update docs and ensure terminal is unset until dependencies are insta…

…lled

.devcontainer/devcontainer.json

@@ -29,7 +29,8 @@
 				"python.defaultInterpreterPath": "/opt/conda/envs/trtools/bin/python",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
-				"python.venvFolders": ["/opt/conda/envs"]
+				"python.venvFolders": ["/opt/conda/envs"],
+				"terminal.integrated.hideOnStartup": "always"
 			}
 		}
 	}

README.rst

@@ -8,6 +8,7 @@
 .. image:: https://codecov.io/gh/gymrek-lab/TRTools/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/gymrek-lab/TRTools
 
+|
 .. image:: https://github.com/codespaces/badge.svg
   :target: https://codespaces.new/gymrek-lab/TRTools
 
@@ -30,23 +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
 ^^^^^^^^
@@ -83,7 +81,7 @@ Note: if you will run or test :code:`simTR`, you will also need to install `ART
 With Docker
 ^^^^^^^^^^^
 
-Please refer to `the biocontainers registry for TRTools <https://biocontainers.pro/tools/trtools>`_.
+Please refer to `the biocontainers registry for TRTools <https://biocontainers.pro/tools/trtools>`_::
 
         docker pull quay.io/biocontainers/trtools:latest