2023.3

bioexcel · Sep 13, 2023 · 100c6c6 · 100c6c6
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diff --git a/README.md b/README.md
@@ -1,8 +1,26 @@
-[![](https://readthedocs.org/projects/biobb-cmip/badge/?version=latest)](https://biobb-cmip.readthedocs.io/en/latest/?badge=latest)
-[![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_cmip)
-[![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_cmip)
-[![](https://img.shields.io/badge/singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_cmip:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/github/v/tag/bioexcel/biobb_cmip?label=Version)](https://GitHub.com/bioexcel/biobb_cmip/tags/)
+[![](https://img.shields.io/pypi/v/biobb-cmip.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-cmip/)
+[![](https://img.shields.io/conda/vn/bioconda/biobb_cmip?label=Conda)](https://anaconda.org/bioconda/biobb_cmip)
+[![](https://img.shields.io/conda/dn/bioconda/biobb_cmip?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_cmip)
+[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_cmip?tab=tags)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_cmip:4.1.0--pyhdfd78af_0)
+
+[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_cmip)
+[![](https://img.shields.io/pypi/pyversions/biobb-cmip.svg?label=Python%20Versions)](https://pypi.org/project/biobb-cmip/)
 [![](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_cmip)
+
+[![](https://readthedocs.org/projects/biobb-cmip/badge/?version=latest&label=Docs)](https://biobb-cmip.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_cmip/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_cmip/junit/report.html)
+[![](https://docs.bioexcel.eu/biobb_cmip/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_cmip/coverage/)
+[![](https://docs.bioexcel.eu/biobb_cmip/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_cmip/flake8/)
+[![](https://img.shields.io/github/last-commit/bioexcel/biobb_cmip?label=Last%20Commit)](https://github.com/bioexcel/biobb_cmip/commits/master)
+[![](https://img.shields.io/github/issues/bioexcel/biobb_cmip.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_cmip/issues/)
 
 # biobb_cmip
 
@@ -15,7 +33,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-cmip.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.2
+v4.1.0 2023.3
 
 ### Installation
 Using PIP:
@@ -25,7 +43,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_cmip>=4.0.0"
+        pip install "biobb_cmip>=4.1.0"
 
 
 * Usage: [Python API documentation](https://biobb-cmip.readthedocs.io/en/latest/modules.html)
@@ -35,7 +53,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_cmip>=4.0.0"
+        conda install -c bioconda "biobb_cmip>=4.1.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-cmip.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-cmip.readthedocs.io/en/latest/command_line.html)
@@ -45,13 +63,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_cmip:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_cmip:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -61,7 +79,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_cmip.sif https://depot.galaxyproject.org/singularity/biobb_cmip:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_cmip.sif https://depot.galaxyproject.org/singularity/biobb_cmip:4.1.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_cmip/__init__.py b/biobb_cmip/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_cmip"
 __all__ = ["cmip"]
-__version__ = "4.0.0"
+__version__ = "4.1.0"
diff --git a/biobb_cmip/docs/source/change_log.md b/biobb_cmip/docs/source/change_log.md
@@ -1,5 +1,12 @@
 # Biobb CMIP changelog
 
+## What's new in version [4.1.0](https://github.com/bioexcel/biobb_cmip/releases/tag/v4.1.0)?
+In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
+
+### New features
+
+* Update to biobb_common 4.1.0 (general)
+
 ## What's new in version [4.0.0](https://github.com/bioexcel/biobb_cmip/releases/tag/4.0.0)?
 All inputs/outputs are now cheked.
 

diff --git a/biobb_cmip/docs/source/conf.py b/biobb_cmip/docs/source/conf.py
@@ -75,9 +75,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.0.0'
+version = u'4.1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'4.0.0'
+release = u'4.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_cmip/docs/source/readme.md b/biobb_cmip/docs/source/readme.md
@@ -1,8 +1,26 @@
-[![](https://readthedocs.org/projects/biobb-cmip/badge/?version=latest)](https://biobb-cmip.readthedocs.io/en/latest/?badge=latest)
-[![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_cmip)
-[![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_cmip)
-[![](https://img.shields.io/badge/singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_cmip:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/github/v/tag/bioexcel/biobb_cmip?label=Version)](https://GitHub.com/bioexcel/biobb_cmip/tags/)
+[![](https://img.shields.io/pypi/v/biobb-cmip.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-cmip/)
+[![](https://img.shields.io/conda/vn/bioconda/biobb_cmip?label=Conda)](https://anaconda.org/bioconda/biobb_cmip)
+[![](https://img.shields.io/conda/dn/bioconda/biobb_cmip?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_cmip)
+[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_cmip?tab=tags)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_cmip:4.1.0--pyhdfd78af_0)
+
+[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_cmip)
+[![](https://img.shields.io/pypi/pyversions/biobb-cmip.svg?label=Python%20Versions)](https://pypi.org/project/biobb-cmip/)
 [![](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_cmip)
+
+[![](https://readthedocs.org/projects/biobb-cmip/badge/?version=latest&label=Docs)](https://biobb-cmip.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_cmip/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_cmip/junit/report.html)
+[![](https://docs.bioexcel.eu/biobb_cmip/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_cmip/coverage/)
+[![](https://docs.bioexcel.eu/biobb_cmip/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_cmip/flake8/)
+[![](https://img.shields.io/github/last-commit/bioexcel/biobb_cmip?label=Last%20Commit)](https://github.com/bioexcel/biobb_cmip/commits/master)
+[![](https://img.shields.io/github/issues/bioexcel/biobb_cmip.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_cmip/issues/)
 
 # biobb_cmip
 
@@ -15,7 +33,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-cmip.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.2
+v4.1.0 2023.3
 
 ### Installation
 Using PIP:
@@ -25,7 +43,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_cmip>=4.0.0"
+        pip install "biobb_cmip>=4.1.0"
 
 
 * Usage: [Python API documentation](https://biobb-cmip.readthedocs.io/en/latest/modules.html)
@@ -35,7 +53,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_cmip>=4.0.0"
+        conda install -c bioconda "biobb_cmip>=4.1.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-cmip.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-cmip.readthedocs.io/en/latest/command_line.html)
@@ -45,13 +63,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_cmip:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_cmip:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -61,7 +79,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_cmip.sif https://depot.galaxyproject.org/singularity/biobb_cmip:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_cmip.sif https://depot.galaxyproject.org/singularity/biobb_cmip:4.1.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_cmip/docs/source/schema.html b/biobb_cmip/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": "4.0.0",
+  "softwareVersion": "4.1.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_cmip",
   "isAccessibleForFree": "True",

diff --git a/biobb_cmip/json_schemas/biobb_cmip.json b/biobb_cmip/json_schemas/biobb_cmip.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_cmip",
     "readthedocs": "https://biobb-cmip.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_cmip",
-    "docker": "https://quay.io/biocontainers/biobb_cmip:4.0.0--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_cmip:4.0.0--pyhdfd78af_0",
-    "version": "4.0.0",
+    "docker": "https://quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_cmip:4.1.0--pyhdfd78af_0",
+    "version": "4.1.0",
     "tools" : [
         {
             "block" : "CmipRun",
@@ -45,15 +45,15 @@
         }
     ],
     "dep_pypi" : [
-        "install_requires=['biobb_common==4.0.0', 'mdanalysis', 'biobb_structure_checking==3.13.0']",
-        "python_requires='>=3.7'"
+        "install_requires=['biobb_common==4.1.0', 'mdanalysis', 'biobb_structure_checking==3.13.4']",
+        "python_requires='>=3.8'"
     ],
     "dep_conda" : [
-        "python >=3.7",
-        "biobb_common ==4.0.0",
+        "python >=3.8",
+        "biobb_common ==4.1.0",
         "cmip ==2.7.0",
         "mdanalysis >=2.0.0",
-        "biobb_structure_checking==3.13.0"
+        "biobb_structure_checking==3.13.4"
     ],
     "keywords" : [
         "classical",

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_cmip",
-    version="4.0.0",
+    version="4.1.0",
     author="Biobb developers",
     author_email="[email protected]",
     description="biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.",
@@ -20,11 +20,11 @@
     packages=setuptools.find_packages(exclude=['docs', 'test']),
     include_package_data=True,
     install_requires=[
-        'biobb_common==4.0.0',
-        'mdanalysis==2.0.0',
-        'biobb_structure_checking==3.13.0'
+        'biobb_common==4.1.0',
+        'mdanalysis>=2.0.0',
+        'biobb_structure_checking==3.13.4'
     ],
-    python_requires='>=3.7',
+    python_requires='>=3.8',
     entry_points={
         "console_scripts": [
             "cmip_run = biobb_cmip.cmip.cmip:main",
@@ -36,9 +36,9 @@
     },
     classifiers=(
         "Development Status :: 5 - Production/Stable",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",