Merge pull request #217 from bacpop/bacpop-43

Small fixes for beebop

MANIFEST.in

@@ -1,5 +1,6 @@
 recursive-include scripts *.py
 recursive-include PopPUNK/data *.gz
+recursive-include PopPUNK/data *.pkl
 recursive-include vendor *
 recursive-include src *
 include CMakeLists.txt

PopPUNK/visualise.py

@@ -290,7 +290,7 @@ def generate_visualisations(query_db,
             combined_seq = rlist
 
         # Fill in qq-distances if required
-        if self == False and tree != "none":
+        if self == False:
             sys.stderr.write("Note: Distances in " + distances + " are from assign mode\n"
                              "Note: Distance will be extended to full all-vs-all distances\n"
                              "Note: Re-run poppunk_assign with --update-db to avoid this\n")

docker2/Dockerfile

@@ -33,11 +33,15 @@ RUN add-apt-repository https://downloads.skewed.de/apt && \
     ln -s /usr/lib/python3/dist-packages/graph_tool \
       /usr/local/lib/python3.10/site-packages
 
-COPY requirements.txt /tmp/requirements.txt
-RUN pip install pybind11 && \
-  pip install -r /tmp/requirements.txt && \
-  rm -f /tmp/requirements.txt
+RUN pip install pybind11[global]
 
 COPY . /src
 WORKDIR /src
-RUN python setup.py install
+RUN pip install .
+
+RUN pip install cmake plotly ffmpeg
+
+RUN git clone -b bacpop-49 https://github.com/bacpop/mandrake.git && \
+    cd mandrake && \
+    python setup.py install && \
+    cd .. && rm -r mandrake

setup.py

@@ -103,6 +103,19 @@ def build_extension(self, ext):
         'Programming Language :: Python :: 3.8',
     ],
     python_requires='>=3.8.0',
+    install_requires=['biopython',
+                      'h5py',
+                      'hdbscan',
+                      'matplotlib',
+                      # 'mandrake', #uncomment when on PyPI
+                      'networkx',
+                      'pandas',
+                      'pp-sketchlib',
+                      'requests',
+                      'scikit-learn',
+                      'tqdm',
+                      'treeswift',
+                      ],
     keywords='bacteria genomics population-genetics k-mer',
     packages=['PopPUNK'],
     entry_points={