2024.2

bioexcel · Nov 5, 2024 · a080f48 · a080f48
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diff --git a/.github/env.yaml b/.github/env.yaml
@@ -7,5 +7,5 @@ dependencies:
   - biobb_common ==5.0.0
   - openbabel ==3.1.1
   - acpype >=2023.10.27
-  - ambertools >=22.5
+  - ambertools <=22.5
 
diff --git a/README.md b/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:5.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--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
-v5.0.0 2024.1
+v5.0.1 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_chemistry>=5.0.0"
+        pip install "biobb_chemistry>=5.0.1"
 
 
 * 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>=5.0.0"
+        conda install -c bioconda "biobb_chemistry>=5.0.1"
 
 
 * 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:5.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_chemistry:5.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_chemistry:5.0.1--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:5.0.0--pyhdfd78af_0
+        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_chemistry/__init__.py b/biobb_chemistry/__init__.py
@@ -4,4 +4,4 @@
 
 name = "biobb_chemistry"
 __all__ = ["acpype", "ambertools", "babelm"]
-__version__ = "5.0.0"
+__version__ = "5.0.1"
diff --git a/biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py b/biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py
@@ -6,6 +6,7 @@
 from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
 from biobb_chemistry.acpype.common import get_binary_path, check_output_path, get_basename, create_unique_name, get_default_value, process_output_gmx
+from typing import Optional
 
 
 class AcpypeConvertAMBERtoGMX(BiobbObject):
@@ -158,15 +159,15 @@ def launch(self) -> int:
         return self.return_code
 
 
-def acpype_convert_amber_to_gmx(input_crd_path: str, input_top_path: str, output_path_gro: str, output_path_top: str, properties: dict = None, **kwargs) -> int:
+def acpype_convert_amber_to_gmx(input_crd_path: str, input_top_path: str, output_path_gro: str, output_path_top: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`AcpypeConvertAMBERtoGMX <acpype.acpype_convert_amber_to_gmx.AcpypeConvertAMBERtoGMX>` class and
     execute the :meth:`launch() <acpype.acpype_convert_amber_to_gmx.AcpypeConvertAMBERtoGMX.launch>` method."""
 
     return AcpypeConvertAMBERtoGMX(input_crd_path=input_crd_path,
-                           input_top_path=input_top_path,
-                           output_path_gro=output_path_gro,
-                           output_path_top=output_path_top,
-                           properties=properties, **kwargs).launch()
+                                   input_top_path=input_top_path,
+                                   output_path_gro=output_path_gro,
+                                   output_path_top=output_path_top,
+                                   properties=properties, **kwargs).launch()
 
 
 def main():
@@ -187,10 +188,10 @@ def main():
 
     # Specific call of each building block
     acpype_convert_amber_to_gmx(input_crd_path=args.input_crd_path,
-                      input_top_path=args.input_top_path,
-                      output_path_gro=args.output_path_gro,
-                      output_path_top=args.output_path_top,
-                      properties=properties)
+                                input_top_path=args.input_top_path,
+                                output_path_gro=args.output_path_gro,
+                                output_path_top=args.output_path_top,
+                                properties=properties)
 
 
 if __name__ == '__main__':

diff --git a/biobb_chemistry/docs/source/change_log.md b/biobb_chemistry/docs/source/change_log.md
@@ -1,5 +1,11 @@
 # Biobb Chemistry changelog
 
+## What's new in version [5.0.1](https://github.com/bioexcel/biobb_chemistry/releases/tag/v5.0.1)?
+
+### Changes
+* [FEATURE](all): AcpypeConvertAMBERtoGMX module
+
+
 ## What's new in version [5.0.0](https://github.com/bioexcel/biobb_chemistry/releases/tag/v5.0.0)?
 
 ### Changes

diff --git a/biobb_chemistry/docs/source/conf.py b/biobb_chemistry/docs/source/conf.py
@@ -18,7 +18,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, str(Path('../../').resolve()))
+sys.path.insert(0, str(Path("../../").resolve()))
 
 # -- General configuration ------------------------------------------------
 
@@ -29,14 +29,14 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx_rtd_theme',
-    'recommonmark'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
+    "recommonmark",
 ]
 
 # Using Google docstring style
@@ -45,38 +45,38 @@
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 # source_suffix = ['.rst', '.md']
 
 # -- Integrate markdown ---------------------------------------------------
 source_parsers = {
-    '.md': 'recommonmark.parser.CommonMarkParser',
+    ".md": "recommonmark.parser.CommonMarkParser",
 }
 
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'biobb_chemistry'
-copyright = u'2024, Bioexcel Project'
-author = u'Bioexcel Project'
+project = "biobb_chemistry"
+copyright = "2024, Bioexcel Project"
+author = "Bioexcel Project"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'5.0.0'
+version = "5.0.1"
 # The full version, including alpha/beta/rc tags.
-release = u'5.0.0'
+release = "5.0.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -111,7 +111,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -125,13 +125,13 @@
 
 # -- Options for HTML output ----------------------------------------------
 def setup(app):
-    app.add_css_file('theme_overrides.css')
-    app.add_js_file('theme_overrides.js')
+    app.add_css_file("theme_overrides.css")
+    app.add_js_file("theme_overrides.js")
 
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -160,7 +160,7 @@ def setup(app):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -223,20 +223,17 @@ def setup(app):
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'biobb_chemistry_doc'
+htmlhelp_basename = "biobb_chemistry_doc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     # 'preamble': '',
-
     # Latex figure (float) alignment
     # 'figure_align': 'htbp',
 }
@@ -245,8 +242,13 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'biobb_chemistry.tex', u'biobb_chemistry Documentation',
-     u'Bioexcel Project', 'manual'),
+    (
+        master_doc,
+        "biobb_chemistry.tex",
+        "biobb_chemistry Documentation",
+        "Bioexcel Project",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -275,8 +277,7 @@ def setup(app):
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'biobb_chemistry', u'biobb_chemistry Documentation',
-     [author], 1)
+    (master_doc, "biobb_chemistry", "biobb_chemistry Documentation", [author], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -289,9 +290,15 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'biobb_chemistry', u'biobb_chemistry Documentation',
-     author, 'biobb_chemistry', 'biobb_chemistry molecular dynamics chemistry building blocks',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "biobb_chemistry",
+        "biobb_chemistry Documentation",
+        author,
+        "biobb_chemistry",
+        "biobb_chemistry molecular dynamics chemistry building blocks",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.

diff --git a/biobb_chemistry/docs/source/readme.md b/biobb_chemistry/docs/source/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:5.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--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
-v5.0.0 2024.1
+v5.0.1 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_chemistry>=5.0.0"
+        pip install "biobb_chemistry>=5.0.1"
 
 
 * 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>=5.0.0"
+        conda install -c bioconda "biobb_chemistry>=5.0.1"
 
 
 * 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:5.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_chemistry:5.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_chemistry:5.0.1--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:5.0.0--pyhdfd78af_0
+        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_chemistry/docs/source/schema.html b/biobb_chemistry/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": "5.0.0",
+  "softwareVersion": "5.0.1",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_chemistry",
   "isAccessibleForFree": "True",