Merge pull request #25 from gwaygenomics/fix-updated-recipe

Update pycytominer version

config/options.yaml

@@ -56,6 +56,7 @@ preprocess:
     foci_cols:
       - Barcode_BarcodeCalled
       - Barcode_MatchedTo_ID
+    exact_match_reads_col: "exact_match_reads_per_cell"
   process-cells:
     perform: true
     force_overwrite: true
@@ -94,7 +95,7 @@ profile:
     perform: true
     force_overwrite: true
     prefilter_features: true
-    output_one_single_cell_file_only: false
+    output_one_single_cell_file_only: true
     cell_quality_column: Metadata_Foci_Cell_Quality
     sanitize_gene_col: true
     merge_columns:
@@ -134,7 +135,7 @@ profile:
       - variance_threshold
       - correlation_threshold
       - drop_na_columns
-      - blacklist
+      - blocklist
       - drop_outliers
     levels:
       - gene

config/utils/config_utils.py

@@ -177,10 +177,10 @@ def process_configuration(
 
     file_info["options"]["example_site"] = sites[0]
 
+    file_info["files"]["single_cell_site_files"] = {}
     if not file_info["options"]["profile"]["single_cell"][
         "output_one_single_cell_file_only"
     ]:
-        file_info["files"]["single_cell_site_files"] = {}
         for site in sites:
             # Define single cell output directory and files
             site_output_dir = pathlib.Path(

environment.yml

@@ -3,18 +3,20 @@ channels:
 - conda-forge
 dependencies:
 - conda-forge::python=3.7.1
-- conda-forge::pandas=1.0.1
-- conda-forge::numpy=1.18.4
+- conda-forge::pandas=1.2
+- conda-forge::numpy=1.20
 - conda-forge::pathlib=1.0.1
 - conda-forge::jupyter=1.0.0
+- conda-forge::jupyterlab=3.0.15
 - conda-forge::ipykernel=5.1.0
 - conda-forge::nb_conda_kernels=2.2.1
 - conda-forge::widgetsnbextension=3.5.1
 - conda-forge::jupyter_contrib_nbextensions=0.5.1
 - conda-forge::matplotlib=3.1.3
-- conda-forge::plotnine=0.6.0
+- conda-forge::plotnine=0.8.0
 - conda-forge::seaborn=0.10.1
 - conda-forge::black=19.10b0
 - conda-forge::nb_black=1.0.7
 - pip:
-  - git+https://github.com/cytomining/pycytominer@ced33f5626c5508f44729e9145c1b051366d6e96
+  - git+https://github.com/cytomining/pycytominer@fdd0e0935ab5446f5c3710e5270c5234d8ef18f1
+  - git+https://github.com/cytomining/cytominer-eval@7f94b1124c9043c5e3717c43eb317a389e4b8efa