2023.4

bioexcel · Apr 11, 2023 · e219621 · e219621
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diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_flexserv.readthedocs.io/en/latest/).
 
 ### Version
-v3.9.1 2022.4
+v4.0.0 2023.1
 
 ### Installation
 Using PIP:
@@ -45,7 +45,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_flexserv>=3.9.1"
+        pip install "biobb_flexserv>=4.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-flexserv.readthedocs.io/en/latest/modules.html)
@@ -55,23 +55,23 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_flexserv>=3.9.1"
+        conda install -c bioconda "biobb_flexserv>=4.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-flexserv.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-flexserv.readthedocs.io/en/latest/command_line.html)
 
-<!---Using DOCKER:
+Using DOCKER:
 
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_flexserv:3.9.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_flexserv:4.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_flexserv:3.9.1--pyhdfd78af_0
+        docker run quay.io/biocontainers/biobb_flexserv:4.0.0--pyhdfd78af_0
 
 Using SINGULARITY:
 
@@ -80,14 +80,13 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_flexserv.sif https://depot.galaxyproject.org/singularity/biobb_flexserv:3.9.1--pyhdfd78af_0
+        singularity pull --name biobb_flexserv.sif https://depot.galaxyproject.org/singularity/biobb_flexserv:4.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
         singularity exec biobb_flexserv.sif <command>
--->
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-flexserv.readthedocs.io/en/latest/command_line.html).
 

diff --git a/biobb_flexserv/__init__.py b/biobb_flexserv/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_flexserv"
 __all__ = ["flexserv","pcasuite"]
-__version__ = "3.9.1"
+__version__ = "4.0.0"
diff --git a/biobb_flexserv/docs/source/change_log.md b/biobb_flexserv/docs/source/change_log.md
@@ -1,5 +1,12 @@
 # Biobb FlexServ changelog
 
+## What's new in version [4.0.0](https://github.com/bioexcel/biobb_flexserv/releases/tag/v4.0.0)?
+In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version.
+
+### New features
+
+* Update to biobb_common 4.0.0 (general)
+
 ## What's new in version [3.9.1](https://github.com/bioexcel/biobb_flexserv/releases/tag/v3.9.1)?
 The version 3.9.1 fixes a bug in Python dependencies. 
 

diff --git a/biobb_flexserv/docs/source/conf.py b/biobb_flexserv/docs/source/conf.py
@@ -71,17 +71,17 @@
 
 # General information about the project.
 project = u'biobb_flexserv'
-copyright = u'2022, Bioexcel Project'
+copyright = u'2023, 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'3.9.1'
+version = u'4.0.0'
 # The full version, including alpha/beta/rc tags.
-release = u'3.9.1'
+release = u'4.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_flexserv/docs/source/readme.md b/biobb_flexserv/docs/source/readme.md
@@ -1,9 +1,27 @@
-[![](https://readthedocs.org/projects/biobb-flexserv/badge/?version=latest)](https://biobb-flexserv.readthedocs.io/en/latest/?badge=latest)
-[![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_flexserv)
-<!---[![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_flexserv?tab=tags)
-[![](https://img.shields.io/badge/singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexserv:3.9.1--pyhdfd78af_0)
--->
+[![](https://img.shields.io/github/v/tag/bioexcel/biobb_flexserv?label=Version)](https://GitHub.com/bioexcel/biobb_flexserv/tags/)
+[![](https://img.shields.io/pypi/v/biobb-flexserv.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-flexserv/)
+[![](https://img.shields.io/conda/vn/bioconda/biobb_flexserv?label=Conda)](https://anaconda.org/bioconda/biobb_flexserv)
+[![](https://img.shields.io/conda/dn/bioconda/biobb_flexserv?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_flexserv)
+[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_flexserv?tab=tags)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexserv:4.0.0--pyhdfd78af_0)
+
+[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_flexserv)
+[![](https://img.shields.io/pypi/pyversions/biobb-flexserv.svg?label=Python%20Versions)](https://pypi.org/project/biobb-flexserv/)
 [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_flexserv)
+
+[![](https://readthedocs.org/projects/biobb-flexserv/badge/?version=latest&label=Docs)](https://biobb-flexserv.readthedocs.io/en/latest/?badge=latest)
+[![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
+[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
+[![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
+
+[![](https://docs.bioexcel.eu/biobb_flexserv/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_flexserv/junit/report.html)
+[![](https://docs.bioexcel.eu/biobb_flexserv/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_flexserv/coverage/)
+[![](https://docs.bioexcel.eu/biobb_flexserv/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_flexserv/flake8/)
+[![](https://img.shields.io/github/last-commit/bioexcel/biobb_flexserv?label=Last%20Commit)](https://github.com/bioexcel/biobb_flexserv/commits/master)
+[![](https://img.shields.io/github/issues/bioexcel/biobb_flexserv.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_flexserv/issues/)
+
 
 # biobb_flexserv
 
@@ -17,7 +35,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_flexserv.readthedocs.io/en/latest/).
 
 ### Version
-v3.9.1 2022.4
+v4.0.0 2023.1
 
 ### Installation
 Using PIP:
@@ -27,7 +45,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_flexserv>=3.9.1"
+        pip install "biobb_flexserv>=4.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-flexserv.readthedocs.io/en/latest/modules.html)
@@ -37,23 +55,23 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_flexserv>=3.9.1"
+        conda install -c bioconda "biobb_flexserv>=4.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-flexserv.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-flexserv.readthedocs.io/en/latest/command_line.html)
 
-<!---Using DOCKER:
+Using DOCKER:
 
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_flexserv:3.9.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_flexserv:4.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_flexserv:3.9.1--pyhdfd78af_0
+        docker run quay.io/biocontainers/biobb_flexserv:4.0.0--pyhdfd78af_0
 
 Using SINGULARITY:
 
@@ -62,14 +80,13 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_flexserv.sif https://depot.galaxyproject.org/singularity/biobb_flexserv:3.9.1--pyhdfd78af_0
+        singularity pull --name biobb_flexserv.sif https://depot.galaxyproject.org/singularity/biobb_flexserv:4.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
         singularity exec biobb_flexserv.sif <command>
--->
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-flexserv.readthedocs.io/en/latest/command_line.html).
 

diff --git a/biobb_flexserv/docs/source/schema.html b/biobb_flexserv/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": "3.9.1",
+  "softwareVersion": "4.0.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_flexserv",
   "isAccessibleForFree": "True",

diff --git a/biobb_flexserv/json_schemas/biobb_flexserv.json b/biobb_flexserv/json_schemas/biobb_flexserv.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_flexserv",
     "readthedocs": "https://biobb-flexserv.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_flexserv",
-    "docker": "https://quay.io/biocontainers/biobb_flexserv:3.9.1--pyhdfd78af_1",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_flexserv:3.9.1--pyhdfd78af_1",
-    "version": "3.9.1",
+    "docker": "https://quay.io/biocontainers/biobb_flexserv:4.0.0--pyhdfd78af_1",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_flexserv:4.0.0--pyhdfd78af_1",
+    "version": "4.0.0",
     "tools" : [
         {
             "block" : "BDRun",
@@ -108,12 +108,12 @@
         }
     ],
     "dep_pypi" : [
-        "install_requires=['biobb_common==3.9.0']",
+        "install_requires=['biobb_common==4.0.0']",
         "python_requires='>=3.7,<3.10'"
     ],
     "dep_conda" : [
         "python >=3.7,<3.10",
-        "biobb_common ==3.9.0",
+        "biobb_common ==4.0.0",
         "flexserv ==1.0.2"
     ],
     "keywords" : [

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_flexserv",
-    version="3.9.1",
+    version="4.0.0",
     author="Biobb developers",
     author_email="adam.hospital@irbbarcelona.org",
     description="biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.",
@@ -19,7 +19,7 @@
     },
     packages=setuptools.find_packages(exclude=['docs', 'test']),
     include_package_data=True,
-    install_requires=['biobb_common==3.9.0'],
+    install_requires=['biobb_common==4.0.0'],
     python_requires='>=3.7,<3.10',
     entry_points={
         "console_scripts": [