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

.github/workflows/inactive_issues.yml

@@ -13,10 +13,10 @@ jobs:
       - uses: actions/stale@v5
         with:
           days-before-issue-stale: 30
-          days-before-issue-close: 14
+          #days-before-issue-close: 14
           stale-issue-label: "stale"
           stale-issue-message: "This issue is stale because it has been open for 30 days with no activity. If there is no more activity in the following 14 days it will be automatically closed."
-          close-issue-message: "This issue was closed because it has been inactive for 14 days since being marked as stale."
+          #close-issue-message: "This issue was closed because it has been inactive for 14 days since being marked as stale."
           days-before-pr-stale: -1
           days-before-pr-close: -1
           repo-token: ${{ secrets.GITHUB_TOKEN }}

.readthedocs.yaml

@@ -5,13 +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_common/docs/source/conf.py
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: "3.8"
    install:
       - requirements: biobb_common/docs/requirements.txt
       - method: pip

README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_common?label=Conda)](https://anaconda.org/bioconda/biobb_common)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_common?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_common)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_1)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)]()
 [![](https://img.shields.io/pypi/pyversions/biobb-common.svg?label=Python%20Versions)]()
@@ -32,10 +32,10 @@ Biobb (BioExcel building blocks) packages are Python building blocks that
 create new layer of compatibility and interoperability over popular
 bioinformatics tools.
 The latest documentation of this package can be found in our readthedocs site:
-[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
+[latest API documentation](http://biobb-common.readthedocs.io/en/latest/).
 
 ### Version
-v4.1.0 2023.1
+v4.1.0 2023.3
 
 ### 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)).

biobb_common/docs/requirements.txt

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

biobb_common/docs/source/_static/theme_overrides.css

@@ -5,12 +5,7 @@ a:visited { color:#9e8830; }
 
 .highlight { background: #fffae4; }
 
-/*.rst-content dl:not(.docutils) dt { background: #d5f0f1; color: #29b3b5; border-top: solid 3px #29b3b5; }*/
-html.writer-html4 .rst-content dl:not(.docutils)>dt, 
-html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)>dt { 
-    background: #d5f0f1; color: #29b3b5; border-top: solid 3px #29b3b5;
-}
-dl.simple dt { border: none!important; background: transparent!important; }
+.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_common/docs/source/conf.py

@@ -36,7 +36,8 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-
+    'sphinx_rtd_theme',
+    'recommonmark'
 ]
 
 # Using Google docstring style
@@ -51,9 +52,9 @@
 # source_suffix = ['.rst', '.md']
 
 # -- Integrate markdown ---------------------------------------------------
-source_parsers = {
-   '.md': 'recommonmark.parser.CommonMarkParser',
-}
+#source_parsers = {
+#   '.md': 'recommonmark.parser.CommonMarkParser',
+#}
 
 source_suffix = ['.rst', '.md']
 
@@ -124,7 +125,7 @@
 
 # -- 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')
 
 

biobb_common/docs/source/readme.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_common?label=Conda)](https://anaconda.org/bioconda/biobb_common)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_common?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_common)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_1)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)]()
 [![](https://img.shields.io/pypi/pyversions/biobb-common.svg?label=Python%20Versions)]()
@@ -32,10 +32,10 @@ Biobb (BioExcel building blocks) packages are Python building blocks that
 create new layer of compatibility and interoperability over popular
 bioinformatics tools.
 The latest documentation of this package can be found in our readthedocs site:
-[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
+[latest API documentation](http://biobb-common.readthedocs.io/en/latest/).
 
 ### Version
-v4.1.0 2023.1
+v4.1.0 2023.3
 
 ### 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)).

biobb_common/json_schemas/biobb_common.json

@@ -1,11 +1,11 @@
 {
     "_id": "biobb_common",
-    "desc": "Biobb_common is the base package required to use the biobb packages.",
+    "desc": "Biobb_common is the base package required to use all the biobb packages.",
     "github": "https://github.com/bioexcel/biobb_common",
     "readthedocs": "https://biobb-common.readthedocs.io/en/latest/",
     "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",
+    "docker": "https://quay.io/biocontainers/biobb_common:4.1.0--pyhdfd78af_1",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_1",
     "version": "4.1.0",
     "tools": [
         {

setup.py

@@ -14,7 +14,7 @@
     keywords="Bioinformatics Workflows BioExcel Compatibility",
     url="https://github.com/bioexcel/biobb_common",
     project_urls={
-        "Documentation": "http://biobb_common.readthedocs.io/en/latest/",
+        "Documentation": "http://biobb-common.readthedocs.io/en/latest/",
         "Bioexcel": "https://bioexcel.eu/",
     },
     packages=setuptools.find_packages(exclude=["docs"]),