2024.2

bioexcel · May 27, 2024 · 923ea8d · 923ea8d
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diff --git 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
@@ -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 <command>
+        docker run quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 <command>
 
 
 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
@@ -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
@@ -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
@@ -66,17 +66,17 @@
 
 # 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
 # |version| and |release|, also used in various other places throughout the
 # 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
@@ -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 <command>
+        docker run quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 <command>
 
 
 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
@@ -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
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_pmx",
-    version="4.1.0",
+    version="4.2.0",
     author="Biobb developers",
     author_email="[email protected]",
     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": [