fix: Broken documentation links (#1226)

Clinical-Genomics · Aug 17, 2023 · d83c4c5 · d83c4c5
1 parent 4fe412c
commit d83c4c5
Show file tree

Hide file tree

Showing 13 changed files with 151 additions and 198 deletions.
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,7 +5,7 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
     python: "3.11"
 

diff --git a/BALSAMIC/assets/__init__.py b/BALSAMIC/assets/__init__.py
@@ -1,9 +0,0 @@
-import pkg_resources
-
-##### FILES #####
-
-cg_logo = "assets/cg.png"
-
-##### Paths #####
-
-cg_logo_path = pkg_resources.resource_filename("BALSAMIC", cg_logo)

diff --git a/BALSAMIC/assets/images/__init__.py b/BALSAMIC/assets/images/__init__.py
diff --git a/BALSAMIC/assets/balsamic_logo.png → BALSAMIC/assets/images/balsamic_logo.png b/BALSAMIC/assets/balsamic_logo.png → BALSAMIC/assets/images/balsamic_logo.png
diff --git a/BALSAMIC/assets/cg.png → BALSAMIC/assets/images/cg.png b/BALSAMIC/assets/cg.png → BALSAMIC/assets/images/cg.png
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -33,6 +33,7 @@ Fixed:
 * vcf2cytosure container missing constants https://github.com/Clinical-Genomics/BALSAMIC/pull/1198
 * Bash commands in vep_somatic_clinical_snv https://github.com/Clinical-Genomics/BALSAMIC/pull/1200
 * Fix SVDB annotation intermediate rule https://github.com/Clinical-Genomics/BALSAMIC/pull/1218
+* Broken documentation links https://github.com/Clinical-Genomics/BALSAMIC/pull/1226
 
 Removed:
 ^^^^^^^

diff --git a/README.rst b/README.rst
@@ -2,7 +2,7 @@
 
     <p align="center">
         <a href="https://github.com/Clinical-Genomics/BALSAMIC">
-            <img  width=480 src="https://raw.githubusercontent.com/Clinical-Genomics/BALSAMIC/master/BALSAMIC/assets/balsamic_logo.png">
+            <img  width=480 src="https://raw.githubusercontent.com/Clinical-Genomics/BALSAMIC/master/BALSAMIC/assets/images/balsamic_logo.png">
         </a>
         <h3 align="center">Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (v 12.0.2)</h3>
         <h3 align="center">FastQ to Annotated VCF</h3>
@@ -11,14 +11,14 @@
 
 
 
-   
+
 BALSAMIC is basically a wrapper for its core workflow manager. The goal is to have a package with well defined cli to
 make it reproducible for user to run somatic calling regaradless of the workflow manger at its core. Right now, BALSAMIC
 is using Snakemake as its core. So one can run the sample using workflows available within this package and standard
 Snakemake cli given that there is a proper config file created.
 
 
-.. list-table:: 
+.. list-table::
    :widths: 20 50
    :header-rows: 0
    :stub-columns: 1
@@ -35,7 +35,7 @@ Snakemake cli given that there is a proper config file created.
      - |test_status_badge|
    * - Container latest release status
      - |docker_latest_release_status|
-   * - Container master and develop status 
+   * - Container master and develop status
      - |docker_latest_build_status|
    * - Code coverage
      - |code_cov_badge|_
@@ -47,18 +47,18 @@ Snakemake cli given that there is a proper config file created.
      - @ashwini06, @ivadym, @khurrammaqbool, @keyvanelhami, @mropat, @imsarath
 
 
-.. |code_cov_badge| image:: https://codecov.io/gh/Clinical-Genomics/BALSAMIC/branch/develop/graph/badge.svg?token=qP68U3PNwV 
+.. |code_cov_badge| image:: https://codecov.io/gh/Clinical-Genomics/BALSAMIC/branch/develop/graph/badge.svg?token=qP68U3PNwV
 .. _code_cov_badge: https://codecov.io/gh/Clinical-Genomics/BALSAMIC
 
 .. |latest_tag| image:: https://img.shields.io/github/v/tag/clinical-genomics/BALSAMIC
 
 .. |test_status_badge| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/pytest_and_coveralls.yml/badge.svg
 
-.. |docker_latest_build_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push.yml/badge.svg 
+.. |docker_latest_build_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push.yml/badge.svg
+
+.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v12.0.2
 
-.. |docker_latest_release_status| image:: https://github.com/Clinical-Genomics/BALSAMIC/actions/workflows/docker_build_push_release.yml/badge.svg?tag=v12.0.2 
-
-.. |snakemake_badge| image:: https://img.shields.io/badge/snakemake-%E2%89%A55.12.3-brightgreen.svg 
+.. |snakemake_badge| image:: https://img.shields.io/badge/snakemake-%E2%89%A55.12.3-brightgreen.svg
 
 .. |singularity_badge| image:: https://img.shields.io/badge/singularity-%E2%89%A53.1.1-brightgreen.svg
 

diff --git a/docs/balsamic_methods.rst b/docs/balsamic_methods.rst
@@ -70,7 +70,7 @@ We used three commercially available products from SeraCare [Material numbers: 0
 1. Foroughi-Asl, H., Jeggari, A., Maqbool, K., Ivanchuk, V., Elhami, K., & Wirta, V. BALSAMIC: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer (Version v8.2.10) [Computer software]. https://github.com/Clinical-Genomics/BALSAMIC
 2. Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data. Accessed June 22, 2020. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 3. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-i890. https://doi.org/10.1093/bioinformatics/bty560
-4. Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]
+4. Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. https://doi.org/10.48550/arXiv.1303.3997
 5. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. https://doi.org/10.1093/bioinformatics/btp352
 6. Picard Tools - By Broad Institute. Accessed June 22, 2020. https://broadinstitute.github.io/picard/
 7. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047-3048. https://doi.org/10.1093/bioinformatics/btw354
@@ -84,10 +84,10 @@ We used three commercially available products from SeraCare [Material numbers: 0
 15. Donald Freed, Rafael Aldana, Jessica A. Weber, Jeremy S. Edwards. The Sentieon Genomics Tools - A fast and accurate solution to variant calling from next-generation sequence data. Bioinformatics. 2016, Volume 32,Issue 8. https://doi.org/10.1093/bioinformatics/btv710
 16. Donald Freed, Renke Pan, Rafael Aldana. TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering. bioRvix. https://doi.org/10.1101/250647
 17. Keiran MR, Peter VL, David CW, David J, Andrew M, Adam PB , Jon WT, Patrick T, Serena Nik-Zainal, Peter J C. ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data. Curr Protoc Bioinformatics. 2016. https://doi.org/10.1002/cpbi.17
-18. Karczewski, K.J., Francioli, L.C., Tiao, G. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443. 2020. https://doi.org/10.1038/s41586-020-2308-7
-19. https://www.seracare.com/Seraseq-ctDNA-Complete-Reference-Material-AF1-0710-0671/
-20. https://www.seracare.com/Seraseq-ctDNA-Complete-Reference-Material-AF05-0710-0672/
-21. https://www.seracare.com/Seraseq-ctDNA-Complete-Reference-Material-AF01-0710-0673/
+18. Karczewski, K.J., Francioli, L.C., Tiao, G. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020). https://doi.org/10.1038/s41586-020-2308-7
+19. Seraseq ctDNA Complete Reference Material AF 1%. https://www.seracare.com/Seraseq-ctDNA-Complete-Reference-Material-AF1-0710-0671/
+20. Seraseq ctDNA Complete Reference Material AF 0.5%. https://www.seracare.com/Seraseq-ctDNA-Complete-Reference-Material-AF05-0710-0672/
+21. Seraseq ctDNA Complete Reference Material AF 0.1%. https://www.seracare.com/Seraseq-ctDNA-Complete-Reference-Material-AF01-0710-0673/
 22. Ameur, A., Dahlberg, J., Olason, P. et al. SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population. Eur J Hum Genet 25, 1253–1260 (2017). https://doi.org/10.1038/ejhg.2017.130
 23. Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov, CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing, GigaScience, Volume 10, Issue 11, November 2021, giab074, https://doi.org/10.1093/gigascience/giab074
-24. Rentzsch P., Witten D., Cooper G.M., Shendure J., Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2018. https://doi.org/10.1093/nar/gky1016. PubMed PMID: 30371827.
+24. Rentzsch P., Witten D., Cooper G.M., Shendure J., Kircher M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2018. https://doi.org/10.1093/nar/gky1016. PubMed PMID: 30371827.
diff --git a/docs/bioinfo_softwares.rst b/docs/bioinfo_softwares.rst
@@ -5,11 +5,10 @@ Tools and software
 BALSAMIC ( **version** = 12.0.2 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each
 one is included: usage and parameters, and relevant external links.
 
-
 ascatNgs
 ~~~~~~~~
 :Source code: `GitHub` `<https://github.com/cancerit/ascatNgs>`_
-:Article: `PNAS` `<https://www.pnas.org/doi/full/10.1073/pnas.1009843107/>`_
+:Article: `PNAS` `<https://doi.org/10.1073/pnas.1009843107>`_
 :Version: `4.5.0`
 
 bcftools
@@ -75,7 +74,7 @@ manta
 multiqc
 ~~~~~~~
 :Source code: `GitHub` `<https://github.com/ewels/MultiQC>`_
-:Article: `Bioinformatics` `<http://dx.doi.org/10.1093/bioinformatics/btw354>`_
+:Article: `Bioinformatics` `<https://doi.org/10.1093/bioinformatics/btw354>`_
 :Version: `1.12`
 
 mosdepth
@@ -142,4 +141,4 @@ vcf2cytosure
 ~~~~~~~~~~~~~
 :Source code: `GitHub` `<https://github.com/NBISweden/vcf2cytosure>`_
 :Article: `-`
-:Version: `0.7.1`
+:Version: `0.7.1`
diff --git a/docs/conf.py b/docs/conf.py
@@ -30,7 +30,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
-    "sphinxcontrib.napoleon",
+    "sphinx.ext.napoleon",
     "sphinx_click",
     "sphinxarg.ext",
     "recommonmark",
@@ -56,7 +56,7 @@
 # a list of builtin themes.
 #
 # html_theme = 'sphinx_rtd_theme'
-html_logo = "../BALSAMIC/assets/balsamic_logo.png"
+html_logo = "../BALSAMIC/assets/images/balsamic_logo.png"
 html_theme = "furo"
 
 # Add any paths that contain custom static files (such as style sheets) here,

diff --git a/docs/git_etiquette.rst b/docs/git_etiquette.rst
@@ -2,35 +2,30 @@
 Git etiquette
 =============
 
-It is recommended to follow a system to standardize the commit messages loosely. Following up from commit messages discussed on https://github.com/Clinical-Genomics/development/pull/97 , the format below is recommended for commit messages:
-
 **Code formatting**
 ^^^^^^^^^^^^^^^^^^^
 
 BALSAMIC is using Black (https://github.com/psf/black) as code formatter.
 
-
 **Conventional commits and PRs**
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 PRs should follow the following keywords in the title: https://www.conventionalcommits.org/en/v1.0.0/
 
 Commit messages are recommended to following the following similar to PRs:
 
-
-#. **feat**\ : Introducing a new features. This includes but not limited to workflows, SnakeMake rule, cli, and plugins. In other words, anything that is new and fundamental change will also go here. Enhancements and optimizations will go into refactor.
-#. **fix**\ : This is essentially a patch. Included but not limited to: bug fixes, hotfixes, and any patch to address a known issue.
-#. **doc**\ : Any changes to the documentation are part of doc subject line, included but not limited to docstrings, cli-help, readme, tutorial, documentation, CHANGELOG, and addition of ipython/jupyter notebook in the form of tutorial.
-#. **test**\ : Any changes to the tests are part of test subject line. This includes adding, removing or updating of the following: unittests, validation/verification dataset, and test related configs.
-#. **refactor**\ : Refactoring refers to a rather broad term. Any style changes, code enhancement, and analysis optimization.
-#. **version**\ : Any changes to .bumpversion config and or change of version will be specified with this. This includes comments within .bumpversion, structure of .bumpversion, etc.
+#. **feat**: Introducing a new features. This includes but not limited to workflows, SnakeMake rule, cli, and plugins. In other words, anything that is new and fundamental change will also go here. Enhancements and optimizations will go into refactor.
+#. **fix**: This is essentially a patch. Included but not limited to: bug fixes, hotfixes, and any patch to address a known issue.
+#. **doc**: Any changes to the documentation are part of doc subject line, included but not limited to docstrings, cli-help, readme, tutorial, documentation, CHANGELOG, and addition of ipython/jupyter notebook in the form of tutorial.
+#. **test**: Any changes to the tests are part of test subject line. This includes adding, removing or updating of the following: unittests, validation/verification dataset, and test related configs.
+#. **refactor**: Refactoring refers to a rather broad term. Any style changes, code enhancement, and analysis optimization.
+#. **version**: Any changes to .bumpversion config and or change of version will be specified with this. This includes comments within .bumpversion, structure of .bumpversion, etc.
 
 **Scope**
 ^^^^^^^^^
 
 Scope is specified within parenthesis. It show the *scope* of the subject line. The following scope are valid:
 
-
 * cli
 * style
 * rule (refers to SnakeMake rules)
@@ -45,7 +40,6 @@ Note: If scope is broad or matching with multiple (it shouldn't, but if it does)
 
 It's better to start Git commit message with the following words:
 
-
 * added
 * removed
 * updated
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -6,6 +6,5 @@ sphinx==4.2.0
 sphinx-argparse==0.3.1
 sphinx-click==3.0.2
 sphinx_rtd_theme==1.0.0
-sphinxcontrib-napoleon==0.7
 furo==2021.10.9
 cyvcf2