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@PauAndrio
PauAndrio committed Oct 23, 2024
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16 changes: 8 additions & 8 deletions README.md
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[![](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:4.2.4--pyhdfd78af_0)
[![](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/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/)
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# biobb_dna

## Introduction
Biobb_dna is a package composed of different analyses for
Biobb_dna is a package composed of different analyses for
nucleic acid trajectories and helical parameters.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
Expand All @@ -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
v4.2.4 2024.1
v5.0.0 2024.2

### Installation
Using PIP:
Expand All @@ -51,7 +51,7 @@ Using PIP:
* Installation:


pip install "biobb_dna>=4.2.4"
pip install "biobb_dna>=5.0.0"


* Usage: [Python API documentation](https://biobb-dna.readthedocs.io/en/latest/modules.html)
Expand All @@ -61,7 +61,7 @@ Using ANACONDA:
* Installation:


conda install -c bioconda "biobb_dna>=4.2.4"
conda install -c bioconda "biobb_dna>=5.0.0"


* 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)
Expand All @@ -71,13 +71,13 @@ Using DOCKER:
* Installation:


docker pull quay.io/biocontainers/biobb_dna:4.2.4--pyhdfd78af_0
docker pull quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0


* Usage:


docker run quay.io/biocontainers/biobb_dna:4.2.4--pyhdfd78af_0 <command>
docker run quay.io/biocontainers/biobb_dna:5.0.0--pyhdfd78af_0 <command>

Using SINGULARITY:

Expand All @@ -86,7 +86,7 @@ Using SINGULARITY:
* Installation:


singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:4.2.4--pyhdfd78af_0
singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:5.0.0--pyhdfd78af_0


* Usage:
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2 changes: 1 addition & 1 deletion biobb_dna/__init__.py
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name = "biobb_dna"
__all__ = ["dna", "curvesplus", "backbone", "stiffness",
"interbp_correlations", "intrabp_correlations"]
__version__ = "4.2.4"
__version__ = "5.0.0"
15 changes: 11 additions & 4 deletions biobb_dna/docs/source/change_log.md
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# Biobb Analysis changelog

## What's new in version [5.0.0](https://github.com/bioexcel/biobb_dna/releases/tag/v5.0.0)?

### Changes

* [FIX] Bug fixes in seqpos of dna timeseries
* [UPDATE] Adding sandbox_path property to the json schemas

## What's new in version [4.2.4](https://github.com/bioexcel/biobb_dna/releases/tag/v4.2.4)?
In version 4.2.4 some bugs in Canion and Curves have been fixed. Added two new tools: CanalUnzip and DnaTimeseriesUnzip.

Expand Down Expand Up @@ -53,28 +60,28 @@ In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version.
* All inputs/outputs are checked for correct file format, extension and type (general)

## What's new in version [3.8.2](https://github.com/bioexcel/biobb_dna/releases/tag/v3.8.2)?
In version 3.8.2 the some dependencies have been updated for the sake of having compatibility woth other BioBB packages.
In version 3.8.2 the some dependencies have been updated for the sake of having compatibility woth other BioBB packages.

### New features

* Updated dependencies (general)

## What's new in version [3.8.1](https://github.com/bioexcel/biobb_dna/releases/tag/v3.8.1)?
In version 3.8.1 the some dependencies have been updated for the sake of having compatibility woth other BioBB packages.
In version 3.8.1 the some dependencies have been updated for the sake of having compatibility woth other BioBB packages.

### New features

* Updated dependencies (general)

## What's new in version [3.8.0](https://github.com/bioexcel/biobb_dna/releases/tag/v3.8.0)?
In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version.
In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version.

### New features

* Update to biobb_common 3.8.1 (general)

## What's new in version [3.7.0](https://github.com/bioexcel/biobb_dna/releases/tag/v3.7.0)?
In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.
In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.

### New features

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94 changes: 47 additions & 47 deletions biobb_dna/docs/source/conf.py
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Expand Up @@ -23,7 +23,7 @@
# -- 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
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source_suffix = ['.rst', '.md']

# The encoding of source files.
#source_encoding = 'utf-8-sig'
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'
Expand All @@ -74,9 +74,9 @@
# built documents.
#
# The short X.Y version.
version = u'4.2.4'
version = u'5.0.0'
# The full version, including alpha/beta/rc tags.
release = u'4.2.4'
release = u'5.0.0'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
Expand All @@ -87,37 +87,37 @@

# 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
Expand All @@ -136,26 +136,26 @@ 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
# "<project> v<release> 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,
Expand All @@ -165,69 +165,69 @@ 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 <link> 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_dna_doc'

# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
latex_elements: dict[str, str] = {
# The paper size ('letterpaper' or 'a4paper').
# 'papersize': 'letterpaper',

Expand All @@ -251,23 +251,23 @@ 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 ---------------------------------------
Expand All @@ -280,7 +280,7 @@ def setup(app):
]

# If true, show URL addresses after external links.
#man_show_urls = False
# man_show_urls = False


# -- Options for Texinfo output -------------------------------------------
Expand All @@ -295,13 +295,13 @@ 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
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