Fixes after a recent guix pull

6 files changed, 21 insertions, 51 deletions

diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index a55cd65..dd76d28 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -159,7 +159,8 @@ functions} for a collection of hashable objects.")
          "1nf6ld3bims1n5vfzhkvcb55pdzh04bbhzf8nil5vvw05nxzarsh"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:cargo-inputs
+     `(#:tests? #f ; doctest fails with newer Rust (dangerous_implicit_autorefs)
+       #:cargo-inputs
        (("rust-atty" ,rust-atty-0.2)
         ("rust-bitflags" ,rust-bitflags-1)
         ("rust-clap-derive" ,rust-clap-derive-3)
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 096ac8e..0d79a0c 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -9,7 +9,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages julia-jll)
-  #:use-module (gnu packages julia-xyz))
+  #:use-module (gnu packages julia-xyz)
+  #:use-module (gnu packages version-control))
 
 (define S specification->package)
 
diff --git a/gn/packages/machine-learning.scm b/gn/packages/machine-learning.scm
index 4d67e9c..3799e9b 100644
--- a/gn/packages/machine-learning.scm
+++ b/gn/packages/machine-learning.scm
@@ -156,7 +156,6 @@ with image data, text data, and sequence data.")
            python-pytest-cov
            python-pytest-timeout
            python-pytest-xdist
-           python-pyux
            python-sphinx
            python-requests))
     (home-page "https://keras.io/")
diff --git a/gn/packages/python-xyz.scm b/gn/packages/python-xyz.scm
index 1e85111..2451d46 100644
--- a/gn/packages/python-xyz.scm
+++ b/gn/packages/python-xyz.scm
@@ -103,11 +103,10 @@ Annotated.")
        (sha256
         (base32 "0cpfd8fdznwlxrjpwy10pl4bj9q393ys1vj90nvsrhwakqcdiil3"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest
-                         python-requests
-                         python-responses
-                         python-poetry-core
-                         python-pytest-asyncio-0.21))
+    (arguments
+     (list
+      #:tests? #f)) ; needs python-pytest-asyncio >= 0.21
+    (native-inputs (list python-poetry-core))
     (home-page "https://github.com/litl/backoff")
     (synopsis "Function decoration for backoff and retry")
     (description "Function decoration for backoff and retry.")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8bb738d..32b2e8a 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -610,46 +610,5 @@ a general image processing tool.")
      renderers (e.g. man pages or LaTeX).")
     (license license:expat)))
 
-(define-public python-jupyter-server
-  (package
-    (name "python-jupyter-server")
-    (version "1.8.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "jupyter-server" version))
-        (sha256
-         (base32
-          "0dqj51fj5ikklbl0gnb939pp80ngnzml5932mljn2lvplph7a34g"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-anyio" ,python-anyio)
-       ("python-argon2-cffi" ,python-argon2-cffi)
-       ("python-ipython-genutils" ,python-ipython-genutils)
-       ("python-jinja2" ,python-jinja2)
-       ("python-jupyter-client" ,python-jupyter-client)
-       ("python-jupyter-core" ,python-jupyter-core)
-       ("python-nbconvert" ,python-nbconvert)
-       ("python-nbformat" ,python-nbformat)
-       ("python-prometheus-client" ,python-prometheus-client)
-       ("python-pyzmq" ,python-pyzmq)
-       ("python-send2trash" ,python-send2trash)
-       ("python-terminado" ,python-terminado)
-       ("python-tornado" ,python-tornado)
-       ("python-traitlets" ,python-traitlets)
-       ("python-websocket-client" ,python-websocket-client)))
-    (native-inputs
-     `(("python-coverage" ,python-coverage)
-       ("python-ipykernel" ,python-ipykernel)
-       ("python-pytest" ,python-pytest)
-       ; ("python-pytest-console-scripts" ,python-pytest-console-scripts) - gone missing
-       ("python-pytest-cov" ,python-pytest-cov)
-       ("python-pytest-mock" ,python-pytest-mock)
-       ; ("python-pytest-tornasync" ,python-pytest-tornasync) - gone missing
-       ("python-requests" ,python-requests)))
-    (home-page "https://jupyter.org")
-    (synopsis
-      "The backend--i.e. core services, APIs, and REST endpoints--to Jupyter web applications.")
-    (description
-      "The backend--i.e. core services, APIs, and REST endpoints--to Jupyter web applications.")
-    (license #f)))
+;; python-jupyter-server removed: version 1.8.0 source gone from PyPI.
+;; Use (gnu packages python-science) python-jupyter-server instead.
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm
index d44e977..c391b2d 100644
--- a/gn/packages/statistics.scm
+++ b/gn/packages/statistics.scm
@@ -123,6 +123,17 @@ interaction networks.")
        (sha256
         (base32 "0yn4nq26na9hzlm08vsxr050ls5nmngpyma49fpfwc9mhxc7njlk"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; test_rmagic.py fails with pytest 9: marks on fixtures
+                ;; are no longer allowed.
+                (invoke "pytest" "-vv"
+                        "--ignore=src/rpy2/ipython/tests/test_rmagic.py")))))))
     (propagated-inputs (list python-jinja2
                              python-packaging
                              python-rpy2-rinterface