Merge pull request #116 from KrishnaswamyLab/dev

scprep 1.0.12

.github/workflows/run_tests.yml

@@ -72,7 +72,7 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         sudo apt-get update -qq
-        sudo apt-get install -y libhdf5-dev libhdf5-serial-dev pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg
+        sudo apt-get install -y pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg
 
     - name: Set up Python
       uses: actions/setup-python@v2
@@ -122,6 +122,7 @@ jobs:
     - name: Coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_SERVICE_NAME: github
       run: |
         coveralls
 

scprep/__init__.py

@@ -15,9 +15,10 @@
 import scprep.reduce
 import scprep.run
 
-import pandas as pd
+import pandas as _pd
+import packaging.version as _packaging_version
 
-if int(pd.__version__.split(".")[1]) < 26:
+if _packaging_version.parse(_pd.__version__) < _packaging_version.parse("2.0"):
 
     def _fill_value(self):
         # Used in reindex_indexer
@@ -26,6 +27,6 @@ def _fill_value(self):
         except AttributeError:
             return self.values.dtype.na_value
 
-    from pandas.core.internals.blocks import ExtensionBlock
+    from pandas.core.internals.blocks import ExtensionBlock as _ExtensionBlock
 
-    setattr(ExtensionBlock, "fill_value", property(_fill_value))
+    setattr(_ExtensionBlock, "fill_value", property(_fill_value))

scprep/plot/histogram.py

@@ -72,6 +72,8 @@ def histogram(
     title=None,
     fontsize=None,
     histtype="stepfilled",
+    label=None,
+    legend=True,
     alpha=None,
     filename=None,
     dpi=None,
@@ -114,6 +116,10 @@ def histogram(
         each other.
         'step' generates a lineplot that is by default unfilled.
         'stepfilled' generates a lineplot that is by default filled.
+    label : str or None, optional (default: None)
+        String, or sequence of strings to match multiple datasets.
+    legend : bool, optional (default: True)
+        Show the legend if ``label`` is given.
     alpha : float, optional (default: 1 for a single dataset, 0.5 for multiple)
         Histogram transparency
     filename : str or None (default: None)
@@ -152,7 +158,7 @@ def histogram(
             if abs_min == 0:
                 abs_min = 0.1
             bins = _symlog_bins(xmin, xmax, abs_min, bins=bins)
-        ax.hist(data, bins=bins, histtype=histtype, alpha=alpha, **kwargs)
+        ax.hist(data, bins=bins, histtype=histtype, alpha=alpha, label=label, **kwargs)
 
         if log == "x" or log is True:
             ax.set_xscale("symlog", linthresh=abs_min)
@@ -172,6 +178,10 @@ def histogram(
             else:
                 for c in cutoff:
                     ax.axvline(c, color="red")
+
+        if label is not None and legend:
+            ax.legend()
+
         # save and show
         if show_fig:
             show(fig)

scprep/run/conversion.py

@@ -46,7 +46,15 @@ def _pysce2rpy(pyobject):
 
 
 def _is_r_object(obj):
-    return "rpy2.robjects" in str(type(obj)) or obj is rpy2.rinterface.NULL
+    return (
+        "rpy2.robjects" in str(type(obj))
+        or "rpy2.rinterface" in str(type(obj))
+        or obj is rpy2.rinterface.NULL
+    )
+
+
+def _is_builtin(obj):
+    return isinstance(obj, (int, str, float))
 
 
 @utils._with_pkg(pkg="rpy2", min_version="3.0")
@@ -83,7 +91,12 @@ def rpy2py(robject):
         else:
             break
     if _is_r_object(robject):
-        warnings.warn("Object not converted: {}".format(robject), RuntimeWarning)
+        warnings.warn(
+            "Object not converted: {} (type {})".format(
+                robject, type(robject).__name__
+            ),
+            RuntimeWarning,
+        )
     return robject
 
 
@@ -119,6 +132,11 @@ def py2rpy(pyobject):
                 pass
         else:
             break
-    if not _is_r_object(pyobject):
-        warnings.warn("Object not converted: {}".format(pyobject), RuntimeWarning)
+    if not _is_r_object(pyobject) and not _is_builtin(pyobject):
+        warnings.warn(
+            "Object not converted: {} (type {})".format(
+                pyobject, type(pyobject).__name__
+            ),
+            RuntimeWarning,
+        )
     return pyobject

scprep/version.py

@@ -1,4 +1,4 @@
 # author: Scott Gigante <scott.gigante@yale.edu>
 # (C) 2018 Krishnaswamy Lab GPLv2
 
-__version__ = "1.0.11"
+__version__ = "1.0.12"

test/test_patch.py

@@ -25,8 +25,8 @@ class CustomBlock(ExtensionBlock):
 
 def test_fill_value():
     values = pd.Series(np.arange(3), dtype=pd.UInt16Dtype())
-    custom_block = CustomBlock(values, placement=slice(1, 2))
+    custom_block = CustomBlock(values, placement=slice(1, 2), ndim=2)
     assert pd.isna(custom_block.fill_value)
     values = pd.Series(np.arange(3), dtype=pd.SparseDtype(float, 0.0))
-    custom_block = CustomBlock(values, placement=slice(1, 2))
+    custom_block = CustomBlock(values, placement=slice(1, 2), ndim=2)
     assert not pd.isna(custom_block.fill_value)

test/test_plot.py

@@ -865,6 +865,7 @@ def test_histogram_multiple(self):
         scprep.plot.histogram(
             [scprep.select.select_rows(self.X, idx=0), [1, 2, 2, 2, 3]],
             color=["r", "b"],
+            label=["one", "two"],
         )
 
     def test_histogram_multiple_cutoff(self):