diff --git a/README.md b/README.md index 19cbb60..8ecec1a 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_flexdyn?label=Conda)](https://anaconda.org/bioconda/biobb_flexdyn) [![](https://img.shields.io/conda/dn/bioconda/biobb_flexdyn?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_flexdyn) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_flexdyn?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexdyn:4.2.0--pyhdfd78af_0) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.0.0--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_flexdyn) [![](https://img.shields.io/pypi/pyversions/biobb-flexdyn.svg?label=Python%20Versions)](https://pypi.org/project/biobb-flexdyn/) @@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-flexdyn.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_flexdyn>=4.2.0" + pip install "biobb_flexdyn>=5.0.0" * Usage: [Python API documentation](https://biobb-flexdyn.readthedocs.io/en/latest/modules.html) @@ -61,7 +61,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_flexdyn>=4.2.0" + conda install -c bioconda "biobb_flexdyn>=5.0.0" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-flexdyn.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-flexdyn.readthedocs.io/en/latest/command_line.html) @@ -71,13 +71,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_flexdyn:4.2.0--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_flexdyn:4.2.0--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0 Using SINGULARITY: @@ -86,7 +86,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_flexdyn.sif https://depot.galaxyproject.org/singularity/biobb_flexdyn:4.2.0--pyhdfd78af_0 + singularity pull --name biobb_flexdyn.sif https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.0.0--pyhdfd78af_0 * Usage: diff --git a/biobb_flexdyn/__init__.py b/biobb_flexdyn/__init__.py index 3833538..2bab734 100644 --- a/biobb_flexdyn/__init__.py +++ b/biobb_flexdyn/__init__.py @@ -1,4 +1,4 @@ from . import flexdyn name = "biobb_flexdyn" __all__ = ["flexdyn"] -__version__ = "4.2.0" +__version__ = "5.0.0" diff --git a/biobb_flexdyn/docs/source/change_log.md b/biobb_flexdyn/docs/source/change_log.md index 0dc8d53..52527c8 100644 --- a/biobb_flexdyn/docs/source/change_log.md +++ b/biobb_flexdyn/docs/source/change_log.md @@ -1,5 +1,11 @@ # Biobb FlexDyn changelog +## What's new in version [5.0.0](https://github.com/bioexcel/biobb_flexdyn/releases/tag/v5.0.0)? + +### Changes + +* [FEATURE] New sandbox_path property + ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_flexdyn/releases/tag/v4.2.0)? In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version. diff --git a/biobb_flexdyn/docs/source/conf.py b/biobb_flexdyn/docs/source/conf.py index 5ecc754..8e0ae72 100644 --- a/biobb_flexdyn/docs/source/conf.py +++ b/biobb_flexdyn/docs/source/conf.py @@ -24,7 +24,7 @@ # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +# needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom @@ -45,7 +45,6 @@ napoleon_google_docstring = True - # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] @@ -54,19 +53,19 @@ # source_suffix = ['.rst', '.md'] # -- Integrate markdown --------------------------------------------------- -#source_parsers = { +# source_parsers = { # '.md': 'recommonmark.parser.CommonMarkParser', -#} +# } source_suffix = ['.rst', '.md'] -#source_suffix = { +# source_suffix = { # '.rst': 'restructuredtext', # '.md': 'markdown', -#} +# } # The encoding of source files. -#source_encoding = 'utf-8-sig' +# source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' @@ -81,9 +80,9 @@ # 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. @@ -94,37 +93,37 @@ # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: -#today = '' +# today = '' # Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# today_fmt = '%B %d, %Y' # 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. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] +# modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. -#keep_warnings = False +# keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False @@ -132,7 +131,7 @@ # -- Options for HTML output ---------------------------------------------- def setup(app): - #app.add_stylesheet('theme_overrides.css') + # app.add_stylesheet('theme_overrides.css') app.add_css_file('theme_overrides.css') app.add_js_file('theme_overrides.js') @@ -144,26 +143,26 @@ def setup(app): # 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 # documentation. -#html_theme_options = {} +# html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] +# html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". -#html_title = None +# html_title = None # A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. -#html_logo = None +# html_logo = None # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -#html_favicon = None +# html_favicon = None # 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, @@ -173,80 +172,80 @@ def setup(app): # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. -#html_extra_path = [] +# html_extra_path = [] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +# html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_domain_indices = True +# html_domain_indices = True # If false, no index is generated. -#html_use_index = True +# html_use_index = True # If true, the index is split into individual pages for each letter. -#html_split_index = False +# html_split_index = False # If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True +# html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True +# html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True +# html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None +# html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' -#html_search_language = 'en' +# html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # Now only 'ja' uses this config value -#html_search_options = {'type': 'default'} +# html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. -#html_search_scorer = 'scorer.js' +# html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'biobb_flexdyn_doc' # -- Options for LaTeX output --------------------------------------------- -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', +latex_elements: dict[str, str] = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', -# Additional stuff for the LaTeX preamble. -#'preamble': '', + # Additional stuff for the LaTeX preamble. + # 'preamble': '', -# Latex figure (float) alignment -#'figure_align': 'htbp', + # Latex figure (float) alignment + # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples @@ -259,23 +258,23 @@ def setup(app): # The name of an image file (relative to this directory) to place at the top of # the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. -#latex_use_parts = False +# latex_use_parts = False # If true, show page references after internal links. -#latex_show_pagerefs = False +# latex_show_pagerefs = False # If true, show URL addresses after external links. -#latex_show_urls = False +# latex_show_urls = False # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_domain_indices = True +# latex_domain_indices = True # -- Options for manual page output --------------------------------------- @@ -288,7 +287,7 @@ def setup(app): ] # If true, show URL addresses after external links. -#man_show_urls = False +# man_show_urls = False # -- Options for Texinfo output ------------------------------------------- @@ -303,13 +302,13 @@ def setup(app): ] # Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +# texinfo_appendices = [] # If false, no module index is generated. -#texinfo_domain_indices = True +# texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False +# texinfo_no_detailmenu = False diff --git a/biobb_flexdyn/docs/source/readme.md b/biobb_flexdyn/docs/source/readme.md index 19cbb60..8ecec1a 100644 --- a/biobb_flexdyn/docs/source/readme.md +++ b/biobb_flexdyn/docs/source/readme.md @@ -3,7 +3,7 @@ [![](https://img.shields.io/conda/vn/bioconda/biobb_flexdyn?label=Conda)](https://anaconda.org/bioconda/biobb_flexdyn) [![](https://img.shields.io/conda/dn/bioconda/biobb_flexdyn?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_flexdyn) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_flexdyn?tab=tags) -[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexdyn:4.2.0--pyhdfd78af_0) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.0.0--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_flexdyn) [![](https://img.shields.io/pypi/pyversions/biobb-flexdyn.svg?label=Python%20Versions)](https://pypi.org/project/biobb-flexdyn/) @@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-flexdyn.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_flexdyn>=4.2.0" + pip install "biobb_flexdyn>=5.0.0" * Usage: [Python API documentation](https://biobb-flexdyn.readthedocs.io/en/latest/modules.html) @@ -61,7 +61,7 @@ Using ANACONDA: * Installation: - conda install -c bioconda "biobb_flexdyn>=4.2.0" + conda install -c bioconda "biobb_flexdyn>=5.0.0" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-flexdyn.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-flexdyn.readthedocs.io/en/latest/command_line.html) @@ -71,13 +71,13 @@ Using DOCKER: * Installation: - docker pull quay.io/biocontainers/biobb_flexdyn:4.2.0--pyhdfd78af_0 + docker pull quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0 * Usage: - docker run quay.io/biocontainers/biobb_flexdyn:4.2.0--pyhdfd78af_0 + docker run quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0 Using SINGULARITY: @@ -86,7 +86,7 @@ Using SINGULARITY: * Installation: - singularity pull --name biobb_flexdyn.sif https://depot.galaxyproject.org/singularity/biobb_flexdyn:4.2.0--pyhdfd78af_0 + singularity pull --name biobb_flexdyn.sif https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.0.0--pyhdfd78af_0 * Usage: diff --git a/biobb_flexdyn/docs/source/schema.html b/biobb_flexdyn/docs/source/schema.html index ee7d2d0..24dc63b 100644 --- a/biobb_flexdyn/docs/source/schema.html +++ b/biobb_flexdyn/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_flexdyn", "isAccessibleForFree": "True", @@ -22,4 +22,4 @@ "priceCurrency":"EUR" } } - + \ No newline at end of file diff --git a/biobb_flexdyn/json_schemas/biobb_flexdyn.json b/biobb_flexdyn/json_schemas/biobb_flexdyn.json index dd0208d..76141a4 100644 --- a/biobb_flexdyn/json_schemas/biobb_flexdyn.json +++ b/biobb_flexdyn/json_schemas/biobb_flexdyn.json @@ -4,81 +4,82 @@ "github": "https://github.com/bioexcel/biobb_flexdyn", "readthedocs": "https://biobb-flexdyn.readthedocs.io/en/latest/", "conda": "https://anaconda.org/bioconda/biobb_flexdyn", - "docker": "https://quay.io/biocontainers/biobb_flexdyn:4.2.0--pyhdfd78af_0", - "singularity": "https://depot.galaxyproject.org/singularity/biobb_flexdyn:4.2.0--pyhdfd78af_0", - "version": "4.2.0", + "docker": "https://quay.io/biocontainers/biobb_flexdyn:5.0.0--pyhdfd78af_0", + "singularity": "https://depot.galaxyproject.org/singularity/biobb_flexdyn:5.0.0--pyhdfd78af_0", + "version": "5.0.0", "rest": false, - "tools" : [ + "tools": [ { - "block" : "ConcoordDisco", - "tool" : "Concoord", - "desc" : "Wrapper of the Concoord_disco software.", - "exec" : "concoord_disco", + "block": "ConcoordDisco", + "tool": "Concoord", + "desc": "Wrapper of the Concoord_disco software.", + "exec": "concoord_disco", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.concoord_disco", "rest": false }, { - "block" : "ConcoordDist", - "tool" : "Concoord", - "desc" : "Wrapper of the Concoord_dist software.", - "exec" : "concoord_dist", + "block": "ConcoordDist", + "tool": "Concoord", + "desc": "Wrapper of the Concoord_dist software.", + "exec": "concoord_dist", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.concoord_dist", "rest": false }, { - "block" : "ImodImc", - "tool" : "Imods", - "desc" : "Wrapper of the imods_imc software.", - "exec" : "imod_imc", + "block": "ImodImc", + "tool": "Imods", + "desc": "Wrapper of the imods_imc software.", + "exec": "imod_imc", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.imod_imc", "rest": false }, { - "block" : "ImodImode", - "tool" : "Imods", - "desc" : "Wrapper of the imods_imode software.", - "exec" : "imod_imode", + "block": "ImodImode", + "tool": "Imods", + "desc": "Wrapper of the imods_imode software.", + "exec": "imod_imode", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.imod_imode", "rest": false }, { - "block" : "ImodImove", - "tool" : "Imods", - "desc" : "Wrapper of the imods_imove software.", - "exec" : "imod_imove", + "block": "ImodImove", + "tool": "Imods", + "desc": "Wrapper of the imods_imove software.", + "exec": "imod_imove", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.imod_imove", "rest": false }, { - "block" : "Nolb_nma", - "tool" : "NOLB", - "desc" : "Wrapper of the Nolb software.", - "exec" : "nolb_nma", + "block": "Nolb_nma", + "tool": "NOLB", + "desc": "Wrapper of the Nolb software.", + "exec": "nolb_nma", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.nolb", "rest": false }, { - "block" : "ProdyANM", - "tool" : "Prody", - "desc" : "Wrapper of the Prody software.", - "exec" : "prody_anm", + "block": "ProdyANM", + "tool": "Prody", + "desc": "Wrapper of the Prody software.", + "exec": "prody_anm", "docs": "https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.prody_anm", "rest": false } ], - "dep_pypi" : [ - "install_requires=['biobb_common==4.2.0']", - "python_requires='>=3.8'" + "dep_pypi": [ + "install_requires=['biobb_common==5.0.0', 'scipy>=1.13.0,<1.14.0']", + "python_requires='>=3.9,<3.12'" ], - "dep_conda" : [ - "python >=3.8", - "biobb_common ==4.2.0", + "dep_conda": [ + "python >=3.9,<3.12", + "sciPy >=1.13.0,<1.14.0", + "biobb_common ==5.0.0", "imods", "concoord", "nolb", "prody" ], - "keywords" : [ + "keywords": [ "3D-Bioinfo", "ELIXIR", "FlexDyn", diff --git a/setup.py b/setup.py index 6091091..d21eee3 100644 --- a/setup.py +++ b/setup.py @@ -38,6 +38,6 @@ "Programming Language :: Python :: 3.9", "License :: OSI Approved :: Apache Software License", "Operating System :: MacOS :: MacOS X", - "Operating System :: POSIX", + "Operating System :: POSIX" ], )