2024.1

bioexcel · May 8, 2024 · 46834cb · 46834cb
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_vs?label=Conda)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_vs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_vs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_vs)
 [![](https://img.shields.io/pypi/pyversions/biobb-vs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-vs/)
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 > At the time of publishing the current version, **autodock_vina has not been compiled for the new ARM mac M1/M2 chips**. So the vina.autodock_vina_run only work in these computers through docker containers.
 
 ### Version
-v4.1.1 2023.3
+v4.1.2 2024.1
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_vs>=4.1.1"
+        pip install "biobb_vs>=4.1.2"
 
 
 * Usage: [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_vs>=4.1.1"
+        conda install -c bioconda "biobb_vs>=4.1.2"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-vs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -87,7 +87,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0
+        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_vs/__init__.py b/biobb_vs/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_vs"
 __all__ = ["fpocket", "vina", "utils"]
-__version__ = "4.1.1"
+__version__ = "4.1.2"
diff --git a/biobb_vs/docs/source/change_log.md b/biobb_vs/docs/source/change_log.md
@@ -1,5 +1,13 @@
 # Biobb Virtual Screening changelog
 
+## What's new in version [4.1.2](https://github.com/bioexcel/biobb_vs/releases/tag/v4.1.2)?
+In version 4.1.2 the code has been updated for being compatible with biopython 1.83 and fpocket version dependency has been fixed to 4.1.
+
+### New features
+
+* Compatibility with biopython 1.83.
+* Fpocket fixed to 4.1 version.
+
 ## What's new in version [4.1.1](https://github.com/bioexcel/biobb_vs/releases/tag/v4.1.1)?
 In version 4.1.1 some minor bugs have been fixed. 
 

diff --git a/biobb_vs/docs/source/conf.py b/biobb_vs/docs/source/conf.py
@@ -76,9 +76,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.1.1'
+version = u'4.1.2'
 # The full version, including alpha/beta/rc tags.
-release = u'4.1.1'
+release = u'4.1.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_vs/docs/source/readme.md b/biobb_vs/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_vs?label=Conda)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_vs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_vs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_vs)
 [![](https://img.shields.io/pypi/pyversions/biobb-vs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-vs/)
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 > At the time of publishing the current version, **autodock_vina has not been compiled for the new ARM mac M1/M2 chips**. So the vina.autodock_vina_run only work in these computers through docker containers.
 
 ### Version
-v4.1.1 2023.3
+v4.1.2 2024.1
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_vs>=4.1.1"
+        pip install "biobb_vs>=4.1.2"
 
 
 * Usage: [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_vs>=4.1.1"
+        conda install -c bioconda "biobb_vs>=4.1.2"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-vs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -87,7 +87,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0
+        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_vs/docs/source/schema.html b/biobb_vs/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": "4.1.1",
+  "softwareVersion": "4.1.2",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_vs",
   "isAccessibleForFree": "True",

diff --git a/biobb_vs/fpocket/common.py b/biobb_vs/fpocket/common.py
@@ -53,7 +53,7 @@ def is_valid_file(ext, argument):
 def check_range(name, property, values, out_log, classname):
     """ Checks the format of a range for fpocket_filter """
 
-    if not type(property) == list or len(property) != 2 or not all(isinstance(n, int) or isinstance(n, float) for n in property):
+    if not isinstance(property, list) or len(property) != 2 or not all(isinstance(n, (int, float)) for n in property):
         fu.log(classname + ': Incorrect format for %s property, exiting' % name, out_log)
         raise SystemExit(classname + ': Incorrect format for %s property, exiting' % name)
 

diff --git a/biobb_vs/json_schemas/biobb_vs.json b/biobb_vs/json_schemas/biobb_vs.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_vs",
     "readthedocs": "https://biobb-vs.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_vs",
-    "docker": "https://quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0",
-    "version": "4.1.1",
+    "docker": "https://quay.io/biocontainers/biobb_vs:4.1.2--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_vs:4.1.2--pyhdfd78af_0",
+    "version": "4.1.2",
     "rest": true,
     "tools" : [
         {

diff --git a/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip b/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_vs",
-    version="4.1.1",
+    version="4.1.2",
     author="Biobb developers",
     author_email="genis.bayarri@irbbarcelona.org",
     description="Biobb_vs is the Biobb module collection to perform virtual screening studies.",