2024.2

bioexcel · Nov 20, 2024 · 94e0c69 · 94e0c69
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_gromacs?label=Conda)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_gromacs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_gromacs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_gromacs)
 [![](https://img.shields.io/pypi/pyversions/biobb-gromacs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-gromacs/)
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-gromacs.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.2
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_gromacs>=4.2.0"
+        pip install "biobb_gromacs>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_gromacs>=4.2.0"
+        conda install -c bioconda "biobb_gromacs>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-gromacs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -88,7 +88,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_gromacs/__init__.py b/biobb_gromacs/__init__.py
@@ -1,6 +1,5 @@
-from . import gromacs
-from . import gromacs_extra
+from . import gromacs, gromacs_extra
 
 name = "biobb_gromacs"
 __all__ = ["gromacs", "gromacs_extra"]
-__version__ = "4.2.0"
+__version__ = "5.0.0"
diff --git a/biobb_gromacs/docs/source/change_log.md b/biobb_gromacs/docs/source/change_log.md
@@ -1,5 +1,22 @@
 # Biobb GROMACS changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v5.0.0)?
+
+### Changes
+
+* [CI/CD](env.yaml): Update biobb_common version.
+* [Typing](ALL): Update typing from python 3.8 style to python 3.9
+* [CI/CD](conf.yml): Adding global properties to test yaml configuration
+* [CI/CD](linting_and_testing.yaml): Update GA test workflow to Python >3.9
+* [DOCS](.readthedocs.yaml): Updating to Python 3.9
+* [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore
+* [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration
+* [CI/CD](py.typed): Adding the py.typed
+* [FIX] Adding execution permissions to append_ligand
+* [UPDATE] Adding sandbox_path property to the json schemas
+* [FEATURE] New sandbox_path property
+* [CI/CD] Update grompp reference files and GA WF
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.2.0)?
 
 ### Changes

diff --git a/biobb_gromacs/docs/source/conf.py b/biobb_gromacs/docs/source/conf.py
@@ -18,7 +18,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, str(Path('../../').resolve()))
+sys.path.insert(0, str(Path("../../").resolve()))
 
 # -- General configuration ------------------------------------------------
 
@@ -29,22 +29,22 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx_rtd_theme',
-    'recommonmark'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
+    "recommonmark",
 ]
 
 # Using Google docstring style
 napoleon_numpy_docstring = False
 napoleon_google_docstring = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -55,7 +55,7 @@
 #    '.md': 'recommonmark.parser.CommonMarkParser',
 # }
 
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # source_suffix = {
 #    '.rst': 'restructuredtext',
@@ -66,21 +66,21 @@
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'biobb_gromacs'
-copyright = u'2024, Bioexcel Project'
-author = u'Bioexcel Project'
+project = "biobb_gromacs"
+copyright = "2024, Bioexcel Project"
+author = "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'4.2.0'
+version = "5.0.0"
 # The full version, including alpha/beta/rc tags.
-release = u'4.2.0'
+release = "5.0.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -97,7 +97,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns: list = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -115,7 +115,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -129,14 +129,13 @@
 
 # -- Options for HTML output ----------------------------------------------
 def setup(app):
-
-    app.add_css_file('theme_overrides.css')
-    app.add_js_file('theme_overrides.js')
+    app.add_css_file("theme_overrides.css")
+    app.add_js_file("theme_overrides.js")
 
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+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
@@ -165,7 +164,7 @@ def setup(app):
 # 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+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
@@ -228,20 +227,17 @@ def setup(app):
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'biobb_gromacs_doc'
+htmlhelp_basename = "biobb_gromacs_doc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
+latex_elements: dict = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     # 'preamble': '',
-
     # Latex figure (float) alignment
     # 'figure_align': 'htbp',
 }
@@ -250,8 +246,13 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'biobb_gromacs.tex', u'biobb_gromacs Documentation',
-     u'Bioexcel Project', 'manual'),
+    (
+        master_doc,
+        "biobb_gromacs.tex",
+        "biobb_gromacs Documentation",
+        "Bioexcel Project",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -279,10 +280,7 @@ def setup(app):
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'biobb_gromacs', u'biobb_gromacs Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "biobb_gromacs", "biobb_gromacs Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -294,10 +292,15 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'biobb_gromacs', u'biobb_gromacs Documentation',
-     author, 'biobb_gromacs',
-     'biobb_gromacs molecular dynamics building blocks',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "biobb_gromacs",
+        "biobb_gromacs Documentation",
+        author,
+        "biobb_gromacs",
+        "biobb_gromacs molecular dynamics building blocks",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.

diff --git a/biobb_gromacs/docs/source/readme.md b/biobb_gromacs/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_gromacs?label=Conda)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_gromacs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_gromacs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_gromacs)
 [![](https://img.shields.io/pypi/pyversions/biobb-gromacs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-gromacs/)
@@ -12,7 +12,7 @@
 
 [![](https://readthedocs.org/projects/biobb-gromacs/badge/?version=latest&label=Docs)](https://biobb-gromacs.readthedocs.io/en/latest/?badge=latest)
 [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
-[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
 [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
 [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
 
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-gromacs.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.2
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_gromacs>=4.2.0"
+        pip install "biobb_gromacs>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_gromacs>=4.2.0"
+        conda install -c bioconda "biobb_gromacs>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-gromacs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -88,7 +88,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_gromacs/docs/source/schema.html b/biobb_gromacs/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_gromacs",
   "isAccessibleForFree": "True",