From a080f48d6a61e32aed709b40e13176aea1e19933 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Tue, 5 Nov 2024 15:06:49 +0100 Subject: [PATCH] 2024.2 --- .github/env.yaml | 2 +- README.md | 14 ++-- biobb_chemistry/__init__.py | 2 +- .../acpype/acpype_convert_amber_to_gmx.py | 19 ++--- biobb_chemistry/docs/source/change_log.md | 6 ++ biobb_chemistry/docs/source/conf.py | 75 ++++++++++--------- biobb_chemistry/docs/source/readme.md | 14 ++-- biobb_chemistry/docs/source/schema.html | 2 +- .../json_schemas/biobb_chemistry.json | 8 +- setup.py | 16 ++-- 10 files changed, 86 insertions(+), 72 deletions(-) diff --git a/.github/env.yaml b/.github/env.yaml index c5d97e94..ecf029a8 100644 --- 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 index 6f40e0d2..fbbeb3c5 100644 --- 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 + docker run quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0 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 index b37fad7f..da7aa980 100644 --- 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 index 8131903b..10287be8 100644 --- 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 ` class and execute the :meth:`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 index db1dcd6c..efd00a68 100644 --- 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 index 2c0a85d1..883fbc21 100644 --- 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 @@ -45,7 +45,7 @@ # 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: @@ -53,30 +53,30 @@ # -- 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 index 6f40e0d2..fbbeb3c5 100644 --- 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 + docker run quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0 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 index d1cc0ebe..a85c3226 100644 --- 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", diff --git a/biobb_chemistry/json_schemas/biobb_chemistry.json b/biobb_chemistry/json_schemas/biobb_chemistry.json index bf4dcb8c..0b22d03f 100644 --- a/biobb_chemistry/json_schemas/biobb_chemistry.json +++ b/biobb_chemistry/json_schemas/biobb_chemistry.json @@ -4,9 +4,9 @@ "github": "https://github.com/bioexcel/biobb_chemistry", "readthedocs": "https://biobb-chemistry.readthedocs.io/en/latest/", "conda": "https://anaconda.org/bioconda/biobb_chemistry", - "docker": "https://quay.io/biocontainers/biobb_chemistry:5.0.0--pyhdfd78af_0", - "singularity": "https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.0--pyhdfd78af_0", - "version": "5.0.0", + "docker": "https://quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0", + "singularity": "https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0", + "version": "5.0.1", "rest": true, "tools": [ { @@ -98,7 +98,7 @@ "python >=3.9", "biobb_common ==5.0.0", "openbabel ==3.1.1", - "ambertools >=22.5", + "ambertools <=22.5", "acpype >=2023.10.27" ], "keywords": [ diff --git a/setup.py b/setup.py index cefb9013..1f9193b1 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="biobb_chemistry", - version="5.0.0", + version="5.0.1", author="Biobb developers", author_email="genis.bayarri@irbbarcelona.org", description="Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.", @@ -15,12 +15,12 @@ url="https://github.com/bioexcel/biobb_chemistry", project_urls={ "Documentation": "https://biobb-chemistry.readthedocs.io/en/latest/", - "Bioexcel": "https://bioexcel.eu/" + "Bioexcel": "https://bioexcel.eu/", }, - packages=setuptools.find_packages(exclude=['docs', 'test']), - package_data={'biobb_chemistry': ['py.typed']}, - install_requires=['biobb_common==5.0.0'], - python_requires='>=3.9', + packages=setuptools.find_packages(exclude=["docs", "test"]), + package_data={"biobb_chemistry": ["py.typed"]}, + install_requires=["biobb_common==5.0.0"], + python_requires=">=3.9", entry_points={ "console_scripts": [ "acpype_params_ac = biobb_chemistry.acpype.acpype_params_ac:main", @@ -32,7 +32,7 @@ "babel_add_hydrogens = biobb_chemistry.babelm.babel_add_hydrogens:main", "babel_convert = biobb_chemistry.babelm.babel_convert:main", "babel_minimize = biobb_chemistry.babelm.babel_minimize:main", - "babel_remove_hydrogens = biobb_chemistry.babelm.babel_remove_hydrogens:main" + "babel_remove_hydrogens = biobb_chemistry.babelm.babel_remove_hydrogens:main", ] }, classifiers=[ @@ -41,6 +41,6 @@ "License :: OSI Approved :: Apache Software License", "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX", - "Operating System :: Unix" + "Operating System :: Unix", ], )