Date: Sun, 26 May 2024 17:51:35 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: c5e70c355be2 - main - biology/py-pyrodigal: update 3.4.0 =?utf-8?Q?=E2=86=92?= 3.4.1 Message-ID: <202405261751.44QHpZMI002959@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=c5e70c355be25f2c803fdebbc8150e68b67e70a9 commit c5e70c355be25f2c803fdebbc8150e68b67e70a9 Author: Älven <alster@vinterdalen.se> AuthorDate: 2024-05-26 17:50:11 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2024-05-26 17:51:27 +0000 biology/py-pyrodigal: update 3.4.0 → 3.4.1 PR: 279310 --- biology/py-pyrodigal/Makefile | 4 ++-- biology/py-pyrodigal/distinfo | 6 +++--- biology/py-pyrodigal/pkg-descr | 26 +++++++++++++------------- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/biology/py-pyrodigal/Makefile b/biology/py-pyrodigal/Makefile index 67eb9672b9b0..7d135a8b0e3a 100644 --- a/biology/py-pyrodigal/Makefile +++ b/biology/py-pyrodigal/Makefile @@ -1,12 +1,12 @@ PORTNAME= pyrodigal -DISTVERSION= 3.4.0 +DISTVERSION= 3.4.1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python binding for Prodigal, an ORF finder for genomes and metagenomes -WWW= https://github.com/althonos/pyrodigal +WWW= https://github.com/althonos/pyrodigal/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/py-pyrodigal/distinfo b/biology/py-pyrodigal/distinfo index d3d07b0b3354..ce200fb3c956 100644 --- a/biology/py-pyrodigal/distinfo +++ b/biology/py-pyrodigal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1716179060 -SHA256 (pyrodigal-3.4.0.tar.gz) = d4714e8f9208b7768f89bca9f47013e9f18f978e4baf43176a67af9cb26c7c79 -SIZE (pyrodigal-3.4.0.tar.gz) = 2577063 +TIMESTAMP = 1716658828 +SHA256 (pyrodigal-3.4.1.tar.gz) = 65963ad8cf651f408758e7fa74cbf793eae9720310f0ef8781ee1a285d435326 +SIZE (pyrodigal-3.4.1.tar.gz) = 2577599 diff --git a/biology/py-pyrodigal/pkg-descr b/biology/py-pyrodigal/pkg-descr index c56d5dda28d0..f33eb8de1a50 100644 --- a/biology/py-pyrodigal/pkg-descr +++ b/biology/py-pyrodigal/pkg-descr @@ -2,17 +2,17 @@ Pyrodigal is a Python module that provides bindings to Prodigal using Cython. Features: The library now features everything from the original Prodigal CLI: -* run mode selection: Choose between single mode, using a training sequence to - count nucleotide hexamers, or metagenomic mode, using pre-trained data from - different organisms (prodigal -p). -* region masking: Prevent genes from being predicted across regions containing - unknown nucleotides (prodigal -m). -* closed ends: Genes will be identified as running over edges if they are larger - than a certain size, but this can be disabled (prodigal -c). +* run mode selection: Choose between single mode, using a training sequence + to count nucleotide hexamers, or metagenomic mode, using pre-trained data + from different organisms (prodigal -p). +* region masking: Prevent genes from being predicted across regions + containing unknown nucleotides (prodigal -m). +* closed ends: Genes will be identified as running over edges if they are + larger than a certain size, but this can be disabled (prodigal -c). * training configuration: During the training process, a custom translation - table can be given (prodigal -g), and the Shine-Dalgarno motif search can be - forcefully bypassed (prodigal -n) -* output files: Output files can be written in a format mostly compatible with - the Prodigal binary, including the protein translations in FASTA format - (prodigal -a), the gene sequences in FASTA format (prodigal -d), or the - potential gene scores in tabular format (prodigal -s). + table can be given (prodigal -g), and the Shine-Dalgarno motif search can + be forcefully bypassed (prodigal -n) +* output files: Output files can be written in a format mostly compatible + with the Prodigal binary, including the protein translations in FASTA + format (prodigal -a), the gene sequences in FASTA format (prodigal -d), + or the potential gene scores in tabular format (prodigal -s).
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