diff --git a/README.md b/README.md index 96ef69972722aa6a4e037e8c86216c135356900b..89fd07eca6edaa3792398ddf8b7e01afcce94819 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/biobb_common/__init__.py b/biobb_common/__init__.py index 539e65836f72ae29f5719fdfde695ed59c729ff2..a677fb4e4f006cc385f5f36cbf16ba007c4f2e29 100644 --- a/biobb_common/__init__.py +++ b/biobb_common/__init__.py @@ -1,2 +1,2 @@ name = "biobb_common" -__version__ = "3.9.0" +__version__ = "4.0.0" diff --git a/biobb_common/docs/source/conf.py b/biobb_common/docs/source/conf.py index 923b1ebfb473f6de4b11e22347ac73ab5f7a409c..f936e4f2efcae0126e68ebaa5a90bdb506ff1e26 100644 --- a/biobb_common/docs/source/conf.py +++ b/biobb_common/docs/source/conf.py @@ -1,14 +1,14 @@ # -*- 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 diff --git a/biobb_common/docs/source/readme.md b/biobb_common/docs/source/readme.md index 96ef69972722aa6a4e037e8c86216c135356900b..89fd07eca6edaa3792398ddf8b7e01afcce94819 100644 --- a/biobb_common/docs/source/readme.md +++ b/biobb_common/docs/source/readme.md @@ -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. diff --git a/biobb_common/docs/source/schema.html b/biobb_common/docs/source/schema.html index ffac06421d6dbffc1da736d4d4db046c5de5e4ec..246c1c4a4603034e558397148cfc8fe7e820a08f 100644 --- a/biobb_common/docs/source/schema.html +++ b/biobb_common/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": "3.9.0", + "softwareVersion": "4.0.0", "applicationSuite": "BioBB BioExcel Building Blocks", "codeRepository": "https://github.com/bioexcel/biobb_common", "isAccessibleForFree": "True", diff --git a/biobb_common/json_schemas/biobb_common.json b/biobb_common/json_schemas/biobb_common.json index c033a2b6ebf0287a0316c8350e35bfa5ec05f1c9..e36a50e3a78a4a90a44b5f3cef27d02293e4bbde 100644 --- a/biobb_common/json_schemas/biobb_common.json +++ b/biobb_common/json_schemas/biobb_common.json @@ -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" diff --git a/biobb_common/tools/file_utils.py b/biobb_common/tools/file_utils.py index 6aea04b1c38776719c788e16870736433678f84d..f660e6cab01bbc512428f2ad2dd8b167fa30ddc4 100644 --- a/biobb_common/tools/file_utils.py +++ b/biobb_common/tools/file_utils.py @@ -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): diff --git a/setup.py b/setup.py index ebf562cb7ddd33ce387c7cc38f8b49defaf05f84..40f8dde2906a56683521c976544df1b89ff821a2 100644 --- a/setup.py +++ b/setup.py @@ -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",