Moving failing packages out

1 files changed, 1 insertions, 1118 deletions

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 4536f6f..8bb738d 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -42,42 +42,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
-  #:use-module (srfi srfi-1)
-  #:use-module (gn packages check))
-
-(define-public python2-rpy2
-  (package
-    (name "python2-rpy2")
-    (version "2.7.6")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "rpy2" version))
-       (sha256
-        (base32
-         "0nhan2qvrw7b7gg5zddwa22kybdv3x1g26vkd7q8lvnkgzrs4dga"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2 ; apparently incompatible with Python 3
-       #:tests? #f))
-    (propagated-inputs
-     `(("python2-six" ,python2-six)
-       ("python2-singledispatch" ,python2-singledispatch)))
-    (inputs
-     `(("readline" ,readline)
-       ("icu4c" ,icu4c)
-       ("pcre" ,pcre)
-       ("r-minimal" ,r-minimal)
-       ("r-survival" ,r-survival)))
-    (native-inputs
-     `(("zlib" ,zlib)))
-    (home-page "http://rpy.sourceforge.net/")
-    (synopsis "Python interface to the R language")
-    (description "rpy2 is a redesign and rewrite of rpy.  It is providing a
-low-level interface to R from Python, a proposed high-level interface,
-including wrappers to graphical libraries, as well as R-like structures and
-functions.")
-    (license license:gpl3+)))
+  #:use-module (srfi srfi-1))
 
 (define-public python-subprocess32 ; guix candidate
   (package
@@ -100,388 +65,6 @@ functions.")
     (license license:gpl2))
 )
 
-(define-public python-rserve
-  (package
-   (name "python-rserve")
-   (version "0.91")
-   (source
-    (origin
-     (method url-fetch)
-                                        ; https://pypi.python.org/packages/27/e8/b23e0e3d38dadc721947bc9f4b6f1b3e5e1e6c26ac67d8ad88376c5555a0/pyRserve-0.9.1.tar.gz#md5=6da1978f908dd7bdc2d22ee5c29238c0
-     (uri (string-append
-           "https://pypi.python.org/packages/27/e8/b23e0e3d38dadc721947bc9f4b6f1b3e5e1e6c26ac67d8ad88376c5555a0/pyRserve-0.9.1.tar.gz"))
-     (sha256
-      (base32
-       "162dg7d0ni035b75qskrjdzd1yyxwnvybcv115aiapcvyfw2vbsm"))))
-   (build-system python-build-system)
-   (propagated-inputs
-    `(
-      ("python-numpy" ,python-numpy)
-      ))
-   (inputs
-    `(("python-setuptools" ,python-setuptools)
-      ("python-pytest" ,python-pytest)
-      ))
-   (home-page "https://pypi.python.org/pypi/pyRserve")
-   (synopsis
-    "RServe.")
-   (description
-    ".")
-   (license license:expat)))
-
-(define-public python-setuptools-old
-  (package
-    (name "python-setuptools-old")
-    (version "40.6.0")
-    (source
-     (origin
-      (method url-fetch)
-      (uri "https://files.pythonhosted.org/packages/37/1b/b25507861991beeade31473868463dad0e58b1978c209de27384ae541b0b/setuptools-40.6.3.zip"
-             )
-      (sha256
-       (base32
-        "1y085dnk574sxw9aymdng9gijvrsbw86hsv9hqnhv7y4d6nlsirv"))
-      (modules '((guix build utils)))
-      (snippet
-       '(begin
-          ;; Remove included binaries which are used to build self-extracting
-          ;; installers for Windows.
-          ;; TODO: Find some way to build them ourself so we can include them.
-          (for-each delete-file (find-files "setuptools" "^(cli|gui).*\\.exe$"))
-          #t))))
-    (build-system python-build-system)
-    ;; FIXME: Tests require pytest, which itself relies on setuptools.
-    ;; One could bootstrap with an internal untested setuptools.
-    (arguments
-     `(#:tests? #f))
-    (home-page "https://pypi.python.org/pypi/setuptools")
-    (synopsis
-     "Library designed to facilitate packaging Python projects")
-    (description
-     "Setuptools is a fully-featured, stable library designed to facilitate
-packaging Python projects, where packaging includes:
-Python package and module definitions,
-distribution package metadata,
-test hooks,
-project installation,
-platform-specific details,
-Python 3 support.")
-    ;; TODO: setuptools now bundles the following libraries:
-    ;; packaging, pyparsing, six and appdirs. How to unbundle?
-    (license (list license:psfl        ; setuptools itself
-                   license:expat       ; six, appdirs, pyparsing
-                   license:asl2.0      ; packaging is dual ASL2/BSD-2
-                   license:bsd-2))))
-
-(define-public python-avro ; guix ready - used by CWL
-(package
-  (name "python-avro")
-  (version "1.8.2")
-  (source
-    (origin
-      (method url-fetch)
-        (uri (pypi-uri "avro" version))
-      (sha256
-        (base32
-          "0nabn1hzj1880qsp7fkg7923c0xdqk4i35s15asmy2xp604f97lg"))))
-  (build-system python-build-system)
-  (inputs
-    `(("python-setuptools" ,python-setuptools)))
-  (home-page "http://hadoop.apache.org/avro")
-  (synopsis
-    "Avro is a serialization and RPC framework.")
-  (description
-    "Avro is a serialization and RPC framework.")
-  (license #f)))
-
-(define-public python2-htmlgen-gn ; guix obsolete
-  (package
-    (name "python2-htmlgen-gn")
-    (version "2.2.2")
-    (source (origin
-              (method url-fetch)
-              ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz
-              (uri (string-append
-                     "https://files.genenetwork.org/software/htmlgen-2.2.2-gn.tar.gz"))
-              (sha256
-               (base32
-                "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r"))
-              ;;(patches (list
-              ;;          (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
-              ;;          (search-patch "python2-htmlgen-Fix-test-for-random.patch")
-              ))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'modernize-imports
-           (lambda _
-             (substitute* "HTMLgen.py"
-               (("whrandom") "random"))
-             (substitute* "HTMLcalendar.py"
-               (("import regex") "import re as regex"))
-             (substitute* "HTMLutil.py"
-               (("import string, regex") "import re as regex\nimport string"))
-             (substitute* "HTMLtest.py"
-               (("import string, regex, regsub") "import re as regex\nimport string")
-               (("regsub.split") "re.split"))
-             #t))
-         (replace 'build
-           (lambda _
-             (invoke "python" "-m" "compileall" ".")))
-         (replace 'check
-           (lambda* (#:key (tests? '()) #:allow-other-keys)
-             (if tests?
-               (invoke "python" "HTMLtest.py")
-               #t)))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (lib (string-append out "/lib/python2.7/site-packages/htmlgen/")))
-               ;; Install libs and headers.
-               (for-each (lambda (file)
-                           (install-file file lib))
-                         (find-files "." "\\.py[c]?$"))
-               #t))))))
-    (home-page "https://packages.debian.org/unstable/python/python-htmlgen")
-    (synopsis "Genenetwork version of Python2 HTMLgen (defunkt project)")
-    (description #f)
-    (license #f)))
-
-(define-public python2-htmlgen-2.2
-  (package
-    (name "python2-htmlgen-2.2")
-    (version "2.2.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://debian/pool/main/h/htmlgen/htmlgen_" version ".orig.tar.gz"))
-              (sha256
-               (base32
-                 "186kb434q6z84g31ysvzi4kcfcvl3pmm57k4jlng4ccgls94x6wb"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'modernize-imports
-           (lambda _
-             (substitute* "HTMLgen.py"
-               (("whrandom") "random"))
-             (substitute* "HTMLcalendar.py"
-               (("import regex") "import re as regex"))
-             (substitute* "HTMLutil.py"
-               (("import string, regex") "import re as regex\nimport string"))
-             (substitute* "HTMLtest.py"
-               (("import string, regex, regsub") "import re as regex\nimport string")
-               (("regsub.split") "re.split"))
-             #t))
-         (replace 'build
-           (lambda _
-             (invoke "python" "-m" "compileall" ".")))
-         (replace 'check
-           (lambda _
-             (invoke "python" "HTMLtest.py")))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (lib (string-append out "/lib/python2.7/site-packages/htmlgen/")))
-               ;; Install libs and headers.
-               (for-each (lambda (file)
-                           (install-file file lib))
-                         (find-files "." "\\.py[c]?$"))
-               #t))))))
-    (home-page "https://packages.debian.org/unstable/python/python-htmlgen")
-    (synopsis "Genenetwork version of Python2 HTMLgen (defunkt project)")
-    (description #f)
-    (license #f)))
-
-(define-public python2-pil1-gn ; guix obsolete
-  (package
-    (name "python2-pil1") ; works with GN2
-    (version "1.1.6")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append
-                   ; "http://files.genenetwork.org/software/contrib/Imaging-"
-                   "http://effbot.org/downloads/Imaging-1.1.6.tar.gz"))
-             (sha256
-              (base32
-               "141zidl3s9v4vfi3nsbg42iq1lc2a932gprqr1kij5hrnn53bmvx"))
-    (modules '((guix build utils)))
-    (snippet
-     ;; Adapt to newer freetype. As the package is unmaintained upstream,
-     ;; there is no use in creating a patch and reporting it.
-     '(substitute* "_imagingft.c"
-                   (("freetype/")
-                    "freetype2/freetype/")))))
-    (build-system python-build-system)
-    (inputs
-      `(("freetype" ,freetype)
-        ("libjpeg" ,libjpeg-turbo)
-        ("libtiff" ,libtiff)
-        ("python2-setuptools" ,python2-setuptools)
-        ("zlib" ,zlib)))
-    (arguments
-     ;; Only the fork python-pillow works with Python 3.
-     `(#:python ,python-2
-       #:tests? #f ; no check target
-       #:phases
-         (alist-cons-before
-          'build 'configure
-          ;; According to README and setup.py, manual configuration is
-          ;; the preferred way of "searching" for inputs.
-          ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter.
-          (lambda* (#:key inputs #:allow-other-keys)
-            (let ((jpeg (assoc-ref inputs "libjpeg"))
-                  (zlib (assoc-ref inputs "zlib"))
-                  (tiff (assoc-ref inputs "libtiff"))
-                  (freetype (assoc-ref inputs "freetype")))
-              (substitute* "setup.py"
-                (("JPEG_ROOT = None")
-                 (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")"))
-                (("ZLIB_ROOT = None")
-                 (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")"))
-                (("TIFF_ROOT = None")
-                 (string-append "TIFF_ROOT = libinclude(\"" tiff "\")"))
-                (("FREETYPE_ROOT = None")
-                 (string-append "FREETYPE_ROOT = libinclude(\""
-                                freetype "\")")))))
-          %standard-phases)))
-    (home-page "http://www.pythonware.com/products/pil/")
-    (synopsis "Python Imaging Library")
-    (description "The Python Imaging Library (PIL) adds image processing
-capabilities to the Python interpreter.")
-    (license (license:x11-style
-               "file://README"
-               "See 'README' in the distribution."))))
-
-(define-public python2-piddle-gn ; guix obsolete
-  (package
-    (name "python2-piddle-gn")
-    (version "1.0.15-gn")
-    (source (origin
-     (method url-fetch)
-     (uri (string-append
-           "https://files.genenetwork.org/software/piddle-1.0.15-gn.tgz"))
-     (sha256
-      (base32
-       "05gjnn31v7p0kh58qixrpcizcxqf3b7zv4a5kk8nsmqwgxh0c6gq"))))
-
-    (build-system python-build-system)
-    (native-inputs
-     `(("python2-setuptools" ,python2-setuptools)))
-    (propagated-inputs
-     `(("python2-pil1" ,python2-pil1-gn)))
-    (arguments
-     `(
-       #:python ,python-2
-       #:tests? #f   ; no 'setup.py test' really!
-    ))
-    (home-page #f)
-    (synopsis "Canvas drawing library for python2 (old!)")
-    (description #f)
-    (license #f)))
-
-(define-public python2-pil1 ; guix obsolete
-  (package
-    (name "python2-pil1") ; this version is NOT used by genenetwork
-    (version "1.1.7")
-    (source (origin
-             (method url-fetch)
-             (uri (string-append "http://effbot.org/downloads/Imaging-"
-                                 version ".tar.gz"))
-             (sha256
-              (base32
-               "04aj80jhfbmxqzvmq40zfi4z3cw6vi01m3wkk6diz3lc971cfnw9"))
-    (modules '((guix build utils)))
-    (snippet
-     ;; Adapt to newer freetype and lcms.  As the package is unmaintained
-     ;; upstream, there is no use in creating a patch and reporting it.
-     '(begin (substitute* "_imagingft.c"
-               (("freetype/")
-                "freetype2/freetype/"))
-             (substitute* '("setup.py"
-                            "_imagingcms.c")
-               (("lcms.h") "lcms2.h"))))))
-    (build-system python-build-system)
-    (inputs
-     `(("freetype" ,freetype)
-       ("lcms" ,lcms) ; not fully supported
-       ("libjpeg" ,libjpeg-turbo)
-       ("libtiff" ,libtiff)
-       ("tcl" ,tcl)
-       ("zlib" ,zlib)))
-    (arguments
-     ;; Only the fork python-pillow works with Python 3.
-     `(#:python ,python-2
-       #:tests? #f ; no check target
-       #:use-setuptools? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'link-libraries
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((freetype (assoc-ref inputs "freetype"))
-                   (jpeg (assoc-ref inputs "libjpeg"))
-                   (lcms (assoc-ref inputs "lcms"))
-                   (tcl (assoc-ref inputs "tcl"))
-                   (tiff (assoc-ref inputs "libtiff"))
-                   (zlib (assoc-ref inputs "zlib")))
-               (substitute* "setup.py"
-                 (("FREETYPE_ROOT .*")
-                  (string-append "FREETYPE_ROOT = libinclude(\"" freetype "\")\n"))
-                 (("JPEG_ROOT .*")
-                  (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")\n"))
-                 (("LCMS_ROOT .*")
-                  (string-append "LCMS_ROOT = libinclude(\"" lcms "\")\n"))
-                 (("^TCL_ROOT .*")
-                  (string-append "TCL_ROOT = libinclude(\"" tcl "\")\n"))
-                 (("TIFF_ROOT .*")
-                  (string-append "TIFF_ROOT = libinclude(\"" tiff "\")\n"))
-                 (("ZLIB_ROOT .*")
-                  (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")\n"))))
-             #t)))))
-    (home-page "http://www.pythonware.com/products/pil/")
-    (synopsis "Python Imaging Library")
-    (description "The @dfn{Python Imaging Library} (PIL) adds image processing
-capabilities to your Python interpreter.  This library supports many file
-formats, and provides powerful image processing and graphics capabilities.
-
-NOTE: This package is superseded by python-pillow")
-    (license (license:x11-style
-               "file://README"
-               "See 'README' in the distribution."))))
-
-; upstream version won't work with gn2
-(define-public python2-piddle
-  (package
-    (name "python2-piddle")
-    (version "1.0.15")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (string-append "mirror://sourceforge/piddle/piddle/"
-                            version "/piddle-" version ".zip"))
-        (sha256
-         (base32
-          "0jaxfsrcgqb5cf2wznxnpdws5khlrdixmg85lrhq2zl9cy6dfdya"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:use-setuptools? #f
-       #:tests? #f)) ; tests are interactive
-    (native-inputs
-     `(("unzip" ,unzip)))
-    (propagated-inputs
-     `(("python2-pil" ,python2-pil1-gn)))
-    (home-page "http://www.strout.net/info/coding/python/piddle/")
-    (synopsis "Plug-In Drawing, Does Little Else")
-    (description "PIDDLE is designed for vector graphics -- i.e., drawing of
-primitives such as lines and ellipses, rather than manipulation of individual
-pixels.")
-    (license license:gpl2+)))
-
 (define-public python2-numarray ; guix: obsolete lib
   (package
     (name "python2-numarray")
@@ -551,9 +134,6 @@ the older versions.")
     (home-page "https://github.com/srittau/python-htmlgen")
     (license license:expat)))
 
-(define-public python2-htmlgen
-  (package-with-python2 python-htmlgen))
-
 (define-public python-asserts
   (package
     (name "python-asserts")
@@ -575,34 +155,6 @@ stand-alone manner.")
     (home-page "https://github.com/srittau/python-asserts")
     (license license:expat)))
 
-(define-public python-version
-(let ((commit "e5aadc720bb74c535f29e5a2de5cd9697efe8d7c"))
-(package
-  (name "python-version")
-  (version "0.1.2")
-  (source
-    (origin
-      (method git-fetch)
-      (uri (git-reference
-      ; (url "https://github.com/genenetwork/pylmm.git")
-        (url "https://github.com/keleshev/version.git") ; version not in pypi
-        (commit commit)))
-      (file-name (string-append name "-" commit))
-      (sha256
-        (base32
-          "1rc8kf72v180qlygkh1y0jwv2fxqpx7n97bqfhbwgnn31iwai9g3"))))
-  (build-system python-build-system)
-  (propagated-inputs
-    `(
-    ("python-more-itertools" ,python-more-itertools)
-    ("python-pytest" ,python-pytest)))
-  (home-page "http://github.com/halst/version")
-  (synopsis "Implementation of semantic version")
-  (description
-    "Implementation of semantic version")
-  (license license:expat)
-)))
-
 (define-public python2-pp
   (package
     (name "python2-pp")
@@ -785,307 +337,6 @@ spreadsheets without the need for COM objects.")
     (description "Extensions to the standard Python datetime module")
     (license license:bsd-3)))
 
-(define-public python-pyshex
-  (package
-    (name "python-pyshex")
-    (version "0.7.14")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "PyShEx" version))
-       (sha256
-        (base32 "1fy664bh6hpmr4cf49fwwxng36kv7s6b2986hbv0cqcypc4ri2cs"))))
-    (arguments
-     '(#:tests? #f          ; Tests try to use the internet.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'drop-rdflib-namespace-rdfnamespace
-           (lambda _
-             ;; _RDFNamespace is in rdflib-5
-             ;; https://github.com/hsolbrig/PyShEx/commit/d138a5b4f2249212f2141b7b9bbaff6696ee9415
-             (substitute* "pyshex/prefixlib.py"
-               (("XMLNS, _RDFNamespace") "XMLNS"))))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (setenv "SKIP_EXTERNAL_URLS" "true")
-               (invoke "python" "-m" "unittest")))))))
-    (build-system python-build-system)
-    (propagated-inputs
-     (list python-cfgraph
-           python-pyshexc-0.7
-           python-rdflib
-           python-requests
-           python-shexjsg
-           python-sparql-slurper
-           python-sparqlwrapper
-           python-urllib3))
-    (native-inputs
-     (list python-pbr python-unittest2))
-    (home-page "https://github.com/hsolbrig/PyShEx")
-    (synopsis "Python ShEx Implementation")
-    (description "This package provides a python ShEx Implementation.")
-    (license license:asl2.0)))
-
-(define-public python-pyshexc
-  (package
-    (name "python-pyshexc")
-    (version "0.9.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "PyShExC" version))
-        (sha256
-         (base32 "1lq4lf0nal1v1d3vbyrr1hfkhmhphy06dyqhyw7b5zls9dfrga9m"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:tests? #f  ; It isn't clear how the tests expect to succeed.
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "unittest" "discover" "-s" "tests")))))))
-    (propagated-inputs
-     (list python-antlr4-python3-runtime
-           python-chardet
-           python-jsonasobj
-           python-pyjsg
-           python-rdflib-shim
-           python-shexjsg))
-    (native-inputs
-     (list python-pbr
-           python-requests
-           python-yadict-compare))
-    (home-page "https://github.com/shexSpec/grammar-python-antlr")
-    (synopsis "Python ShExC Parser")
-    (description "This package converts the @dfn{Shape Expression Compact}
-(ShExC) into @dfn{Python JSON Schema Binding} (pyjsg) objects.")
-    (license license:asl2.0)))
-
-(define-public python-pyshexc-0.7
-  (package
-    (inherit python-pyshexc)
-    (name "python-pyshexc")
-    (version "0.7.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/shexSpec/grammar")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name "shexspec-grammar" version))
-        (sha256
-         (base32 "08wsknjq8zyi3hk01w6yl6z8jld63l6l64n43gjhj0jphbm4s9iz"))
-        (modules '((guix build utils)))
-        (snippet
-         '(begin
-            (substitute* "parsers/python/setup.cfg"
-              (("python-requires = 3") "python_requires = >=3.6"))))))
-    (arguments
-     `(#:tests? #f  ; Tests try to access the internet.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'chdir
-           (lambda _
-             (chdir "parsers/python")
-             (setenv "PBR_VERSION" ,version)))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (substitute* "tests/__init__.py"
-                 (("schemas_base =.*")
-                  (string-append "schemas_base = \""
-                                 (assoc-ref inputs "test-suite")
-                                 "/schemas\"\n")))
-               (substitute* "tests/test_shexr.py"
-                 (("https://raw.githubusercontent.com/shexSpec/shexTest/master/validation/manifest")
-                  (string-append (assoc-ref inputs "test-suite")
-                                 "/validation/manifest")))
-               (substitute* "tests/test_issue_9.py"
-                 (("https://raw.githubusercontent.com/shexSpec/shexTest/master/schemas/1dotNS2.shex")
-                  (search-input-file inputs "/schemas/1dotNS2.shex")))
-               (symlink (assoc-ref inputs "test-suite")
-                        "../../../shexTest")
-               (invoke "python" "-m" "unittest" "discover" "-s" "tests")))))))
-    (propagated-inputs
-     (list python-antlr4-python3-runtime
-           python-certifi
-           python-jsonasobj
-           python-rdflib-shim
-           python-requests
-           python-shexjsg))
-    (native-inputs
-     `(("python-pbr" ,python-pbr)
-       ("python-unittest2" ,python-unittest2)
-       ("python-yadict-compare" ,python-yadict-compare)
-       ("test-suite"
-        ,(origin
-           (method git-fetch)
-           (uri (git-reference
-                  (url "https://github.com/shexSpec/shexTest")
-                  (commit "v2.0.2")))
-           (file-name (git-file-name name version))
-           (sha256
-            (base32
-             "1x788nyrwycfr55wbg0ay6mc8mi6wwsg81h614rx9pw6rvrsppps"))))))
-    (home-page "https://github.com/shexSpec/grammar/tree/master/parsers/python")))
-
-(define-public python-antlr4-python3-runtime
-  (package
-    (name "python-antlr4-python3-runtime")
-    (version "4.9.3")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "antlr4-python3-runtime" version))
-        (sha256
-         (base32 "06w8fz73rk8vzjz9rydfk56g4mbqpyl81yhypc14jab886dlc97j"))))
-    (build-system python-build-system)
-    (home-page "https://www.antlr.org/")
-    (synopsis "ANTLR runtime for Python")
-    (description "This package provides the ANTLR runtime for Python.")
-    (license license:bsd-3)))
-
-(define-public python-jsonasobj
-  (package
-    (name "python-jsonasobj")
-    (version "1.2.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "jsonasobj" version))
-        (sha256
-         (base32
-          "1yj8y3k3fb7lk043f1zhmhb2lzjlfpnxajb92rpxmjzja93yxx0y"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:tests? #f   ; Tests not included in release tarball.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-source
-           (lambda _
-             (substitute* "setup.py"
-               (("yadict_compare") "['dict_compare"))
-             #t)))))
-    (native-inputs
-     `(("python-yadict-compare" ,python-yadict-compare)))
-    (home-page "https://github.com/hsolbrig/jsonasobj")
-    (synopsis "JSON as python objects")
-    (description
-     "This package provides an extension to the core python json library that
-treats name/value pairs as first class attributes whenever possible.")
-    (license license:asl2.0)))
-
-(define-public python-shexjsg
-  (package
-    (name "python-shexjsg")
-    (version "0.8.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "ShExJSG" version))
-        (sha256
-         (base32 "1dnhpk6n6vzadkv13y7r6y2mi1pzv4y19vmxh91k9ykpqngn4ypi"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (if tests?
-               (begin (add-installed-pythonpath inputs outputs)
-                      ;; Tries to download files from the internet.
-                      (substitute* "tests/test_shexj.py"
-                        (("skipIf\\(False") "skipIf(True"))
-                      (invoke "python" "-m" "unittest"))))))))
-    (propagated-inputs
-     (list python-pyjsg))
-    (native-inputs
-     (list python-jsonasobj
-           python-pbr
-           python-rdflib-shim
-           python-requests
-           python-yadict-compare))
-    (home-page "https://github.com/hsolbrig/ShExJSG")
-    (synopsis "Astract Syntax Tree for the ShEx 2.0 language")
-    (description "This package provides an astract syntax tree for the
-ShEx 2.0 language.")
-    (license license:cc0)))
-
-(define-public python-yadict-compare
-  (package
-    (name "python-yadict-compare")
-    (version "1.2.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "yadict_compare" version))
-        (sha256
-         (base32
-          "1kkcw82cp6mf3jailckd9gya4r7wjyz4gc5azsj2njj4wqn081rw"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (with-directory-excursion "test"
-               (invoke "python" "-m" "unittest" "discover" "-s" "test")))))))
-    (native-inputs
-     `(("python-unittest2" ,python-unittest2)))
-    (home-page "https://github.com/hsolbrig/dict_compare")
-    (synopsis "Dictionary comparison tool with filtering and reporting")
-    (description
-     "A dictionary comparison tool that allows the injection of filters and
-handles recursion and lists.")
-    (license license:bsd-3)))
-
-(define-public python-pyjsg
-  (package
-    (name "python-pyjsg")
-    (version "0.11.10")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "PyJSG" version))
-        (sha256
-         (base32 "1ylbx2pc06qsvb8cqnr8nysvmw55f8nkm05ybcwjpyik53zy7mjb"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         ;; From tox.ini
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (for-each
-                 (lambda (dir)
-                   (invoke "python" "-m" "unittest" "discover" "-s" dir))
-                 '("tests/test_issues"
-                   ;"tests/test_basics"
-                   "tests/test_jsglib"
-                   "tests/test_parser_impl"
-                   "tests/test_python_generator"
-                   "tests_standalone"
-                   "tests_standalone_2"))))))))
-    (propagated-inputs
-     (list python-antlr4-python3-runtime
-           python-jsonasobj))
-    (native-inputs
-     (list python-pbr
-           python-requests
-           python-unittest2
-           python-yadict-compare))
-    (home-page "https://github.com/hsolbrig/pyjsg")
-    (synopsis "Python JSON Schema Grammar bindings")
-    (description
-     "A tool to create Python classes that represent JSON objects defined in JSG.")
-    (license license:asl2.0)))
-
 (define-public python-sparql-slurper
   (package
     (name "python-sparql-slurper")
@@ -1108,67 +359,6 @@ handles recursion and lists.")
     (description "This package provides a SPARQL Slurper for rdflib.")
     (license license:asl2.0)))
 
-(define-public python-sparqlslurper
-  (package
-    (name "python-sparqlslurper")
-    (version "0.5.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "sparqlslurper" version))
-              (sha256
-               (base32 "0ipma74dr5jvsxwaa9al147mn9vv3v5r9lb9hajm4qgwcjqfp0lj"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:tests? #f  ; Tests try to use the internet.
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "unittest")))))))
-    (propagated-inputs
-     (list python-rdflib-shim
-           python-sparqlwrapper))
-    (native-inputs
-     (list python-pbr python-unittest2))
-    (home-page "http://github.com/hsolbrig/sparqlslurper")
-    (synopsis "SPARQL Slurper for rdflib")
-    (description "This package provides an implementation of a
-@code{rdflibGraph} that acts as a cache for a SPARQL endpoint.  SPARQL Slurper
-translates the @code{Graph.triples()} function into the corresponding SPARQL
-query and resolves it against an endpoint.")
-    (license license:cc0)))
-
-(define-public python2-ruamel.ordereddict
-  (package
-    (name "python2-ruamel.ordereddict")
-    (version "0.4.14")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "ruamel.ordereddict" version))
-        (sha256
-         (base32
-          "0jldrcanmz0284r2y6kbi82vslkaf5hf5q90v7rqxcdjdv952418"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (if tests?
-               (begin (add-installed-pythonpath inputs outputs)
-                      (invoke "python" "test/testordereddict.py"))
-               #t))))))
-    (home-page "https://sourceforge.net/projects/ruamel-ordereddict/")
-    (synopsis "Version of dict that keeps keys in insertion resp. sorted order")
-    (description
-     "This package provides a version of dict that keeps keys in insertion resp.
-sorted order.")
-    (license license:expat)))
-
 (define-public python-pandas-plink
   (package
     (name "python-pandas-plink")
@@ -1252,159 +442,6 @@ sorted order.")
         (base32
          "1vc0rd50wbny0qdjjc7z14xvjdsfcmzavx3njxpxr2dvhx3b6j79"))))))
 
-(define-public python-varint
-  (package
-    (name "python-varint")
-    (version "1.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "varint" version))
-       (sha256
-        (base32
-         "19ac46adalgva1chlh0rxv6cinpikxfd92kabbbfjpmcfwiw1v56"))))
-    (build-system python-build-system)
-    (home-page
-     "http://github.com/fmoo/python-varint")
-    (synopsis "Simple python varint implementation")
-    (description
-     "Simple python varint implementation")
-    (license license:expat)))
-
-(define-public python-multiaddr
-  (package
-    (name "python-multiaddr")
-    (version "0.0.9")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "multiaddr" version))
-       (sha256
-        (base32
-         "1kqfmcbv8plpicbygwpdljin7n82iyxklc0w1ywxbhzdi58nkcih"))))
-    (build-system python-build-system)
-    (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-pytest-runner" ,python-pytest-runner)))
-    (propagated-inputs
-     `(("python-base58" ,python-base58)
-       ("python-idna" ,python-idna)
-       ("python-netaddr" ,python-netaddr)
-       ("python-six" ,python-six)
-       ("python-varint" ,python-varint)))
-    (home-page
-     "https://github.com/multiformats/py-multiaddr")
-    (synopsis
-     "Python implementation of jbenet's multiaddr")
-    (description
-     "Python implementation of jbenet's multiaddr")
-    (license license:expat)))
-
-(define-public python-ipfshttpclient
-  (package
-    (name "python-ipfshttpclient")
-    (version "0.7.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "ipfshttpclient" version))
-       (sha256
-        (base32
-         "14rnqk61fqa6c1ql412q723g7spgpv2pch96h7p8gb632hy07cgy"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'bumpup-max-version
-           (lambda _
-             (substitute* "ipfshttpclient/client/__init__.py"
-               (("VERSION_MAXIMUM   = \"0.7.0\"")
-                "VERSION_MAXIMUM   = \"0.8.1\""))
-             #t)))))
-    (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-pytest-runner" ,python-pytest-runner)))
-    (propagated-inputs
-     `(("python-httpx" ,python-httpx)
-       ("python-multiaddr" ,python-multiaddr)
-       ("python-requests" ,python-requests)))
-    (home-page
-     "https://ipfs.io/ipns/12D3KooWEqnTdgqHnkkwarSrJjeMP2ZJiADWLYADaNvUb6SQNyPF/")
-    (synopsis "Python IPFS HTTP CLIENT library")
-    (description "Python IPFS HTTP CLIENT library")
-    (license license:expat)))
-
-(define-public python-jupyter-server-proxy
-  (package
-    (name "python-jupyter-server-proxy")
-    (version "3.0.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "jupyter-server-proxy" version))
-        (sha256
-         (base32 "0vglj7v7wq73a9dya60q2vrxxpglg11w66l7crkzzrfpbblr814p"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-aiohttp" ,python-aiohttp)
-       ("python-jupyter-server" ,python-jupyter-server)
-       ("python-simpervisor" ,python-simpervisor)))
-    (home-page "https://jupyter-server-proxy.readthedocs.io/")
-    (synopsis "Jupyter server extension to supervise and proxy web services")
-    (description
-     "Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like @code{/rstudio} next to others like @code{/lab}.  Alongside the python package that provides the main functionality, the JupyterLab extension (@code{@@jupyterlab/server-proxy}) provides buttons in the JupyterLab launcher window to get to RStudio for example.")
-    (license license:bsd-3)))
-
-(define-public python-jupyter-server-proxy-1    ; bundled javascript?
-  (package
-    (name "python-jupyter-server-proxy")
-    (version "1.6.0")
-    (source
-      (origin
-        ;; Tests not included in release.
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/jupyterhub/jupyter-server-proxy")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "03yry0jz6xlvy28h3w514pw0q9w51lnr1lpcigqmhnf5x7g9bfyy"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f  ; Running the test suite isn't fully documented.
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               ;; see .github/workflows/test.yaml and CONTRIBUTING.md
-               (setenv "JUPYTER_TOKEN" "secret")
-               (setenv "HOME" (getcwd))
-               (invoke "jupyter" "serverextension" "enable" "jupyter_server_proxy")
-               (system "jupyter-notebook --config=./tests/resources/jupyter_server_config.py &")
-               (sleep 5)
-               (invoke "pytest" "--verbose"))
-             #t)))))
-    (propagated-inputs
-     `(("python-aiohttp" ,python-aiohttp)
-       ("python-notebook" ,python-notebook)
-       ("python-simpervisor" ,python-simpervisor)))
-    (native-inputs
-     `(("python-pytest" ,python-pytest)))
-    (home-page "https://jupyter-server-proxy.readthedocs.io/")
-    (synopsis "Jupyter server extension to supervise and proxy web services")
-    (description
-     "Jupyter Server Proxy lets you run arbitrary external processes (such as
-RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your
-notebook server and provide authenticated web access to them using a path like
-@code{/rstudio} next to others like @code{/lab}.  Alongside the python package
-that provides the main functionality, the JupyterLab extension
-(@code{@@jupyterlab/server-proxy}) provides buttons in the JupyterLab launcher
-window to get to RStudio for example.")
-    (license license:bsd-3)))
-
-;; Waiting for this to be merged upstream then I'll remove it
 (define-public python-flask-debugtoolbar
   (package
     (name "python-flask-debugtoolbar")
@@ -1488,160 +525,6 @@ file format spec.")
 
 ;; Note: This package is only needed for rdflib < 6.0; supersede when
 ;; the above are removed.
-(define-public python-rdflib-jsonld
-  (package
-    (name "python-rdflib-jsonld")
-    (version "0.6.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "rdflib-jsonld" version))
-        (sha256
-         (base32
-          "0qrshlqzv5g5bign7kjja3xf7hyk7xgayr3yd0qlqda1kl0x6z0h"))))
-    (build-system python-build-system)
-    (native-inputs
-     (list python-nose))
-    (propagated-inputs
-     (list python-rdflib))
-    (home-page "https://github.com/RDFLib/rdflib-jsonld")
-    (synopsis "rdflib extension adding JSON-LD parser and serializer")
-    (description "This package provides an rdflib extension adding JSON-LD
-parser and serializer.")
-    (license license:bsd-3)))
-
-(define-public python-rdflib-shim
-  (package
-    (name "python-rdflib-shim")
-    (version "1.0.3")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "rdflib_shim" version))
-              (sha256
-               (base32
-                "03gwsjcinbyyqrhs2jfhs6mr7j69dfn5djihd0mv9al654gd2mfr"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (substitute* "requirements.txt"
-                    (("rdflib-jsonld==0.6.1") "rdflib-jsonld"))))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "unittest" "discover" "-s" "tests")))))))
-    (propagated-inputs
-     (list python-rdflib python-rdflib-jsonld))
-    (native-inputs
-     (list python-pbr))
-    (home-page "http://hsolbrig.github.io/rdflib-shim")
-    (synopsis "Shim for rdflib 5 and 6 incompatibilities")
-    (description "Shim for rdflib 5 and 6 incompatibilities")
-    (license license:cc0)))
-
-(define-public python-h5py-2
-  (package
-    (name "python-h5py")
-    (version "2.10.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "h5py" version))
-              (sha256
-               (base32
-                "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ;no test target
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'fix-hdf5-paths
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      (setenv "HDF5_DIR"
-                              (assoc-ref inputs "hdf5")))))))
-    (propagated-inputs (list python-six python-numpy))
-    (inputs (list hdf5-1.10))
-    (native-inputs (list python-cython python-pkgconfig pkg-config))
-    (home-page "https://www.h5py.org/")
-    (synopsis "Read and write HDF5 files from Python")
-    (description
-     "The h5py package provides both a high- and low-level interface to the
-HDF5 library from Python.  The low-level interface is intended to be a
-complete wrapping of the HDF5 API, while the high-level component supports
-access to HDF5 files, datasets and groups using established Python and NumPy
-concepts.")
-    (license license:bsd-3)))
-
-(define-public python-typing-extensions-4.10
-  (package
-    (inherit python-typing-extensions)
-    (version "4.10.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "typing_extensions" version))
-              (sha256
-               (base32
-                "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh"))))))
-
-(define-public python-addict
-  (package
-    (name "python-addict")
-    (version "2.4.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "addict" version))
-              (sha256
-               (base32
-                "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk"))))
-    (build-system pyproject-build-system)
-    (home-page "https://github.com/mewwts/addict")
-    (synopsis "Python dictionary with attribute accessible values")
-    (description "@code{python-addict} provides dictionaries whose items can
-be get and set using both attribute and item syntax.")
-    (license license:expat)))
-
-(define-public python-enlighten
-  (package
-    (name "python-enlighten")
-    (version "1.12.4")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "enlighten" version))
-              (sha256
-               (base32
-                "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs
-     (list python-blessed python-prefixed))
-    (home-page "https://github.com/Rockhopper-Technologies/enlighten")
-    (synopsis "Console progress bar library")
-    (description "@code{python-enlighten} is a console progress bar library
-for Python.  The main advantage of Enlighten is that it allows writing to
-stdout and stderr without any redirection or additional code---just print or
-log as you normally would.  Enlighten also includes experimental support for
-Jupyter Notebooks.")
-    (license license:mpl2.0)))
-
-(define-public python-prefixed
-  (package
-    (name "python-prefixed")
-    (version "0.7.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "prefixed" version))
-              (sha256
-               (base32
-                "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b"))))
-    (build-system pyproject-build-system)
-    (home-page "https://github.com/Rockhopper-Technologies/prefixed")
-    (synopsis "Prefixed alternative numeric library")
-    (description "@code{python-prefixed} provides an alternative
-implementation of the built-in float which supports formatted output with
-SI (decimal) and IEC (binary) prefixes.")
-    (license license:mpl2.0)))
-
 (define-public python-pillow-9
   (package
     (name "python-pillow-9")