Change pp-sketchlib calls to kwargs

.github/workflows/python-package-conda.yml

@@ -6,21 +6,25 @@ jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
+      matrix:
+        python-version: [ '3.8', '3.9' ]
+        sketchlib-version: [ '1.7.4', '2.0.0' ]
       max-parallel: 5
-
+    name: linux python_${{ matrix.python-version }}_pp-sketchlib_${{ matrix.sketchlib-version }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.python-version }}
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
         conda env update --file environment.yml --name base
+        conda install -y -c conda-forge pp-sketchlib=${{ matrix.sketchlib-version }}
     - name: Lint with flake8
       run: |
         conda install flake8

LICENSE_kseq

@@ -1,5 +1,5 @@
 The MIT License
-Copyright (c) 20082-2012 by Heng Li <lh3@me.com>
+Copyright (c) 2008-2012 by Heng Li <lh3@me.com>
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
 "Software"), to deal in the Software without restriction, including

NOTICE

@@ -1,5 +1,5 @@
 
-   Copyright 2020 Zhirong Yang, John Lees
+   Copyright 2020-2022 Zhirong Yang, John Lees, Gerry Tonkin-Hill
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

README.md

@@ -1,7 +1,7 @@
 # mandrake <img src='docs/images/mandragora.png' align="right" height="139" />
 
 <!-- badges: start -->
-[![Build and run tests](https://github.com/johnlees/mandrake/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/johnlees/mandrake/actions/workflows/python-package-conda.yml)
+[![Build and run tests](https://github.com/bacpop/mandrake/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/bacpop/mandrake/actions/workflows/python-package-conda.yml)
 [![Anaconda package](https://anaconda.org/conda-forge/mandrake/badges/version.svg
 )](https://anaconda.org/conda-forge/mandrake)
 [![Documentation Status](https://readthedocs.org/projects/mandrake/badge/?version=latest)](https://mandrake.readthedocs.io/)
@@ -19,6 +19,9 @@ See https://mandrake.readthedocs.io/en/latest/installation.html for more details
 2. Run `conda create -n mandrake_env mandrake` to install into a clean environment.
 3. Run `conda activate mandrake_env` to use the environment.
 
+Refer to the [conda-forge](https://conda-forge.org/docs/user/tipsandtricks.html#installing-cuda-enabled-packages-like-tensorflow-and-pytorch) documentation if
+you want to install a CUDA (GPU) enabled version.
+
 ### Semi-manual
 
 You will need some dependencies, which you can install through `conda`:

mandrake/__init__.py

@@ -3,4 +3,4 @@
 
 '''Visualisation of pathogen population structure'''
 
-__version__ = '1.2.1'
+__version__ = '1.2.2'

mandrake/__main__.py

@@ -109,7 +109,7 @@ def main():
         if args.kNN < 0:
             raise ValueError("Invalid value for kNN")
         kNN = args.kNN
-        threshold = -1
+        threshold = -1.0
     elif args.threshold is not None:
         if args.threshold <= 0 or args.threshold > 1:
             raise ValueError("Invalid value for threshold")

mandrake/dists.py

@@ -61,31 +61,36 @@ def sketchlibDists(sketch_db, dist_col, kNN, threshold, cpus, use_gpu, device_id
             jaccard = False
         if threshold > 0:
             raise ValueError("Use kNN with --sketches")
-        I, J, dists = pp_sketchlib.querySelfSparse(sketch_db,
-                                                   names,
-                                                   kmers,
-                                                   True,
-                                                   jaccard,
-                                                   kNN,
-                                                   dist_col,
-                                                   cpus)
+        I, J, dists = pp_sketchlib.querySelfSparse(ref_db_name=sketch_db,
+                                                   rList=names,
+                                                   klist=kmers,
+                                                   random_correct=True,
+                                                   jaccard=jaccard,
+                                                   kNN=kNN,
+                                                   dist_cutoff=0,
+                                                   dist_col=dist_col,
+                                                   num_threads=cpus,
+                                                   use_gpu=use_gpu,
+                                                   device_id=device_id)
     else:
         # older versions of sketchlib do a dense query then sparsify the
         # return. Ok for smaller data, but runs out of memory on big datasets
         # sketchlib API needs positive int for kNN
         if kNN < 0:
             kNN = 0
-        I, J, dists = pp_sketchlib.queryDatabaseSparse(sketch_db,
-                                                      sketch_db,
-                                                      names,
-                                                      names,
-                                                      kmers,
-                                                      True,
-                                                      threshold,
-                                                      kNN,
-                                                      dist_col == 0,
-                                                      cpus,
-                                                      use_gpu,
-                                                      device_id)
+        if threshold <= 0:
+            threshold = 0.0
+        I, J, dists = pp_sketchlib.queryDatabaseSparse(ref_db_name=sketch_db,
+                                                       query_db_name=sketch_db,
+                                                       rList=names,
+                                                       qList=names,
+                                                       klist=kmers,
+                                                       random_correct=True,
+                                                       dist_cutoff=threshold,
+                                                       kNN=kNN,
+                                                       core=(dist_col == 0),
+                                                       num_threads=cpus,
+                                                       use_gpu=use_gpu,
+                                                       device_id=device_id)
 
     return I, J, dists, names

setup.py

@@ -107,9 +107,9 @@ def build_extension(self, ext):
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'License :: OSI Approved :: Apache Software License',
-        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
     ],
-    python_requires='>=3.7.0',
+    python_requires='>=3.8.0',
     keywords='bacteria genomics population-genetics k-mer visualisation',
     packages=['mandrake'],
     entry_points={

test/run_test.py

@@ -28,14 +28,13 @@
 sys.stderr.write("Running with each input type\n")
 subprocess.run(python_cmd + " ../mandrake-runner.py --alignment sub5k_hiv_refs_prrt_trim.fas --kNN 50 --cpus 2 --maxIter 1000000", shell=True, check=True)
 subprocess.run(python_cmd + " ../mandrake-runner.py --sketches listeria.h5 --kNN 50 --cpus 2 --maxIter 1000000", shell=True, check=True)
+subprocess.run(python_cmd + " ../mandrake-runner.py --sketches listeria.h5 --use-accessory --kNN 50 --cpus 2 --maxIter 1000000", shell=True, check=True)
 subprocess.run(python_cmd + " ../mandrake-runner.py --accessory gene_presence_absence.Rtab --kNN 50 --cpus 2 --maxIter 1000000", shell=True, check=True)
 
 sys.stderr.write("kNN and threshold both work\n")
 subprocess.run(python_cmd + " ../mandrake-runner.py --alignment sub5k_hiv_refs_prrt_trim.fas --threshold 0.1 --cpus 2 --maxIter 1000000", shell=True, check=True)
-subprocess.run(python_cmd + " ../mandrake-runner.py --sketches listeria.h5 --threshold 0.1 --use-accessory --cpus 2 --maxIter 1000000", shell=True, check=True)
 subprocess.run(python_cmd + " ../mandrake-runner.py --accessory gene_presence_absence.Rtab --threshold 0.2 --cpus 2 --maxIter 1000000", shell=True, check=True)
 
-# test updating order is correct
 sys.stderr.write("Processing can be turned off\n")
 # This won't necessarily work
 # subprocess.run(python_cmd + " ../mandrake-runner.py --sketches listeria.h5 --kNN 50 --maxIter 10000000 --no-preprocessing", shell=True, check=True)