PR#1: Update to 0.2.8 (close RHBZ#2067101) - rpms/python-probeinterface

rpms / python-probeinterface

#1 Update to 0.2.8 (close RHBZ#2067101)

Merged 2 years ago by music. Opened 2 years ago by music.

rpms/ music/python-probeinterface v0.2.8 into rawhide

Update to 0.2.8 (close RHBZ#2067101)

Benjamin A. Beasley • 2 years ago

61e5e45

.gitignore

file modified

		`@@ -1,2 +1,3 @@`
		`/probeinterface-0.2.6.tar.gz`
		`/probeinterface-0.2.7.tar.gz`
		`+ /probeinterface-0.2.8.tar.gz`

97.patch

file added

+62

		`@@ -0,0 +1,62 @@`
		`+ From 8728c2e2ff673bd7c1715ee2f052949d63defdd6 Mon Sep 17 00:00:00 2001`
		`+ From: "Benjamin A. Beasley" <code@musicinmybrain.net>`
		`+ Date: Wed, 23 Mar 2022 07:23:42 -0400`
		`+ Subject: [PATCH] =?UTF-8?q?Adjust=20examples=20to=20use=20to=5F3d(axes=3D?=`
		`+ =?UTF-8?q?=E2=80=A6)?=`
		`+ MIME-Version: 1.0`
		`+ Content-Type: text/plain; charset=UTF-8`
		`+ Content-Transfer-Encoding: 8bit`
		`+`
		`+ API changed in d2cd928. Fixes:`
		`+`
		`+ TypeError: to_3d() got an unexpected keyword argument 'plane'`
		`+`
		`+ when running the examples.`
		`+ ---`
		`+ examples/ex_01_generate_probe_from_sratch.py \| 4 ++--`
		`+ examples/ex_02_probe_2d_probe_3d.py \| 6 +++---`
		`+ 2 files changed, 5 insertions(+), 5 deletions(-)`
		`+`
		`+ diff --git a/examples/ex_01_generate_probe_from_sratch.py b/examples/ex_01_generate_probe_from_sratch.py`
		`+ index e26947f..e979285 100644`
		`+ --- a/examples/ex_01_generate_probe_from_sratch.py`
		`+ +++ b/examples/ex_01_generate_probe_from_sratch.py`
		`+ @@ -60,10 +60,10 @@`
		`+ plot_probe(probe)`
		`+`
		`+ ##############################################################################`
		+ -# A 2d `Probe` can be transformed to a 3d `Probe` by indicating the `plane`
		+ +# A 2d `Probe` can be transformed to a 3d `Probe` by indicating the `axes`
		`+ # on which contacts will lie (Here the 'y' coordinate will be 0 for all contacts):`
		`+`
		`+ -probe_3d = probe.to_3d(plane='xz')`
		`+ +probe_3d = probe.to_3d(axes='xz')`
		`+ plot_probe(probe_3d)`
		`+`
		`+ plt.show()`
		`+ diff --git a/examples/ex_02_probe_2d_probe_3d.py b/examples/ex_02_probe_2d_probe_3d.py`
		`+ index 2755872..a3efd55 100644`
		`+ --- a/examples/ex_02_probe_2d_probe_3d.py`
		`+ +++ b/examples/ex_02_probe_2d_probe_3d.py`
		`+ @@ -33,10 +33,10 @@`
		`+ ##############################################################################`
		`+ # Let's transform it into a 3d probe.`
		`+ #`
		`+ -# Here the plane is 'xz' so y will be 0 for all contacts.`
		`+ +# Here the axes are 'xz' so y will be 0 for all contacts.`
		`+ # The shape of probe_3d.contact_positions is now (n_elec, 3)`
		`+`
		`+ -probe_3d = probe_2d.to_3d(plane='xz')`
		`+ +probe_3d = probe_2d.to_3d(axes='xz')`
		`+ print(probe_2d.contact_positions.shape)`
		`+ print(probe_3d.contact_positions.shape)`
		`+`
		`+ @@ -55,7 +55,7 @@`
		`+ # We can create another probe lying on another plane:`
		`+`
		`+`
		`+ -other_3d = probe_2d.to_3d(plane='yz')`
		`+ +other_3d = probe_2d.to_3d(axes='yz')`
		`+ plot_probe(other_3d)`
		`+`
		`+ ##############################################################################`

python-probeinterface.spec

file modified

+5 -2

		`@@ -5,7 +5,7 @@`
		`%bcond_without doc_pdf`

		`Name: python-probeinterface`
		`- Version: 0.2.7`
		`+ Version: 0.2.8`
		`Release: %autorelease`
		`Summary: Handles probe layout, geometry, and wiring to device`

		`@@ -24,6 +24,9 @@`
		`Source1: %{probe_url}/neuronexus/A1x32-Poly3-10mm-50-177/A1x32-Poly3-10mm-50-177.json`
		`Source2: %{probe_url}/cambridgeneurotech/ASSY-156-P-1/ASSY-156-P-1.json`

		`+ # Adjust examples to use to_3d(axes=…)`
		`+ Patch0: %{url}/pull/97.patch`
		`+`
		`BuildArch: noarch`

		`BuildRequires: python3-devel`
		`@@ -87,7 +90,7 @@`


		`%prep`
		`- %autosetup -n probeinterface-%{version}`
		`+ %autosetup -n probeinterface-%{version} -p1`

		`# Do not require exact dependency versions to build documentation:`
		`sed -r -i 's/==/>=/' requirements_rtd.txt`

sources

file modified

+1 -1

		`@@ -1,1 +1,1 @@`
		`- SHA512 (probeinterface-0.2.7.tar.gz) = 531066bf1999c56f09551e47820d74d657ca614e144e502e6539ff2bbe00a01dc28455b9ad657d783bcb608846037adfd404897857324501f77c49abfccc0d14`
		`+ SHA512 (probeinterface-0.2.8.tar.gz) = 7eac5d987222571971c2f7af3fc758520c984612b8bd58b197f19deddb506c8c8b664f472687cc7b8621cc33e86b89793ed4db2960aa74931138cacd8930190e`

music commented 2 years ago

This breaks the API by renaming:

probeinterface.probe.select_dimensions to probeinterface.probe.select_axes
the plane keyword argument of probeinterface.probe.to_3d to axes
the dimensions keyword argument of probeinterface.probe.to_3d to axes

The only dependent package, python-neo, does not use the affected parts of the API.

music commented 2 years ago

Upstream release notes:

probeinterface 0.2.8
--------------------


March, 23rd 2022

* wiring CambridgeNeurotec mini-amp-64
* expose function select_dimensions (2d>3d and 3d>2d)
* add to_dict/from_dict in ProbeGroup
* Add "text_on_contact" in plot_probe()
* Add read_openephys function for Neuropux-PXI plugin

music commented 2 years ago

Announced to the devel list. Merge and build no earlier than 2022-03-30.

ankursinha commented 2 years ago

+1 (but weird of upstream to break API without even noting it in the changelog)

music commented 2 years ago

If they hadn’t forgotten to update the examples to match, or if I hadn’t been running the examples as extra tests, I might have missed it. I always review source diffs, but sometimes less carefully when upstream seems to keep careful changelogs.

Pull-Request has been merged by music

2 years ago