couple fixes for plotting in new docker file

Dockerfile

@@ -8,6 +8,7 @@ RUN apt-get --allow-releaseinfo-change update && apt-get install -y \
   build-essential \
   cmake \
   emacs \
+  fonts-lato \
   libboost-dev \
   libgsl-dev \
   libncurses-dev \
@@ -17,10 +18,13 @@ RUN apt-get --allow-releaseinfo-change update && apt-get install -y \
   libz-dev \
   ncbi-blast+ \
   python3-pyqt5 \
-  vim
+  vim \
+  xvfb
 USER $MAMBA_USER
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
-RUN micromamba install -y -cconda-forge -cbioconda -cbiocore python biopython pandas psutil pysam scons seaborn zlib pyyaml scikit-learn mafft # -cbioconda is for pysam, -cbiocore is for mafft
+RUN micromamba install -y -c conda-forge -c bioconda -cbiocore -c etetoolkit \
+    python biopython pandas psutil pysam scons seaborn zlib pyyaml scikit-learn \
+    mafft circlify ete3 # ete_toolchain
 RUN pip install colored-traceback dendropy levenshtein
 COPY --chown=$MAMBA_USER:$MAMBA_USER_GID . /partis
 WORKDIR /partis

python/plotting.py

@@ -1043,21 +1043,23 @@ def plot_legend_only(leg_entries, plotdir, plotname, title=None, n_digits=None):
             tlab = utils.round_to_n_digits(tlab, 2)
         ax.plot([None], [None], label=str(tlab), color=lfo['color'], linewidth=lfo.get('linewidth', 5), linestyle=lfo.get('linestyle', '-'), alpha=lfo.get('alpha', 0.6))  # str() is to convert None to 'None', otherwise it doesn't show up
     handles, labels = ax.get_legend_handles_labels()
-    figlegend.legend(handles, labels, 'center', title=title)
+    figlegend.legend(handles, labels, loc='center', title=title)
     figlegend.savefig(lfn)
     return lfn
 
 # ----------------------------------------------------------------------------------------
-def mpl_init(figsize=None, fsize=20, label_fsize=15):
+def mpl_init(figsize=None, fsize=20, label_fsize=15, fweight='bold'):
     if 'seaborn' not in sys.modules:
         import seaborn  # really #$*$$*!ing slow to import, but only importing part of it doesn't seem to help
     sys.modules['seaborn'].set_style('ticks')
     mpl.rcParams.update({
         'font.size': fsize, 'axes.titlesize': fsize, 'axes.labelsize': fsize,
         'xtick.labelsize': label_fsize, 'ytick.labelsize': label_fsize,  # NOTE this gets (maybe always?) overriden by xticklabelsize/yticklabelsize in mpl_finis()
         'legend.fontsize': fsize,
-        'font.family': 'Lato', 'font.weight': 600,
-        'axes.labelweight': 600, 'axes.titleweight': 600,
+        'font.family': 'Lato',
+        'font.weight': fweight,
+        'axes.labelweight': fweight,
+        'axes.titleweight': fweight,
         'figure.autolayout': True})
     fig, ax = plt.subplots(figsize=figsize)
     fig.tight_layout()