2024.2

README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_cp2k?label=Conda)](https://anaconda.org/bioconda/biobb_cp2k)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_cp2k?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_cp2k)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_cp2k?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_cp2k:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_cp2k:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_cp2k)
 [![](https://img.shields.io/pypi/pyversions/biobb-cp2k.svg?label=Python%20Versions)](https://pypi.org/project/biobb-cp2k/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-cp2k.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_cp2k>=4.2.0"
+        pip install "biobb_cp2k>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-cp2k.readthedocs.io/en/latest/modules.html)
@@ -61,7 +61,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_cp2k>=4.2.0"
+        conda install -c bioconda "biobb_cp2k>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-cp2k.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-cp2k.readthedocs.io/en/latest/command_line.html)
@@ -71,13 +71,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_cp2k:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_cp2k:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_cp2k:4.2.0--pyhdfd78af_0
+        docker run quay.io/biocontainers/biobb_cp2k:5.0.0--pyhdfd78af_0
 
 Using SINGULARITY:
 
@@ -86,7 +86,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_cp2k.sif https://depot.galaxyproject.org/singularity/biobb_cp2k:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_cp2k.sif https://depot.galaxyproject.org/singularity/biobb_cp2k:5.0.0--pyhdfd78af_0
 
 
 * Usage:

biobb_cp2k/__init__.py

@@ -1,4 +1,4 @@
 from . import cp2k
 name = "biobb_cp2k"
 __all__ = ["cp2k"]
-__version__ = "4.2.0"
+__version__ = "5.0.0"

biobb_cp2k/docs/source/change_log.md

@@ -1,5 +1,12 @@
 # Biobb CP2K changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_cp2k/releases/tag/v5.0.0)?
+
+### Changes
+
+* [FEATURE](__init__): Importing submodules when a module is loaded
+* [FEATURE] New sandbox_path property
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_cp2k/releases/tag/v4.2.0)?
 In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version.
 

biobb_cp2k/docs/source/conf.py

@@ -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
@@ -44,7 +44,6 @@
 napoleon_google_docstring = True
 
 
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -53,19 +52,19 @@
 # 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'
@@ -80,9 +79,9 @@
 # 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.
@@ -93,45 +92,45 @@
 
 # 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
 
 
 # -- 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')
 
@@ -143,26 +142,26 @@ 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,
@@ -172,80 +171,80 @@ 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 <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_cp2k_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
@@ -258,23 +257,23 @@ 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 ---------------------------------------
@@ -287,7 +286,7 @@ def setup(app):
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -302,13 +301,13 @@ 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