2023.3 Release v4.1.0

README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_common?label=Conda)](https://anaconda.org/bioconda/biobb_common)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_common?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_common)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)]()
 [![](https://img.shields.io/pypi/pyversions/biobb-common.svg?label=Python%20Versions)]()
@@ -35,7 +35,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.0 2023.1
 
 ### 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)).

biobb_common/__init__.py

 name = "biobb_common"
-__version__ = "4.0.0"
+__version__ = "4.1.0"

biobb_common/docs/source/conf.py

@@ -73,9 +73,9 @@ author = u'Bioexcel Project'
 # 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'2023.1'
+release = u'2023.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

biobb_common/docs/source/readme.md

-[![](https://readthedocs.org/projects/biobb-common/badge/?version=latest)](https://biobb-common.readthedocs.io/en/latest/?badge=latest)
-[![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_common)
-[![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
-[![](https://img.shields.io/badge/singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:3.9.0--pyhdfd78af_0)
+[![](https://img.shields.io/github/v/tag/bioexcel/biobb_common?label=Version)](https://GitHub.com/bioexcel/biobb_common/tags/)
+[![](https://img.shields.io/pypi/v/biobb-common.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-common/)
+[![](https://img.shields.io/conda/vn/bioconda/biobb_common?label=Conda)](https://anaconda.org/bioconda/biobb_common)
+[![](https://img.shields.io/conda/dn/bioconda/biobb_common?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_common)
+[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_0)
+
+[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)]()
+[![](https://img.shields.io/pypi/pyversions/biobb-common.svg?label=Python%20Versions)]()
 [![](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://readthedocs.org/projects/biobb-common/badge/?version=latest&label=Docs)](https://biobb-common.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://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://img.shields.io/badge/Tests-Passing-brightgreen)]()
+[![](https://img.shields.io/badge/Coverage-90%25-brightgreen)]()
+[![](https://img.shields.io/github/last-commit/bioexcel/biobb_common?label=Last%20Commit)]()
+[![](https://img.shields.io/github/issues/bioexcel/biobb_common.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_common/issues/)
+
 
 
 # biobb_common
@@ -17,7 +35,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.0 2023.1
 
 ### 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)).

biobb_common/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_common",
   "isAccessibleForFree": "True",
@@ -22,4 +22,4 @@
     "priceCurrency":"EUR"
   }
 }
-</script>
+</script>
\ No newline at end of file

biobb_common/json_schemas/biobb_common.json

@@ -6,25 +6,25 @@
     "conda": "https://anaconda.org/bioconda/biobb_common",
     "docker": "https://quay.io/biocontainers/biobb_common:3.8.1--pyhdfd78af_0",
     "singularity": "https://depot.galaxyproject.org/singularity/biobb_common:3.8.1--pyhdfd78af_0",
-    "version": "4.0.0",
-    "tools" : [
+    "version": "4.1.0",
+    "tools": [
         {
-            "block" : "",
-            "tool" : "in house",
-            "desc" : "Biobb Base structure & common elements."
+            "block": "",
+            "tool": "in house",
+            "desc": "Biobb Base structure & common elements."
         }
     ],
-    "dep_pypi" : [
-        "install_requires=['pyyaml', 'requests', 'biopython==1.79']",
-        "python_requires='>=3.7,<=3.10'"
+    "dep_pypi": [
+        "install_requires=['pyyaml', 'requests', 'biopython']",
+        "python_requires='>=3.8'"
     ],
-    "dep_conda" : [
-        "python >=3.7,<=3.10",
+    "dep_conda": [
+        "python >=3.8",
         "pyyaml",
         "requests",
-        "biopython ==1.79"
+        "biopython"
     ],
-    "keywords" : [
+    "keywords": [
         "common"
     ]
-}
+}
\ No newline at end of file

setup.py

@@ -22,7 +22,6 @@ setuptools.setup(
     python_requires=">=3.8",
     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",