gnu: crossmap: Update to 0.7.3.

* gnu/packages/bioinformatics.scm (crossmap): Update to 0.7.3.
[source] <snippet>: Adjust it for a new location of egg info directory.

Change-Id: Ic826c4c42c2386dc9d1b301667be1dbb5d2db3eb
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pynbody: Use python-ipython-minimal for tests.

* gnu/packages/astronomy.scm (python-pynbody)[native-inputs]: Remove
python-ipython; add python-ipython-minimal.

Change-Id: I2a87ff21b94cff7b3b3b2eb5c150b362fadede60
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pycollada: Update to 0.9.2.

* gnu/packages/python-xyz.scm (python-pycollada): Update to 0.9.2.
[native-inputs]: Remove python-wheel.

Change-Id: I3cc70c7eeda9e4c54a0457ba430e4c6cbe1697f3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-notebook: Fix build.

* gnu/packages/jupyter.scm (python-notebook)[arguments] <test-flags>:
Skip one test.
[propagated-inputs]: Swap python-jupyter-client@8 with
python-jupyter-client@7.

Change-Id: I37b420120395924c524f1936723e2a2c6228761d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-jupyter-client-7.

* gnu/packages/jupyter.scm (python-jupyter-client-7): New variable.

Change-Id: I6164464161b0725d97c8eaf6ac1b46b03b1f13e3
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-console: Move to jupyter.

* gnu/packages/python-xyz.scm (python-jupyter-console): Move from here ...
* gnu/packages/jupyter.scm: ... to here.

Change-Id: I687d44df58fab4d62a3eac92f2dab1eebdc89921
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-console: Update to 6.6.3.

* gnu/packages/python-xyz.scm (python-jupyter-console): Update to 6.6.3.
[arguments] <test-flags>: Skip one test.
<phases>: Add 'pre-check.
[propagated-inputs]: Add python-ipython, python-jupyter-core,
python-pyzmq, and python-traitlets.
[native-inputs]: Remove python-setuptools; add python-flaky and
python-hatchling.

Change-Id: Ia7d12b313cfcc890a5173813b92d97872ece742b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ipykernel: Update to 7.1.0.

* gnu/packages/jupyter.scm (python-ipykernel): Update to 7.1.0.
Remove artifacts.
[arguments] <modules>: Drop them as not required.
<test-flags>: Skip just one shaky test.
<phases>: Remove 'relax-a-bit, and 'hide-deprecation-warnings; add
'fix-pytest-config.

Change-Id: I49512675b1d2f4ab1e74ec02aab92ae6673016b2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-client: Update to 8.7.0.

* gnu/packages/jupyter.scm (python-jupyter-client): Update to 8.7.0.
[inputs]: Add net-tools and openssh.
[propagated-inputs]: Remove python-entrypoints and python-nest-asyncio.
[native-inputs]: Remove python-pytest-asyncio, python-async-generator, and
python-ipython; add python-anyio and python-pytest-jupyter-minimal.

Change-Id: I0c058aa67c6fcb71c5fcfaca34c72a15d132b0ee
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-pytest-jupyter-minimal.

* gnu/packages/jupyter.scm (python-pytest-jupyter-minimal): New variable.

Change-Id: I0192ea6c58702664651fe838c5f38a82a5fad6d2
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Remove python-jupyter-console-minimal.

Variable is not public and not in use by any other packages.

* gnu/packages/python-xyz.scm (python-jupyter-console-minimal): Delete variable.

Fixes: guix/guix#4881
Change-Id: I3b13ec6522f8c7c61a39e8f2262b652fbcb4210b
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-client: Move to jupyter.

* gnu/packages/python-xyz.scm (python-jupyter-client,
python-jupyter-client-bootstrap): Move from here ...
* gnu/packages/jupyter.scm: ... to here.

Change-Id: I036632e68c808877de14da7f91863be50cdafd61
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-client: Simplfy bootstrapping.

* gnu/packages/python-xyz.scm (python-jupyter-client): Take over
definition of python-jupyter-client-bootsrap with adjustments.
[arguments] <phases>: Remove 'hide-zmq-deprecation-warnings, and
'set-tool-file-name, it uses Python's "subprocess.Popen" now; add
'fix-pytest-config, and 'pre-check'; use default 'check.
(python-jupyter-client-bootsrap): Inherit from python-jupyter-client

Change-Id: I2cf3aceb4d33995853cd36e79034a5867e51444e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-core: Update to 5.9.1.

* gnu/packages/jupyter.scm (python-jupyter-core): Update to 5.9.1.
[arguments] <tests-flags>: Rework skipped tests.
[phases]{disable-migration}: Rewrite "touch" with Guile.
[native-inputs]: Remove python-pytest-timeout.

Change-Id: I1b272eafeac129af05fd1c92f4ec72bb73be17f9
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-jupyter-core: Move to jupyter.

* gnu/packages/python-xyz.scm (python-jupyter-core): Move from here ...
* gnu/packages/jupyter.scm: ... to here.

Change-Id: Id577b47b0a6c9a8754e6dc4f07e5ac8ba4ea106d
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: Add python-ipython-minimal.

* gnu/packages/python-xyz.scm (python-ipython-minimal): New variable.

Change-Id: Ib68f3a7f2d45064aa83c7d034011ce4b43391ab6
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-ipython: Update to 9.8.0.

* gnu/packages/python-xyz.scm (python-ipython): Update to 9.8.0.
[arguments] <test-backend, test-flags>: Move custom {check} options
here.
<phases>: Remove 'make-docs-reproducible, resolved upstream; add
'pre-check and use default 'check.
[inputs]: Remove readline and which.
[propagated-inputs]: Remove python-colorama and python-exceptiongroup;
add python-ipython-pygments-lexers.
[native-inputs]: Remove python-pickleshare, python-pytest-asyncio-0.21,
and python-wheel; add python-pytest-asyncio and python-trio.

Change-Id: I3f96109e70772cb07b6a24bb83058473f182e3ed
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-contourpy: Update to 1.3.3.

* gnu/packages/python-xyz.scm (python-contourpy): Update to 1.3.3.

Change-Id: Id764c632d375f6e68782adf5385f227eefaebefd
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pythran: Clean up artifacts.

* gnu/packages/python-science.scm (python-pythran): Adjust style and
remove unused parts.
[source] <url>: Use a direct URL string.
[arguments] <test-flags, phase:pre-check>: Drop them as not used.
[native-inputs]: Remove openblas, python-pytest, python-pytest-xdist,
and python-wheel.
[home-page]: Move above [synopsis].

Change-Id: I7708981548ce68351c00fbf4e8f8e806a18f798a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-pytest-doctestplus: Update to 1.6.0.

* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to 1.6.0.
[phases] {patch-git-path}: Switch to search-input-file.
[propagated-inputs]: Remove python-setuptools; add python-packaging.
[native-inputs]: Remove python-pytest and python-wheel; add
python-pytest-bootstrap and python-setuptools.

Change-Id: Ie3fae7a1a639bf2b3a77dde3cdfd4696a929696e
Signed-off-by: Rutherther <rutherther@ditigal.xyz>