2025.2

RubenChM · RubenChM · commit aef403b1e92e · 2025-12-22T11:50:47.000+01:00
diff --git a/.github/env.yaml b/.github/env.yaml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==5.1.1
+  - biobb_common ==5.2.0
   - biobb_structure_checking >=3.15.6
diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         os: [self-hosted]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_structure_utils?label=Conda)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_structure_utils?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_structure_utils?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.1.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.2.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_structure_utils)
 [![](https://img.shields.io/pypi/pyversions/biobb-structure-utils.svg?label=Python%20Versions)](https://pypi.org/project/biobb-structure-utils/)
@@ -36,7 +36,7 @@ Biobb_structure_utils is the Biobb module collection to modify or extract inform
 [latest API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/).
 
 ### Version
-v5.1.0 2025.1
+v5.2.0 2025.2
 
 ### Installation
 
@@ -47,7 +47,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_structure_utils>=5.1.0"
+        pip install "biobb_structure_utils>=5.2.0"
 
 
 * Usage: [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html)
@@ -57,7 +57,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_structure_utils>=5.1.0"
+        conda install -c bioconda "biobb_structure_utils>=5.2.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-structure-utils.readthedocs.io/en/latest/command_line.html)
@@ -67,13 +67,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_structure_utils:5.2.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_structure_utils:5.2.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -82,7 +82,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.1.0--pyhdfd78af_0
+        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.2.0--pyhdfd78af_0
 
 
 * Usage:
diff --git a/biobb_structure_utils/__init__.py b/biobb_structure_utils/__init__.py
@@ -2,4 +2,4 @@
 
 name = "biobb_structure_utils"
 __all__ = ["utils"]
-__version__ = "5.1.0"
+__version__ = "5.2.0"
diff --git a/biobb_structure_utils/docs/source/change_log.md b/biobb_structure_utils/docs/source/change_log.md
@@ -1,5 +1,11 @@
 # Biobb Structure Utils changelog
 
+## What's new in version [5.2.0](https://github.com/bioexcel/biobb_amber/releases/tag/v5.2.0)?
+
+### Changes
+
+* [UPDATE] Update to biobb_common 5.2.0
+
 ## What's new in version [5.1.0](https://github.com/bioexcel/biobb_structure_utils/releases/tag/v5.1.0)?
 
 ### Changes
diff --git a/biobb_structure_utils/docs/source/conf.py b/biobb_structure_utils/docs/source/conf.py
@@ -73,9 +73,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "5.1.0"
+version = "5.2.0"
 # The full version, including alpha/beta/rc tags.
-release = "5.1.0"
+release = "5.2.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/biobb_structure_utils/docs/source/readme.md b/biobb_structure_utils/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_structure_utils?label=Conda)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_structure_utils?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_structure_utils?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.1.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.2.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_structure_utils)
 [![](https://img.shields.io/pypi/pyversions/biobb-structure-utils.svg?label=Python%20Versions)](https://pypi.org/project/biobb-structure-utils/)
@@ -36,7 +36,7 @@ Biobb_structure_utils is the Biobb module collection to modify or extract inform
 [latest API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/).
 
 ### Version
-v5.1.0 2025.1
+v5.2.0 2025.2
 
 ### Installation
 
@@ -47,7 +47,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_structure_utils>=5.1.0"
+        pip install "biobb_structure_utils>=5.2.0"
 
 
 * Usage: [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html)
@@ -57,7 +57,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_structure_utils>=5.1.0"
+        conda install -c bioconda "biobb_structure_utils>=5.2.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-structure-utils.readthedocs.io/en/latest/command_line.html)
@@ -67,13 +67,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_structure_utils:5.2.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_structure_utils:5.2.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -82,7 +82,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.1.0--pyhdfd78af_0
+        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.2.0--pyhdfd78af_0
 
 
 * Usage:
diff --git a/biobb_structure_utils/docs/source/schema.html b/biobb_structure_utils/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": "5.1.0",
+  "softwareVersion": "5.2.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_structure_utils",
   "isAccessibleForFree": "True",
diff --git a/biobb_structure_utils/json_schemas/biobb_structure_utils.json b/biobb_structure_utils/json_schemas/biobb_structure_utils.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_structure_utils",
     "readthedocs": "https://biobb-structure-utils.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_structure_utils",
-    "docker": "https://quay.io/biocontainers/biobb_structure_utils:5.1.0--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.1.0--pyhdfd78af_0",
-    "version": "5.1.0",
+    "docker": "https://quay.io/biocontainers/biobb_structure_utils:5.2.0--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_structure_utils:5.2.0--pyhdfd78af_0",
+    "version": "5.2.0",
     "rest": true,
     "tools": [
         {
@@ -131,12 +131,12 @@
         }
     ],
     "dep_pypi": [
-        "install_requires=['biobb_common==5.1.1', 'biobb_structure_checking>=3.15.6']",
-        "python_requires='>=3.9'"
+        "install_requires=['biobb_common==5.2.0', 'biobb_structure_checking>=3.15.6']",
+        "python_requires='>=3.10'"
     ],
     "dep_conda": [
-        "python >=3.9",
-        "biobb_common ==5.1.1",
+        "python >=3.10",
+        "biobb_common ==5.2.0",
         "biobb_structure_checking >=3.15.6"
     ],
     "dep_conda_extra": [],
diff --git a/biobb_structure_utils/utils/extract_model.py b/biobb_structure_utils/utils/extract_model.py
@@ -144,9 +144,7 @@ def launch(self) -> int:
             self.copy_to_host()
 
             # Remove temporal files
-            self.tmp_files.extend([
-                tmp_folder
-            ])
+            self.tmp_files.append(tmp_folder)
             self.remove_tmp_files()
 
             self.check_arguments(output_files_created=True, raise_exception=False)
diff --git a/biobb_structure_utils/utils/extract_molecule.py b/biobb_structure_utils/utils/extract_molecule.py
@@ -142,9 +142,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([
-            tmp_folder
-        ])
+        self.tmp_files.append(tmp_folder)
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_structure_utils",
-    version="5.1.0",
+    version="5.2.0",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="biobb_structure_utils is the Biobb module collection to perform basic manipulations on 3d structures.",
@@ -19,8 +19,8 @@
     },
     packages=setuptools.find_packages(exclude=["docs", "test"]),
     package_data={"biobb_structure_utils": ["py.typed"]},
-    install_requires=["biobb_common==5.1.1", "biobb_structure_checking>=3.15.6"],
-    python_requires=">=3.9",
+    install_requires=["biobb_common==5.2.0", "biobb_structure_checking>=3.15.6"],
+    python_requires=">=3.10",
     entry_points={
         "console_scripts": [
             "cat_pdb = biobb_structure_utils.utils.cat_pdb:main",
@@ -42,7 +42,7 @@
     },
     classifiers=[
         "Development Status :: 5 - Production/Stable",
-        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",
