build-system/pyproject: Remove uneeded use of pyproject-guile-json.

* gnu/packages/bioinformatics.scm (python-bed-reader, python-gseapy)
* gnu/packages/chemistry.scm (gemmi, ringdecomposerlib, rdkit)
* gnu/packages/cinnamon.scm (libxapp)
* gnu/packages/cups.scm (hplip)
* gnu/packages/djvu.scm (ocrodjvu)
* gnu/packages/finance.scm (electron-cash)
* gnu/packages/gnome.scm (terminator)
* gnu/packages/image-processing.scm (insight-toolkit)
* gnu/packages/machine-learning.scm (onnxruntime, tensorflow-lite,
koboldcpp, python-tokenizers)
* gnu/packages/maths.scm (gmsh, z3, fp16)
* gnu/packages/music.scm (quodlibet)
* gnu/packages/photo.scm (lensfun)
* gnu/packages/python-science.scm (python-clarabel)
* gnu/packages/python-xyz.scm (python-orjson, python-libcst,
python-rpds-py, python-streamtracer, python-tiktoken)
* gnu/packages/rpm.scm (createrepo-c)
* gnu/packages/rust-apps.scm (maturin)
* gnu/packages/sugar.scm (sugar, sugar-datastore)
* gnu/packages/version-control.scm (mercurial, hg-commitsigs)
* gnu/packages/vpn.scm (python-proton-vpn-local-agent)
[arguments]<#:phases>: Remove uneeded use of pyproject-guile-json
extension.

* gnu/packages/python-xyz.scm (python-streamtracer)[arguments]
<#:phases>: Also rewrite 'check phase replacement.

Change-Id: I779c354120ada3d94f07a127b9ec5011e73254c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu/packages/bioinformatics.scm

@@ -2195,7 +2195,6 @@ Format (GFF) with Biopython integration.")
         (ice-9 match)
         (ice-9 rdelim))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'configure 'set-data-path
             (lambda _
@@ -2290,7 +2289,7 @@ version = ~s
                   (delete-file-recursively
                    (string-append site "/bed_reader/tests"))
                   (delete-file-recursively
-                   (string-append #$output "/.pytest_cache"))))))))))
+                   (string-append #$output "/.pytest_cache")))))))))
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-pytest-datadir
@@ -25484,7 +25483,6 @@ CSIv1, CSIv2 and FAI files.")
         ((guix build pyproject-build-system) #:prefix py:)
         (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'install 'prepare-python-module
             (lambda _
@@ -25540,7 +25538,7 @@ exclude =
               (when tests?
                 (invoke "pytest" "-vv" "tests"
                         ;; These tests need access to the internet
-                        "-k" "not test_enrichr and not test_prerank"))))))))
+                        "-k" "not test_enrichr and not test_prerank")))))))
     (inputs
      (cons python-wrapper (cargo-inputs 'python-gseapy)))
     (native-inputs

gnu/packages/chemistry.scm

@@ -1062,7 +1062,6 @@ integrals for Gaussian type functions.")
               (string-append "-DPYTHON_INSTALL_DIR="
                              (site-packages %build-inputs %outputs)))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'patch-includes
               (lambda _
@@ -1101,7 +1100,7 @@ integrals for Gaussian type functions.")
                   (with-directory-excursion "../source"
                     (setenv "PYTHONPATH" "../build/py")
                     (invoke "python3" "-m" "unittest" "discover" "-v"
-                            "-s" "tests")))))))))
+                          "-s" "tests"))))))))
     (inputs (list python zlib))
     (native-inputs
      (list fast-float
@@ -1471,7 +1470,6 @@ and rendering molecules.")
                   (guix build utils)
                   ((guix build pyproject-build-system) #:prefix py:))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-before 'configure 'patch-cmake
               (lambda _
@@ -1514,7 +1512,7 @@ and rendering molecules.")
             (add-after 'install 'check
               (assoc-ref %standard-phases 'check))
             (add-before 'check 'add-install-to-pythonpath
-              (assoc-ref py:%standard-phases 'add-install-to-pythonpath))))))
+            (assoc-ref py:%standard-phases 'add-install-to-pythonpath)))))
     (inputs (list python))
     (native-inputs (list doxygen python python-cython-0 python-sphinx))
     (home-page "https://github.com/rareylab/RingDecomposerLib")
@@ -1632,7 +1630,6 @@ Tanimoto scoring.")
                "-DCMAKE_INCLUDE_PATH="
                (search-input-directory %build-inputs "/include/avalontoolkit")))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'copy-external-dependencies
               (lambda _
@@ -1692,7 +1689,7 @@ Tanimoto scoring.")
                               ;; Circular import
                               "pythonSourceTests"
                               ) "|")
-                           ")"))))))))))
+                         ")")))))))))
     (inputs
      (list avalon-toolkit
            cairo

gnu/packages/cinnamon.scm

@@ -82,7 +82,6 @@
                "-Dpy-overrides-dir="
                (py:site-packages %build-inputs %outputs) "/gi/overrides"))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-before 'configure 'set-gtk-module-path
               (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -102,7 +101,7 @@
                    (string-quote (string-append #$output "/bin/pastebin")))
                   (("'xdg-open'")
                    (string-quote (search-input-file inputs
-                                                    "/bin/xdg-open"))))))))))
+                                                  "/bin/xdg-open")))))))))
     (inputs
      (list dbus
            glib                         ; for gio

gnu/packages/cups.scm

@@ -647,7 +647,6 @@ should only be used as part of the Guix cups-pk-helper service.")
               "--enable-qt5"
               "--disable-qt4")
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'set-gcc-14-cflags
               ;; We set CFLAGS here because adding setting it in
@@ -743,7 +742,7 @@ should only be used as part of the Guix cups-pk-helper service.")
                                      bin target)))
                          (chmod file #o755)))
                               (find-files "." (lambda (file stat)
-                                                (eq? 'symlink (stat:type stat)))))))))))))
+                                     (eq? 'symlink (stat:type stat))))))))))))
     ;; Note that the error messages printed by the tools in the case of
     ;; missing dependencies are often downright misleading.
     ;; TODO: hp-toolbox still fails to start with:

gnu/packages/djvu.scm

@@ -386,7 +386,6 @@ and background layers of images, which can then be encoded into a DjVu file.")
                              ,@%pyproject-build-system-modules)
         #:test-target "test"
         #:phases
-        (with-extensions (list (pyproject-guile-json))
           #~(modify-phases %standard-phases
               (delete 'configure)
               (add-after 'unpack 'fix-for-python-3.11
@@ -431,7 +430,7 @@ and background layers of images, which can then be encoded into a DjVu file.")
                                      "/bin")))))
                             '("bin/djvu2hocr"
                               "bin/hocr2djvused"
-                              "bin/ocrodjvu"))))))))
+                            "bin/ocrodjvu")))))))
       (native-inputs
        (list (libc-utf8-locales-for-target) libxml2 python-pynose python-pillow))
       (inputs

gnu/packages/finance.scm

@@ -767,7 +767,6 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
                   (guix build qt-utils)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'create-output-directories
               (lambda _
@@ -786,7 +785,7 @@ other machines/servers.  Electrum does not download the Bitcoin blockchain.")
             (add-after 'install 'wrap-qt
               (lambda* (#:key inputs #:allow-other-keys)
                 (wrap-qt-program "electron-cash"
-                                 #:output #$output #:inputs inputs)))))))
+                               #:output #$output #:inputs inputs))))))
     (native-inputs (list python-setuptools))
     (inputs
      (list bash-minimal

gnu/packages/gnome.scm

@@ -12250,7 +12250,6 @@ advanced image management tool")
                    #:prefix glib-or-gtk:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'handle-dbus-python
               (lambda _
@@ -12268,7 +12267,7 @@ advanced image management tool")
                   `("GI_TYPELIB_PATH" =
                     (,(getenv "GI_TYPELIB_PATH"))))))
             (add-after 'wrap 'glib-or-gtk-wrap
-              (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))))))
+            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (native-inputs
      (list gettext-minimal
            `(,glib "bin") ;for glib-compile-resources

gnu/packages/image-processing.scm

@@ -1388,7 +1388,6 @@ libraries designed for computer vision research and implementation.")
                 "-DBUILD_TESTING=OFF")
 
         #:phases
-        (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'do-not-tune
               (lambda _
@@ -1448,7 +1447,7 @@ libraries designed for computer vision research and implementation.")
               (lambda* (#:key inputs outputs tests? #:allow-other-keys)
                 (when tests?
                   (py:add-installed-pythonpath inputs outputs)
-                  (invoke "python3" "-c" "import itk"))))))))
+                  (invoke "python3" "-c" "import itk")))))))
       (inputs (list eigen
                     expat
                     fftw

gnu/packages/machine-learning.scm

@@ -2222,7 +2222,6 @@ with a single function call.")
               ;; XXX: Fixes build with gcc@14.
               "-DCMAKE_CXX_FLAGS=-Wl,-z,noexecstack")
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'unpack 'chdir
             (lambda _
@@ -2285,7 +2284,7 @@ with a single function call.")
               ((assoc-ref py:%standard-phases 'sanity-check)
                #:inputs `(("sanity-check.py" . ,#$(default-sanity-check.py))
                           ,@inputs)
-               #:outputs `(("out" . ,#$output:python)))))))))
+               #:outputs `(("out" . ,#$output:python))))))))
     (outputs (list "out" "python"))
     (inputs
      (list abseil-cpp-20250127
@@ -3682,7 +3681,6 @@ Python.")
          "-DFARMHASH_SOURCE_DIR=/tmp/farmhash"
          (string-append "-Dgemmlowp_ROOT=" #$(this-package-input "gemmlowp")))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'unpack 'chdir
             (lambda _
@@ -3808,7 +3806,7 @@ find_library(ML_DTYPES_LIBRARIES
               ((assoc-ref py:%standard-phases 'sanity-check)
                #:inputs `(("sanity-check.py" . ,#$(default-sanity-check.py))
                           ,@inputs)
-               #:outputs `(("out" . ,#$output:python)))))))))
+               #:outputs `(("out" . ,#$output:python))))))))
     (inputs
      (list abseil-cpp
            cpuinfo
@@ -4714,7 +4712,6 @@ different backends")
               "LLAMA_PORTABLE=1"
               "LLAMA_USE_BUNDLED_GLSLC=0")    ;; TODO: add CLBLAS
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (delete 'configure)
             (replace 'install
@@ -4733,7 +4730,7 @@ different backends")
                 (wrap-program (search-input-file outputs "bin/koboldcpp.py")
                   `("GUIX_PYTHONPATH" =
                     (,(getenv "GUIX_PYTHONPATH")
-                     ,(python:site-packages inputs outputs))))))))))
+                   ,(python:site-packages inputs outputs)))))))))
     (inputs
      (list bash-minimal
            openblas
@@ -6033,7 +6030,6 @@ definite approximations of Optimal Transport (Wasserstein) distances.
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'check 'python-check
             (lambda _
@@ -6057,7 +6053,7 @@ definite approximations of Optimal Transport (Wasserstein) distances.
                 (copy-file "PKG-INFO" (string-append info "/METADATA"))
                 (copy-recursively
                  "py_src/tokenizers"
-                 (string-append lib "tokenizers")))))))))
+                 (string-append lib "tokenizers"))))))))
     (native-inputs
      (list pkg-config python-minimal python-pytest))
     (inputs

gnu/packages/maths.scm

@@ -3777,7 +3777,6 @@ supports the propositional fragment of PDDL2.2.")
                   (guix build cmake-build-system)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'patch-paths
               (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -3795,7 +3794,7 @@ supports the propositional fragment of PDDL2.2.")
                                               "/lib/libgmsh.so")))
                   (substitute* "api/gmsh.py"
                     (("find_library\\(\"gmsh\"\\)")
-                     (simple-format #f "\"~a\"" libgmsh))))))))))
+                   (simple-format #f "\"~a\"" libgmsh)))))))))
     (inputs
      (list fltk
            fontconfig
@@ -8670,7 +8669,6 @@ arrays, uninterpreted functions and their combinations.")
                #$(version-major+minor (package-version python-wrapper))
                "/site-packages"))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (replace 'check
               (lambda* (#:key parallel-build? tests? #:allow-other-keys)
@@ -8690,7 +8688,7 @@ arrays, uninterpreted functions and their combinations.")
                                             "/z3/lib/libz3.so"))
                        (z3-lib (string-append #$output "/lib/libz3.so")))
                   (mkdir-p (dirname dest))
-                  (symlink z3-lib dest))))))))
+                (symlink z3-lib dest)))))))
     (native-inputs
      (list which python-wrapper))
     (synopsis "Theorem prover")
@@ -10815,7 +10813,6 @@ when an application performs repeated divisions by the same divisor.")
           (guix build cmake-build-system)
           (guix build utils))
         #:phases
-        (with-extensions (list (pyproject-guile-json))
           #~(modify-phases %standard-phases
               (add-after 'install 'move-python-files
                 (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -10829,7 +10826,7 @@ when an application performs repeated divisions by the same divisor.")
                                 (rename-file file
                                              (string-append target "/"
                                                             (basename file))))
-                              (find-files include "\\.py$")))))))))
+                            (find-files include "\\.py$"))))))))
       (native-inputs (list python-wrapper))
       (inputs (list psimd googletest-1.8 googlebenchmark))
       (synopsis "C++ library for half-precision floating point formats")

gnu/packages/music.scm

@@ -7812,7 +7812,6 @@ streaming audio server.")
                   ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-before 'check 'pre-check
               (lambda _
@@ -7837,7 +7836,7 @@ streaming audio server.")
                        `("GI_TYPELIB_PATH" ":" = (,gi-typelib-path))
                        `("GST_PLUGIN_SYSTEM_PATH" ":" suffix
                          (,gst-plugins-path))))
-                   '("exfalso" "operon" "quodlibet")))))))))
+                 '("exfalso" "operon" "quodlibet"))))))))
     (native-inputs (list xvfb-run gettext-minimal python-pytest
                          python-setuptools))
     (inputs

gnu/packages/photo.scm

@@ -549,7 +549,6 @@ scene to produce an image that looks much like a tone-mapped image.")
           #~'("-DBUILD_FOR_SSE=OFF" "-DBUILD_FOR_SSE2=OFF"))
       #:tests? #f ; There are no tests to run.
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'unpack 'fix-egg
             (lambda _
@@ -565,7 +564,7 @@ scene to produce an image that looks much like a tone-mapped image.")
                               (,(getenv "GUIX_PYTHONPATH")
                                ,(py:site-packages inputs outputs)))))
                         (list "bin/lensfun-update-data"
-                              "bin/lensfun-add-adapter"))))))))
+                              "bin/lensfun-add-adapter")))))))
     (native-inputs
      (list pkg-config))
     (inputs

gnu/packages/python-science.scm

@@ -628,12 +628,11 @@ written in C.")
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'build 'build-python-module
             (assoc-ref py:%standard-phases 'build))
           (add-after 'build-python-module 'install-python-module
-            (assoc-ref py:%standard-phases 'install))))
+            (assoc-ref py:%standard-phases 'install)))
       #:features '(list "python")
       #:install-source? #false))
     (inputs

gnu/packages/python-xyz.scm

@@ -6367,12 +6367,11 @@ help formatter.")
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'build 'build-python-module
             (assoc-ref py:%standard-phases 'build))
           (add-after 'build-python-module 'install-python-module
-            (assoc-ref py:%standard-phases 'install))))
+            (assoc-ref py:%standard-phases 'install)))
       #:install-source? #false))
     (inputs
      (cons maturin (cargo-inputs 'python-orjson)))
@@ -22516,7 +22515,6 @@ members = [
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'unpack 'prepare-source
             (lambda _
@@ -22541,7 +22539,7 @@ members = [
           ;;           #:test-flags '()
           ;;           args)))
           (replace 'install
-            (assoc-ref py:%standard-phases 'install))))))
+            (assoc-ref py:%standard-phases 'install)))))
     (native-inputs
      (list python-minimal-wrapper
            python-hypothesmith
@@ -36162,12 +36160,11 @@ line by line or column by column or a combination of both.")
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'build 'build-python-module
             (assoc-ref py:%standard-phases 'build))
           (add-after 'build-python-module 'install-python-module
-            (assoc-ref py:%standard-phases 'install))))
+            (assoc-ref py:%standard-phases 'install)))
       #:install-source? #false))
     (inputs
      (cons maturin (cargo-inputs 'python-rpds-py)))
@@ -37023,7 +37020,6 @@ functionality and customization to your projects with their own plugins.")
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'build 'build-python-module
             (assoc-ref py:%standard-phases 'build))
@@ -37032,10 +37028,9 @@ functionality and customization to your projects with their own plugins.")
           (add-after 'install-python-module 'add-install-to-pythonpath
             (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
           (add-after 'check 'check-python-module
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
+            (lambda args
                 (with-directory-excursion #$output
-                  (invoke "pytest" "-vv")))))))
+                (apply (assoc-ref py:%standard-phases 'check) args)))))
       #:install-source? #false))
     (native-inputs
      (list maturin
@@ -38148,7 +38143,6 @@ to TIFF, BigTIFF, and ImageJ hyperstack compatible files.")
         ((guix build pyproject-build-system) #:prefix py:)
         (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (replace 'build
             (assoc-ref py:%standard-phases 'build))
@@ -38162,7 +38156,7 @@ to TIFF, BigTIFF, and ImageJ hyperstack compatible files.")
               (assoc-ref py:%standard-phases 'create-entrypoints)
               (assoc-ref py:%standard-phases 'compile-bytecode)))
           (replace 'install
-            (assoc-ref py:%standard-phases 'install))))))
+            (assoc-ref py:%standard-phases 'install)))))
     (propagated-inputs (list python-regex python-requests))
     (inputs (cargo-inputs 'python-tiktoken))
     (native-inputs

gnu/packages/rpm.scm

@@ -160,7 +160,6 @@ information on multiple streams, default data and translations).")
                   ((guix build pyproject-build-system) #:prefix py:)
                   (guix build utils))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'fix-python-site-prefix
               (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -173,7 +172,7 @@ information on multiple streams, default data and translations).")
                 (substitute* "CMakeLists.txt"
                   (("execute_process.*OUTPUT_VARIABLE BASHCOMP_DIR.*")
                    (format #f "set (BASHCOMP_DIR ~a\
-/share/bash-completion/completions)~%" #$output)))))))))
+/share/bash-completion/completions)~%" #$output))))))))
     (native-inputs
      (list bash-completion pkg-config python))
     (inputs

gnu/packages/rust-apps.scm

@@ -1902,7 +1902,6 @@ specified image or color, easing the process of theme creation.")
          "--skip=metadata::test::test_merge_metadata_from_pyproject_toml_with_customized_python_source_dir"
          "--skip=pyproject_toml::tests::test_warn_missing_maturin_version")
       #:phases
-      (with-extensions (list (pyproject-guile-json))
       #~(modify-phases %standard-phases
           (add-after 'build 'build-python-module
             (lambda _
@@ -1949,7 +1948,7 @@ specified image or color, easing the process of theme creation.")
                 (mkdir-p (string-append share "/nushell/vendor/autoload"))
                 (with-output-to-file
                     (string-append share "/nushell/vendor/autoload/maturin")
-                  (lambda _ (invoke maturin "completions" "nushell"))))))))))
+                  (lambda _ (invoke maturin "completions" "nushell")))))))))
     (propagated-inputs
      (list python-tomli))
     (inputs (cons bzip2 (cargo-inputs 'maturin)))

gnu/packages/sugar.scm

@@ -79,7 +79,6 @@
       `(((guix build pyproject-build-system) #:prefix py:)
         ,@%glib-or-gtk-build-system-default-modules)
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'patch-build-system
               (lambda _
@@ -142,7 +141,7 @@
                                             ,(py:site-packages inputs outputs)))
                      `("GI_TYPELIB_PATH" prefix
                        (,(getenv "GI_TYPELIB_PATH")))))
-                 (find-files (string-append #$output "/bin") "^sugar.*"))))))))
+               (find-files (string-append #$output "/bin") "^sugar.*")))))))
     (inputs
      (list bash-minimal
            ethtool
@@ -257,7 +256,6 @@ activities and other Sugar components.")
       `(((guix build pyproject-build-system) #:prefix py:)
         ,@%glib-or-gtk-build-system-default-modules)
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (add-after 'unpack 'patch-build-system
               (lambda _
@@ -284,7 +282,7 @@ activities and other Sugar components.")
                  (list (search-input-file outputs "bin/copy-from-journal")
                        (search-input-file outputs "bin/copy-to-journal")
                        (search-input-file outputs
-                                          "bin/datastore-service")))))))))
+                                        "bin/datastore-service"))))))))
     (inputs
      (list bash-minimal
            coreutils

gnu/packages/version-control.scm

@@ -2719,7 +2719,6 @@ execution of any hook written in any language before every commit.")
                   (guix build utils))
       #:make-flags #~(list (string-append "PREFIX=" #$output))
       #:phases
-      (with-extensions (list (pyproject-guile-json))
         #~(modify-phases %standard-phases
             (delete 'configure)
             (add-after 'unpack 'patch-tests
@@ -2814,7 +2813,7 @@ execution of any hook written in any language before every commit.")
                 ((assoc-ref py:%standard-phases 'sanity-check)
                  #:inputs `(("sanity-check.py" . ,#$(default-sanity-check.py))
                             ,@inputs)
-                 #:outputs outputs)))))))
+               #:outputs outputs))))))
     (native-inputs
      (list python-docutils
            ;; The following inputs are only needed to run the tests.
@@ -2891,13 +2890,12 @@ history.  It implements the changeset evolution concept for Mercurial.")
                               #$(this-package-native-input "python"))
                              "/site-packages/hgext3rd/commitsigs.py")))
         #:phases
-        (with-extensions (list (pyproject-guile-json))
           #~(modify-phases %standard-phases
               (add-after 'unpack 'patch-paths
                 (lambda _
                   (substitute* "commitsigs.py"
                     (("b'(gpg|openssl)'," _ bin)
-                     (format #f "b'~a'," (which bin))))))))))
+                   (format #f "b'~a'," (which bin)))))))))
       (native-inputs
        (list python))
       (inputs

gnu/packages/vpn.scm

@@ -1028,7 +1028,6 @@ packages.")
                     ((guix build pyproject-build-system) #:prefix py:)
                     (guix build utils))
         #:phases
-        (with-extensions (list (pyproject-guile-json))
           #~(modify-phases %standard-phases
               (add-after 'unpack 'chdir
                 (lambda _
@@ -1088,7 +1087,7 @@ name = ~s~%"
                 (lambda args
                   (chdir "..")
                   (apply (assoc-ref py:%standard-phases 'check)
-                         (cons* #:test-flags (list) args))))))))
+                       (cons* #:test-flags (list) args)))))))
       (native-inputs
        (list python-flit-core
              python-pytest