ruff apply unsafe fixes

Author: berombau

pyproject.toml

@@ -114,9 +114,6 @@ ignore = [
 ]
 extend-include = ["*.ipynb"]
 
-[tool.ruff.format]
-docstring-code-format = true
-
 [tool.ruff.pydocstyle]
 convention = "numpy"
 

src/FlowSOM/io/read_fcs.py

@@ -8,7 +8,7 @@
 
 
 def read_FCS(filepath):
-    """Reads in an FCS file
+    """Reads in an FCS file.
 
     :param filepath: An array containing a full path to the FCS file
     :type filepath: str

src/FlowSOM/main.py

@@ -21,7 +21,7 @@ class FlowSOM:
     """A class that contains all the FlowSOM data using MuData objects."""
 
     def __init__(self, inp=None, cols_to_use: np.ndarray | None = None, n_clus=10, seed: int | None = None, **kwargs):
-        """Initialize the FlowSOM AnnData object
+        """Initialize the FlowSOM AnnData object.
 
         :param inp: A file path to an FCS file or a AnnData FCS file to cluster
         :type inp: str / ad.AnnData
@@ -42,7 +42,7 @@ def __init__(self, inp=None, cols_to_use: np.ndarray | None = None, n_clus=10, s
             self._update_derived_values()
 
     def read_input(self, inp):
-        """Converts input to a FlowSOM AnnData object
+        """Converts input to a FlowSOM AnnData object.
 
         :param inp: A file path to an FCS file or a AnnData FCS file to cluster
         :type inp: str / ad.AnnData
@@ -74,7 +74,7 @@ def read_input(self, inp):
         return self.mudata
 
     def build_SOM(self, cols_to_use: np.ndarray | None = None, outlier_MAD=4, **kwargs):
-        """Initialize the SOM clustering and update FlowSOM object
+        """Initialize the SOM clustering and update FlowSOM object.
 
         :param cols_to_use:  An array of the columns to use for clustering
         :type cols_to_use: np.array
@@ -112,7 +112,7 @@ def SOM(
         importance=None,
         seed=None,
     ):
-        """Perform SOM clustering
+        """Perform SOM clustering.
 
         :param inp:  An array of the columns to use for clustering
         :type inp: np.array
@@ -181,7 +181,7 @@ def SOM(
         return codes, clusters, dists, xdim, ydim
 
     def _update_derived_values(self):
-        """Update the derived values such as median values and CV values"""
+        """Update the derived values such as median values and CV values."""
         # get dataframe of intensities and cluster labels on cell level
         df = self.mudata["cell_data"].to_df()  # [self.adata.X[:, 0].argsort()]
         df = pd.concat([self.mudata["cell_data"].obs["clustering"], df], axis=1)
@@ -243,7 +243,7 @@ def _update_derived_values(self):
             self.mudata["cluster_data"].uns["metacluster_MFIs"] = metacluster_median_values
 
     def build_MST(self):
-        """Make a minimum spanning tree"""
+        """Make a minimum spanning tree."""
         adjacency = cdist(
             self.mudata["cluster_data"].obsm["codes"],
             self.mudata["cluster_data"].obsm["codes"],
@@ -274,7 +274,7 @@ def _dist_mst(self, codes):
         return codes
 
     def metacluster(self, n_clus):
-        """Perform a (consensus) hierarchical clustering
+        """Perform a (consensus) hierarchical clustering.
 
         :param n_clus: The number of metaclusters
         :type n_clus: int
@@ -298,7 +298,7 @@ def consensus_hierarchical_clustering(
         return metaclusters
 
     def test_outliers(self, mad_allowed: int = 4, fsom_reference=None, plot_file=None, channels=None):
-        """Test if any cells are too far from their cluster centers
+        """Test if any cells are too far from their cluster centers.
 
         :param mad_allowed: Number of median absolute deviations allowed. Default = 4.
         :type mad_allowed: int
@@ -392,7 +392,7 @@ def test_outliers(self, mad_allowed: int = 4, fsom_reference=None, plot_file=Non
         return result
 
     def new_data(self, inp, mad_allowed=4):
-        """Map new data to a FlowSOM grid
+        """Map new data to a FlowSOM grid.
 
         :param inp: An anndata or filepath to an FCS file
         :type inp: ad.AnnData / str
@@ -428,7 +428,7 @@ def new_data(self, inp, mad_allowed=4):
         return fsom_new
 
     def subset(self, ids):
-        """Take a subset from a FlowSOM object
+        """Take a subset from a FlowSOM object.
 
         :param ids: An array of ids to subset
         :type ids: np.array
@@ -447,7 +447,7 @@ def get_cluster_data(self):
 
 def flowsom_clustering(inp, cols_to_use=None, n_clus=10, xdim=10, ydim=10, seed=None, **kwargs):
     """Perform FlowSOM clustering on an anndata object and returns the anndata
-       object with the FlowSOM clusters and metaclusters added as variable
+       object with the FlowSOM clusters and metaclusters added as variable.
 
     :param inp: An anndata or filepath to an FCS file
     :type inp: ad.AnnData / str

src/FlowSOM/pl/_plot_helper_functions.py

@@ -11,7 +11,7 @@
 
 
 def FlowSOM_colors():
-    """Colormap of default FlowSOM colors"""
+    """Colormap of default FlowSOM colors."""
     cmap = matplotlib.colors.LinearSegmentedColormap.from_list(
         "FlowSOM_colors",
         ["#00007F", "#0000E1", "#007FFF", "#00E1E1", "#7FFF7F", "#E1E100", "#FF7F00", "#E10000", "#7F0000"],
@@ -20,7 +20,7 @@ def FlowSOM_colors():
 
 
 def gg_color_hue():
-    """Colormap of default ggplot colors"""
+    """Colormap of default ggplot colors."""
     cmap = matplotlib.colors.ListedColormap(
         ["#F8766D", "#D89000", "#A3A500", "#39B600", "#00BF7D", "#00BFC4", "#00B0F6", "#9590FF", "#E76BF3", "#FF62BC"]
     )
@@ -67,7 +67,7 @@ def plot_FlowSOM(
     ref_node_size: int = None,
     equal_node_size: bool = False,
 ):
-    """Plots the base layer of a FlowSOM result
+    """Plots the base layer of a FlowSOM result.
 
     :param fsom: A FlowSOM object
     :type fsom: A object from the class FlowSOM
@@ -185,7 +185,7 @@ def plot_FlowSOM(
 
 
 def plot_star_legend(fig, ax, markers, coords=(0, 0), cmap=FlowSOM_colors(), max_star_height=1, star_height=1):
-    """Function makes the legend of the FlowSOM star plot
+    """Function makes the legend of the FlowSOM star plot.
 
     :param markers:
     :type markers:

src/FlowSOM/pl/plot_functions.py

@@ -35,7 +35,7 @@ def plot_2D_scatters(
     plot_file: str = "2DScatterPlots.png",
     title=None,
 ):
-    """Function to draw 2D scatter plots of FlowSOM (meta)clusters
+    """Function to draw 2D scatter plots of FlowSOM (meta)clusters.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -165,7 +165,7 @@ def plot_2D_scatters(
 
 
 def plot_labels(fsom, labels, max_node_size=0, text_size=20, text_color="black", title=None, **kwargs):
-    """Plot labels for each cluster
+    """Plot labels for each cluster.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -201,7 +201,7 @@ def plot_numbers(fsom, level="clusters", max_node_size=0, **kwargs):
     :param level: Should be either "clusters" (default) or "metaclusters".
     :type level: str
     :param max_node_size: Determines the maximum node size. Default is 0.
-    :type max_node_size: float
+    :type max_node_size: float.
     """
     assert level in ["clusters", "metaclusters"], "level should be clusters or metaclusters"
     if level == "clusters":
@@ -214,7 +214,7 @@ def plot_numbers(fsom, level="clusters", max_node_size=0, **kwargs):
 def plot_variable(
     fsom, variable, cmap=FlowSOM_colors(), labels=None, text_size=5, text_color="black", lim=None, title=None, **kwargs
 ):
-    """Plot FlowSOM grid or tree, colored by node values given in variable
+    """Plot FlowSOM grid or tree, colored by node values given in variable.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -258,7 +258,7 @@ def plot_variable(
 
 
 def plot_marker(fsom, marker, ref_markers=None, lim=None, cmap=FlowSOM_colors(), **kwargs):
-    """Plot FlowSOM grid or tree, colored by node values for a specific marker
+    """Plot FlowSOM grid or tree, colored by node values for a specific marker.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -287,7 +287,7 @@ def plot_marker(fsom, marker, ref_markers=None, lim=None, cmap=FlowSOM_colors(),
 
 
 def plot_stars(fsom, markers=None, cmap=FlowSOM_colors(), title=None, **kwargs):
-    """Plot star charts
+    """Plot star charts.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -340,7 +340,7 @@ def plot_pies(
     **kwargs,
 ):
     """Plot FlowSOM grid or tree, with pies indicating another clustering or
-    manual gating result
+    manual gating result.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -395,7 +395,7 @@ def plot_pies(
 
 
 def FlowSOMmary(fsom, plot_file="./FlowSOMmary.pdf"):
-    """Makes a visual FlowSOMmary of a FlowSOM object
+    """Makes a visual FlowSOMmary of a FlowSOM object.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM

src/FlowSOM/pp/fcs_functions.py

@@ -25,7 +25,7 @@ def aggregate_flowframes(filenames, c_total, channels=None, keep_order=False):
     :type keep_order: boolean
     :param silent: If False, prints an update every time it starts processing a
     new file. Default = False.
-    :type silent: boolean
+    :type silent: boolean.
     """
     nFiles = len(filenames)
     cFile = int(np.ceil(c_total / nFiles))

src/FlowSOM/tl/_consensus_clustering.py

@@ -24,7 +24,7 @@ class ConsensusCluster:
       * L -> smallest number of clusters to try
       * K -> biggest number of clusters to try
       * H -> number of resamplings for each cluster number
-      * resample_proportion -> percentage to sample
+      * resample_proportion -> percentage to sample.
     """
 
     def __init__(self, cluster, K, H, resample_proportion=0.9, linkage="average"):
@@ -39,14 +39,14 @@ def _internal_resample(self, data, proportion):
         """
         Args:
           * data -> (examples,attributes) format
-          * proportion -> percentage to sample
+          * proportion -> percentage to sample.
         """
         resampled_indices = np.random.choice(range(data.shape[0]), size=int(data.shape[0] * proportion), replace=False)
         return resampled_indices, data[resampled_indices, :]
 
     def fit(self, data):
         """
-        Fits a consensus matrix for each number of clusters
+        Fits a consensus matrix for each number of clusters.
 
         Args:
           * data -> (examples,attributes) format
@@ -75,5 +75,5 @@ def fit(self, data):
         self.Mk = Mk
 
     def predict(self, n_clus=10):
-        """Predicts on the consensus matrix, for best found cluster number"""
+        """Predicts on the consensus matrix, for best found cluster number."""
         return self.cluster_(n_clusters=n_clus, linkage=self.linkage, metric="precomputed").fit_predict(1 - self.Mk)

src/FlowSOM/tl/getter_functions.py

@@ -8,7 +8,7 @@
 
 
 def get_channels(obj, markers: np.ndarray, exact=True):
-    """Gets the channels of the provided markers based on a FlowSOM object or an FCS file
+    """Gets the channels of the provided markers based on a FlowSOM object or an FCS file.
 
     :param obj: A FlowSOM object or a FCS AnnData object
     :type obj: FlowSOM / AnnData
@@ -55,7 +55,7 @@ def get_channels(obj, markers: np.ndarray, exact=True):
 
 
 def get_markers(obj, channels, exact=True):
-    """Gets the markers of the provided channels based on a FlowSOM object or an FCS file
+    """Gets the markers of the provided channels based on a FlowSOM object or an FCS file.
 
     :param obj: A FlowSOM object or a FCS AnnData object
     :type obj: FlowSOM / AnnData
@@ -106,7 +106,7 @@ def get_markers(obj, channels, exact=True):
 
 
 def get_counts(fsom, level="metaclusters"):
-    """Get counts of number of cells in clusters or metaclusters
+    """Get counts of number of cells in clusters or metaclusters.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -128,7 +128,7 @@ def get_counts(fsom, level="metaclusters"):
 
 
 def get_percentages(fsom, level="metaclusters"):
-    """Get percentages of number of cells in clusters or metaclusters
+    """Get percentages of number of cells in clusters or metaclusters.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -142,7 +142,7 @@ def get_percentages(fsom, level="metaclusters"):
 
 
 def get_cluster_percentages_positive(fsom, cutoffs, cols_used=False, pretty_colnames=False):
-    """Get percentage-positive values for all clusters
+    """Get percentage-positive values for all clusters.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -183,7 +183,7 @@ def get_cluster_percentages_positive(fsom, cutoffs, cols_used=False, pretty_coln
 
 
 def get_metacluster_percentages_positive(fsom, cutoffs, cols_used=False, pretty_colnames=False):
-    """Get percentage-positive values for all metaclusters
+    """Get percentage-positive values for all metaclusters.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM
@@ -232,7 +232,7 @@ def get_features(
     positive_cutoffs=None,
     filenames=None,
 ):
-    """Map FCS files on an existing FlowSOM object
+    """Map FCS files on an existing FlowSOM object.
 
     :param fsom: A FlowSOM object
     :type fsom: FlowSOM