Merge pull request #118 from KrishnaswamyLab/dev

v1.0.12.post1

.github/workflows/run_tests.yml

@@ -34,12 +34,14 @@ jobs:
 
     - name: Install tools
       run: |
-        python -m pip install --upgrade "pip<=21.0"
-        pip install --use-deprecated=legacy-resolver -U wheel setuptools
-        pip install --use-deprecated=legacy-resolver -U black flake8
+        python -m pip install --upgrade pip
+        pip install -U wheel setuptools
+        pip install -U black flake8
+
     - name: Lint with Black
       run: |
         black . --check --diff
+
     - name: Lint with flake8
       run: |
         flake8 scprep
@@ -101,6 +103,13 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-renv-${{ steps.setup-r.outputs.installed-r-version }}-
 
+    - name: Install package & dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --upgrade wheel setuptools
+        pip install --upgrade .[test]
+        python -c "import scprep"
+
     - name: Install R packages
       run: |
         if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
@@ -109,13 +118,6 @@ jobs:
         renv::install("bioc::slingshot")
       shell: Rscript {0}
 
-    - name: Install package & dependencies
-      run: |
-        python -m pip install --upgrade "pip<=21.0"
-        pip install --use-deprecated=legacy-resolver -U wheel setuptools
-        pip install --use-deprecated=legacy-resolver -U .[test,r]
-        python -c "import scprep"
-
     - name: Run tests
       run: nose2 -vvv
 

scprep/__init__.py

@@ -15,18 +15,6 @@
 import scprep.reduce
 import scprep.run
 
-import pandas as _pd
-import packaging.version as _packaging_version
+from . import _patch
 
-if _packaging_version.parse(_pd.__version__) < _packaging_version.parse("2.0"):
-
-    def _fill_value(self):
-        # Used in reindex_indexer
-        try:
-            return self.values.dtype.fill_value
-        except AttributeError:
-            return self.values.dtype.na_value
-
-    from pandas.core.internals.blocks import ExtensionBlock as _ExtensionBlock
-
-    setattr(_ExtensionBlock, "fill_value", property(_fill_value))
+_patch.patch_fill_value()

scprep/_patch.py

@@ -0,0 +1,17 @@
+import packaging.version
+import pandas as pd
+
+
+def patch_fill_value():
+    if packaging.version.parse(pd.__version__) < packaging.version.parse("2.0"):
+
+        def _fill_value(self):
+            # Used in reindex_indexer
+            try:
+                return self.values.dtype.fill_value
+            except AttributeError:
+                return self.values.dtype.na_value
+
+        from pandas.core.internals.blocks import ExtensionBlock
+
+        setattr(ExtensionBlock, "fill_value", property(_fill_value))

scprep/plot/jitter.py

@@ -195,12 +195,12 @@ def jitter(
 
         # Plotting means
         if plot_means:
+            plot_x_means = [
+                i for i in range(len(params.x_labels)) if np.any(params.x_coords == i)
+            ]
             ax.scatter(
-                np.arange(len(params.x_labels)),
-                [
-                    np.nanmean(params.y[params.x_coords == i])
-                    for i in range(len(params.x_labels))
-                ],
+                plot_x_means,
+                [np.nanmean(params.y[params.x_coords == i]) for i in plot_x_means],
                 c=means_c,
                 edgecolors="black",
                 lw=1.5,

scprep/plot/utils.py

@@ -14,7 +14,10 @@ def _with_default(param, default):
 
 
 def _mpl_is_gui_backend():
-    backend = mpl.get_backend()
+    try:
+        backend = mpl.get_backend()
+    except Exception:
+        return False
     if backend in ["module://ipykernel.pylab.backend_inline", "agg"]:
         return False
     else:

scprep/version.py

@@ -1,4 +1,4 @@
 # author: Scott Gigante <scott.gigante@yale.edu>
 # (C) 2018 Krishnaswamy Lab GPLv2
 
-__version__ = "1.0.12"
+__version__ = "1.0.13"

setup.py

@@ -8,6 +8,7 @@
     "scikit-learn>=0.19.1",
     "decorator>=4.3.0",
     "pandas>=0.25",
+    "packaging",
 ]
 
 optional_requires = [
@@ -41,7 +42,7 @@
     doc_requires += ["autodocsumm!=0.2.0"]
 else:
     test_requires += ["matplotlib>=3.0", "rpy2>=3.0", "black"]
-    optional_requires += ["anndata2ri"]
+    optional_requires += ["anndata2ri>=1.0.6"]
     doc_requires += ["autodocsumm"]
 
 version_py = os.path.join(os.path.dirname(__file__), "scprep", "version.py")

test/_test_lazyload.py

@@ -14,11 +14,11 @@ def test_lazyload():
     for module in scprep._lazyload._importspec.keys():
         if module == "anndata2ri" and sys.version_info[:2] < (3, 6):
             continue
-        if module in preloaded_modules:
-            assert getattr(scprep._lazyload, module).__class__ is type(scprep)
+        assert module not in scprep_loaded, module
+        if module in postloaded_modules:
+            assert getattr(scprep._lazyload, module).__class__ is type(scprep), module
         else:
             assert (
                 getattr(scprep._lazyload, module).__class__
                 is scprep._lazyload.AliasModule
-            )
-        assert module not in scprep_loaded, module
+            ), module

test/test_hdf5.py

@@ -68,7 +68,7 @@ def test_get_node_invalid():
 def test_get_values_invalid():
     utils.assert_raises_message(
         TypeError,
-        "Expected h5py.Dataset or tables.CArray. " "Got <class 'str'>",
+        "Expected h5py.Dataset or tables.CArray. Got <class 'str'>",
         scprep.io.hdf5.get_values,
         "invalid",
     )

test/test_lazyload.py

@@ -1,4 +1,5 @@
 import subprocess
+import mock
 import os
 import scprep
 import sys
@@ -23,18 +24,16 @@ def test_lazyload():
 
 
 def test_builtins():
-    for module in scprep._lazyload._importspec.keys():
-        if module == "anndata2ri" and sys.version_info[:2] < (3, 6):
+    for module_name in scprep._lazyload._importspec.keys():
+        if module_name == "anndata2ri" and sys.version_info[:2] < (3, 6):
             continue
-        try:
-            del sys.modules[module]
-        except KeyError:
-            pass
-        assert (
-            getattr(scprep._lazyload, module).__class__ is scprep._lazyload.AliasModule
-        )
-        try:
-            getattr(scprep._lazyload, module).__version__
-        except AttributeError:
-            pass
-        assert getattr(scprep._lazyload, module).__class__ is type(scprep)
+        with mock.patch.dict(sys.modules):
+            if module_name in sys.modules:
+                del sys.modules[module_name]
+            module = getattr(scprep._lazyload, module_name)
+            assert module.__class__ is scprep._lazyload.AliasModule, (
+                module_name,
+                module,
+            )
+            module.__package__
+            assert module.__class__ is type(scprep), (module_name, module)