From 76977be14ae7fbd718d4151ecd2907d4e11b83b1 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Mon, 20 Jul 2026 15:58:55 +0930 Subject: [PATCH] Add protocols paper citation and bump version to 1.3.1 phold citation now also prints the Pharokka/Phold/Phynteny protocols paper alongside the existing Phold citation. Also syncs the VERSION file, which had drifted out of sync with pyproject.toml. --- HISTORY.md | 4 ++++ pyproject.toml | 2 +- src/phold/utils/CITATION | 4 ++++ src/phold/utils/VERSION | 2 +- 4 files changed, 10 insertions(+), 2 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index e691c83..f9cfb63 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,5 +1,9 @@ # History +1.3.1 (2026-07-20) +------------------ +* `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) ------------------ * 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 diff --git a/pyproject.toml b/pyproject.toml index c5f89a8..954759f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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" diff --git a/src/phold/utils/CITATION b/src/phold/utils/CITATION index aec1520..2ab2be3 100644 --- a/src/phold/utils/CITATION +++ b/src/phold/utils/CITATION @@ -1,2 +1,6 @@ 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 + diff --git a/src/phold/utils/VERSION b/src/phold/utils/VERSION index 7e099ec..6261a05 100644 --- a/src/phold/utils/VERSION +++ b/src/phold/utils/VERSION @@ -1 +1 @@ -1.2.6 \ No newline at end of file +1.3.1 \ No newline at end of file