Update docs with changes

README.md

@@ -21,15 +21,24 @@ Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, B
 Fast and flexible bacterial genomic epidemiology with PopPUNK. *Genome Research* **29**:304-316 (2019).
 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.
+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 and roadmap
 
 The [roadmap](https://poppunk.bacpop.org/roadmap.html) can be found in the documentation.
 
-### 2023-01-18
+### 2024-08-07
+PopPUNK 2.7.0 comes with two changes:
+- Distance matrices `<db_name>.dists.npy` are no longer required or written when using
+`poppunk_assign`, with or without `--update-db`. These can be very large, especially
+with many samples, so this saves space and memory in model reuse and distribution. Note that
+the `<db_name>.dists.pkl` file is still required (but this is small).
+- We have added a `--stable` flag to `poppunk_assign`. Rather than merging hybrid clusters,
+new samples will simply be assigned to their nearest neighbour. This implies `--serial` and
+cannot be run with `--update-db`. This behaviour mimics the 'stable nomenclature' of schemes
+such as [LIN](https://doi.org/10.1093/molbev/msac135).
 
+### 2023-01-18
 We have retired the PopPUNK website. Databases have been expanded, and can be
 found here: https://www.bacpop.org/poppunk/.
 
@@ -45,11 +54,13 @@ change clusters).
 If this is a common problem let us know, as we could write a script to 'upgrade'
 HDBSCAN models.
 See issue [#213](https://github.com/bacpop/PopPUNK/issues/213) for more details.
+
 ### 2021-03-15
 We have fixed a number of bugs with may affect the use of `poppunk_assign` with
 `--update-db`. We have also fixed a number of bugs with GPU distances. These are
 'advanced' features and are not likely to be encountered in most cases, but if you do wish to use either of these features please make sure that you are using
 `PopPUNK >=v2.4.0` with `pp-sketchlib >=v1.7.0`.
+
 ### 2020-09-30
 We have discovered a bug affecting the interaction of pp-sketchlib and PopPUNK.
 If you have used `PopPUNK >=v2.0.0` with `pp-sketchlib <v1.5.1` label order may

docs/index.rst

@@ -58,7 +58,7 @@ The advantages of PopPUNK are broadly that:
 - It is fast, and scalable to over :math:`10^{5}` genomes in a single run.
 - Assigning new query sequences to a cluster using an existing database is scalable even beyond this.
 - Cluster names remain consistent between studies, and other cluster labels such as MLST
-  can be appended.
+  can be appended. **Please note that when used as documented PopPUNK outputs stable nomenclature**.
 - Databases can be updated online (as sequences arrive).
 - Online updating is equivalent to building databases from scratch.
 - Databases can be kept small and managable by only keeping representative isolates.

docs/roadmap.rst

@@ -11,14 +11,9 @@ 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
+3. 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.
 
@@ -27,8 +22,6 @@ 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.