From ec202001ef4915886e079c81868b5f62af5521c2 Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Thu, 16 May 2024 21:07:15 -0700 Subject: [PATCH] Add CITATION.cff (#219) * add CITATION.cff * update affliation and abstract * Update Ivan's orcid * black update * relax sphinx dependencies --------- Co-authored-by: Ivan Ivanov --- CITATION.cff | 61 +++++++++++++++++++++++++++++++++++++++++++++++ iohub/upti.py | 1 - iohub/zarrfile.py | 1 - setup.cfg | 14 +++++------ 4 files changed, 68 insertions(+), 9 deletions(-) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..7afeed65 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,61 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: iohub +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Ziwen + family-names: Liu + email: ziwen.liu@czbiohub.org + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0001-7482-1299' + - given-names: Ivan + family-names: Ivanov + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0001-6389-0213' + affiliation: Chan Zuckerberg Biohub San Francisco + - given-names: Jordão + family-names: Bragantini + orcid: 'https://orcid.org/0000-0001-7652-2735' + email: jordao.bragantini@czbiohub.org + affiliation: Chan Zuckerberg Biohub San Francisco + - given-names: Talon + family-names: Chandler + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0002-3033-674X' + - given-names: Ahmet Can + family-names: Solak + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0002-1381-8309' + - given-names: Eduardo + family-names: Hirata-Miyasaki + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0002-1016-2447' + - given-names: Cameron + family-names: Foltz + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0001-8933-2172' + - given-names: Li-Hao + family-names: Yeh + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0003-2803-5996' + - given-names: Shalin + family-names: Mehta + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: 'https://orcid.org/0000-0002-2542-3582' +repository-code: 'https://github.com/czbiohub-sf/iohub/' +url: 'https://czbiohub-sf.github.io/iohub/' +abstract: Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata +keywords: + - python + - image-metadata + - bioimaging + - ndimensional-arrays +license: BSD-3-Clause +commit: a4d43a2a8cd8d4abce00e475f9f1699d451eba9f +version: 0.1.0 +date-released: '2024-02-14' diff --git a/iohub/upti.py b/iohub/upti.py index 4eb29e8e..6cc3c212 100644 --- a/iohub/upti.py +++ b/iohub/upti.py @@ -10,7 +10,6 @@ class UPTIReader(ReaderBase): - """ Reader for UPTI raw data. Accepts both new live UPTI and older UPTI format. diff --git a/iohub/zarrfile.py b/iohub/zarrfile.py index 3ca03818..0689e99f 100644 --- a/iohub/zarrfile.py +++ b/iohub/zarrfile.py @@ -13,7 +13,6 @@ class ZarrReader(ReaderBase): - """ .. deprecated:: 0.0.1 `ZarrReader` will be removed in future iohub releases, diff --git a/setup.cfg b/setup.cfg index 9f31d092..b73eb098 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,10 +54,10 @@ dev = ome-zarr>=0.6.1 doc = matplotlib - numpydoc==1.1.0 - sphinx==4.2.0 - pydata-sphinx-theme==0.13.3 - sphinx-copybutton==0.4.0 - sphinx-multiversion==0.2.4 - sphinx-sitemap==2.5.0 - sphinx-gallery==0.13.0 + numpydoc>=1.1.0 + sphinx>=4.2.0 + pydata-sphinx-theme>=0.15.2 + sphinx-copybutton>=0.4.0 + sphinx-multiversion>=0.2.4 + sphinx-sitemap>=2.5.0 + sphinx-gallery>=0.13.0