Add a warning to the README about v0.3.1

README.rst

@@ -36,6 +36,31 @@ The current release contains the following modules. More modules will be added i
 
 Please refer to `the documentation <https://cellbender.readthedocs.io/en/latest/>`_ for a quick start tutorial.
 
+.. warning::
+   The release tagged v0.3.1 included a bug which caused output count matrices to be incorrect. `The bug 
+   <https://github.com/broadinstitute/CellBender/blame/e2fb5977cb187cb4b12172c9f77ed556bca92cb0/cellbender/remove_background/estimation.py#L241>`_, 
+   introduced in `#303 <https://github.com/broadinstitute/CellBender/pull/303>`_, compromised output denoised count matrices 
+   (due to an integer overflow) and would often show up as negative entries in the output count matrices. The bug also existed on 
+   the master branch until `#347 <https://github.com/broadinstitute/CellBender/pull/347>`_.
+
+   For now, we recommend using either v0.3.0 or the master branch (after #347) until v0.3.2 is released, and then using v0.3.2.
+
+   Outputs generated with v0.3.1 (or the master branch between #303 and #347) can be salvaged by making use of the 
+   checkpoint file, which is not compromised. The following command will re-run the (inexpensive, CPU-only) 
+   estimation of the output count matrix using the saved posterior in the checkpoint file. Note the use of the new 
+   input argument ``--force-use-checkpoint`` which will allow use of a checkpoint file produced by a different CellBender version:
+
+   .. code-block:: console
+
+     (cellbender) $ cellbender remove-background \
+           --input my_raw_count_matrix_file.h5 \
+           --output my_cellbender_output_file.h5 \
+           --checkpoint path/to/ckpt.tar.gz \
+           --force-use-checkpoint
+
+   where ``path/to/ckpt.tar.gz`` is the path to the checkpoint file generated by the original run. Ensure that you pair up the right 
+   ``--input`` with the right ``--checkpoint``.
+
 Installation and Usage
 ----------------------