diff --git a/README.md b/README.md index 155105d..91f1b3f 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_dna?label=Conda)](https://anaconda.org/bioconda/biobb_dna) [![](https://img.shields.io/conda/dn/bioconda/biobb_dna?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_dna) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_dna?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_dna:5.0.0--pyhdfd78af_0) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_dna:5.0.1--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_dna) [![](https://img.shields.io/pypi/pyversions/biobb-dna.svg?label=Python%20Versions)](https://pypi.org/project/biobb-dna/) @@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-dna.readthedocs.io/en/latest/). ### Version -v5.0.0 2024.2 +v5.0.1 2024.2 ### Installation Using PIP: @@ -51,7 +51,7 @@ Using PIP: * Installation: - pip install "biobb_dna>=5.0.0" + pip install "biobb_dna>=5.0.1" * Usage: [Python API documentation](https://biobb-dna.readthedocs.io/en/latest/modules.html) @@ -61,7 +61,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_dna>=5.0.0" + conda install -c bioconda "biobb_dna>=5.0.1" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-dna.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-dna.readthedocs.io/en/latest/command_line.html) @@ -71,13 +71,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_dna:5.0.1--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_dna:5.0.1--pyhdfd78af_0 Using SINGULARITY: @@ -86,7 +86,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:5.0.0--pyhdfd78af_0 + singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:5.0.1--pyhdfd78af_0 * Usage: diff --git a/biobb_dna/__init__.py b/biobb_dna/__init__.py index d62983f..9b64fa0 100644 --- a/biobb_dna/__init__.py +++ b/biobb_dna/__init__.py @@ -1,10 +1,19 @@ -from . import dna -from . import curvesplus -from . import backbone -from . import stiffness -from . import interbp_correlations -from . import intrabp_correlations +from . import ( + backbone, + curvesplus, + dna, + interbp_correlations, + intrabp_correlations, + stiffness, +) + name = "biobb_dna" -__all__ = ["dna", "curvesplus", "backbone", "stiffness", - "interbp_correlations", "intrabp_correlations"] -__version__ = "5.0.0" +__all__ = [ + "dna", + "curvesplus", + "backbone", + "stiffness", + "interbp_correlations", + "intrabp_correlations", +] +__version__ = "5.0.1" diff --git a/biobb_dna/docs/source/change_log.md b/biobb_dna/docs/source/change_log.md index 39cebbb..50bf776 100644 --- a/biobb_dna/docs/source/change_log.md +++ b/biobb_dna/docs/source/change_log.md @@ -1,5 +1,11 @@ # Biobb Analysis changelog +## What's new in version [5.0.1](https://github.com/bioexcel/biobb_dna/releases/tag/v5.0.1)? + +### Changes + +* [FIX](all): Accept lists in different formats on input properties. + ## What's new in version [5.0.0](https://github.com/bioexcel/biobb_dna/releases/tag/v5.0.0)? ### Changes diff --git a/biobb_dna/docs/source/conf.py b/biobb_dna/docs/source/conf.py index 6c5496a..7b422e3 100644 --- a/biobb_dna/docs/source/conf.py +++ b/biobb_dna/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: @@ -56,27 +56,27 @@ # '.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_dna' -copyright = u'2024, Bioexcel Project' -author = u'Bioexcel Project' +project = "biobb_dna" +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_dna_doc' +htmlhelp_basename = "biobb_dna_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_dna.tex', u'biobb_dna Documentation', - u'Bioexcel Project', 'manual'), + ( + master_doc, + "biobb_dna.tex", + "biobb_dna Documentation", + "Bioexcel Project", + "manual", + ), ] # The name of an image file (relative to this directory) to place at the top of @@ -274,10 +276,7 @@ def setup(app): # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'biobb_dna', u'biobb_dna Documentation', - [author], 1) -] +man_pages = [(master_doc, "biobb_dna", "biobb_dna Documentation", [author], 1)] # If true, show URL addresses after external links. # man_show_urls = False @@ -289,9 +288,15 @@ def setup(app): # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'biobb_dna', u'biobb_dna Documentation', - author, 'biobb_dna', 'biobb_dna template building block', - 'Miscellaneous'), + ( + master_doc, + "biobb_dna", + "biobb_dna Documentation", + author, + "biobb_dna", + "biobb_dna template building block", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. diff --git a/biobb_dna/docs/source/readme.md b/biobb_dna/docs/source/readme.md index 155105d..91f1b3f 100644 --- a/biobb_dna/docs/source/readme.md +++ b/biobb_dna/docs/source/readme.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_dna?label=Conda)](https://anaconda.org/bioconda/biobb_dna) [![](https://img.shields.io/conda/dn/bioconda/biobb_dna?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_dna) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_dna?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_dna:5.0.0--pyhdfd78af_0) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_dna:5.0.1--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_dna) [![](https://img.shields.io/pypi/pyversions/biobb-dna.svg?label=Python%20Versions)](https://pypi.org/project/biobb-dna/) @@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-dna.readthedocs.io/en/latest/). ### Version -v5.0.0 2024.2 +v5.0.1 2024.2 ### Installation Using PIP: @@ -51,7 +51,7 @@ Using PIP: * Installation: - pip install "biobb_dna>=5.0.0" + pip install "biobb_dna>=5.0.1" * Usage: [Python API documentation](https://biobb-dna.readthedocs.io/en/latest/modules.html) @@ -61,7 +61,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_dna>=5.0.0" + conda install -c bioconda "biobb_dna>=5.0.1" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-dna.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-dna.readthedocs.io/en/latest/command_line.html) @@ -71,13 +71,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_dna:5.0.1--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_dna:5.0.1--pyhdfd78af_0 Using SINGULARITY: @@ -86,7 +86,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:5.0.0--pyhdfd78af_0 + singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:5.0.1--pyhdfd78af_0 * Usage: diff --git a/biobb_dna/docs/source/schema.html b/biobb_dna/docs/source/schema.html index 7afd78a..26dd6a5 100644 --- a/biobb_dna/docs/source/schema.html +++ b/biobb_dna/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_dna", "isAccessibleForFree": "True", diff --git a/biobb_dna/json_schemas/biobb_dna.json b/biobb_dna/json_schemas/biobb_dna.json index 0fd5e80..5f1c4f5 100644 --- a/biobb_dna/json_schemas/biobb_dna.json +++ b/biobb_dna/json_schemas/biobb_dna.json @@ -4,9 +4,9 @@ "github": "https://github.com/bioexcel/biobb_dna", "readthedocs": "https://biobb-dna.readthedocs.io/en/latest/", "conda": "https://anaconda.org/bioconda/biobb_dna", - "docker": "https://quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0", - "singularity": "https://depot.galaxyproject.org/singularity/biobb_dna:5.0.0--pyhdfd78af_0", - "version": "5.0.0", + "docker": "https://quay.io/biocontainers/biobb_dna:5.0.1--pyhdfd78af_0", + "singularity": "https://depot.galaxyproject.org/singularity/biobb_dna:5.0.1--pyhdfd78af_0", + "version": "5.0.1", "rest": true, "tools": [ { diff --git a/setup.py b/setup.py index 046300f..0ccb6e0 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setuptools.setup( name="biobb_dna", - version="5.0.0", + version="5.0.1", author="Biobb developers", author_email="genis.bayarri@irbbarcelona.com", description="Biobb_dna is a package composed of different analyses for nucleic acid trajectories.", @@ -15,15 +15,12 @@ url="https://github.com/bioexcel/biobb_dna", project_urls={ "Documentation": "http://biobb-dna.readthedocs.io/en/latest/", - "Bioexcel": "https://bioexcel.eu/" + "Bioexcel": "https://bioexcel.eu/", }, - packages=setuptools.find_packages(exclude=['adapters', 'docs', 'test']), - package_data={'biobb_dna': ['py.typed']}, - install_requires=[ - 'biobb_common==5.0.0', - 'pandas>=1.3.0', - 'scikit-learn>=0.24.2'], - python_requires='>=3.9', + packages=setuptools.find_packages(exclude=["adapters", "docs", "test"]), + package_data={"biobb_dna": ["py.typed"]}, + install_requires=["biobb_common==5.0.0", "pandas>=1.3.0", "scikit-learn>=0.24.2"], + python_requires=">=3.9", entry_points={ "console_scripts": [ "biobb_curves = biobb_dna.curvesplus.biobb_curves:main", @@ -44,7 +41,7 @@ "intrahpcorr = biobb_dna.intrabp_correlations.intrahpcorr:main", "intraseqcorr = biobb_dna.intrabp_correlations.intraseqcorr:main", "average_stiffness = biobb_dna.stiffness.average_stiffness:main", - "basepair_stiffness = biobb_dna.stiffness.basepair_stiffness:main" + "basepair_stiffness = biobb_dna.stiffness.basepair_stiffness:main", ] }, classifiers=[ @@ -53,6 +50,6 @@ "License :: OSI Approved :: Apache Software License", "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX", - "Operating System :: Unix" + "Operating System :: Unix", ], )