2024.1

bioexcel · May 24, 2024 · 3c9244a · 3c9244a
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_structure_utils?label=Conda)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_structure_utils?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_structure_utils?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.2.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_structure_utils)
 [![](https://img.shields.io/pypi/pyversions/biobb-structure-utils.svg?label=Python%20Versions)](https://pypi.org/project/biobb-structure-utils/)
@@ -36,7 +36,7 @@ Biobb_structure_utils is the Biobb module collection to modify or extract inform
 [latest API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/).
 
 ### Version
-v4.1.0 2023.3
+v4.2.0 2024.1
 
 ### Installation
 
@@ -47,7 +47,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_structure_utils>=4.1.0"
+        pip install "biobb_structure_utils>=4.2.0"
 
 
 * Usage: [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html)
@@ -57,7 +57,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_structure_utils>=4.1.0"
+        conda install -c bioconda "biobb_structure_utils>=4.2.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-structure-utils.readthedocs.io/en/latest/command_line.html)
@@ -67,13 +67,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_structure_utils:4.2.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_structure_utils:4.2.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -82,7 +82,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0
+        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.2.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_structure_utils/__init__.py b/biobb_structure_utils/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_structure_utils"
 __all__ = ["utils"]
-__version__ = "4.1.0"
+__version__ = "4.2.0"
diff --git a/biobb_structure_utils/docs/source/change_log.md b/biobb_structure_utils/docs/source/change_log.md
@@ -1,5 +1,12 @@
 # Biobb Structure Utils changelog
 
+## What's new in version [4.2.0](https://github.com/bioexcel/biobb_structure_utils/releases/tag/v4.2.0)?
+In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version.
+
+### New features
+
+* Update to biobb_common 4.2.0 (general)
+
 ## What's new in version [4.1.0](https://github.com/bioexcel/biobb_structure_utils/releases/tag/v4.1.0)?
 In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version. Also biobb_structure_checking has been updated from 3.12.1 to 3.13.4.
 

diff --git a/biobb_structure_utils/docs/source/conf.py b/biobb_structure_utils/docs/source/conf.py
@@ -73,9 +73,9 @@
 # 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_structure_utils/docs/source/readme.md b/biobb_structure_utils/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_structure_utils?label=Conda)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_structure_utils?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_structure_utils?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.2.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_structure_utils)
 [![](https://img.shields.io/pypi/pyversions/biobb-structure-utils.svg?label=Python%20Versions)](https://pypi.org/project/biobb-structure-utils/)
@@ -36,7 +36,7 @@ Biobb_structure_utils is the Biobb module collection to modify or extract inform
 [latest API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/).
 
 ### Version
-v4.1.0 2023.3
+v4.2.0 2024.1
 
 ### Installation
 
@@ -47,7 +47,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_structure_utils>=4.1.0"
+        pip install "biobb_structure_utils>=4.2.0"
 
 
 * Usage: [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html)
@@ -57,7 +57,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_structure_utils>=4.1.0"
+        conda install -c bioconda "biobb_structure_utils>=4.2.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-structure-utils.readthedocs.io/en/latest/command_line.html)
@@ -67,13 +67,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_structure_utils:4.2.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_structure_utils:4.2.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -82,7 +82,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0
+        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.2.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_structure_utils/docs/source/schema.html b/biobb_structure_utils/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_structure_utils",
   "isAccessibleForFree": "True",

diff --git a/biobb_structure_utils/json_schemas/biobb_structure_utils.json b/biobb_structure_utils/json_schemas/biobb_structure_utils.json
@@ -4,9 +4,9 @@
     "github" : "https://github.com/bioexcel/biobb_structure_utils",
     "readthedocs" : "https://biobb-structure-utils.readthedocs.io/en/latest/",
     "conda" : "https://anaconda.org/bioconda/biobb_structure_utils",
-    "docker" : "https://quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0",
-    "singularity" : "https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0",
-    "version" : "4.1.0",
+    "docker" : "https://quay.io/biocontainers/biobb_structure_utils:4.2.0--pyhdfd78af_0",
+    "singularity" : "https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.2.0--pyhdfd78af_0",
+    "version" : "4.2.0",
     "rest": true,
     "tools" : [
         {
@@ -131,12 +131,12 @@
         }
     ],
     "dep_pypi" : [
-        "install_requires=['biobb_common==4.1.0', 'biobb_structure_checking==3.13.4']",
+        "install_requires=['biobb_common==4.2.0', 'biobb_structure_checking==3.13.4']",
         "python_requires='>=3.8'"
     ],
     "dep_conda" : [
         "python >=3.8",
-        "biobb_common ==4.1.0",
+        "biobb_common ==4.2.0",
         "biobb_structure_checking ==3.13.4"
     ],
     "dep_conda_extra" : [

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_structure_utils",
-    version="4.1.0",
+    version="4.2.0",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="biobb_structure_utils is the Biobb module collection to perform basic manipulations on 3d structures.",
@@ -18,7 +18,7 @@
         "Bioexcel": "https://bioexcel.eu/"
     },
     packages=setuptools.find_packages(exclude=['docs', 'test']),
-    install_requires=['biobb_common==4.1.0', 'biobb_structure_checking==3.13.4'],
+    install_requires=['biobb_common==4.2.0', 'biobb_structure_checking==3.13.4'],
     python_requires='>=3.8',
     entry_points={
         "console_scripts": [