Change some missed "arboretum" to "arboreto" renamings.

notebooks/pySCENIC - Full pipeline.ipynb

@@ -421,9 +421,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Run GRNboost from `arboretum` to infer co-expression modules\n",
+    "### Run GRNboost from `arboreto` to infer co-expression modules\n",
     "\n",
-    "The arboretum package is used for this phase of the pipeline."
+    "The arboreto package is used for this phase of the pipeline."
    ]
   },
   {

notebooks/pySCENIC - Percentiles as threshold for modules.ipynb

@@ -98,8 +98,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from arboretum.utils import load_tf_names\n",
-    "from arboretum.algo import grnboost2\n",
+    "from arboreto.utils import load_tf_names\n",
+    "from arboreto.algo import grnboost2\n",
     "import pandas as pd\n",
     "import os\n",
     "from dask.distributed import LocalCluster, Client\n",

requirements.conda.yml

@@ -58,7 +58,7 @@ dependencies:
 - zict=0.1.3=py36h3a3bf81_0
 - zlib=1.2.11=ha838bed_2
 - pip:
-  - arboretum==0.1.3
+  - arboreto==0.1.5
   - attrs==17.4.0
   - boltons==18.0.0
   - dill==0.2.7.1

src/pyscenic/prune.py

@@ -55,8 +55,8 @@ def _prepare_client(client_or_address, num_workers):
     :return: a tuple: (Client instance, shutdown callback function).
     :raises: ValueError if no valid client input was provided.
     """
-    # Credits to Thomas Moerman (arboretum package):
-    # https://github.com/tmoerman/arboretum/blob/b065c6eade325ace104b2bb772ad15c78d573b1b/arboretum/algo.py#L139-L185
+    # Credits to Thomas Moerman (arboreto package):
+    # https://github.com/tmoerman/arboreto/blob/482ce8598da5385eb0e01a50362cb2b1e6f66a41/arboreto/algo.py#L145-L191
 
     if client_or_address is None or str(client_or_address).lower() == 'local':
         local_cluster = LocalCluster(n_workers=num_workers,