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Add protocols paper citation and bump version to 1.3.1 #136

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4 changes: 4 additions & 0 deletions HISTORY.md
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# History

1.3.1 (2026-07-20)
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* `phold citation` now also prints our [protocols paper](https://doi.org/10.1002/cpz1.70405) citation alongside the existing Phold citation

1.3.0 (2026-07-02)
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* Adds multi-GPU support - use `--gpus` (e.g. `--gpus 0,2`) to specify which CUDA device indices `phold` and Foldseek-GPU should use. Defaults to all visible CUDA GPUs. Has no effect on MPS/XPU systems
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -5,7 +5,7 @@ requires = ["setuptools>=61.0", "wheel>=0.37.1"]
[project]
# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
name = "phold"
version = "1.3.0" # change VERSION too
version = "1.3.1" # change VERSION too
description = "Phage Annotations using Protein Structures"
readme = "README.md"
requires-python = ">=3.8, <4"
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4 changes: 4 additions & 0 deletions src/phold/utils/CITATION
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Bouras G, Grigson SR, Mirdita M, Heinzinger M, Papudeshi B, Mallawaarachchi V, Green R, Kim SR, Mihalia V, Psaltis AJ, Wormald P-J, Vreugde S, Steinegger M, Edwards RA: "Protein Structure Informed Bacteriophage Genome Annotation with Phold", Nucleic Acids Research, Volume 54, Issue 1, 13 January 2026, gkaf1448, https://doi.org/10.1093/nar/gkaf1448

Please also consider citing our protocols paper:

Bouras G, Grigson SR, Durr L, Papudeshi B, Mallawaarachchi V, Vreugde S, Edwards RA: "Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny", Current Protocols, Volume 6, Number 7, 6 July 2026, https://doi.org/10.1002/cpz1.70405

2 changes: 1 addition & 1 deletion src/phold/utils/VERSION
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1.2.6
1.3.1
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