Merge pull request #133 from scottgigante-immunai/rpy2/converter

Clear warnings and test errors

.github/workflows/run_tests.yml

@@ -30,6 +30,10 @@ jobs:
       with:
         access_token: ${{ github.token }}
 
+    - name: Get current date
+      id: date
+      run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
+
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
@@ -63,8 +67,9 @@ jobs:
       if: startsWith(runner.os, 'Linux')
       with:
         path: ${{ env.RENV_PATHS_ROOT }}
-        key: ${{ runner.os }}-renv-${{ steps.setup-r.outputs.installed-r-version }}-${{ hashFiles('**/renv.lock') }}
+        key: ${{ runner.os }}-renv-${{ steps.setup-r.outputs.installed-r-version }}-${{ hashFiles('**/renv.lock') }}-${{ steps.date.outputs.date }}
         restore-keys: |
+          ${{ runner.os }}-renv-${{ steps.setup-r.outputs.installed-r-version }}-${{ hashFiles('**/renv.lock') }}-
           ${{ runner.os }}-renv-${{ steps.setup-r.outputs.installed-r-version }}-
 
     - name: Install python tools

scprep/run/conversion.py

@@ -76,10 +76,10 @@ def rpy2py(robject):
     for converter in [
         _rpynull2py,
         _rpysce2py,
-        rpy2.robjects.pandas2ri.rpy2py,
+        rpy2.robjects.pandas2ri.converter.rpy2py,
         _rpylist2py,
-        rpy2.robjects.numpy2ri.rpy2py,
-        rpy2.robjects.conversion.rpy2py,
+        rpy2.robjects.numpy2ri.converter.rpy2py,
+        rpy2.robjects.default_converter.rpy2py,
     ]:
         if _is_r_object(robject):
             try:
@@ -119,9 +119,9 @@ def py2rpy(pyobject):
     for converter in [
         _pynull2rpy,
         _pysce2rpy,
-        rpy2.robjects.pandas2ri.py2rpy,
-        rpy2.robjects.numpy2ri.py2rpy,
-        rpy2.robjects.conversion.py2rpy,
+        rpy2.robjects.pandas2ri.converter.py2rpy,
+        rpy2.robjects.numpy2ri.converter.py2rpy,
+        rpy2.robjects.default_converter.py2rpy,
     ]:
         if not _is_r_object(pyobject):
             try:

scprep/run/dyngen.py

@@ -6,10 +6,12 @@
     args="""lib=.libPaths()[1], dependencies=NA,
             repos='http://cran.rstudio.com', verbose=TRUE""",
     body="""
-       install.packages(c("dynwrap", "dyngen"),
-                        lib=lib,
-                        repos=repos,
-                        dependencies=dependencies)
+        install.packages(
+            c("dynwrap", "dyngen"),
+            lib=lib,
+            repos=repos,
+            dependencies=dependencies
+        )
     """,
 )
 

scprep/stats.py

@@ -11,7 +11,6 @@
 import numbers
 import numpy as np
 import pandas as pd
-import scipy.sparse
 import warnings
 
 plt = matplotlib.pyplot
@@ -550,7 +549,7 @@ def differential_expression(
     X, Y, measure="difference", direction="both", gene_names=None, n_jobs=-2
 ):
     """Calculate the most significant genes between two datasets.
-    
+
     If using ``measure="emd"``, the test statistic is multiplied by the sign of
     the mean differencein order to allow for distinguishing between positive
     and negative shifts. To ignore this, use ``direction="both"`` to sort by the

scprep/version.py

@@ -1 +1 @@
-__version__ = "1.2.0"
+__version__ = "1.2.1"

setup.py

@@ -25,7 +25,7 @@
     "mock",
     "h5py",
     "matplotlib>=3.0",
-    "rpy2>=3.0",
+    "rpy2>=3.4.3",
     "black",
 ]