2024.2

bioexcel · Oct 16, 2024 · 0f55c8e · 0f55c8e
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diff --git a/.github/env.yaml b/.github/env.yaml
@@ -4,8 +4,8 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==4.2.0
+  - biobb_common ==5.0.0
   - pocl
-  - gromacs ==2022.2
-  - ambertools >=22.0
+  - gromacs >=2022.2
+  - ambertools >=22.5
 
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis)
 [![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-analysis.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.1
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -51,7 +51,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_analysis>=4.2.0"
+        pip install "biobb_analysis>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html)
@@ -61,7 +61,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_analysis>=4.2.0"
+        conda install -c bioconda "biobb_analysis>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html)
@@ -71,13 +71,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_analysis:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_analysis:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_analysis:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_analysis:5.0.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -87,7 +87,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:5.0.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_analysis/__init__.py b/biobb_analysis/__init__.py
@@ -3,4 +3,4 @@
 
 name = "biobb_analysis"
 __all__ = ["ambertools", "gromacs"]
-__version__ = "4.2.0"
+__version__ = "5.0.0"
diff --git a/biobb_analysis/docs/source/change_log.md b/biobb_analysis/docs/source/change_log.md
@@ -1,5 +1,14 @@
 # Biobb Analysis changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_analysis/releases/tag/v5.0.0)?
+
+### Changes
+
+* [FEATURE](__init__): Importing submodules when a module is loaded
+* [UPDATE] Adding sandbox_path property to the json schemas
+* [FEATURE] New sandbox_path property
+* [FIX] temporal folder
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_analysis/releases/tag/v4.2.0)?
 In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version.
 
@@ -60,14 +69,14 @@ In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version.
 * Update to Ambertools 22.0 (ambertools module)
 
 ## What's new in version [3.7.0](https://github.com/bioexcel/biobb_analysis/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_analysis/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
 

diff --git a/biobb_analysis/docs/source/conf.py b/biobb_analysis/docs/source/conf.py
@@ -53,9 +53,9 @@
 # source_suffix = ['.rst', '.md']
 
 # -- Integrate markdown ---------------------------------------------------
-#source_parsers = {
+# source_parsers = {
 #   '.md': 'recommonmark.parser.CommonMarkParser',
-#}
+# }
 
 source_suffix = ['.rst', '.md']
 
@@ -75,9 +75,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.2.0'
+version = u'5.0.0'
 # The full version, including alpha/beta/rc tags.
-release = u'4.2.0'
+release = u'5.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -94,7 +94,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns: list[str] = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -228,7 +228,7 @@ def setup(app):
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
 

diff --git a/biobb_analysis/docs/source/readme.md b/biobb_analysis/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis)
 [![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-analysis.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.1
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -51,7 +51,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_analysis>=4.2.0"
+        pip install "biobb_analysis>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html)
@@ -61,7 +61,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_analysis>=4.2.0"
+        conda install -c bioconda "biobb_analysis>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html)
@@ -71,13 +71,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_analysis:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_analysis:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_analysis:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_analysis:5.0.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -87,7 +87,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:5.0.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_analysis/docs/source/schema.html b/biobb_analysis/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": "4.2.0",
+  "softwareVersion": "5.0.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_analysis",
   "isAccessibleForFree": "True",
@@ -22,4 +22,4 @@
     "priceCurrency":"EUR"
   }
 }
-</script>
+</script>
diff --git a/biobb_analysis/gromacs/gmx_trjconv_str_ens.py b/biobb_analysis/gromacs/gmx_trjconv_str_ens.py
@@ -2,6 +2,7 @@
 
 """Module containing the GMX TrjConvStr 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
 from biobb_common.tools import file_utils as fu
@@ -133,7 +134,7 @@ def launch(self) -> int:
         if self.container_path:
             output = self.container_volume_path + '/' + self.output_name + '.' + self.output_type
         else:
-            output = self.stage_io_dict.get("unique_dir") + '/' + self.output_name + '.' + self.output_type
+            output = self.stage_io_dict.get("unique_dir", "") + '/' + self.output_name + '.' + self.output_type
 
         self.cmd = [self.binary_path, 'trjconv',
                     '-f', self.stage_io_dict["in"]["input_traj_path"],
@@ -174,8 +175,8 @@ def launch(self) -> int:
                                            self.output_name + '*.pdb', self.out_log)
 
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            self.io_dict['in'].get("stdin_file_path")
+            self.stage_io_dict.get("unique_dir", ""),
+            self.io_dict['in'].get("stdin_file_path", "")
         ])
         self.remove_tmp_files()
 
@@ -184,7 +185,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def gmx_trjconv_str_ens(input_traj_path: str, input_top_path: str, output_str_ens_path: str, input_index_path: str = None, properties: dict = None, **kwargs) -> int:
+def gmx_trjconv_str_ens(input_traj_path: str, input_top_path: str, output_str_ens_path: str, input_index_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`GMXTrjConvStrEns <gromacs.gmx_trjconv_str_ens.GMXTrjConvStrEns>` class and
     execute the :meth:`launch() <gromacs.gmx_trjconv_str_ens.GMXTrjConvStrEns.launch>` method."""