marius Bakke]

* gnu/packages/python.scm (python-fonttools): Update to 3.28.0.
[arguments]: Remove.
[native-inputs]: Add PYTHON-PYTEST and PYTHON-PYTEST-RUNNER.
---
 gnu/packages/python.scm | 20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index d0df96f7d..f15fb13d6 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5894,28 +5894,18 @@ add functionality and customization to your projects with their own plugins.")
 (define-public python-fonttools
   (package
     (name "python-fonttools")
-    (version "3.15.1")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "fonttools" version ".zip"))
               (sha256
                (base32
-                "1hhj97izwliy0vybmza72d90l5d4mcn50y8akq7kyccfl82vdx4d"))))
+                "0vsvjhidpb5kywpjgz1j3fywzkddxkb0afqai18qa3h6lqjyxwpb"))))
     (build-system python-build-system)
-    (arguments
-     '(#:test-target "check"
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-setuppy
-           ;; Remove the undocumented "extra_path" argument, which adds an
-           ;; intervening directories between site-packages and the package
-           ;; directory.
-           (lambda _
-             (substitute* "setup.py"
-               (("^[ \t]*extra_path *= *'FontTools',") ""))
-             #t)))))
     (native-inputs
-     `(("unzip" ,unzip)))
+     `(("unzip" ,unzip)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
     (home-page "https://github.com/behdad/fonttools")
     (synopsis "Tools to manipulate font files")
     (description
-- 
2.18.0

[bug#32260] [PATCH 19/21] gnu: docbook-xsl: Delete bundled jars.

[Marius Bakke]

[-- Attachment #1: Type: text/plain, Size: 292 bytes --]

One of these patches is not like the others...

Marius Bakke <mbakke@fastmail.com> writes:

> * gnu/packages/docbook.scm (docbook-xsl)[source](modules, snippet): New fields.

This is for core-updates and has nothing to do with this series (apart
from being caught up in the middle!).

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[bug#32260] [PATCH 02/21] gnu: python: Update to 3.7.0.

[Efraim]

[-- Attachment #1: Type: text/plain, Size: 282 bytes --]

Here's a patch with the changes I made to make it build on aarch64-linux.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: 0001-gnu-python-3.7-Update-deleted-tests.patch --]
[-- Type: text/plain, Size: 1284 bytes --]

From c829655b54445eaf17943ff7ab9487e2111ff5d0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 26 Jul 2018 17:12:01 +0300
Subject: [PATCH] gnu: python-3.7: Update deleted tests.

* gnu/packages/python.scm (python-3.7)[source]: Update the list of files
to be deleted in the snippet.
---
 gnu/packages/python.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7a42d9bc5..513a362a4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -341,9 +341,9 @@ data types.")
               (snippet
                '(begin
                   (for-each delete-file
-                            '("Lib/ctypes/test/test_structures.py" ; fails on aarch64
-                              "Lib/ctypes/test/test_win32.py" ; fails on aarch64
-                              "Lib/test/test_fcntl.py")) ; fails on aarch64
+                            '("Lib/ctypes/test/test_win32.py" ; fails on aarch64
+                              "Lib/test/test_fcntl.py" ; fails on aarch64
+                              "Lib/test/test_posix.py")) ; fails on aarch64
                   #t))))
     (arguments
      (substitute-keyword-arguments (package-arguments python-2)
-- 
2.18.0

bug#32260: [PATCH 00/21] Python updates

[Marius Bakke]

[-- Attachment #1: Type: text/plain, Size: 1445 bytes --]

Marius Bakke <mbakke@fastmail.com> writes:

> This series updates Python to 3.7 and bumps many of the python-*
> packages to the latest upstream releases.
>
> Also, Python 3.7 is now reproducible on my system.  As well as most of
> the library packages.  Woohoo!  :-)
>
> Do we have time for a 'python-updates' round before core-updates?
> Relatedly, can the existing 'python-updates' branch be deleted?
>
> Marius Bakke (21):
>   gnu: python: Remove outdated comment and phases.
>   gnu: python: Update to 3.7.0.
>   gnu: python: Rebuild bytecode after removing tests.
>   gnu: python: Build reproducibly.
>   gnu: python-py: Add missing dependency on setuptools-scm.
>   gnu: python-py: Update to 1.5.4.
>   gnu: python-py: Update home page.
>   gnu: python-pyflakes: Update to 2.0.0.
>   gnu: python-more-itertools: Update to 4.2.0.
>   gnu: python-pycodestyle: Update to 2.4.0.
>   gnu: python-setuptools: Update to 40.0.0.
>   gnu: python-pytest-runner: Update to 4.2.
>   gnu: python-flake8: Update to 3.5.0.
>   gnu: python-hypothesis: Update to 3.66.6.
>   gnu: python-pytest-cov: Update to 2.5.1.
>   gnu: Add python-invoke.
>   gnu: python-pytest: Update to 3.6.3.
>   gnu: python-pytest-mock: Update to 1.10.0.
>   gnu: docbook-xsl: Delete bundled jars.
>   gnu: gdb: Fix build with Python >= 3.7.
>   gnu: python-fonttools: Update to 3.28.0.

These are now in 'core-updates' since I didn't get a response regarding
'python-updates'.

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[bug#32260] [PATCH 00/21] Python updates

[Ludovic Courtès]

Hello,

Marius Bakke <mbakke@fastmail.com> skribis:

> Marius Bakke <mbakke@fastmail.com> writes:
>
>> This series updates Python to 3.7 and bumps many of the python-*
>> packages to the latest upstream releases.
>>
>> Also, Python 3.7 is now reproducible on my system.  As well as most of
>> the library packages.  Woohoo!  :-)
>>
>> Do we have time for a 'python-updates' round before core-updates?
>> Relatedly, can the existing 'python-updates' branch be deleted?
>>
>> Marius Bakke (21):
>>   gnu: python: Remove outdated comment and phases.
>>   gnu: python: Update to 3.7.0.
>>   gnu: python: Rebuild bytecode after removing tests.
>>   gnu: python: Build reproducibly.
>>   gnu: python-py: Add missing dependency on setuptools-scm.
>>   gnu: python-py: Update to 1.5.4.
>>   gnu: python-py: Update home page.
>>   gnu: python-pyflakes: Update to 2.0.0.
>>   gnu: python-more-itertools: Update to 4.2.0.
>>   gnu: python-pycodestyle: Update to 2.4.0.
>>   gnu: python-setuptools: Update to 40.0.0.
>>   gnu: python-pytest-runner: Update to 4.2.
>>   gnu: python-flake8: Update to 3.5.0.
>>   gnu: python-hypothesis: Update to 3.66.6.
>>   gnu: python-pytest-cov: Update to 2.5.1.
>>   gnu: Add python-invoke.
>>   gnu: python-pytest: Update to 3.6.3.
>>   gnu: python-pytest-mock: Update to 1.10.0.
>>   gnu: docbook-xsl: Delete bundled jars.
>>   gnu: gdb: Fix build with Python >= 3.7.
>>   gnu: python-fonttools: Update to 3.28.0.
>
> These are now in 'core-updates' since I didn't get a response regarding
> 'python-updates'.

Makes sense.  Thank you!

Ludo’.