2024.2

bioexcel · May 29, 2024 · fbaba44 · fbaba44
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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:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.1--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
-v4.2.0 2023.3
+v4.2.1 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_pmx>=4.2.0"
+        pip install "biobb_pmx>=4.2.1"
 
 
 * 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>=4.2.0"
+        conda install -c bioconda "biobb_pmx>=4.2.1"
 
 
 * 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:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_pmx:4.2.1--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_pmx:4.2.1--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:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.1--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__ = "4.2.0"
+__version__ = "4.2.1"
diff --git a/biobb_pmx/docs/source/change_log.md b/biobb_pmx/docs/source/change_log.md
@@ -1,5 +1,14 @@
 # Biobb PMX changelog
 
+## What's new in version [4.2.1](https://github.com/bioexcel/biobb_pmx/releases/tag/v4.2.1)?
+
+### Changes
+
+* [DOCS] Update JSON
+* [TEST] Updating GMXLIB of docker test
+* [CI/CD] Update actions/checkout to v4
+* [FIX] Fix type hints
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v4.2.0)?
 
 ### Changes

diff --git a/biobb_pmx/docs/source/conf.py b/biobb_pmx/docs/source/conf.py
@@ -74,9 +74,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.2.0'
+version = u'4.2.1'
 # The full version, including alpha/beta/rc tags.
-release = u'4.2.0'
+release = u'4.2.1'
 
 # 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:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.1--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
-v4.2.0 2023.3
+v4.2.1 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_pmx>=4.2.0"
+        pip install "biobb_pmx>=4.2.1"
 
 
 * 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>=4.2.0"
+        conda install -c bioconda "biobb_pmx>=4.2.1"
 
 
 * 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:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_pmx:4.2.1--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_pmx:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_pmx:4.2.1--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:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.2.1--pyhdfd78af_0
 
 
 * Usage:

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": "4.2.0",
+  "softwareVersion": "4.2.1",
   "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="4.2.0",
+    version="4.2.1",
     author="Biobb developers",
     author_email="[email protected]",
     description="Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.",