From 0c6325098d998f9d0f6055da7557a3a035d714c3 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Thu, 7 Sep 2023 12:36:00 +0200 Subject: [PATCH 1/9] Fixed JSON --- biobb_common/json_schemas/biobb_common.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/biobb_common/json_schemas/biobb_common.json b/biobb_common/json_schemas/biobb_common.json index f62896c..9815a82 100644 --- a/biobb_common/json_schemas/biobb_common.json +++ b/biobb_common/json_schemas/biobb_common.json @@ -4,8 +4,8 @@ "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_0", + "singularity": "https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--pyhdfd78af_0", "version": "4.1.0", "tools": [ { From 02b236587cec193e0dcf0415673a1975b231b493 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Thu, 7 Sep 2023 12:37:11 +0200 Subject: [PATCH 2/9] Fixed JSON --- README.md | 4 ++-- biobb_common/docs/source/readme.md | 4 ++-- biobb_common/json_schemas/biobb_common.json | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index b4b0ba3..ee97a1d 100644 --- a/README.md +++ b/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)]() @@ -35,7 +35,7 @@ The latest documentation of this package can be found in our readthedocs site: [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)). diff --git a/biobb_common/docs/source/readme.md b/biobb_common/docs/source/readme.md index b4b0ba3..ee97a1d 100644 --- a/biobb_common/docs/source/readme.md +++ b/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)]() @@ -35,7 +35,7 @@ The latest documentation of this package can be found in our readthedocs site: [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)). diff --git a/biobb_common/json_schemas/biobb_common.json b/biobb_common/json_schemas/biobb_common.json index 9815a82..9f8d525 100644 --- a/biobb_common/json_schemas/biobb_common.json +++ b/biobb_common/json_schemas/biobb_common.json @@ -4,8 +4,8 @@ "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:4.1.0--pyhdfd78af_0", - "singularity": "https://depot.galaxyproject.org/singularity/biobb_common:4.1.0--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": [ { From dec577fbee1a18c523dacf1e7100200c8355da68 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Thu, 5 Oct 2023 15:42:35 +0200 Subject: [PATCH 3/9] Disabled closing inactive issues --- .github/workflows/inactive_issues.yml | 4 ++-- biobb_common/json_schemas/biobb_common.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/inactive_issues.yml b/.github/workflows/inactive_issues.yml index 62e1839..1cb4248 100644 --- a/.github/workflows/inactive_issues.yml +++ b/.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 }} \ No newline at end of file diff --git a/biobb_common/json_schemas/biobb_common.json b/biobb_common/json_schemas/biobb_common.json index 9f8d525..08b0b1c 100644 --- a/biobb_common/json_schemas/biobb_common.json +++ b/biobb_common/json_schemas/biobb_common.json @@ -1,6 +1,6 @@ { "_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", From d047019a258de5058ee42365bf56f84ac27a5dda Mon Sep 17 00:00:00 2001 From: gbayarri Date: Thu, 5 Oct 2023 15:50:50 +0200 Subject: [PATCH 4/9] Fixing Read the Docs --- biobb_common/docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biobb_common/docs/requirements.txt b/biobb_common/docs/requirements.txt index 163f583..eb508c5 100644 --- a/biobb_common/docs/requirements.txt +++ b/biobb_common/docs/requirements.txt @@ -1 +1 @@ -docutils==0.17.1 \ No newline at end of file +#docutils==0.17.1 \ No newline at end of file From 44eb4728c89ea4e3cc2204c3491c42c130612816 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Thu, 5 Oct 2023 15:53:11 +0200 Subject: [PATCH 5/9] Fixing Read the Docs --- biobb_common/docs/source/_static/theme_overrides.css | 7 +------ biobb_common/docs/source/conf.py | 2 +- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/biobb_common/docs/source/_static/theme_overrides.css b/biobb_common/docs/source/_static/theme_overrides.css index 667af0a..6e3bf7e 100755 --- a/biobb_common/docs/source/_static/theme_overrides.css +++ b/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; } diff --git a/biobb_common/docs/source/conf.py b/biobb_common/docs/source/conf.py index 50fc645..0a9c4b7 100644 --- a/biobb_common/docs/source/conf.py +++ b/biobb_common/docs/source/conf.py @@ -124,7 +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') From ce3a660e5d465ab5e5a4a7f229d59ba41f48445d Mon Sep 17 00:00:00 2001 From: gbayarri Date: Thu, 5 Oct 2023 15:57:16 +0200 Subject: [PATCH 6/9] Fixing Read the Docs --- biobb_common/docs/requirements.txt | 4 +++- biobb_common/docs/source/conf.py | 9 +++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/biobb_common/docs/requirements.txt b/biobb_common/docs/requirements.txt index eb508c5..cde97f2 100644 --- a/biobb_common/docs/requirements.txt +++ b/biobb_common/docs/requirements.txt @@ -1 +1,3 @@ -#docutils==0.17.1 \ No newline at end of file +#docutils==0.17.1 +sphinx_rtd_theme +recommonmark \ No newline at end of file diff --git a/biobb_common/docs/source/conf.py b/biobb_common/docs/source/conf.py index 0a9c4b7..358296f 100644 --- a/biobb_common/docs/source/conf.py +++ b/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'] From 2c20d9a0a594679e883e9e7c8edc731878968ec4 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Fri, 27 Oct 2023 15:36:53 +0200 Subject: [PATCH 7/9] README --- README.md | 2 +- biobb_common/docs/source/readme.md | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ee97a1d..fd278d9 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ 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 2023.3 diff --git a/biobb_common/docs/source/readme.md b/biobb_common/docs/source/readme.md index ee97a1d..fd278d9 100644 --- a/biobb_common/docs/source/readme.md +++ b/biobb_common/docs/source/readme.md @@ -32,7 +32,7 @@ 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 2023.3 diff --git a/setup.py b/setup.py index ae6e423..5d18e1d 100644 --- a/setup.py +++ b/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"]), From 1aad4536d274851abb257c572e861293d3ce83d4 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Mon, 30 Oct 2023 11:57:09 +0100 Subject: [PATCH 8/9] Fixing Read the Docs --- .readthedocs.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 91d019f..7b347e5 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,11 @@ # 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 From 492f9aa8683961938af5c47700d7804911c337c1 Mon Sep 17 00:00:00 2001 From: gbayarri Date: Mon, 30 Oct 2023 11:57:55 +0100 Subject: [PATCH 9/9] Fixing Read the Docs --- .readthedocs.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7b347e5..6164430 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -16,7 +16,6 @@ sphinx: # 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