2024.2

.github/env.yaml

@@ -4,8 +4,8 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==4.2.0
+  - biobb_common ==5.0.0
   - openbabel ==3.1.1
-  - acpype ==2022.7.21
-  - ambertools >=22.0
+  - acpype >=2023.10.27
+  - ambertools >=22.5
 

README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_chemistry?label=Conda)](https://anaconda.org/bioconda/biobb_chemistry)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_chemistry?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_chemistry)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_chemistry?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:4.2.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_chemistry)
 [![](https://img.shields.io/pypi/pyversions/biobb-chemistry.svg?label=Python%20Versions)](https://pypi.org/project/biobb-chemistry/)
@@ -40,7 +40,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-chemistry.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.1 2024.1
+v5.0.0 2024.1
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_chemistry>=4.2.1"
+        pip install "biobb_chemistry>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-chemistry.readthedocs.io/en/latest/modules.html)
@@ -60,7 +60,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_chemistry>=4.2.1"
+        conda install -c bioconda "biobb_chemistry>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-chemistry.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-chemistry.readthedocs.io/en/latest/command_line.html)
@@ -70,13 +70,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_chemistry:4.2.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_chemistry:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_chemistry:4.2.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_chemistry:5.0.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -85,7 +85,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:4.2.1--pyhdfd78af_0
+        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.0--pyhdfd78af_0
 
 
 * Usage:

biobb_chemistry/__init__.py

@@ -4,4 +4,4 @@
 
 name = "biobb_chemistry"
 __all__ = ["acpype", "ambertools", "babelm"]
-__version__ = "4.2.1"
+__version__ = "5.0.0"

biobb_chemistry/ambertools/reduce_remove_hydrogens.py

@@ -2,9 +2,9 @@
 
 """Module containing the ReduceRemoveHydrogens class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
-import biobb_common.tools.file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
 from biobb_chemistry.ambertools.common import get_binary_path, check_input_path, check_output_path
 
@@ -115,7 +115,7 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -124,7 +124,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def reduce_remove_hydrogens(input_path: str, output_path: str, properties: dict = None, **kwargs) -> int:
+def reduce_remove_hydrogens(input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ReduceRemoveHydrogens <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens>` class and
     execute the :meth:`launch() <ambertools.reduce_remove_hydrogens.ReduceRemoveHydrogens.launch>` method."""
 

biobb_chemistry/docs/source/change_log.md

@@ -1,5 +1,11 @@
 # Biobb Chemistry changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_chemistry/releases/tag/v5.0.0)?
+
+### Changes
+
+* [FEATURE](__init__): Importing submodules when a module is loaded
+
 ## What's new in version [4.2.1](https://github.com/bioexcel/biobb_chemistry/releases/tag/v4.2.1)?
 In version 4.2.1 some improvements have been introduced in the babel tools.
 
@@ -32,29 +38,29 @@ In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version.
 * Update to biobb_common 4.0.0 (general)
 
 ## What's new in version [3.9.0](https://github.com/bioexcel/biobb_chemistry/releases/tag/v3.9.0)?
-In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version. 
+In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version.
 
 ### New features
 
 * Update to biobb_common 3.9.0 (general)
 * All inputs/outputs are checked for correct file format, extension and type (general)
 
 ## What's new in version [3.8.0](https://github.com/bioexcel/biobb_chemistry/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 3.8.1 (general)
 
 ## What's new in version [3.7.0](https://github.com/bioexcel/biobb_chemistry/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_chemistry/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