Merge pull request #292 from bacpop/roadmap

Add the roadmap to the docs

README.md

@@ -22,7 +22,9 @@ doi:[10.1101/gr.241455.118](https://doi.org/10.1101/gr.241455.118)
 You can also run your command with `--citation` to get a [list of citations](https://poppunk.readthedocs.io/en/latest/citing.html) and a
 suggested methods paragraph.
 
-## News
+## News and roadmap
+
+The [roadmap](https://poppunk.readthedocs.io/en/latest/roadmap.html) can be found in the documentation.
 
 ### 2023-01-18
 

docs/index.rst

@@ -48,6 +48,7 @@ in the `paper <https://doi.org/10.1101/gr.241455.118>`_.
    poppunk_iterate.rst
    citing.rst
    api.rst
+   roadmap.rst
    miscellaneous.rst
 
 Why use PopPUNK?

docs/roadmap.rst

@@ -0,0 +1,53 @@
+Roadmap
+====================================
+
+.. |nbsp| unicode:: 0xA0
+   :trim:
+
+This document describes our future plans for additions to PopPUNK, `pp-sketchlib <https://github.com/bacpop/pp-sketchlib>`__ and `BeeBOP <https://github.com/bacpop/beebop/>`__
+and BeeBOP. Tasks are in order of priority.
+
+PopPUNK
+-------
+1. Containerise the workflow. See `#193 <https://github.com/bacpop/PopPUNK/issues/193>`__, `#277 <https://github.com/bacpop/PopPUNK/issues/277>`__, `#278 <https://github.com/bacpop/PopPUNK/issues/278>`__.
+2. Add full worked tutorials back to the documentation `#275 <https://github.com/bacpop/PopPUNK/issues/275>`__.
+3. Make the update pipeline more robust. See `#273 <https://github.com/bacpop/PopPUNK/issues/273>`__.
+4. Codebase optimsation and refactoring
+    - Modularisation of the network code `#249 <https://github.com/bacpop/PopPUNK/issues/249>`__.
+    - Removing old functions `#103 <https://github.com/bacpop/PopPUNK/issues/103>`__
+5. Add more species databases:
+    - N. meningitidis `#267 <https://github.com/bacpop/PopPUNK/issues/267>`__.
+    - H. influenzae `#276 <https://github.com/bacpop/PopPUNK/issues/276>`__.
+6. Stable names for lineage/subclustering modes.
+
+Other enhancements listed on the `issue page <https://github.com/bacpop/pp-sketchlib/issues>`__ are currently not planned.
+
+pp-sketchlib
+------------
+
+1. Update installation in package managers
+    - Update for new macOS `#92 <https://github.com/bacpop/ska.rust#planned-features>`__
+    - Rebuild conda recipe for CUDA12 and newer HDF5 `#46 <https://github.com/conda-forge/pp-sketchlib-feedstock/pull/46>`__
+2. Allow amino-acids as input `#89 <https://github.com/bacpop/pp-sketchlib/issues/89>`__.
+
+Other enhancements listed on the `issue page <https://github.com/bacpop/pp-sketchlib/issues>`__ are currently not planned.
+
+BeeBOP
+------
+
+1. Update backend database to v8 `#42 <https://github.com/bacpop/beebop/pull/42>`__.
+2. Update CI images.
+3. Add more info on landing page.
+    - News page.
+    - About page.
+    - Methods description.
+4. Add custom cluster names (e.g. GPSCs)
+5. Integration tests for error logging.
+6. Persist user data.
+    - Persist microreact tokens `#41 <https://github.com/bacpop/beebop/pull/41>`__.
+    - Allow user to change or delete tokens
+7. Add linage/subclusters to results page `#23 <https://github.com/bacpop/beebop/pull/23>`__.
+8. Report sample quality to user.
+9. Front-end update for large numbers of input files.
+10. Add serotype prediction for *S. pneumoniae*.
+11. Add multiple species databases.