From 2c990974c2ba82157a99e2fc8408a0a50231d2fb Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Mon, 13 May 2024 14:07:47 -0700 Subject: [PATCH 1/5] add CITATION.cff --- CITATION.cff | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..b75a4624 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,63 @@ +# 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: CZ Biohub + orcid: 'https://orcid.org/0000-0002-4675-5287' + 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: CZ Biohub + orcid: 'https://orcid.org/0000-0001-8933-2172' + - given-names: Li-Hao + family-names: Yeh + affiliation: CZ Biohub + 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: >- + N-dimensional bioimaging data I/O with OME metadata in + Python +keywords: + - python + - image-metadata + - bioimaging + - ndimensional-arrays +license: BSD-3-Clause +commit: a4d43a2a8cd8d4abce00e475f9f1699d451eba9f +version: 0.1.0 +date-released: '2024-02-14' From fce737002001b4875140e48163bbcb5eb073e00f Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Tue, 14 May 2024 06:44:45 +0800 Subject: [PATCH 2/5] update affliation and abstract --- CITATION.cff | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index b75a4624..2b1911c0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -37,11 +37,11 @@ authors: orcid: 'https://orcid.org/0000-0002-1016-2447' - given-names: Cameron family-names: Foltz - affiliation: CZ Biohub + affiliation: Chan Zuckerberg Biohub San Francisco orcid: 'https://orcid.org/0000-0001-8933-2172' - given-names: Li-Hao family-names: Yeh - affiliation: CZ Biohub + affiliation: Chan Zuckerberg Biohub San Francisco orcid: 'https://orcid.org/0000-0003-2803-5996' - given-names: Shalin family-names: Mehta @@ -49,9 +49,7 @@ authors: orcid: 'https://orcid.org/0000-0002-2542-3582' repository-code: 'https://github.com/czbiohub-sf/iohub/' url: 'https://czbiohub-sf.github.io/iohub/' -abstract: >- - N-dimensional bioimaging data I/O with OME metadata in - Python +abstract: Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata keywords: - python - image-metadata From 9da28ee3c90ee23ed68f5b39e55eb3d28c11762a Mon Sep 17 00:00:00 2001 From: Ivan Ivanov Date: Tue, 14 May 2024 09:34:03 -0700 Subject: [PATCH 3/5] Update Ivan's orcid --- CITATION.cff | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 2b1911c0..7afeed65 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -15,8 +15,8 @@ authors: orcid: 'https://orcid.org/0000-0001-7482-1299' - given-names: Ivan family-names: Ivanov - affiliation: CZ Biohub - orcid: 'https://orcid.org/0000-0002-4675-5287' + 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 From f4994a9469c954b9dfe01a531661cd5051cb4a65 Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Wed, 15 May 2024 04:13:32 +0800 Subject: [PATCH 4/5] black update --- iohub/upti.py | 1 - iohub/zarrfile.py | 1 - 2 files changed, 2 deletions(-) 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, From 44066af856923536c87b3a8aba22e93fc2f09c41 Mon Sep 17 00:00:00 2001 From: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Date: Fri, 17 May 2024 12:04:09 +0800 Subject: [PATCH 5/5] relax sphinx dependencies --- setup.cfg | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) 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