Merge branch 'master' of github.com:bioexcel/biobb_structure_utils

.github/env.yaml

@@ -5,5 +5,4 @@ channels:
   - anaconda
 dependencies:
   - biobb_common ==4.1.0
-  - biobb_structure_checking ==3.12.1
-
+  - biobb_structure_checking ==3.13.4

.github/workflows/fair-software.yml

@@ -0,0 +1,15 @@
+name: fair-software
+
+on: push
+
+jobs:
+  verify:
+    name: "fair-software"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: fair-software/[email protected]
+        name: Measure compliance with fair-software.eu recommendations
+        env:
+          PYCHARM_HOSTED: "Trick colorama into displaying colored output" 
+        with:
+          MY_REPO_URL: "https://github.com/${{ github.repository }}"

.github/workflows/linting_and_testing.yml

@@ -10,6 +10,8 @@ on:
       - 'LICENSE'
       - 'setup.py'
       - 'README.md'
+      - 'CITATION.cff'
+      - 'references.jsonld'
       - '**/docs/**'
       - '**/json_schemas/**'
 
@@ -23,7 +25,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - run: echo "Repository -> ${{ github.repository }}"
       - run: echo "Branch -> ${{ github.ref }}"
@@ -83,7 +85,7 @@ jobs:
           genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt  --output-file ./reports/flake8/flake8badge.svg
 
       - name: Checkout biobb_common
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: bioexcel/biobb_common
           path: './biobb_common'

.readthedocs.yaml

@@ -5,14 +5,17 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: biobb_structure_utils/docs/source/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
-   version: "3.7"
-   install:
-      - requirements: biobb_structure_utils/docs/requirements.txt
-      - method: pip
-        path: .
+  install:
+    - requirements: biobb_structure_utils/docs/requirements.txt
+    - method: pip
+      path: .

CITATION.cff

@@ -0,0 +1,84 @@
+# YAML 1.2
+---
+abstract: "BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments."
+authors:
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Andrio"
+    given-names: "Pau"
+    orcid: "https://orcid.org/0000-0003-2116-3880"
+  -
+    affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
+    family-names: "Hospital"
+    given-names: "Adam"
+    orcid: "https://orcid.org/0000-0002-8291-8071"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Conejero"
+    given-names:  "Javier"
+    orcid: "https://orcid.org/0000-0001-6401-6229"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Jordà"
+    given-names: "Luis"
+    orcid: "https://orcid.org/0000-0002-9407-9703"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Del Pino"
+    given-names: "Marc"
+    orcid: "https://orcid.org/0000-0001-5565-7577"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Laia"
+    given-names: "Codó"
+    orcid: "https://orcid.org/0000-0002-6797-8746"
+  -
+    affiliation: "School of computer Science, the University of Manchester"
+    family-names: Werkhoven
+    given-names: Ben
+    name-particle: van
+    orcid: "https://orcid.org/0000-0002-7508-3272"
+  -
+    affiliation: "University of Manchester (UOM)"
+    family-names: "Soiland-Reyes"
+    given-names: "Stian"
+    orcid: "https://orcid.org/0000-0001-9842-9718"
+  -
+    affiliation: "University of Manchester (UOM)"
+    family-names: "Goble"
+    given-names: "Carole"
+    orcid: "https://orcid.org/0000-0003-1219-2137"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Lezzi"
+    given-names: "Daniele"
+    orcid: "https://orcid.org/0000-0001-5081-7244"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Rosa M"
+    given-names: "Badia"
+    orcid: "https://orcid.org/0000-0003-2941-5499"
+  -
+    affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)"
+    family-names: "Orozco"
+    given-names: "Modesto"
+    orcid: "https://orcid.org/0000-0002-8608-3278"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
+    family-names: "Gelpí"
+    given-names: "Josep Ll."
+    orcid: "https://orcid.org/0000-0002-0566-7723"
+    email: "[email protected]"
+
+cff-version: "1.2.0"
+date-released: "2019-09-10"
+keywords:
+  - "BioExcel"
+  - "BioBB"
+  - "Bioinformatics"
+  - "Computational Biology"
+  - "Biomolecular Workflows"
+license: "Apache-2.0"
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/bioexcel/biobb"
+title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"

README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_structure_utils?label=Conda)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_structure_utils?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_structure_utils)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_structure_utils?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.0.0--pyhdfd78af_1)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_structure_utils)
 [![](https://img.shields.io/pypi/pyversions/biobb-structure-utils.svg?label=Python%20Versions)](https://pypi.org/project/biobb-structure-utils/)
@@ -22,6 +22,12 @@
 [![](https://img.shields.io/github/last-commit/bioexcel/biobb_structure_utils?label=Last%20Commit)](https://github.com/bioexcel/biobb_structure_utils/commits/master)
 [![](https://img.shields.io/github/issues/bioexcel/biobb_structure_utils.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_structure_utils/issues/)
 
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847)
+
+[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
+
+[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
 
 # biobb_structure_utils
 
@@ -30,7 +36,7 @@ Biobb_structure_utils is the Biobb module collection to modify or extract inform
 [latest API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.0 2023.3
 
 ### Installation
 
@@ -41,7 +47,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_structure_utils>=4.0.0"
+        pip install "biobb_structure_utils>=4.1.0"
 
 
 * Usage: [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html)
@@ -51,7 +57,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_structure_utils>=4.0.0"
+        conda install -c bioconda "biobb_structure_utils>=4.1.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-structure-utils.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-structure-utils.readthedocs.io/en/latest/command_line.html)
@@ -61,13 +67,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_1
+        docker pull quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_1 <command>
+        docker run quay.io/biocontainers/biobb_structure_utils:4.1.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -76,7 +82,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.0.0--pyhdfd78af_1
+        singularity pull --name biobb_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0
 
 
 * Usage:
@@ -91,8 +97,8 @@ The command list and specification can be found at the [Command Line documentati
 ### 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) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2024 [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_structure_utils/__init__.py

@@ -1,3 +1,3 @@
 name = "biobb_structure_utils"
 __all__ = ["utils"]
-__version__ = "4.0.0"
+__version__ = "4.1.0"

biobb_structure_utils/docs/requirements.txt

@@ -1 +1,3 @@
-docutils==0.17.1
+# docutils==0.17.1
+sphinx_rtd_theme
+recommonmark

biobb_structure_utils/docs/source/_static/theme_overrides.css

@@ -5,7 +5,7 @@ a:visited { color:#9e8830; }
 
 .highlight { background: #fffae4; }
 
-.rst-content dl:not(.docutils) dt { background: #d5f0f1; color: #29b3b5; border-top: solid 3px #29b3b5; }
+.rst-content dl:not(.docutils) dt { background: #d5f0f1!important; color: #29b3b5!important; border-top: solid 3px #29b3b5!important; }
 .rst-content .viewcode-link, .rst-content .viewcode-back { color: #dcbc3c; }
 .rst-versions .rst-current-version { color: #29b3b5; }
 

biobb_structure_utils/docs/source/_static/theme_overrides.js

@@ -1,8 +1,8 @@
 $(document).ready(function() {
 	var path = '';
 
-	if($('.icon.icon-home').attr('href') == '../index.html') path = '../';
-	else if($('.icon.icon-home').attr('href') == '../../index.html') path = '../../';
+	if($('.wy-side-nav-search .icon.icon-home').attr('href') == '../index.html') path = '../';
+	else if($('.wy-side-nav-search .icon.icon-home').attr('href') == '../../index.html') path = '../../';
 
-	$('.icon.icon-home').html('<img src="' + path + '_static/logo.png" class="logo" alt="Logo">');
+	$('.wy-side-nav-search .icon.icon-home').html('<img src="' + path + '_static/logo.png" class="logo" alt="Logo">');
 });

biobb_structure_utils/docs/source/change_log.md

@@ -1,11 +1,12 @@
 # Biobb Structure Utils changelog
 
 ## What's new in version [4.1.0](https://github.com/bioexcel/biobb_structure_utils/releases/tag/v4.1.0)?
-In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
+In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version. Also biobb_structure_checking has been updated from 3.12.1 to 3.13.4.
 
 ### New features
 
 * Update to biobb_common 4.1.0 (general)
+* Update to biobb_structure_checking 3.13.4 (utils module)
 
 ## What's new in version [4.0.0](https://github.com/bioexcel/biobb_structure_utils/releases/tag/v4.0.0)?
 In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version.

biobb_structure_utils/docs/source/conf.py

@@ -35,7 +35,8 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-
+    'sphinx_rtd_theme',
+    'recommonmark'
 ]
 
 # Using Google docstring style
@@ -64,17 +65,17 @@
 
 # General information about the project.
 project = u'biobb_structure_utils'
-copyright = u'2022, Bioexcel Project'
+copyright = u'2024, Bioexcel Project'
 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'4.0.0'
+version = u'4.1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'4.0.0'
+release = u'4.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -123,7 +124,7 @@
 
 # -- Options for HTML output ----------------------------------------------
 def setup(app):
-    app.add_stylesheet('theme_overrides.css')
+    app.add_css_file('theme_overrides.css')
     app.add_js_file('theme_overrides.js')