Merge pull request #252 from bacpop/path-fix

Path fix for distance plot, update docs with new DB page
bacpop · Jan 18, 2023 · ed2b14f · ed2b14f
2 parents 9b6cad3 + de05c8d
commit ed2b14f
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Showing 9 changed files with 20 additions and 127 deletions.
diff --git a/PopPUNK/__main__.py b/PopPUNK/__main__.py
@@ -288,7 +288,7 @@ def main():
         if args.max_search_depth is not None and args.max_search_depth < max(rank_list):
             sys.stderr.write("The maximum search depth must be greater than the highest lineage rank\n")
             sys.exit(1)
-            
+
     if args.create_db == False:
         # Check and set required parameters for other modes
         if args.ref_db is None:
@@ -363,8 +363,7 @@ def main():
         # Plot results
         if not args.no_plot:
             plot_scatter(distMat,
-                         os.path.join(os.path.dirname(args.output),
-                                      os.path.basename(args.output) + "_distanceDistribution"),
+                         f"{args.output}/{os.path.basename(args.output)}_distanceDistribution",
                          args.output + " distances")
 
     #******************************#
@@ -600,7 +599,7 @@ def main():
                                     prefix = output,
                                     suffix = '_rank_' + str(rank) + '_graph',
                                     use_gpu = args.gpu_graph)
-                
+
                 # Identify clusters from output
                 lineage_clusters[rank] = \
                     printClusters(indivNetworks[rank],

diff --git a/README.md b/README.md
@@ -8,12 +8,10 @@
 [![PyPI version](https://badge.fury.io/py/poppunk.svg)](https://badge.fury.io/py/poppunk)
 <!-- badges: end -->
 
-See our website: <https://www.poppunk.net>
-
 ## Description
 
-See the [documentation](http://poppunk.readthedocs.io/en/latest/) and the
-[paper](https://doi.org/10.1101/gr.241455.118).
+See the [documentation](http://poppunk.readthedocs.io/en/latest/) the
+[paper](https://doi.org/10.1101/gr.241455.118), and [databases](https://www.bacpop.org/poppunk/).
 
 If you find PopPUNK useful, please cite us:
 
@@ -26,6 +24,11 @@ suggested methods paragraph.
 
 ## News
 
+### 2023-01-18
+
+We will retire the PopPUNK website. Databases have been expanded, and can be
+found here: https://www.bacpop.org/poppunk/.
+
 ### 2022-08-04
 The change in scikit-learn's API in v1.0.0 and above mean that HDBSCAN models
 fitted with `sklearn <=v0.24` will give an error when loaded. If you run into this,

diff --git a/docs/conf.py b/docs/conf.py
@@ -79,9 +79,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.5.0'
+version = '2.6.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.5.0'
+release = '2.6.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/index.rst b/docs/index.rst
@@ -42,7 +42,6 @@ in the `paper <https://doi.org/10.1101/gr.241455.118>`_.
    visualisation.rst
    mst.rst
    subclustering.rst
-   online.rst
    gpu.rst
    troubleshooting.rst
    scripts.rst
@@ -74,7 +73,7 @@ The advantages of PopPUNK are broadly that:
   `phandango <http://jameshadfield.github.io/phandango/>`_.
 - Everything is available within a single python executable.
 
-Citation:
+Citation
 ---------
 If you find PopPUNK useful, please cite as:
 
@@ -84,7 +83,7 @@ doi:`10.1101/gr.241455.118 <https://dx.doi.org/10.1101/gr.241455.118>`__
 
 See :doc:`citing` for more details.
 
-Index:
+Index
 ------
 
 * :ref:`genindex`

diff --git a/docs/model_distribution.rst b/docs/model_distribution.rst
@@ -4,7 +4,7 @@ If you have fitted a model yourself, you may be interested in distributing it so
 others can use it for your species. This will give consistent cluster names across datasets,
 mean the high-quality tested fit can be reused, and speeds up future analysis.
 
-Please contact us at poppunk@poppunk.net. We would be happy to add your sketches and
+Please contact us at poppunk@bacpop.org. We would be happy to add your sketches and
 fitted model to our other `databases <https://poppunk.net/pages/databases.html>`__.
 
 Database contents

diff --git a/docs/model_fitting.rst b/docs/model_fitting.rst
@@ -5,7 +5,7 @@ Fitting new models (``--fit-model``)
    :trim:
 
 If you cannot find an existing model for your species in the
-`list <https://poppunk.net/pages/databases.html>`__ you will want to fit your own.
+`list <https://www.bacpop.org/poppunk/>`__ you will want to fit your own.
 This process is flexible, and there are five different models you can use depending
 on the population structure of your dataset.
 

diff --git a/docs/online.rst b/docs/online.rst
diff --git a/docs/overview.rst b/docs/overview.rst
@@ -17,7 +17,7 @@ are the current minimum supported versions.
 
 Use query assignment mode
 ^^^^^^^^^^^^^^^^^^^^^^^^^
-If a database is available for your species (see https://poppunk.net/pages/databases.html)
+If a database is available for your species (see https://www.bacpop.org/poppunk/)
 we would strongly recommend downloading it to use to cluster your genomes. This
 has many advantages:
 
@@ -65,14 +65,10 @@ See :doc:`visualisation` for details on options.
 Use an online interface
 -----------------------
 If available, you may want to use one of the browser-based interfaces to
-PopPUNK. These include `PopPUNK-web <https://web.poppunk.net/>`__ and
+PopPUNK. These include `beebop <https://beebop.dide.ic.ac.uk/>`__ and
 `pathogen.watch <https://pathogen.watch/genomes/all?genusId=1301&speciesId=1313>`__
 (*S. pneumoniae* only).
 
-.. warning::
-   PopPUNK-web is temporarily down while we work on an updated and better supported
-   version.
-
 Using these interfaces requires nothing to be installed or set up, doesn't require any
 genome data to be shared with us, and will return interactive visualisations. If your
 species isn't available, or you have large batches of genomes to cluster you will

diff --git a/docs/query_assignment.rst b/docs/query_assignment.rst
@@ -3,14 +3,14 @@ Query assignment (``poppunk_assign``)
 This is the recommended mode to use PopPUNK, as long as a database is available for
 your species. If there is no database available, you can fit your own (:doc:`model_fitting`).
 
-Briefly, `download your reference database <https://poppunk.net/pages/databases.html>`__ and run::
+Briefly, `download your reference database <https://www.bacpop.org/poppunk/>`__ and run::
 
     poppunk_assign --db database --query qfile.txt \
     --output poppunk_clusters --threads 8
 
 Downloading a database
 ----------------------
-Current PopPUNK databases can be found here: https://poppunk.net/pages/databases.html
+Current PopPUNK databases can be found here: https://www.bacpop.org/poppunk/
 
 We refer to sequences in the database as references, and those being added
 as queries. The clusters assigned by PopPUNK are variable-length-k-mer clusters (VLKCs).