use stable instead of latest RTD

since latest may refer to code that's still in development

CHANGELOG.md

@@ -126,7 +126,7 @@ Current limitations:
 * StatSTR now can calculate the entropy of the allele distribution at
     each locus with the \--entropy flag
 * The [TRTools documentation
-    website](https://trtools.readthedocs.io/en/latest/) now displays the
+    website](https://trtools.readthedocs.io/en/stable/) now displays the
     release notes.
 
 ### Command line interface changes

README.rst

@@ -21,7 +21,7 @@ TRTools
 
 TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing. It supports multiple recent genotyping tools (see below).
 
-See full documentation and examples at https://trtools.readthedocs.io/en/latest/.
+See full documentation and examples at https://trtools.readthedocs.io/en/stable/.
 
 If you use TRTools in your work, please cite: Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek. (2020) TRTools: a toolkit for genome-wide analysis of tandem repeats. Bioinformatics. (https://doi.org/10.1093/bioinformatics/btaa736)
 
@@ -82,14 +82,14 @@ Tools
 -----
 TRTools includes the following tools.
 
-* `mergeSTR <https://trtools.readthedocs.io/en/latest/source/mergeSTR.html>`_: a tool to merge VCF files across multiple samples genotyped using the same tool
-* `dumpSTR <https://trtools.readthedocs.io/en/latest/source/dumpSTR.html>`_: a tool for filtering VCF files with TR genotypes
-* `qcSTR <https://trtools.readthedocs.io/en/latest/source/qcSTR.html>`_: a tool for generating various quality control plots for a TR callset
-* `statSTR <https://trtools.readthedocs.io/en/latest/source/statSTR.html>`_: a tool for computing various statistics on VCF files
-* `compareSTR <https://trtools.readthedocs.io/en/latest/source/compareSTR.html>`_: a tool for comparing TR callsets
-* `associaTR <https://trtools.readthedocs.io/en/latest/source/associaTR.html>`_: a tool for testing TR length-phenotype associations (e.g., running a TR GWAS)
-* `prancSTR <https://trtools.readthedocs.io/en/latest/source/prancSTR.html>`_: a tool for identifying somatic mosacisim at TRs. Currently only compatible with HipSTR VCF files. (*beta mode*)
-* `simTR <https://trtools.readthedocs.io/en/latest/source/simTR.html>`_: a tool for simulating next-generation sequencing reads from TR regions. (*beta mode*)
+* `mergeSTR <https://trtools.readthedocs.io/en/stable/source/mergeSTR.html>`_: a tool to merge VCF files across multiple samples genotyped using the same tool
+* `dumpSTR <https://trtools.readthedocs.io/en/stable/source/dumpSTR.html>`_: a tool for filtering VCF files with TR genotypes
+* `qcSTR <https://trtools.readthedocs.io/en/stable/source/qcSTR.html>`_: a tool for generating various quality control plots for a TR callset
+* `statSTR <https://trtools.readthedocs.io/en/stable/source/statSTR.html>`_: a tool for computing various statistics on VCF files
+* `compareSTR <https://trtools.readthedocs.io/en/stable/source/compareSTR.html>`_: a tool for comparing TR callsets
+* `associaTR <https://trtools.readthedocs.io/en/stable/source/associaTR.html>`_: a tool for testing TR length-phenotype associations (e.g., running a TR GWAS)
+* `prancSTR <https://trtools.readthedocs.io/en/stable/source/prancSTR.html>`_: a tool for identifying somatic mosacisim at TRs. Currently only compatible with HipSTR VCF files. (*beta mode*)
+* `simTR <https://trtools.readthedocs.io/en/stable/source/simTR.html>`_: a tool for simulating next-generation sequencing reads from TR regions. (*beta mode*)
 
 Type :code:`<command> --help` to see a full set of options.
 
@@ -102,8 +102,8 @@ It additionally includes a python library, :code:`trtools`, which can be accesse
 Usage
 -----
 
-We recommend new users start with the example commands described in the `command-line interface for each tool <https://trtools.readthedocs.io/en/latest/UTILITIES.html>`_.
-We also suggest going through our `vignettes <https://trtools.readthedocs.io/en/latest/VIGNETTES.html>`_ that walk through some example workflows using TRTools.
+We recommend new users start with the example commands described in the `command-line interface for each tool <https://trtools.readthedocs.io/en/stable/UTILITIES.html>`_.
+We also suggest going through our `vignettes <https://trtools.readthedocs.io/en/stable/VIGNETTES.html>`_ that walk through some example workflows using TRTools.
 
 Supported TR Callers
 --------------------
@@ -115,7 +115,7 @@ TRTools supports VCFs from the following TR genotyping tools:
 * HipSTR_
 * PopSTR_ version 2 or higher
 
-See our description of the `features and example use-cases <https://trtools.readthedocs.io/en/latest/CALLERS.html>`_ of each of these tools.
+See our description of the `features and example use-cases <https://trtools.readthedocs.io/en/stable/CALLERS.html>`_ of each of these tools.
 
 ..
     please ensure this list of links remains the same as the one in the main README
@@ -145,16 +145,14 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 #. Install TRTools from source `as above <From source_>`_.
 #. Additionally, install :code:`pytest`, `pytest-cov <https://anaconda.org/conda-forge/pytest-cov>`_, :code:`sphinx>=3` and :code:`sphinx_rtd_theme`, in your environment.
 #. Fork the TRTools repository.
-#. The :code:`develop` branch contains the latest pre-release codebase. Create a branch off of :code:`develop` titled with the name of your feature.
-#. Make your changes. 
+#. Make your changes.
 #. Document your changes.
 
-   * Add bullet point(s) to the 'Unreleased Changes' section of :code:`RELEASE_NOTES.rst` describing all the user facing changes you've made (if that section doesn't exist, create it at the top of the file). See prior releases in that file for examples.
    * Ensure all functions, modules, classes etc. conform to `numpy docstring standards <https://numpydoc.readthedocs.io/en/latest/format.html>`_.
 
     If applicable, update the REAMDEs in the directories of the files you changed with new usage information.
 
-   * New doc pages for `the website <https://trtools.readthedocs.io/en/latest/>`_ can be created under :code:`<project-root>/doc` and linked to as appropriate.
+   * New doc pages for `the website <https://trtools.readthedocs.io/en/stable/>`_ can be created under :code:`<project-root>/doc` and linked to as appropriate.
    * If you have added significant amounts of documentation in any of these ways, build the documentation locally to ensure it looks good.
 
     :code:`cd` to the :code:`doc` directory and run :code:`make clean && make html`, then view :code:`doc/_build/html/index.html` and navigate from there
@@ -163,13 +161,10 @@ We appreciate contributions to TRTools. If you would like to contribute a fix or
 
    * :code:`cd` to the root of the project and run :code:`python -m pytest --cov=. --cov-report term-missing` to make sure that (1) all tests pass and (2) any code you have added is covered by tests. (Code coverage may **not** go down).
 
-#. Submit a pull request **to the develop branch** of the central repository with a description of what changes you have made.
+#. Submit a pull request (PR) **to the master branch** of the central repository with a description of what changes you have made. Title the PR according to the `conventional commits spec <https://www.conventionalcommits.org>`_.
    A member of the TRTools team will reply and continue the contribution process from there, possibly asking for additional information/effort on your part.
 
 Publishing
 ----------
-If you are a TRTools maintainer and wish to publish changes from the develop branch into master and distribute them to PyPI and bioconda,
-please see PUBLISHING.rst in the root of the git repo.
+If you are a TRTools maintainer and wish to publish changes and distribute them to PyPI and bioconda, please see PUBLISHING.rst in the root of the git repo.
 If you are a community member and would like that to happen, contact us (see above).
-
-

trtools/compareSTR/README.rst

@@ -17,7 +17,7 @@ CompareSTR optionally will stratify results based on a user-specified FORMAT fie
 
 Note: CompareSTR is designed to be used as a QC tool. While it may be able to pick up certain biological differences in some applications (e.g. identifying de novo mutations by comparing parent and child callsets or somatic mutations by comparing callsets from different tissues), use-case specific analyses may be better performed by more specialized tools.
 
-Note: CompareSTR has the ability to stratify comparisons based on quality scores. However, beware that quality scores output by different genotypers may not be directly comparable. You can use `qcSTR <https://trtools.readthedocs.io/en/latest/source/qcSTR.html>`_ to visualize the distribution of quality scores in each VCF file seprately.
+Note: CompareSTR has the ability to stratify comparisons based on quality scores. However, beware that quality scores output by different genotypers may not be directly comparable. You can use `qcSTR <https://trtools.readthedocs.io/en/stable/source/qcSTR.html>`_ to visualize the distribution of quality scores in each VCF file seprately.
 
 Usage
 -----
@@ -83,7 +83,7 @@ compareSTR outputs the following text files and plots:
 * :code:`<outprefix>-samplecompare.tab`: Has columns sample, metric-conc-seq, metric-conc-len, numcalls. One line per sample
 * :code:`<outprefix>-samplecompare.pdf`: Plots the length concordance metric for each sample considered.
 
-See `Example Commands`_ below for example compareSTR commands for different supported TR genotypers based on example data files in this repository. More detailed use cases are also given in the vignettes https://trtools.readthedocs.io/en/develop/VIGNETTES.html.
+See `Example Commands`_ below for example compareSTR commands for different supported TR genotypers based on example data files in this repository. More detailed use cases are also given in the vignettes https://trtools.readthedocs.io/en/stable/VIGNETTES.html
 
 Instructions on Compressing and Indexing VCF files
 --------------------------------------------------

trtools/qcSTR/README.rst

@@ -68,7 +68,7 @@ metrics. Alternatively, you may specify the type(s) of quality plot(s) you wish
 the :code:`--quality` option. In that case you will get a file named
 :code:`<outprefix>-quality-<type>.pdf` for each type of plot you requested. Quality plot
 examples are shown below. To learn more about how qcSTR infers quality scores for VCFs from
-different genotypers, see `here <https://trtools.readthedocs.io/en/latest/LIBRARY_SPEC.html>`_
+different genotypers, see `here <https://trtools.readthedocs.io/en/stable/LIBRARY_SPEC.html>`_
 
 Note: quality score plots are useful when considered in the context of a single genotyper run,
 and can also be used to compare different invocations of the same genotyper. However,