fix mamba err

Author: cactuskid

notebooks/Foldtree.ipynb

@@ -179,16 +179,22 @@
         "#mamba config --set auto_update_conda false\n",
         "\n",
         "export CONDA_AUTO_UPDATE_CONDA=false\n",
-        "eval \"$(mamba shell hook --shell bash)\"\n",
         "\n",
         "if ! mamba env list | grep -qE '^\\s*foldtree\\s'; then\n",
         "    mamba create -n foldtree -y\n",
         "fi\n",
         "\n",
+        "eval \"$(mamba shell hook --shell bash)\"\n",
+        "\n",
         "mamba activate foldtree\n",
         "\n",
         "# Create the foldtree environment\n",
-        "mamba install -q -c bioconda -c conda-forge -c nodefaults python=\"${PYTHON_VERSION}\" foldseek snakemake snakedeploy snakefmt iqtree muscle quicktree fasttree=2.1.11 clustalo=1.2.4 python-wget ete3 statsmodels toytree toyplot tqdm requests biopython\n"
+        "mamba install -q -c bioconda -c conda-forge -c nodefaults python=\"${PYTHON_VERSION}\" foldseek snakemake snakedeploy snakefmt iqtree muscle quicktree fasttree=2.1.11 clustalo=1.2.4 python-wget ete3 statsmodels toytree toyplot tqdm requests biopython\n",
+        "pip install ujson\n",
+        "\n",
+        "mamba activate base\n",
+        "\n",
+        "mamba install -q -c bioconda -c conda-forge -c nodefaults python=\"${PYTHON_VERSION}\"  snakemake"
       ]
     },
     {

src/grabplddt.py

@@ -6,6 +6,8 @@
 all_structs ={}
 for struct in glob.glob(path):
     all_structs[struct] = AFDB_tools.descr(struct)
+    #unpack scipy stats describe object into a dictionary
+    all_structs[struct] = { k:v for k,v in zip( ['nobs', 'minmax', 'mean', 'variance', 'skewness', 'kurtosis'], all_structs[struct].tolist())}
 #write to log file
 with open(snakemake.log[0], 'w' ) as lfout:
     lfout.write(str(all_structs))