From 5f3efc06e083e8d4b7ecb5ed1d94bb91c5475997 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 11 Sep 2026 20:58:46 +0000 Subject: [PATCH 01/10] Add CITATION.cff for published ScreenPro2 publication Co-authored-by: abearab <53412130+abearab@users.noreply.github.com> --- CITATION.cff | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..bbe36ea --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,28 @@ +cff-version: 1.2.0 +title: ScreenPro2 +message: >- + If you use this software, please cite the associated publication below. +authors: + - family-names: O'Loughlin + given-names: Timothy A. + - family-names: Arab + given-names: Abolfazl + - family-names: Misiukiewicz + given-names: Sebastian + - family-names: Gilbert + given-names: Luke A. +preferred-citation: + type: article + title: Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response + authors: + - family-names: O'Loughlin + given-names: T.A. + - family-names: Arab + given-names: A. + - family-names: Misiukiewicz + given-names: S. + - family-names: Gilbert + given-names: L.A. + journal: Nature Chemical Biology + year: 2026 + doi: 10.1038/s41589-026-02312-z From fb1a893b68a081400e188dcf48fa1a5a8caa5d2a Mon Sep 17 00:00:00 2001 From: Abolfazl Arab Date: Fri, 11 Sep 2026 14:03:04 -0700 Subject: [PATCH 02/10] clear citation authors Removed Misiukiewicz from authors list in CITATION.cff. --- CITATION.cff | 4 ---- 1 file changed, 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index bbe36ea..313da7e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,8 +7,6 @@ authors: given-names: Timothy A. - family-names: Arab given-names: Abolfazl - - family-names: Misiukiewicz - given-names: Sebastian - family-names: Gilbert given-names: Luke A. preferred-citation: @@ -19,8 +17,6 @@ preferred-citation: given-names: T.A. - family-names: Arab given-names: A. - - family-names: Misiukiewicz - given-names: S. - family-names: Gilbert given-names: L.A. journal: Nature Chemical Biology From 2713661718086a198446bff33bae59cf1a5307a7 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 11 Sep 2026 21:04:28 +0000 Subject: [PATCH 03/10] Update README citation notes with published paper Co-authored-by: abearab <53412130+abearab@users.noreply.github.com> --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ce6ed78..2d42f5c 100644 --- a/README.md +++ b/README.md @@ -339,7 +339,9 @@ by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research As ## Citation If you use ScreenPro2 in your research, please cite the following paper. - Coming soon... +O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. _Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response_. _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z + +Citation metadata is also available in [`CITATION.cff`](CITATION.cff). ## Development ### Testing From 7feb5c7975add4130ab0b9fdbf6252fe2c2e29a8 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 11 Sep 2026 21:09:55 +0000 Subject: [PATCH 04/10] Add NCB DOI badge and dual citation notes in README Co-authored-by: abearab <53412130+abearab@users.noreply.github.com> --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 2d42f5c..6b3bafa 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934) +[![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z) [![PyPI version](https://badge.fury.io/py/ScreenPro2.svg)](https://badge.fury.io/py/ScreenPro2) [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest) [![Downloads](https://static.pepy.tech/badge/screenpro2)](https://pepy.tech/project/screenpro2) @@ -337,9 +338,11 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research Associate in the Gilbert lab at UCSF and Arc Institute. ## Citation -If you use ScreenPro2 in your research, please cite the following paper. +If you use ScreenPro2 in your research, please cite both the software release (Zenodo) and the published paper (Nat Chem Biol). -O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. _Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response_. _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z +- **Software (Zenodo)**: ScreenPro2. https://doi.org/10.5281/zenodo.18807934 + +- **Paper (Nat Chem Biol)**: O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. _Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response_. _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z Citation metadata is also available in [`CITATION.cff`](CITATION.cff). From 488dc8d3554adfde0ecc89f3de488324c3cf9b9d Mon Sep 17 00:00:00 2001 From: Abolfazl Arab Date: Fri, 11 Sep 2026 14:54:20 -0700 Subject: [PATCH 05/10] Improve citation formatting for Nat Chem Biol paper Updated paper citation formatting in README.md. --- README.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/README.md b/README.md index 6b3bafa..7f81244 100644 --- a/README.md +++ b/README.md @@ -342,10 +342,6 @@ If you use ScreenPro2 in your research, please cite both the software release (Z - **Software (Zenodo)**: ScreenPro2. https://doi.org/10.5281/zenodo.18807934 -- **Paper (Nat Chem Biol)**: O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. _Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response_. _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z +- **Paper (Nat Chem Biol)**: O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z Citation metadata is also available in [`CITATION.cff`](CITATION.cff). - -## Development -### Testing -Tests can be easily run using the `pytest` framework. From 425626d4b82ac19a55c4f68df67e950c2a3b774d Mon Sep 17 00:00:00 2001 From: Abolfazl Arab Date: Fri, 11 Sep 2026 14:59:05 -0700 Subject: [PATCH 06/10] Revise DOI badges and citation details in README Updated citation format and DOI badge links in README. --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 7f81244..40ea016 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934) -[![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z) +[![zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934) +[![NCB](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z) [![PyPI version](https://badge.fury.io/py/ScreenPro2.svg)](https://badge.fury.io/py/ScreenPro2) [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest) [![Downloads](https://static.pepy.tech/badge/screenpro2)](https://pepy.tech/project/screenpro2) @@ -340,8 +340,8 @@ by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research As ## Citation If you use ScreenPro2 in your research, please cite both the software release (Zenodo) and the published paper (Nat Chem Biol). -- **Software (Zenodo)**: ScreenPro2. https://doi.org/10.5281/zenodo.18807934 +- **Software (Zenodo)**: +> Arab, A., Gilbert, L.A. et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467 -- **Paper (Nat Chem Biol)**: O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z - -Citation metadata is also available in [`CITATION.cff`](CITATION.cff). +- **Paper (Nature Chemical Biology)**: +> O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z From 08ad24906401e0f712b6beb75ded5437403349dc Mon Sep 17 00:00:00 2001 From: Abolfazl Arab Date: Fri, 11 Sep 2026 14:59:47 -0700 Subject: [PATCH 07/10] Update citation format in README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 40ea016..492a626 100644 --- a/README.md +++ b/README.md @@ -341,7 +341,7 @@ by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research As If you use ScreenPro2 in your research, please cite both the software release (Zenodo) and the published paper (Nat Chem Biol). - **Software (Zenodo)**: -> Arab, A., Gilbert, L.A. et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467 +> Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467 - **Paper (Nature Chemical Biology)**: -> O’Loughlin, T.A., Arab, A., Gilbert, L.A. et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z +> O’Loughlin, T.A., Arab, A., et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z From e69f1b4f94676023d574db26571c076a0529f378 Mon Sep 17 00:00:00 2001 From: Abolfazl Arab Date: Fri, 11 Sep 2026 15:00:40 -0700 Subject: [PATCH 08/10] Update citation instructions in README.md Removed the mention of 'Zenodo' from the citation instructions. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 492a626..3ca4642 100644 --- a/README.md +++ b/README.md @@ -338,7 +338,7 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research Associate in the Gilbert lab at UCSF and Arc Institute. ## Citation -If you use ScreenPro2 in your research, please cite both the software release (Zenodo) and the published paper (Nat Chem Biol). +If you use ScreenPro2 in your research, please cite both the software release and the published paper. - **Software (Zenodo)**: > Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467 From 33137730842c433627e7c40630c7f2b2e8dd6c98 Mon Sep 17 00:00:00 2001 From: Abolfazl Arab Date: Fri, 11 Sep 2026 15:44:29 -0700 Subject: [PATCH 09/10] Update README.md From 44b043fca8a0873b65133dee4121e08715f57f7b Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 11 Sep 2026 22:46:57 +0000 Subject: [PATCH 10/10] Bump version to 0.7.0 and add final publication note Co-authored-by: abearab <53412130+abearab@users.noreply.github.com> --- README.md | 2 ++ pyproject.toml | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3ca4642..fe033b8 100644 --- a/README.md +++ b/README.md @@ -340,6 +340,8 @@ by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research As ## Citation If you use ScreenPro2 in your research, please cite both the software release and the published paper. +**Final publication note**: The final ScreenPro2 publication is now available in _Nature Chemical Biology_ (2026): https://doi.org/10.1038/s41589-026-02312-z + - **Software (Zenodo)**: > Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467 diff --git a/pyproject.toml b/pyproject.toml index 3e1949d..9c47f2b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "ScreenPro2" description = "Flexible analysis of high-content CRISPR screening" -version = "0.6.1" +version = "0.7.0" authors = [ "Abolfazl Arab ", "Nick Youngblut ",