2024.2

CITATION.cff

@@ -39,7 +39,7 @@ repository-code: "https://github.com/bioexcel/biobb"
 title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
 doi: "10.1038/s41597-019-0177-4"
 url: "https://mmb.irbbarcelona.org/biobb/"
-version: 4.2.0
+version: 5.0.0
 preferred-citation:
   type: "article"
   authors:

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:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--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
-v4.2.0 2024.1
+v5.0.0 2024.1
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_vs>=4.2.0"
+        pip install "biobb_vs>=5.0.0"
 
 
 * 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>=4.2.0"
+        conda install -c bioconda "biobb_vs>=5.0.0"
 
 
 * 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:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_vs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_vs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_vs:5.0.0--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:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--pyhdfd78af_0
 
 
 * Usage:

biobb_vs/__init__.py

@@ -1,6 +1,5 @@
-from . import fpocket
-from . import vina
-from . import utils
+from . import fpocket, utils, vina
+
 name = "biobb_vs"
 __all__ = ["fpocket", "vina", "utils"]
-__version__ = "4.2.0"
+__version__ = "5.0.0"

biobb_vs/docs/source/change_log.md

@@ -1,5 +1,19 @@
 # Biobb Virtual Screening changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_vs/releases/tag/v5.0.0)?
+
+### Changes
+
+* [FIX](all): Accept lists in different formats on input properties.
+* [CI/CD](env.yaml): Update biobb_common version.
+* [CI/CD](linting_and_testing.yml): Update set-up micromamba.
+* [CI/CD](linting_and_testing): Update GA test workflow to Python >3.9
+* [DOCS](.readthedocs.yaml): Updating to Python 3.9
+* [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore
+* [FEATURE](__init__): Importing submodules when a module is loaded
+* [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration
+* [FEATURE] New sandbox_path property
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_vs/releases/tag/v4.2.0)?
 In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version.
 
@@ -16,7 +30,7 @@ In version 4.1.2 the code has been updated for being compatible with biopython 1
 * 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. 
+In version 4.1.1 some minor bugs have been fixed.
 
 ### New features
 
@@ -30,7 +44,7 @@ In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
 * Update to biobb_common 4.1.0 (general)
 
 ## What's new in version [4.0.0](https://github.com/bioexcel/biobb_vs/releases/tag/v4.0.0)?
-In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version. Also Autodock Vina has been updated from 1.1.2 to 1.2.3. 
+In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version. Also Autodock Vina has been updated from 1.1.2 to 1.2.3.
 
 ### New features
 
@@ -46,35 +60,35 @@ In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version.
 * All inputs/outputs are checked for correct file format, extension and type (general)
 
 ## What's new in version [3.8.1](https://github.com/bioexcel/biobb_vs/releases/tag/v3.8.1)?
-In version 3.8.1 the AutoDockVinaRun and FPocketRun tools have added the ability to be executed through docker. 
+In version 3.8.1 the AutoDockVinaRun and FPocketRun tools have added the ability to be executed through docker.
 
 ### New features
 
 * Added docker containers for AutoDockVinaRun and FPocketRun tools
 
 ## What's new in version [3.8.0](https://github.com/bioexcel/biobb_vs/releases/tag/v3.8.0)?
-In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version. 
+In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version.
 
 ### New features
 
 * Update to biobb_common 3.8.0 (general)
 
 ## What's new in version [3.7.1](https://github.com/bioexcel/biobb_vs/releases/tag/v3.7.1)?
-In version 3.7.1 some minor bugs have been fixed. 
+In version 3.7.1 some minor bugs have been fixed.
 
 ### Other changes
 
 * Minor bug fixes in AutoDockVinaRun
 
 ## What's new in version [3.7.0](https://github.com/bioexcel/biobb_vs/releases/tag/v3.7.0)?
-In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version. 
+In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.
 
 ### New features
 
 * Update to biobb_common 3.7.0 (general)
 
 ## What's new in version [3.6.0](https://github.com/bioexcel/biobb_vs/releases/tag/v3.6.0)?
-In version 3.6.0 the dependency biobb_common has been updated to 3.6.0 version. 
+In version 3.6.0 the dependency biobb_common has been updated to 3.6.0 version.
 
 ### New features