build: remove Dockerfile, add codespace config, and bump min python

.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

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>`_::
+
+        docker pull quay.io/biocontainers/trtools:latest
+
 Tools
 -----
 TRTools includes the following tools.