From 46834cb2b74aff54a3c38e22cc9f061e8e946087 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Wed, 8 May 2024 10:09:56 +0200 Subject: [PATCH] 2024.1 --- README.md | 14 +++++++------- biobb_vs/__init__.py | 2 +- biobb_vs/docs/source/change_log.md | 8 ++++++++ biobb_vs/docs/source/conf.py | 4 ++-- biobb_vs/docs/source/readme.md | 14 +++++++------- biobb_vs/docs/source/schema.html | 2 +- biobb_vs/fpocket/common.py | 2 +- biobb_vs/json_schemas/biobb_vs.json | 6 +++--- .../fpocket/ref_output_filter_pockets.zip | Bin 40885 -> 40885 bytes setup.py | 2 +- 10 files changed, 31 insertions(+), 23 deletions(-) diff --git a/README.md b/README.md index f012428..ea6b40c 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_vs?label=Conda)](https://anaconda.org/bioconda/biobb_vs) [![](https://img.shields.io/conda/dn/bioconda/biobb_vs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_vs) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_vs?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_vs) [![](https://img.shields.io/pypi/pyversions/biobb-vs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-vs/) @@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site: > At the time of publishing the current version, **autodock_vina has not been compiled for the new ARM mac M1/M2 chips**. So the vina.autodock_vina_run only work in these computers through docker containers. ### Version -v4.1.1 2023.3 +v4.1.2 2024.1 ### Installation Using PIP: @@ -52,7 +52,7 @@ Using PIP: * Installation: - pip install "biobb_vs>=4.1.1" + pip install "biobb_vs>=4.1.2" * Usage: [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) @@ -62,7 +62,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_vs>=4.1.1" + conda install -c bioconda "biobb_vs>=4.1.2" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-vs.readthedocs.io/en/latest/command_line.html) @@ -72,13 +72,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0 Using SINGULARITY: @@ -87,7 +87,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0 + singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0 * Usage: diff --git a/biobb_vs/__init__.py b/biobb_vs/__init__.py index c143325..78c1867 100644 --- a/biobb_vs/__init__.py +++ b/biobb_vs/__init__.py @@ -1,3 +1,3 @@ name = "biobb_vs" __all__ = ["fpocket", "vina", "utils"] -__version__ = "4.1.1" +__version__ = "4.1.2" diff --git a/biobb_vs/docs/source/change_log.md b/biobb_vs/docs/source/change_log.md index e5c1830..e74985f 100644 --- a/biobb_vs/docs/source/change_log.md +++ b/biobb_vs/docs/source/change_log.md @@ -1,5 +1,13 @@ # Biobb Virtual Screening changelog +## What's new in version [4.1.2](https://github.com/bioexcel/biobb_vs/releases/tag/v4.1.2)? +In version 4.1.2 the code has been updated for being compatible with biopython 1.83 and fpocket version dependency has been fixed to 4.1. + +### New features + +* Compatibility with biopython 1.83. +* Fpocket fixed to 4.1 version. + ## What's new in version [4.1.1](https://github.com/bioexcel/biobb_vs/releases/tag/v4.1.1)? In version 4.1.1 some minor bugs have been fixed. diff --git a/biobb_vs/docs/source/conf.py b/biobb_vs/docs/source/conf.py index 02b6bb0..344bac9 100644 --- a/biobb_vs/docs/source/conf.py +++ b/biobb_vs/docs/source/conf.py @@ -76,9 +76,9 @@ # built documents. # # The short X.Y version. -version = u'4.1.1' +version = u'4.1.2' # The full version, including alpha/beta/rc tags. -release = u'4.1.1' +release = u'4.1.2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/biobb_vs/docs/source/readme.md b/biobb_vs/docs/source/readme.md index f012428..ea6b40c 100644 --- a/biobb_vs/docs/source/readme.md +++ b/biobb_vs/docs/source/readme.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_vs?label=Conda)](https://anaconda.org/bioconda/biobb_vs) [![](https://img.shields.io/conda/dn/bioconda/biobb_vs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_vs) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_vs?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_vs) [![](https://img.shields.io/pypi/pyversions/biobb-vs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-vs/) @@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site: > At the time of publishing the current version, **autodock_vina has not been compiled for the new ARM mac M1/M2 chips**. So the vina.autodock_vina_run only work in these computers through docker containers. ### Version -v4.1.1 2023.3 +v4.1.2 2024.1 ### Installation Using PIP: @@ -52,7 +52,7 @@ Using PIP: * Installation: - pip install "biobb_vs>=4.1.1" + pip install "biobb_vs>=4.1.2" * Usage: [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) @@ -62,7 +62,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_vs>=4.1.1" + conda install -c bioconda "biobb_vs>=4.1.2" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-vs.readthedocs.io/en/latest/command_line.html) @@ -72,13 +72,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0 Using SINGULARITY: @@ -87,7 +87,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0 + singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0 * Usage: diff --git a/biobb_vs/docs/source/schema.html b/biobb_vs/docs/source/schema.html index a54160b..525ba75 100644 --- a/biobb_vs/docs/source/schema.html +++ b/biobb_vs/docs/source/schema.html @@ -10,7 +10,7 @@ "applicationSubCategory": "http://www.edamontology.org/topic_3892", "citation": "https://www.nature.com/articles/s41597-019-0177-4", "license": "https://www.apache.org/licenses/LICENSE-2.0", - "softwareVersion": "4.1.1", + "softwareVersion": "4.1.2", "applicationSuite": "BioBB BioExcel Building Blocks", "codeRepository": "https://github.com/bioexcel/biobb_vs", "isAccessibleForFree": "True", diff --git a/biobb_vs/fpocket/common.py b/biobb_vs/fpocket/common.py index ff79047..a858abd 100644 --- a/biobb_vs/fpocket/common.py +++ b/biobb_vs/fpocket/common.py @@ -53,7 +53,7 @@ def is_valid_file(ext, argument): def check_range(name, property, values, out_log, classname): """ Checks the format of a range for fpocket_filter """ - if not type(property) == list or len(property) != 2 or not all(isinstance(n, int) or isinstance(n, float) for n in property): + if not isinstance(property, list) or len(property) != 2 or not all(isinstance(n, (int, float)) for n in property): fu.log(classname + ': Incorrect format for %s property, exiting' % name, out_log) raise SystemExit(classname + ': Incorrect format for %s property, exiting' % name) diff --git a/biobb_vs/json_schemas/biobb_vs.json b/biobb_vs/json_schemas/biobb_vs.json index 7647931..858acbc 100644 --- a/biobb_vs/json_schemas/biobb_vs.json +++ b/biobb_vs/json_schemas/biobb_vs.json @@ -4,9 +4,9 @@ "github": "https://github.com/bioexcel/biobb_vs", "readthedocs": "https://biobb-vs.readthedocs.io/en/latest/", "conda": "https://anaconda.org/bioconda/biobb_vs", - "docker": "https://quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0", - "singularity": "https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0", - "version": "4.1.1", + "docker": "https://quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0", + "singularity": "https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0", + "version": "4.1.2", "rest": true, "tools" : [ { diff --git a/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip b/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip index 4656b1c1b793b427722fc438d64a1c42c05db6e4..b19344474f767480c98f02976ede785eda026e06 100644 GIT binary patch delta 166 zcmdnGpK0rUCcXe~W)=|!5YP!+5wVePl_(2{v3ZZ^G#Lmh%&1rx!aD291{J%WSi=Jm z3(t$=hp=|mCh