Merge branch 'master' into ref/GetLengthGenotypes

.devcontainer/devcontainer.json

@@ -0,0 +1,41 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
+{
+	"name": "Ubuntu",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/base:jammy",
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/miniforge:1": {
+			"version": "latest",
+			"variant": "Mambaforge"
+		}
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "mamba env create -y -n trtools --file .devcontainer/environment.yml && conda run -n trtools pip install --user -e .",
+
+	// Configure tool-specific properties.
+	"customizations": {
+		"vscode": {
+			"extensions": ["ms-python.python"],
+			"settings": {
+				"python.condaPath": "/opt/conda/condabin/conda",
+				"python.defaultInterpreterPath": "/opt/conda/envs/trtools/bin/python",
+				"python.terminal.activateEnvironment": true,
+				"python.terminal.activateEnvInCurrentTerminal": true,
+				"python.venvFolders": ["/opt/conda/envs"],
+				"terminal.integrated.environmentChangesRelaunch": true,
+				"terminal.integrated.hideOnStartup": "always"
+			}
+		}
+	}
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/environment.yml

@@ -0,0 +1,14 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bioconda::art
+  - conda-forge::pip
+  - bioconda::bcftools
+  - conda-forge::pytest
+  - conda-forge::pytest-cov
+  - conda-forge::python=3.8 # the lowest version of python that we formally support
+  - conda-forge::sphinx=3.0.4
+  - conda-forge::sphinx_rtd_theme
+  - conda-forge::sphinx-autodoc-typehints

PUBLISHING.rst

@@ -11,12 +11,9 @@ Maintainers should reach consensus before going ahead with publishing changes.
 Note that the publishing to PyPI step below will require credentials
 that are only made available to core maintainers of TRTools.
 
-We use a simplified version of
-`git flow <http://web.archive.org/web/20200520162709/https://nvie.com/posts/a-successful-git-branching-model/>`_
-to maintain and publish trtools.
-We use the master branch as the default branch with the latest stable codebase.
+Note that we use the master branch as the default branch with the latest stable codebase.
 The builds from this branch are distributed to PyPI and conda.
-The develop branch contains new features that have yet to make their way into master.
+Other branches are used for development.
 
 New Dependencies
 ----------------
@@ -31,13 +28,14 @@ If you've added dependencies to trtools or its tests, those dependencies should
 Publishing Steps
 ----------------
 
-Once changes have been made to develop that are ready to be published, first choose the new version number according to `semantic versioning <https://semver.org>`_. Then set up the environment you're going to publish TRTools from:
+Once changes have been made to a branch that are ready to be published, first choose the new version number according to `semantic versioning <https://semver.org>`_.
+Then set up the environment you're going to publish TRTools from:
 
 #. Create a clean environment.
 #. Install setuptools with version >= 40.8.0
 #. Additionally, install ``pytest``, ``wheel``, ``build``, and ``twine``
 #. Clone the `trtools repo <https://github.com/gymrek-lab/TRTools>`_
-#. Check out the develop branch
+#. Check out the branch with the new work
 #. Run :code:`pip install --upgrade pip && pip install -e .`
 
 Then go through the steps of merging the changes into the master branch:
@@ -46,7 +44,7 @@ Then go through the steps of merging the changes into the master branch:
 #. Update the version number listed in the :code:`pyproject.toml` file.
 #. Change the 'Unreleased Changes' section of :code:`RELEASE_NOTES.rst` to the new version number.
 #. Check if any changes have been made that have not yet been documented in the release notes. If so, document them.
-#. Submit a pull request from develop into master on the github website.
+#. Submit a pull request from this branch into master on the github website.
 #. If the code review checks pass, merge the pull request.
 #. Tag the merge commit with the package version in vX.Y.Z format. (For more details on tagging, see `below`)
 

README.rst

@@ -2,10 +2,13 @@
 .. a location that the doc/index.rst uses for including this file
 .. before_header
 
+.. image:: https://github.com/codespaces/badge.svg
+  :width: 160
+  :target: https://codespaces.new/gymrek-lab/TRTools
+
 .. image:: https://github.com/gymrek-lab/trtools/workflows/Tests/badge.svg
     :target: https://github.com/gymrek-lab/trtools/workflows/Tests/badge.svg
 
-
 .. image:: https://codecov.io/gh/gymrek-lab/TRTools/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/gymrek-lab/TRTools
 
@@ -28,23 +31,20 @@ If you use TRTools in your work, please cite: Nima Mousavi, Jonathan Margoliash,
 Install
 -------
 
+Note: TRTools supports Python versions 3.8 and up. We do not officially support python versions 3.6 and 3.7 as they are `end of life <https://devguide.python.org/versions/#status-of-python-versions>`_, but we believe TRTools likely works with them from previous testing results.
+
 With conda
 ^^^^^^^^^^
 
 ::
 
         conda install -c conda-forge -c bioconda trtools
 
-Optionally install :code:`bcftools` which is used to prepare input files for TRTools by running:
+Optionally install :code:`bcftools` which is used to prepare input files for TRTools (and :code:`ART` which is used by simTR) by running:
 
 ::
 
-        conda install -c conda-forge -c bioconda bcftools
-
-Note: Bioconda only supports python versions 3.6-3.8 currently,
-so that is all TRTools supports in conda.
-If you are using a different version of python we support (3.5 or >= 3.9),
-install TRTools using pip.
+        conda install -c conda-forge -c bioconda bcftools art
 
 With pip
 ^^^^^^^^
@@ -78,6 +78,13 @@ Note: make sure TRTools is not installed in the environment via a different meth
 
 Note: if you will run or test :code:`simTR`, you will also need to install `ART <https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm>`_. The simTR tests will only run if the executable :code:`art_illumina` is found on your :code:`PATH`. If it has been installed, :code:`which art_illumina` should return a path.
 
+With Docker
+^^^^^^^^^^^
+
+Please refer to `the biocontainers registry for TRTools <https://biocontainers.pro/tools/trtools>`_ for all of our images. To use the most recent release, run the following command::
+
+        docker pull quay.io/biocontainers/trtools:latest
+
 Tools
 -----
 TRTools includes the following tools.
@@ -145,7 +152,7 @@ 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.
+#. Create a branch off of :code:`master` titled with the name of your feature.
 #. Make your changes. 
 #. Document your changes.
 
@@ -163,7 +170,7 @@ 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 to the master branch of the central repository with a description of what changes you have made.
    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

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 ]
 description = "Toolkit for genome-wide analysis of STRs"
 readme = "README.rst"
-requires-python = ">=3.5"
+requires-python = ">=3.6"
 license = {text = "MIT"}
 classifiers = [
     "Programming Language :: Python :: 3.5",

trtools/prancSTR/README.rst

@@ -132,4 +132,4 @@ Below are :code:`prancSTR` examples using HipSTR VCFs. Data files can be found a
 
 Citations
 ----------------
-A preprint describing simTR and prancSTR is currently being prepared. The latest version of manuscript can be found in :code:`paper_draft` folder of this tool.
+The latest manuscript for citation of the tool can be found at https://doi.org/10.1101/2023.11.22.568371