Flake cleaning

.github/workflows/devel.yml

@@ -23,7 +23,7 @@ jobs:
         sudo apt-get install -y libcurl4-openssl-dev
         python -m pip install --upgrade pip
         pip install wheel
-        pip install pytest flake8 scikit-learn skranger omnipath scanpy adjustText pypath-omnipath psutil .
+        pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -52,7 +52,7 @@ jobs:
         export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig"
         python -m pip install --upgrade pip
         pip install wheel
-        pip install pytest flake8 scikit-learn skranger omnipath scanpy adjustText pypath-omnipath psutil .
+        pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/main.yml

@@ -21,7 +21,7 @@ jobs:
         sudo apt-get install -y libcurl4-openssl-dev
         python -m pip install --upgrade pip
         pip install wheel
-        pip install pytest-cov flake8 scikit-learn skranger omnipath scanpy adjustText pypath-omnipath psutil .
+        pip install pytest-cov flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -55,7 +55,7 @@ jobs:
         export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig"
         python -m pip install --upgrade pip
         pip install wheel
-        pip install pytest flake8 scikit-learn skranger omnipath scanpy adjustText pypath-omnipath psutil .
+        pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

decoupler/__init__.py

@@ -20,7 +20,7 @@
 from .decouple import decouple, run_consensus  # noqa: F401
 from .consensus import cons  # noqa: F401
 from .omnip import show_resources, get_resource, get_progeny, get_dorothea, translate_net, get_collectri  # noqa: F401
-from .omnip import get_ksn_omnipath
+from .omnip import get_ksn_omnipath  # noqa: F401
 from .plotting import plot_volcano, plot_violins, plot_barplot, plot_metrics_scatter, plot_metrics_boxplot  # noqa: F401
 from .plotting import plot_metrics_scatter_cols, plot_psbulk_samples, plot_filter_by_expr, plot_filter_by_prop  # noqa: F401
 from .plotting import plot_volcano_df, plot_targets  # noqa: F401

decoupler/omnip.py

@@ -361,7 +361,7 @@ def get_dorothea(
 
 def get_collectri(
         organism: str | int = 'human',
-        split_complexes = False,
+        split_complexes=False,
         ) -> pd.DataFrame:
     """
     CollecTRI gene regulatory network.