From 923ea8dbb0770f8577fe710f95024c8e8fcf082d Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Mon, 27 May 2024 17:35:36 +0200 Subject: [PATCH] 2024.2 --- .github/env.yaml | 2 +- README.md | 14 +++++++------- biobb_pmx/__init__.py | 2 +- biobb_pmx/docs/source/change_log.md | 14 ++++++++++++++ biobb_pmx/docs/source/conf.py | 6 +++--- biobb_pmx/docs/source/readme.md | 25 ++++++++++++++++--------- biobb_pmx/docs/source/schema.html | 2 +- setup.py | 4 ++-- 8 files changed, 45 insertions(+), 24 deletions(-) diff --git a/.github/env.yaml b/.github/env.yaml index 740c7dd..0e51750 100644 --- a/.github/env.yaml +++ b/.github/env.yaml @@ -4,7 +4,7 @@ channels: - bioconda - anaconda dependencies: - - biobb_common ==4.1.0 + - biobb_common ==4.2.0 - pmx_biobb ==4.1.3 - pillow - imagehash diff --git a/README.md b/README.md index 3fc5fe0..0eec4f0 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_pmx?label=Conda)](https://anaconda.org/bioconda/biobb_pmx) [![](https://img.shields.io/conda/dn/bioconda/biobb_pmx?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_pmx) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_pmx?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pmx:4.1.0--pyhdfd78af_1) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.0--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_pmx) [![](https://img.shields.io/pypi/pyversions/biobb-pmx.svg?label=Python%20Versions)](https://pypi.org/project/biobb-pmx/) @@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-pmx.readthedocs.io/en/latest/). ### Version -v4.1.0 2023.3 +v4.2.0 2023.3 ### Installation Using PIP: @@ -50,7 +50,7 @@ Using PIP: * Installation: - pip install "biobb_pmx>=4.1.0" + pip install "biobb_pmx>=4.2.0" * Usage: [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) @@ -60,7 +60,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_pmx>=4.1.0" + conda install -c bioconda "biobb_pmx>=4.2.0" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html) @@ -70,13 +70,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_pmx:4.1.0--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_pmx:4.1.0--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 Using SINGULARITY: @@ -86,7 +86,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.1.0--pyhdfd78af_0 + singularity pull --name biobb_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.0--pyhdfd78af_0 * Usage: diff --git a/biobb_pmx/__init__.py b/biobb_pmx/__init__.py index 9d576dc..cf0264a 100644 --- a/biobb_pmx/__init__.py +++ b/biobb_pmx/__init__.py @@ -2,4 +2,4 @@ name = "biobb_pmx" __all__ = ["pmxbiobb"] -__version__ = "4.1.0" +__version__ = "4.2.0" diff --git a/biobb_pmx/docs/source/change_log.md b/biobb_pmx/docs/source/change_log.md index 1834ef9..f306013 100644 --- a/biobb_pmx/docs/source/change_log.md +++ b/biobb_pmx/docs/source/change_log.md @@ -1,5 +1,19 @@ # Biobb PMX changelog +## What's new in version [4.2.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v4.2.0)? + +### Changes + +* [UPDATE] Updating json schemas +* [DOCS] Adding description to all modules +* [FIX] Adding additional paths +* [DOCS] Adding fair software badge and GA +* [DOCS] Added references file +* [CI/CD] Adding Castiel Gitlab push sync github Action +* [DOCS] Fixing Read the Docs +* [DOCS] Updating README +* [DOCS] Change json file + ## What's new in version [4.1.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v4.1.0)? In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version. New Python minimum version is 3.8.0. diff --git a/biobb_pmx/docs/source/conf.py b/biobb_pmx/docs/source/conf.py index d3ced1a..3fd82a9 100644 --- a/biobb_pmx/docs/source/conf.py +++ b/biobb_pmx/docs/source/conf.py @@ -66,7 +66,7 @@ # General information about the project. project = u'biobb_pmx' -copyright = u'2021, Bioexcel Project' +copyright = u'2024, Bioexcel Project' author = u'Bioexcel Project' # The version info for the project you're documenting, acts as replacement for @@ -74,9 +74,9 @@ # built documents. # # The short X.Y version. -version = u'4.1.0' +version = u'4.2.0' # The full version, including alpha/beta/rc tags. -release = u'4.1.0' +release = u'4.2.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/biobb_pmx/docs/source/readme.md b/biobb_pmx/docs/source/readme.md index 314c5dd..0eec4f0 100644 --- a/biobb_pmx/docs/source/readme.md +++ b/biobb_pmx/docs/source/readme.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_pmx?label=Conda)](https://anaconda.org/bioconda/biobb_pmx) [![](https://img.shields.io/conda/dn/bioconda/biobb_pmx?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_pmx) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_pmx?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pmx:4.1.0--pyhdfd78af_1) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.0--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_pmx) [![](https://img.shields.io/pypi/pyversions/biobb-pmx.svg?label=Python%20Versions)](https://pypi.org/project/biobb-pmx/) @@ -22,6 +22,13 @@ [![](https://img.shields.io/github/last-commit/bioexcel/biobb_pmx?label=Last%20Commit)](https://github.com/bioexcel/biobb_pmx/commits/master) [![](https://img.shields.io/github/issues/bioexcel/biobb_pmx.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_pmx/issues/) +[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) +[![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847) + +[](https://bestpractices.coreinfrastructure.org/projects/8847/badge) + +[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL) + # biobb_pmx @@ -34,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-pmx.readthedocs.io/en/latest/). ### Version -v4.1.0 2023.3 +v4.2.0 2023.3 ### Installation Using PIP: @@ -43,7 +50,7 @@ Using PIP: * Installation: - pip install "biobb_pmx>=4.1.0" + pip install "biobb_pmx>=4.2.0" * Usage: [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) @@ -53,7 +60,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_pmx>=4.1.0" + conda install -c bioconda "biobb_pmx>=4.2.0" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-pmx.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-pmx.readthedocs.io/en/latest/command_line.html) @@ -63,13 +70,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_pmx:4.1.0--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_pmx:4.1.0--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 Using SINGULARITY: @@ -79,7 +86,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.1.0--pyhdfd78af_0 + singularity pull --name biobb_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.0--pyhdfd78af_0 * Usage: @@ -94,8 +101,8 @@ The command list and specification can be found at the [Command Line documentati ### Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). -* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/) -* (c) 2015-2022[Institute for Research in Biomedicine](https://www.irbbarcelona.org/) +* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) +* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. diff --git a/biobb_pmx/docs/source/schema.html b/biobb_pmx/docs/source/schema.html index a91e040..997843b 100644 --- a/biobb_pmx/docs/source/schema.html +++ b/biobb_pmx/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": "4.1.0", + "softwareVersion": "4.2.0", "applicationSuite": "BioBB BioExcel Building Blocks", "codeRepository": "https://github.com/bioexcel/biobb_pmx", "isAccessibleForFree": "True", diff --git a/setup.py b/setup.py index b68bf30..2943272 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="biobb_pmx", - version="4.1.0", + version="4.2.0", author="Biobb developers", author_email="pau.andrio@bsc.es", description="Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.", @@ -18,7 +18,7 @@ "Bioexcel": "https://bioexcel.eu/" }, packages=setuptools.find_packages(exclude=['docs']), - install_requires=['biobb_common==4.1.0', 'pmx-biobb==4.1.3'], + install_requires=['biobb_common==4.2.0', 'pmx-biobb==4.1.3'], python_requires='>=3.8', entry_points={ "console_scripts": [