update dockerfile

Dockerfile

@@ -1,5 +1,9 @@
-FROM continuumio/anaconda
+FROM mambaorg/micromamba:1.5.6
+COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
+RUN micromamba install -y -n base -f /tmp/env.yaml && \
+    micromamba clean --all --yes
 
+USER root
 RUN apt-get --allow-releaseinfo-change update && apt-get install -y \
   build-essential \
   cmake \
@@ -12,13 +16,13 @@ RUN apt-get --allow-releaseinfo-change update && apt-get install -y \
   libyaml-dev \
   libz-dev \
   ncbi-blast+ \
-  python-pyqt5 \
+  python3-pyqt5 \
   vim
-
-RUN conda install -y -cbioconda -cbiocore python biopython pandas psutil pysam scons seaborn zlib pyyaml scikit-learn mafft # -cbioconda is for pysam, -cbiocore is for mafft
-RUN conda update -y numpy  # the previous command downgrades numpy (I'm not sure why), which breaks the seaborn import
-RUN pip install colored-traceback dendropy==4.4.0 levenshtein
-COPY . /partis
+USER $MAMBA_USER
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+RUN micromamba install -y -cconda-forge -cbioconda -cbiocore python biopython pandas psutil pysam scons seaborn zlib pyyaml scikit-learn mafft # -cbioconda is for pysam, -cbiocore is for mafft
+RUN pip install colored-traceback dendropy levenshtein
+COPY --chown=$MAMBA_USER:$MAMBA_USER_GID . /partis
 WORKDIR /partis
 RUN ./bin/build.sh
 CMD ./test/test.py --quick