Skip to content
Snippets Groups Projects
Commit 0d7ab69a authored by Pau Andrio's avatar Pau Andrio
Browse files

Release 2023.1

parent cb24d03b
No related branches found
Tags v4.0.0
No related merge requests found
Hide whitespace changes
Inline Side-by-side
README.md
+ 3
− 3
View file @ 0d7ab69a
......@@ -17,13 +17,13 @@ The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
### Version
v3.9.0 2022.4
v4.0.0 2023.1
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
......
biobb_common/__init__.py
+ 1
− 1
View file @ 0d7ab69a
name = "biobb_common"
__version__ = "3.9.0"
__version__ = "4.0.0"
biobb_common/docs/source/conf.py
+ 60
− 62
View file @ 0d7ab69a
# -*- coding: utf-8 -*-
#
# Pymdsetup documentation build configuration file, created by
# sphinx-quickstart on Wed Nov 22 09:36:44 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
......@@ -24,7 +24,7 @@ sys.path.insert(0, str(Path('../../').resolve()))
# -- 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
......@@ -43,8 +43,6 @@ extensions = [
napoleon_numpy_docstring = False
napoleon_google_docstring = True
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
......@@ -60,7 +58,7 @@ source_parsers = {
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'
......@@ -73,24 +71,24 @@ author = u'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'3.9.0'
version = u'4.0.0'
# The full version, including alpha/beta/rc tags.
release = u'2022.3'
release = u'2023.1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# 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.
......@@ -98,27 +96,27 @@ exclude_patterns = []
# 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
......@@ -137,26 +135,26 @@ 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
# 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,
......@@ -166,62 +164,62 @@ 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
# 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_common_doc'
......@@ -229,18 +227,18 @@ htmlhelp_basename = 'biobb_common_doc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# 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
# (source start file, target name, title,
......@@ -252,23 +250,23 @@ latex_documents = [
# 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 ---------------------------------------
......@@ -281,7 +279,7 @@ man_pages = [
]
# If true, show URL addresses after external links.
#man_show_urls = False
# man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
......@@ -296,13 +294,13 @@ texinfo_documents = [
]
# 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
biobb_common/docs/source/readme.md
+ 3
− 3
View file @ 0d7ab69a
......@@ -17,13 +17,13 @@ The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
### Version
v3.9.0 2022.4
v4.0.0 2023.1
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
......
biobb_common/docs/source/schema.html
+ 1
− 1
View file @ 0d7ab69a
......@@ -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": "3.9.0",
"softwareVersion": "4.0.0",
"applicationSuite": "BioBB BioExcel Building Blocks",
"codeRepository": "https://github.com/bioexcel/biobb_common",
"isAccessibleForFree": "True",
......
biobb_common/json_schemas/biobb_common.json
+ 3
− 3
View file @ 0d7ab69a
......@@ -6,7 +6,7 @@
"conda": "https://anaconda.org/bioconda/biobb_common",
"docker": "https://quay.io/biocontainers/biobb_common:3.8.1--pyhdfd78af_0",
"singularity": "https://depot.galaxyproject.org/singularity/biobb_common:3.8.1--pyhdfd78af_0",
"version": "3.9.0",
"version": "4.0.0",
"tools" : [
{
"block" : "",
......@@ -16,10 +16,10 @@
],
"dep_pypi" : [
"install_requires=['pyyaml', 'requests', 'biopython==1.79']",
"python_requires='>=3.7,<3.10'"
"python_requires='>=3.7,<=3.10'"
],
"dep_conda" : [
"python >=3.7,<3.10",
"python >=3.7,<=3.10",
"pyyaml",
"requests",
"biopython ==1.79"
......
biobb_common/tools/file_utils.py
+ 1
− 0
View file @ 0d7ab69a
......@@ -124,6 +124,7 @@ def zip_list(zip_file: str, file_list: typing.Iterable[str], out_log: logging.Lo
out_log (:obj:`logging.Logger`): Input log object.
"""
file_list.sort()
Path(zip_file).parent.mkdir(parents=True, exist_ok=True)
with zipfile.ZipFile(zip_file, 'w') as zip_f:
inserted = []
for index, f in enumerate(file_list):
......
setup.py
+ 2
− 2
View file @ 0d7ab69a
......@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
setuptools.setup(
name="biobb_common",
version="3.9.0",
version="4.0.0",
author="Biobb developers",
author_email="pau.andrio@bsc.es",
description="Biobb_common is the base package required to use the biobb packages.",
......@@ -19,7 +19,7 @@ setuptools.setup(
},
packages=setuptools.find_packages(exclude=['docs']),
install_requires=['pyyaml', 'requests', 'biopython==1.79'],
python_requires='>=3.7,<3.10',
python_requires='>=3.7,<=3.10',
classifiers=(
"Development Status :: 3 - Alpha",
"Programming Language :: Python :: 3.7",
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment