From d51b8ac9474a09b3baea4aa8cb1745d6ce9121cd Mon Sep 17 00:00:00 2001
From: Marius Bakke <marius@gnu.org>
Date: Sat, 22 May 2021 19:46:02 +0200
Subject: gnu: Remove python2-notebook.

Some of its requirements no longer support Python 2 which has left this
package broken for a while.

* gnu/packages/python-xyz.scm (python2-notebook): Remove variable.
(python-notebook)[properties]: Remove.
---
 gnu/packages/python-xyz.scm | 21 ---------------------
 1 file changed, 21 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bd716f3dac..2b02efa0c4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11200,29 +11200,8 @@ (define-public python-notebook
     (description
      "The Jupyter HTML notebook is a web-based notebook environment for
 interactive computing.")
-    (properties `((python2-variant . ,(delay python2-notebook))))
     (license license:bsd-3)))
 
-(define-public python2-notebook
-  (let ((base (package-with-python2
-                (strip-python2-variant python-notebook))))
-    (package/inherit base
-      (native-inputs
-       `(("python2-mock" ,python2-mock)
-         ,@(package-native-inputs base)))
-      (arguments
-       (substitute-keyword-arguments (package-arguments base)
-         ((#:phases phases)
-          `(modify-phases ,phases
-             (add-before 'check 'disable-test-case
-              ;; The test requires network access to localhost. Curiously it
-              ;; fails with Python 2 only. Simply make the test-case return
-              ;; immediately.
-              (lambda _
-                (substitute*
-                    "notebook/services/nbconvert/tests/test_nbconvert_api.py"
-                  (("formats = self.nbconvert_api") "return #")))))))))))
-
 (define-public python-widgetsnbextension
   (package
     (name "python-widgetsnbextension")
-- 
cgit v1.2.3


From 8a0e94f69be6bbe2edf89ace385d7062f90970c1 Mon Sep 17 00:00:00 2001
From: Marius Bakke <marius@gnu.org>
Date: Sat, 22 May 2021 19:48:01 +0200
Subject: gnu: Remove python2-ipython-cluster-helper.

Some of its requirements no longer support Python 2 which has left this
package broken for a while.

* gnu/packages/python-xyz.scm (python2-ipython-cluster-helper): Remove variable.
---
 gnu/packages/python-xyz.scm | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2b02efa0c4..c501b65a55 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7554,9 +7554,6 @@ (define-public python-ipython-cluster-helper
 cluster down and deletes the throwaway profile.")
     (license license:expat)))
 
-(define-public python2-ipython-cluster-helper
-  (package-with-python2 python-ipython-cluster-helper))
-
 (define-public python-traitlets
   (package
     (name "python-traitlets")
-- 
cgit v1.2.3


From dbcf2b61b1f48cbe84d51873f4e4de60897b914c Mon Sep 17 00:00:00 2001
From: Marius Bakke <marius@gnu.org>
Date: Sun, 23 May 2021 14:07:34 +0200
Subject: gnu: Fix erroneous uses of 'package/inherit'.

These packages use a different source/version from the inherited package, and
thus should not inherit replacements.

* gnu/packages/check.scm (googletest-1.8, python-pytest-runner-2): Use record
inheritance instead of PACKAGE/INHERIT.
* gnu/packages/crates-io.scm (rust-bindgen-0.49, rust-bytes-0.4,
rust-colored-1.9.1, rust-difference-1, rust-docopt-0.8, rust-html5ever-0.23,
rust-http-0.1, rust-http-body-0.1, rust-loom-0.2, rust-loom-0.1,
rust-pulldown-cmark-0.0.8, rust-ring-0.13, rust-rustls-0.12, rust-sct-0.3,
rust-term-0.2, rust-untrusted-0.6, rust-webpki-0.18, rust-webpki-roots-0.17,
rust-webpki-roots-0.14): Likewise.
* gnu/packages/emacs.scm (emacs-next, emacs-next-pgtk, guile-emacs): Likewise.
* gnu/packages/guile.scm (guile-2.2.4): Likewise.
* gnu/packages/maths.scm (hdf5-1.10, hdf5-1.12): Likewise.
* gnu/packages/protobuf.scm (protobuf-3.6, protobuf-3.5, python-protobuf-3.6):
Likewise.
* gnu/packages/python-web.scm (python2-html2text): Likewise.
* gnu/packages/python-xyz.scm (python-pygments/fixed, python2-numpy,
python2-urwid, python2-markdown, python2-fonttools): Likewise.
* gnu/packages/racket.scm (racket): Likewise.
* gnu/packages/sequoia.scm (sequoia4pEp): Likewise.
---
 gnu/packages/check.scm      |  8 +++----
 gnu/packages/crates-io.scm  | 57 ++++++++++++++++++++++++++++++---------------
 gnu/packages/emacs.scm      |  9 ++++---
 gnu/packages/guile.scm      |  4 ++--
 gnu/packages/maths.scm      |  6 +++--
 gnu/packages/protobuf.scm   | 10 ++++----
 gnu/packages/python-web.scm |  3 ++-
 gnu/packages/python-xyz.scm | 18 +++++++-------
 gnu/packages/racket.scm     |  4 ++--
 gnu/packages/sequoia.scm    |  3 ++-
 10 files changed, 76 insertions(+), 46 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 63ed2175ef..7b20d863e6 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -697,8 +697,8 @@ (define-public googletest
     (license license:bsd-3)))
 
 (define-public googletest-1.8
-  (package/inherit
-   googletest
+  (package
+    (inherit googletest)
    (version "1.8.1")
    (source (origin
              (method git-fetch)
@@ -1188,8 +1188,8 @@ (define-public python2-pytest-runner
 ;; python-bleach 3.1.0 requires this ancient version of pytest-runner.
 ;; Remove once no longer needed.
 (define-public python-pytest-runner-2
-  (package/inherit
-   python-pytest-runner
+  (package
+    (inherit python-pytest-runner)
    (version "2.12.2")
    (source (origin
              (method url-fetch)
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index 313c57e90f..318b2c695b 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
@@ -4416,7 +4416,8 @@ (define-public rust-bindgen-0.37
         ("rust-shlex" ,rust-shlex-0.1))))))
 
 (define-public rust-bindgen-0.49
-  (package/inherit rust-bindgen-0.50
+  (package
+    (inherit rust-bindgen-0.50)
     (name "rust-bindgen")
     (version "0.49.4")
     (source
@@ -5949,7 +5950,8 @@ (define-public rust-bytes-0.5
        (("rust-serde" ,rust-serde-1))))))
 
 (define-public rust-bytes-0.4
-  (package/inherit rust-bytes-0.5
+  (package
+    (inherit rust-bytes-0.5)
     (name "rust-bytes")
     (version "0.4.12")
     (source
@@ -7660,7 +7662,8 @@ (define-public rust-colored-1
     (license license:mpl2.0)))
 
 (define-public rust-colored-1.9.1
-  (package/inherit rust-colored-1
+  (package
+    (inherit rust-colored-1)
     (name "rust-colored")
     (version "1.9.1")
     (source
@@ -11575,7 +11578,8 @@ (define-public rust-difference-2
     (license license:expat)))
 
 (define-public rust-difference-1
-  (package/inherit rust-difference-2
+  (package
+    (inherit rust-difference-2)
     (name "rust-difference")
     (version "1.0.0")
     (source
@@ -12123,7 +12127,8 @@ (define-public rust-docopt-1
     (license (list license:expat license:unlicense))))
 
 (define-public rust-docopt-0.8
-  (package/inherit rust-docopt-1
+  (package
+    (inherit rust-docopt-1)
     (name "rust-docopt")
     (version "0.8.3")
     (source
@@ -18312,7 +18317,8 @@ (define-public rust-html5ever-0.24
         ("rust-typed-arena" ,rust-typed-arena-1))))))
 
 (define-public rust-html5ever-0.23
-  (package/inherit rust-html5ever-0.24
+  (package
+    (inherit rust-html5ever-0.24)
     (name "rust-html5ever")
     (version "0.23.0")
     (source
@@ -18387,7 +18393,8 @@ (define-public rust-http-0.2
     (license (list license:asl2.0 license:expat))))
 
 (define-public rust-http-0.1
-  (package/inherit rust-http-0.2
+  (package
+    (inherit rust-http-0.2)
     (name "rust-http")
     (version "0.1.17")
     (source
@@ -18454,7 +18461,8 @@ (define-public rust-http-body-0.3
         ("rust-http" ,rust-http-0.2))))))
 
 (define-public rust-http-body-0.1
-  (package/inherit rust-http-body-0.3
+  (package
+    (inherit rust-http-body-0.3)
     (name "rust-http-body")
     (version "0.1.0")
     (source
@@ -22410,7 +22418,8 @@ (define-public rust-loom-0.3
         ("rust-serde-json" ,rust-serde-json-1))))))
 
 (define-public rust-loom-0.2
-  (package/inherit rust-loom-0.3
+  (package
+    (inherit rust-loom-0.3)
     (name "rust-loom")
     (version "0.2.13")
     (source
@@ -22432,7 +22441,8 @@ (define-public rust-loom-0.2
         ("rust-serde-json" ,rust-serde-json-1))))))
 
 (define-public rust-loom-0.1
-  (package/inherit rust-loom-0.3
+  (package
+    (inherit rust-loom-0.3)
     (name "rust-loom")
     (version "0.1.1")
     (source
@@ -30534,7 +30544,8 @@ (define-public rust-pulldown-cmark-0.1
         ("rust-getopts" ,rust-getopts-0.2))))))
 
 (define-public rust-pulldown-cmark-0.0.8
-  (package/inherit rust-pulldown-cmark-0.4
+  (package
+    (inherit rust-pulldown-cmark-0.4)
     (name "rust-pulldown-cmark")
     (version "0.0.8")
     (source
@@ -33150,7 +33161,8 @@ (define-public rust-ring-0.14
         ("rust-cc" ,rust-cc-1))))))
 
 (define-public rust-ring-0.13
-  (package/inherit rust-ring-0.16
+  (package
+    (inherit rust-ring-0.16)
     (name "rust-ring")
     (version "0.13.5")
     (source
@@ -35111,7 +35123,8 @@ (define-public rust-rustls-0.14
         ("rust-webpki" ,rust-webpki-0.18))))))
 
 (define-public rust-rustls-0.12
-  (package/inherit rust-rustls-0.16
+  (package
+    (inherit rust-rustls-0.16)
     (name "rust-rustls")
     (version "0.12.0")
     (source
@@ -36158,7 +36171,8 @@ (define-public rust-sct-0.4
         ("rust-untrusted" ,rust-untrusted-0.6))))))
 
 (define-public rust-sct-0.3
-  (package/inherit rust-sct-0.6
+  (package
+    (inherit rust-sct-0.6)
     (name "rust-sct")
     (version "0.3.0")
     (source
@@ -41958,7 +41972,8 @@ (define-public rust-term-0.4
         ("rust-winapi" ,rust-winapi-0.2))))))
 
 (define-public rust-term-0.2
-  (package/inherit rust-term-0.4
+  (package
+    (inherit rust-term-0.4)
     (name "rust-term")
     (version "0.2.14")
     (source
@@ -47060,7 +47075,8 @@ (define-public rust-untrusted-0.7
     (license license:isc)))
 
 (define-public rust-untrusted-0.6
-  (package/inherit rust-untrusted-0.7
+  (package
+    (inherit rust-untrusted-0.7)
     (name "rust-untrusted")
     (version "0.6.2")
     (source
@@ -48681,7 +48697,8 @@ (define-public rust-webpki-0.19
        (("rust-base64" ,rust-base64-0.9))))))
 
 (define-public rust-webpki-0.18
-  (package/inherit rust-webpki-0.21
+  (package
+    (inherit rust-webpki-0.21)
     (name "rust-webpki")
     (version "0.18.1")
     (source
@@ -48767,7 +48784,8 @@ (define-public rust-webpki-roots-0.18
         (base32 "1d4ss607rgi9pj01zzqa13c1p3m35z314yh6lmjaj4kzvwv5gkci"))))))
 
 (define-public rust-webpki-roots-0.17
-  (package/inherit rust-webpki-roots-0.18
+  (package
+    (inherit rust-webpki-roots-0.18)
     (name "rust-webpki-roots")
     (version "0.17.0")
     (source
@@ -48818,7 +48836,8 @@ (define-public rust-webpki-roots-0.15
         ("rust-webpki" ,rust-webpki-0.18))))))
 
 (define-public rust-webpki-roots-0.14
-  (package/inherit rust-webpki-roots-0.18
+  (package
+    (inherit rust-webpki-roots-0.18)
     (name "rust-webpki-roots")
     (version "0.14.0")
     (source
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 5316d25151..1a2b98bec2 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -305,7 +305,8 @@ (define* (emacs-byte-compile-directory dir)
 (define-public emacs-next
   (let ((commit "2ea34662c20f71d35dd52a5ed996542c7386b9cb")
         (revision "0"))
-    (package/inherit emacs
+    (package
+      (inherit emacs)
       (name "emacs-next")
       (version (git-version "28.0.50" revision commit))
       (source
@@ -326,7 +327,8 @@ (define-public emacs-next
 (define-public emacs-next-pgtk
   (let ((commit "ae18c8ec4f0ef37c8c9cda473770ff47e41291e2")
         (revision "1"))
-    (package/inherit emacs-next
+    (package
+      (inherit emacs-next)
       (name "emacs-next-pgtk")
       (version (git-version "28.0.50" revision commit))
       (source
@@ -450,7 +452,8 @@ (define-public emacs-wide-int
 (define-public guile-emacs
   (let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b")
         (revision "0"))
-    (package/inherit emacs
+    (package
+      (inherit emacs)
       (name "guile-emacs")
       (version (git-version "0.0.0" revision commit))
       (source (origin
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 74c0709ea4..5de4f68093 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -269,8 +269,8 @@ (define-public guile-2.2
 (define-deprecated guile-2.2/bug-fix guile-2.2)
 
 (define-public guile-2.2.4
-  (package/inherit
-   guile-2.2
+  (package
+    (inherit guile-2.2)
    (version "2.2.4")
    (source (origin
              (inherit (package-source guile-2.2))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8cd64e7697..5062cc0347 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1230,7 +1230,8 @@ (define-public hdf5-1.8
               "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 
 (define-public hdf5-1.10
-  (package/inherit hdf5-1.8
+  (package
+    (inherit hdf5-1.8)
     (version "1.10.7")
     (source
      (origin
@@ -1249,7 +1250,8 @@ (define-public hdf5-1.10
        (patches (search-patches "hdf5-config-date.patch"))))))
 
 (define-public hdf5-1.12
-  (package/inherit hdf5-1.8
+  (package
+    (inherit hdf5-1.8)
     (version "1.12.0")
     (source
      (origin
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 995d543059..857adf1703 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -123,7 +123,8 @@ (define-public protobuf
 
 ;; Tensorflow requires version 3.6 specifically.
 (define-public protobuf-3.6
-  (package/inherit protobuf
+  (package
+    (inherit protobuf)
     (version "3.6.1")
     (source (origin
               (method url-fetch)
@@ -136,8 +137,8 @@ (define-public protobuf-3.6
 
 ;; The 3.5 series are the last versions that do not require C++ 11.
 (define-public protobuf-3.5
-  (package/inherit
-   protobuf
+  (package
+    (inherit protobuf)
    (version "3.5.1")
    (source (origin
               (method url-fetch)
@@ -289,7 +290,8 @@ (define-public python2-protobuf
 
 ;; For tensorflow.
 (define-public python-protobuf-3.6
-  (package/inherit python-protobuf
+  (package
+    (inherit python-protobuf)
     (name "python-protobuf")
     (version (package-version protobuf-3.6) )
     (source
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 72eb93541b..4468a9b8cd 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -707,7 +707,8 @@ (define-public python-html2text
 
 (define-public python2-html2text
   (let ((base (package-with-python2 python-html2text)))
-    (package/inherit base
+    (package
+      (inherit base)
       ;; This is the last version with support for Python 2.
       (version "2019.8.11")
       (source (origin
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c501b65a55..5a3c6b670e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3980,7 +3980,8 @@ (define-public python-pygments
     (properties `((python2-variant . ,(delay python2-pygments))))))
 
 (define python-pygments/fixed
-  (package/inherit python-pygments
+  (package
+    (inherit python-pygments)
     (version "2.7.4")
     (source
      (origin
@@ -4969,8 +4970,8 @@ (define-public python-numpy
 (define-public python2-numpy
   (let ((numpy (package-with-python2
                 (strip-python2-variant python-numpy))))
-    (package/inherit
-     numpy
+    (package
+      (inherit numpy)
       (version "1.16.5")
       (source (origin
                 (method url-fetch)
@@ -8087,7 +8088,8 @@ (define-public python-urwid
 (define-public python2-urwid
   (let ((base (package-with-python2
                (strip-python2-variant python-urwid))))
-    (package/inherit base
+    (package
+      (inherit base)
       (version "2.1.0")
       (source
        (origin
@@ -9528,8 +9530,8 @@ (define-public python-markdown
 ;; Markdown 3.2 dropped support for Python 2.
 (define-public python2-markdown
   (let ((base (package-with-python2 (strip-python2-variant python-markdown))))
-    (package/inherit
-     base
+    (package
+      (inherit base)
      (version "3.1.1")
      (source (origin
                (method url-fetch)
@@ -9697,8 +9699,8 @@ (define-public python-fonttools
 ;; Fonttools 4.x dropped support for Python 2, so stick with 3.x here.
 (define-public python2-fonttools
   (let ((base (package-with-python2 (strip-python2-variant python-fonttools))))
-    (package/inherit
-     base
+    (package
+      (inherit base)
      (version "3.44.0")
      (source (origin
                (method url-fetch)
diff --git a/gnu/packages/racket.scm b/gnu/packages/racket.scm
index 18af14b2ec..be33270b30 100644
--- a/gnu/packages/racket.scm
+++ b/gnu/packages/racket.scm
@@ -173,8 +173,8 @@ (define out (assoc-ref outputs "out"))
 
 
 (define-public racket
-  (package/inherit
-      racket-minimal
+  (package
+    (inherit racket-minimal)
     (name "racket")
     (version (package-version racket-minimal)) ; needed for origin uri to work
     (source
diff --git a/gnu/packages/sequoia.scm b/gnu/packages/sequoia.scm
index cb1e2a4872..c83926ef6c 100644
--- a/gnu/packages/sequoia.scm
+++ b/gnu/packages/sequoia.scm
@@ -221,7 +221,8 @@ (define-public sequoia
 
 (define-public sequoia4pEp
   ;; Currently pEp Engine requires sequoia in not-so-current version
-  (package/inherit sequoia
+  (package
+    (inherit sequoia)
     (name "sequoia")
     (version "0.15.0-pEp")
     (source
-- 
cgit v1.2.3


From 029a3fe46b6549c17085f661bb7b934d7ca0fa3e Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 24 May 2021 11:10:26 +0300
Subject: gnu: python-nltk-3.4: Add missing input.

* gnu/packages/python-xyz.scm (python-nltk-3.4)[propagated-inputs]: Add
python-six.
---
 gnu/packages/python-xyz.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5a3c6b670e..e011d37e91 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15484,7 +15484,8 @@ (define-public python-nltk-3.4
        (method url-fetch)
        (uri (pypi-uri "nltk" version ".zip"))
        (sha256
-        (base32 "153x2clrnigs74jdgnn3qmljdjj4gprmvpdvh49i18ls4m8mbm5y"))))))
+        (base32 "153x2clrnigs74jdgnn3qmljdjj4gprmvpdvh49i18ls4m8mbm5y"))))
+    (propagated-inputs `(("python-six" ,python-six)))))
 
 (define-public python2-nltk
   (package-with-python2 python-nltk))
-- 
cgit v1.2.3


From 67ac4348d4f4631b65201f66e0ba56f54143ad1b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 24 May 2021 11:11:34 +0300
Subject: gnu: python-nltk: Add missing inputs.

* gnu/packages/python-xyz.scm (python-nltk)[propagated-inputs]: Add
python-click, python-joblib, python-regex, python-tqdm.
---
 gnu/packages/python-xyz.scm | 5 +++++
 1 file changed, 5 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e011d37e91..954536b283 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15463,6 +15463,11 @@ (define-public python-nltk
      '(;; The tests require some extra resources to be downloaded.
        ;; TODO Try packaging these resources.
        #:tests? #f))
+    (propagated-inputs
+     `(("python-click" ,python-click)
+       ("python-joblib" ,python-joblib)
+       ("python-regex" ,python-regex)
+       ("python-tqdm" ,python-tqdm)))
     (native-inputs
      `(("unzip" ,unzip)))
     (home-page "http://nltk.org/")
-- 
cgit v1.2.3


From 4ea6161046e664470b036f4692ea115e33ef6003 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 24 May 2021 16:13:35 +0300
Subject: gnu: python-matplotlib: Don't hardcode python version.

* gnu/packages/python-xyz.scm (python-matplotlib)[arguments]: In custom
'install-jquery-ui phase programmatically get the version of python.
---
 gnu/packages/python-xyz.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 954536b283..25f986e9b6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5563,8 +5563,11 @@ (define-public python-matplotlib
              #t))
          (add-before 'install 'install-jquery-ui
            (lambda* (#:key outputs inputs #:allow-other-keys)
-             (let ((dir (string-append (assoc-ref outputs "out")
-                                       "/lib/python3.7/site-packages/matplotlib/backends/web_backend/")))
+             (let* ((python-version (python-version
+                                      (assoc-ref inputs "python")))
+                    (dir (string-append (assoc-ref outputs "out")
+                                       "/lib/python" python-version "/site-packages"
+                                       "/matplotlib/backends/web_backend/")))
                (mkdir-p dir)
                (invoke "unzip"
                        (assoc-ref inputs "jquery-ui")
-- 
cgit v1.2.3


From 3aea1433f110c4c0acb75920b10c92de92996adb Mon Sep 17 00:00:00 2001
From: Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
Date: Tue, 25 May 2021 01:15:08 +0200
Subject: gnu: python2-shapely: Remove package.

* gnu/packages/python-xyz.scm (python2-shapely): Delete variable.
---
 gnu/packages/python-xyz.scm | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 25f986e9b6..770beb0336 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -861,9 +861,6 @@ (define-public python-logwrap
 and function call return values in a human-readable way.")
     (license license:asl2.0)))
 
-(define-public python2-shapely
-  (package-with-python2 python-shapely))
-
 (define-public python-clyent
   (package
     (name "python-clyent")
-- 
cgit v1.2.3


From 35311e3b25c161175f983be888606b3b371acad0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 27 May 2021 15:12:52 +0300
Subject: gnu: Add python-simpervisor.

* gnu/packages/python-xyz.scm (python-simpervisor): New variable.
---
 gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 770beb0336..b10b55357f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24900,6 +24900,41 @@ (define-public python-nest-asyncio
 @code{loop.run_until_complete}.")
     (license license:bsd-3)))
 
+(define-public python-simpervisor
+  (package
+    (name "python-simpervisor")
+    (version "0.4")
+    (source
+      (origin
+        ;; Tests not included in release.
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/yuvipanda/simpervisor")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1brsisx7saf4ic0dih1n5y7rbdbwn1ywv9pl32bch3061r46prvv"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f  ; Test suite can't find aiohttp.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "--maxfail" "3" "--verbose"))
+             #t)))))
+    (native-inputs
+     `(("python-aiohttp" ,python-aiohttp)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-asyncio" ,python-pytest-asyncio)))
+    (home-page "https://github.com/yuvipanda/simpervisor")
+    (synopsis "Simple async process supervisor")
+    (description
+     "This package provides a simple async process supervisor in Python.")
+    (license license:bsd-3)))
+
 (define-public python-parallel
   (package
     (name "python-parallel")
-- 
cgit v1.2.3


From 0b31e45b49af76d02ad760162ffe69d6c3cb854f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 27 May 2021 20:58:45 +0200
Subject: gnu: Add python-logutils.

* gnu/packages/python-xyz.scm (python-logutils): New variable.
---
 gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b10b55357f..973da15cad 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -25194,6 +25194,27 @@ (define-public python-helpdev
 environment.")
     (license license:expat)))
 
+(define-public python-logutils
+  (package
+    (name "python-logutils")
+    (version "0.3.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "logutils" version))
+       (sha256
+        (base32
+         "10lsi5wv5ysnvf9ya4ncbix6mmipnv5067sf2cglc2f2sljql1dw"))))
+    (build-system python-build-system)
+    (home-page "https://bitbucket.org/vinay.sajip/logutils/")
+    (synopsis "Logging utilities")
+    (description "This package provides a set of handlers for the Python
+standard library logging package.  Some of these handlers are out-of-scope
+for the standard library, and so they are packaged here.  Others are updated
+versions which have appeared in recent Python releases, but are usable with
+older versions of Python and so are packaged here.")
+    (license license:bsd-3)))
+
 (define-public python-qtsass
   (package
     (name "python-qtsass")
-- 
cgit v1.2.3


From 167fc141d4e6f054e546322eb06e07dacb3309a3 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 27 May 2021 20:59:16 +0200
Subject: gnu: Add python-helper.

* gnu/packages/python-xyz.scm (python-helper): New variable.
---
 gnu/packages/python-xyz.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 973da15cad..3540d8fb05 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -25215,6 +25215,29 @@ (define-public python-logutils
 older versions of Python and so are packaged here.")
     (license license:bsd-3)))
 
+(define-public python-helper
+  (package
+    (name "python-helper")
+    (version "2.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "helper" version))
+              (sha256
+               (base32
+                "1d2j64wgbggzv5rhvil10zndp2w78wa5np5w0psj122ws9qr9wsa"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-mock" ,python-mock)))
+    (propagated-inputs
+     `(("python-logutils" ,python-logutils)
+       ("python-pyyaml" ,python-pyyaml)))
+    (home-page "https://github.com/gmr/helper")
+    (synopsis "Library for writing configurable applications and daemons")
+    (description
+     "This package provides procedures for quickly writing configurable
+applications and daemons.")
+    (license license:bsd-3)))
+
 (define-public python-qtsass
   (package
     (name "python-qtsass")
-- 
cgit v1.2.3


From bb5a3e91e93830622026084af909aabe53693d25 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 28 May 2021 10:09:10 +0200
Subject: gnu: Add python-argopt.

* gnu/packages/python-xyz.scm (python-argopt): New variable.
---
 gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3540d8fb05..c4f19b4c6f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -219,6 +219,31 @@ (define-module (gnu packages python-xyz)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26))
 
+(define-public python-argopt
+  (package
+   (name "python-argopt")
+   (version "0.7.0")
+   (source (origin
+            (method url-fetch)
+            (uri (pypi-uri "argopt" version))
+            (sha256
+             (base32
+              "0ybs7kkp0cpl8zn1lvf7481xhssg1bbhh5la2cjzdm5yibashyxa"))))
+   (build-system python-build-system)
+   (native-inputs
+    `(("python-coverage" ,python-coverage)
+      ("python-nose" ,python-nose)
+      ("python-setuptools" ,python-setuptools) ; Won't build without this.
+      ("python-setuptools-scm" ,python-setuptools-scm)))
+   (propagated-inputs
+    `(("python-toml" ,python-toml)
+      ("python-flake8" ,python-flake8)))
+   (home-page "https://github.com/casperdcl/argopt")
+   (synopsis "Generate a command-line interface from a docstring")
+   (description "This package provides tools to define a command line interface
+from a docstring rather than the other way around.")
+   (license license:mpl2.0)))
+
 (define-public python-colorful
   (package
     (name "python-colorful")
-- 
cgit v1.2.3


From 4ad3f818c9e2d200bf5c9cf0cf986b1a185d9d5b Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 28 May 2021 10:47:16 +0200
Subject: gnu: Add python-cachetools.

* gnu/packages/python-xyz.scm (python-cachetools): New variable.
---
 gnu/packages/python-xyz.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c4f19b4c6f..d978942402 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -244,6 +244,24 @@ (define-public python-argopt
 from a docstring rather than the other way around.")
    (license license:mpl2.0)))
 
+(define-public python-cachetools
+  (package
+    (name "python-cachetools")
+    (version "4.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "cachetools" version))
+              (sha256
+               (base32
+                "1zqc098gk6y614lxwqd9z2gm8lldgvrpid133pnlm4m048gfvdb1"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/tkem/cachetools/")
+    (synopsis "Extensible memoizing collections and decorators")
+    (description "This module provides various memoizing collections and
+decorators, including variants of the Python standard library's
+@code{lru_cache} function decorator.")
+    (license license:expat)))
+
 (define-public python-colorful
   (package
     (name "python-colorful")
-- 
cgit v1.2.3


From fc71a45afdb4e7ee45d1c952c56c3b83cafaac1e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 29 May 2021 20:24:55 +0200
Subject: gnu: python-cookiecutter: Update to 1.7.3.

* gnu/packages/python-xyz.scm (python-cookiecutter): Update to 1.7.3.
---
 gnu/packages/python-xyz.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d978942402..e4cc0009c5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12850,14 +12850,13 @@ (define-public python-whichcraft
 (define-public python-cookiecutter
   (package
     (name "python-cookiecutter")
-    (version "1.7.2")
+    (version "1.7.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cookiecutter" version))
        (sha256
-        (base32
-         "1b2xa5dypk1vf8aq599fd8zw4y0pwvq3hgl7ia8aiv8gg3ab5dpg"))))
+        (base32 "0mx49whhwcxmvcak27zr7p7ndzkn3w7psfd7fzh3n91fi1r4v6kb"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-freezegun" ,python-freezegun)
-- 
cgit v1.2.3


From 2a600ae5ff92f6164020d0cec51190f28fdc904c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 29 May 2021 23:22:15 +0200
Subject: gnu: python-fastjsonschema: Update to 2.15.1.

* gnu/packages/python-xyz.scm (python-fastjsonschema): Update to 2.15.1.
---
 gnu/packages/python-xyz.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e4cc0009c5..b3ed73f04a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10788,14 +10788,13 @@ (define-public python-json-spec
 (define-public python-fastjsonschema
   (package
     (name "python-fastjsonschema")
-    (version "2.15.0")
+    (version "2.15.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "fastjsonschema" version))
         (sha256
-          (base32
-            "0xknp399gpdjf08lrq2yvv66s7nsc51fgbm6vph7vyyg1ckbmv71"))))
+          (base32 "1ln2j60jzyn6p8i8ljygfgrji58hc23452g7nllkcjdk4p93c7v7"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; Fail with a strange backtrace ending in importlib.
-- 
cgit v1.2.3


From 71854b7dfe034dc47655c6fa885bd255fde3c160 Mon Sep 17 00:00:00 2001
From: Stefan Reichör <stefan@xsteve.at>
Date: Sat, 29 May 2021 22:28:37 +0200
Subject: gnu: Add python-easy-ansi.

* gnu/packages/python-xyz.scm (python-easy-ansi): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
---
 gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b3ed73f04a..886a890049 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16549,6 +16549,30 @@ (define-public python-ansi2html
 (define-public python2-ansi2html
   (package-with-python2 python-ansi2html))
 
+(define-public python-easy-ansi
+  (package
+    (name "python-easy-ansi")
+    (version "0.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/joeysbytes/easy-ansi")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0albh55ynzs98qy9pln4qaxw5qhhh3lk09jy9bx19gycrp1c3lc3"))))
+    (build-system python-build-system)
+    (home-page "https://gitlab.com/joeysbytes/easy-ansi")
+    (synopsis "Terminal framework API")
+    (description
+     "Easy ANSI is a terminal framework API to give you an easy way to use
+colors, cursor control movements, and line/box drawing.  It is not meant as a
+replacement to more full-featured frameworks (such as curses or urwid), but as
+a tool to quickly create nice-looking screens in your terminal window.  You
+can even create animations with the cursor controls.")
+    (license license:expat)))
+
 (define-public python-ddt
   (package
     (name "python-ddt")
-- 
cgit v1.2.3


From b346a7c7db6b3d6e5a2bdd964fc99038f99f29a7 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 1 Jun 2021 10:13:38 +0200
Subject: gnu: Add python-stdlib-list.

* gnu/packages/python-xyz.scm (python-stdlib-list): New variable.
---
 gnu/packages/python-xyz.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 886a890049..05c1b6d8d6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9692,6 +9692,26 @@ (define-public python-crashtest
      "Python library that makes exceptions handling and inspection easier.")
     (license license:expat)))
 
+(define-public python-stdlib-list
+  (package
+    (name "python-stdlib-list")
+    (version "0.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "stdlib-list" version))
+              (sha256
+               (base32
+                "17vdn4q0sdlndc2fr9svapxx6366hnrhkn0fswp1xmr0jxqh7rd1"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; Tests require more dependencies.
+    (native-inputs
+     `(("python-sphinx" ,python-sphinx)))
+    (home-page "https://github.com/jackmaney/python-stdlib-list")
+    (synopsis "Python Standard Libraries")
+    (description "This package contains a list of Python Standard Libraries.")
+    (license license:expat)))
+
 (define-public python-straight-plugin
   (package
     (name "python-straight-plugin")
-- 
cgit v1.2.3


From 50dfbbf8ef52111067071c788e19fc21d54c40d6 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 1 Jun 2021 10:18:00 +0200
Subject: gnu: Add python-sinfo.

* gnu/packages/python-xyz.scm (python-sinfo): New variable.
---
 gnu/packages/python-xyz.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 05c1b6d8d6..a5cc04edaf 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2189,6 +2189,25 @@ (define-public python-eventlet
 from the Python interpreter, or as a small part of a larger application.")
   (license license:expat)))
 
+(define-public python-sinfo
+  (package
+    (name "python-sinfo")
+    (version "0.3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "sinfo" version))
+              (sha256
+               (base32
+                "0kdsp883mx0lfyykv0p12bvs203kdm3skb8bw5wf2pc7kb393sl1"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-stdlib-list" ,python-stdlib-list)))
+    (home-page "https://gitlab.com/joelostblom/session_info")
+    (synopsis "Output module version information loaded in a Python session")
+    (description "This package outputs version information for modules loaded
+in the current session, Python, and the OS.")
+    (license license:bsd-3)))
+
 (define-public python-six
   (package
     (name "python-six")
-- 
cgit v1.2.3


From bb934ab79d014198404c3678e8a278c1b334b6fb Mon Sep 17 00:00:00 2001
From: Marius Bakke <marius@gnu.org>
Date: Fri, 4 Jun 2021 14:50:59 +0200
Subject: gnu: python-pydantic: Update to 1.8.2.

* gnu/packages/python-xyz.scm (python-pydantic): Update to 1.8.2.
[arguments]: Disable some new tests.
[native-inputs]: Add PYTHON-PYTEST-MOCK.
[propagated-inputs]: Add PYTHON-TYPING-EXTENSIONS.
---
 gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a5cc04edaf..f21fb53cc5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4527,7 +4527,7 @@ (define-public python-jsonrpc-server
 (define-public python-pydantic
   (package
     (name "python-pydantic")
-    (version "1.6.1")
+    (version "1.8.2")
     (source
      (origin
        (method git-fetch)
@@ -4536,24 +4536,39 @@ (define-public python-pydantic
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1380s9k77g6q15by9fkxndczjk89q6xpz09jdrqip535xws2z3j8"))))
+        (base32 "06162dss6mvi7wiy2lzxwvzajwxgy8b2fyym7qipaj7zibcqalq2"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
        (modify-phases %standard-phases
-         ;; Reported upstream:
-         ;; <https://github.com/samuelcolvin/pydantic/issues/1580>.
-         ;; Disable the faulty test as the fix is unclear.
          (add-before 'check 'disable-test
            (lambda _
+             ;; Reported upstream:
+             ;; <https://github.com/samuelcolvin/pydantic/issues/1580>.
+             ;; Disable the faulty test as the fix is unclear.
              (substitute* "tests/test_validators.py"
                (("test_assert_raises_validation_error")
                 "_test_assert_raises_validation_error"))
-             #t))
+
+             ;; These fail because of <https://bugs.python.org/issue40398>.
+             ;; Remove after Python has been upgraded to >= 3.9.
+             (substitute* "tests/test_generics.py"
+               (("assert replace_types\\(Callable, \\{T: int\\}\\) == Callable")
+                ""))
+             (substitute* "tests/test_schema.py"
+               (("test_unenforced_constraints_schema")
+               "_test_unenforced_constraints_schema"))
+
+             ;; Disable tests for the Hypothesis plugin because it is tricky
+             ;; to configure in the build container.
+             (delete-file "tests/test_hypothesis_plugin.py")))
          (replace 'check
-           (lambda _ (invoke "pytest" "-vv" "tests"))))))
+           (lambda _ (invoke "pytest" "-vv"))))))
     (native-inputs
-     `(("python-pytest" ,python-pytest)))
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-mock" ,python-pytest-mock)))
+    (propagated-inputs
+     `(("python-typing-extensions" ,python-typing-extensions)))
     (home-page "https://github.com/samuelcolvin/pydantic")
     (synopsis "Python data validation and settings management")
     (description
-- 
cgit v1.2.3


From e639da604f987bae41f1c00bf0726331937a925f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 1 Jun 2021 10:20:10 +0200
Subject: gnu: python-anndata: Update to 0.7.6.

* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
---
 gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f21fb53cc5..f3404178ba 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21061,28 +21061,41 @@ (define-public python-zarr
 (define-public python-anndata
   (package
     (name "python-anndata")
-    (version "0.7.1")
+    (version "0.7.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "anndata" version))
        (sha256
         (base32
-         "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09"))))
+         "1ch8yp0xmag6z0kl01pljm35lbbwax7lrimfhiclpkd4m6xngk53"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     `(#:tests? #f ; The tarball from PyPi doesn't include tests.
+       #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'delete-inconvenient-tests
-           (lambda _
-             ;; This test depends on python-scikit-learn.
-             (delete-file "anndata/tests/test_inplace_subset.py")
-             #t))
          (delete 'check)
-         (add-after 'install 'check
+         (add-before 'build 'relax-dependency-requirements
+           (lambda _
+             ;; We need to upgrade python-pandas to avoid
+             ;; https://github.com/pandas-dev/pandas/issues/35446
+             (substitute* "pyproject.toml"
+               (("pandas>=1.1.1") "pandas>=1.0.5"))))
+         (replace 'build
+           (lambda _
+             ;; ZIP does not support timestamps before 1980.
+             (setenv "SOURCE_DATE_EPOCH" "315532800")
+             (invoke "flit" "build")))
+         (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-vv"))))))
+             (let ((out (assoc-ref outputs "out")))
+               (for-each (lambda (wheel)
+                           (format #true wheel)
+                           (invoke "python" "-m" "pip" "install"
+                                   wheel (string-append "--prefix=" out)))
+                         (find-files "dist" "\\.whl$")))
+             #t)))))
     (propagated-inputs
      `(("python-h5py" ,python-h5py)
        ("python-importlib-metadata" ,python-importlib-metadata)
@@ -21095,6 +21108,8 @@ (define-public python-anndata
     (native-inputs
      `(("python-joblib" ,python-joblib)
        ("python-pytest" ,python-pytest)
+       ("python-toml" ,python-toml)
+       ("python-flit" ,python-flit)
        ("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "https://github.com/theislab/anndata")
     (synopsis "Annotated data for data analysis pipelines")
-- 
cgit v1.2.3


From d71751526f330f5dcfce6e50e00fbddce0676811 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 5 Jun 2021 09:24:24 +0200
Subject: gnu: python-numpy-documentation: Use patched texlive-amsfonts.

* gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Use
texlive-amsfonts/patched.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f3404178ba..8a1aabdca8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5203,7 +5203,7 @@ (define-public python-numpy-documentation
                                         texlive-fonts-ec
                                         texlive-generic-ifxetex
                                         texlive-generic-pdftex
-                                        texlive-amsfonts
+                                        texlive-amsfonts/patched
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ
-- 
cgit v1.2.3


From ace97406f2ba198b8f866f37fd17ebbee73739bc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 5 Jun 2021 09:24:54 +0200
Subject: gnu: python-matplotlib-documentation: Use patched texlive-amsfonts.

* gnu/packages/python-xyz.scm (python-matplotlib-documentation)[native-inputs]:
Use texlive-amsfonts/patched.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8a1aabdca8..e28fb648b0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5743,7 +5743,7 @@ (define-public python-matplotlib-documentation
        ("python-ipykernel" ,python-ipykernel)
        ("python-mock" ,python-mock)
        ("graphviz" ,graphviz)
-       ("texlive" ,(texlive-union (list texlive-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts/patched
                                         texlive-latex-amsmath
                                         texlive-latex-enumitem
                                         texlive-latex-expdlist
-- 
cgit v1.2.3


From 45aae518e77eedde534c6017363a275d9c4e0eb8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 5 Jun 2021 09:25:22 +0200
Subject: gnu: python-ipython-documentation: Use patched texlive-amsfonts.

* gnu/packages/python-xyz.scm (python-ipython-documentation)[native-inputs]:
Use texlive-amsfonts/patched.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e28fb648b0..dfbeeabe59 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8107,7 +8107,7 @@ (define-public python-ipython-documentation
      `(("python-sphinx" ,python-sphinx)
        ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme)
        ;; FIXME: It's possible that a smaller union would work just as well.
-       ("texlive" ,(texlive-union (list texlive-amsfonts
+       ("texlive" ,(texlive-union (list texlive-amsfonts/patched
                                         texlive-fonts-ec
                                         texlive-generic-ifxetex
                                         texlive-generic-pdftex
-- 
cgit v1.2.3


From f9ef881e4dea6f7fdbe5c4be59d54b34f2b62f36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 5 Jun 2021 09:25:43 +0200
Subject: gnu: python-pypandoc: Use patched texlive-amsfonts.

* gnu/packages/python-xyz.scm (python-pypandoc)[native-inputs]: Use
texlive-amsfonts/patched.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index dfbeeabe59..b63c2852d5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24844,7 +24844,7 @@ (define-public python-pypandoc
     (propagated-inputs
      `(("wheel" ,python-wheel)))
     (native-inputs
-     `(("texlive" ,(texlive-union (list texlive-amsfonts
+     `(("texlive" ,(texlive-union (list texlive-amsfonts/patched
                                         texlive-fonts-ec
                                         texlive-latex-hyperref
                                         texlive-latex-oberdiek
-- 
cgit v1.2.3


From 78469645fd26036c0742abf56d59768b49dc65c4 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Sun, 6 Jun 2021 02:06:49 +0200
Subject: gnu: Add python-sparse.

* gnu/packages/python-xyz.scm(python-sparse): New variable.
---
 gnu/packages/python-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b63c2852d5..a4fe31a01f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -67,7 +67,7 @@
 ;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil@zoho.com>
@@ -5147,6 +5147,51 @@ (define-public python-colormath
 (define-public python2-colormath
   (package-with-python2 python-colormath))
 
+(define-public python-sparse
+  (package
+    (name "python-sparse")
+    (version "0.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sparse" version))
+       (sha256
+        (base32
+         "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "-m" "pytest" "-v")))))))
+    (propagated-inputs
+     `(("python-numba" ,python-numba)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)))
+    (native-inputs
+     `(("python-dask" ,python-dask)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-black" ,python-pytest-black)
+       ("python-pytest-cov" ,python-pytest-cov)))
+    (home-page "https://github.com/pydata/sparse/")
+    (synopsis "Library for multi-dimensional sparse arrays")
+    (description
+     "This package implements sparse arrays of arbitrary dimension on top of
+@code{numpy} and @code{scipy.sparse}.  Sparse array is a matrix in which most
+of the elements are zero.  @code{python-sparse} generalizes the
+@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but
+extends beyond just rows and columns to an arbitrary number of dimensions.
+Additionally, this project maintains compatibility with the
+@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface
+used in @code{scipy.sparse}.  These differences make this project useful in
+certain situations where @code{scipy.sparse} matrices are not well suited, but
+it should not be considered a full replacement.  It lacks layouts that are not
+easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and
+depends on @code{scipy.sparse} for some computations.")
+    (license license:bsd-3)))
+
 (define-public python-spectra
   (package
     (name "python-spectra")
-- 
cgit v1.2.3


From d8fed768a899bd0a3a84a88572135a1d7bde2400 Mon Sep 17 00:00:00 2001
From: Hartmut Goebel <h.goebel@crazy-compilers.com>
Date: Tue, 25 May 2021 10:17:20 +0200
Subject: gnu: Add python-asn1tools.

* gnu/packages/python-xyz.scm (python-asn1tools): New variable.
---
 gnu/packages/python-xyz.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/python-xyz.scm')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a4fe31a01f..6a6d7f4b26 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19,7 +19,7 @@
 ;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
 ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
-;;; Copyright © 2016, 2018, 2019 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2016, 2018, 2019, 2021 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org>
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2016, 2017 Troy Sankey <sankeytms@gmail.com>
@@ -10471,6 +10471,30 @@ (define-public python2-ipaddress
  module to older versions of Python.")
     (license license:psfl)))
 
+(define-public python-asn1tools
+  (package
+    (name "python-asn1tools")
+    (version "0.158.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asn1tools" version))
+       (sha256
+        (base32 "1k88a1azmyvp2ab6qcf2i40dig5abhyn7cmlyhmwwh8kr3syvma0"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-bitstruct" ,python-bitstruct)
+       ("python-diskcache" ,python-diskcache)
+       ("python-prompt-toolkit" ,python-prompt-toolkit)
+       ("python-pyparsing" ,python-pyparsing)))
+    (home-page "https://github.com/eerimoq/asn1tools")
+    (synopsis  "ASN.1 parsing, encoding and decoding")
+    (description "This package provides ASN.1 parsing, encoding and decoding
+for Python, including constraints checking.  It supports several
+codecs (e.g. BER, PER, UPER, XER) as well as limited C source code generating
+for OER and UPER.")
+    (license license:expat)))
+
 (define-public python2-ipaddr
   (package
     (name "python2-ipaddr")
-- 
cgit v1.2.3