Merge pull request #23 from saeyslab/export_pyflowsom

export pyflowsom

Author: berombau

pyproject.toml

@@ -66,7 +66,7 @@ optional-dependencies.doc = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
-optional-dependencies.test = [ "coverage", "pytest" ]
+optional-dependencies.test = [ "coverage", "pyflowsom", "pytest" ]
 urls.Documentation = "https://flowsom.readthedocs.io/en/latest/"
 urls.Home-page = "https://github.com/saeyslab/FlowSOM_Python"
 urls.Source = "https://github.com/saeyslab/FlowSOM_Python"

src/flowsom/models/__init__.py

@@ -5,3 +5,5 @@
 from .consensus_cluster import ConsensusCluster  # isort:skip
 from .flowsom_estimator import FlowSOMEstimator  # isort:skip
 from .batch_flowsom_estimator import BatchFlowSOMEstimator  # isort:skip
+from .pyFlowSOM_som_estimator import PyFlowSOM_SOMEstimator  # isort:skip
+from .pyflowsom_estimator import PyFlowSOMEstimator  # isort:skip

src/flowsom/models/pyFlowSOM_som_estimator.py

@@ -1,5 +1,4 @@
 import numpy as np
-from pyFlowSOM import map_data_to_nodes, som
 from sklearn.utils.validation import check_is_fitted
 
 from . import BaseClusterEstimator
@@ -54,6 +53,8 @@ def fit(
         according to importance
         :type importance: np.array
         """
+        from pyFlowSOM import map_data_to_nodes, som
+
         alpha = self.alpha
         X = X.astype("double")
 
@@ -77,7 +78,10 @@ def fit(
 
     def predict(self, X, y=None):
         """Predict labels using the model."""
+        from pyFlowSOM import map_data_to_nodes
+
         check_is_fitted(self)
+
         X = X.astype("double")
         clusters, dists = map_data_to_nodes(self.codes, X)
         self.labels_ = clusters.astype(int) - 1

tests/models/test_pyFlowSOM.py

@@ -1,21 +1,21 @@
 import pytest
 from sklearn.metrics import v_measure_score
 
-# optional import if pyFlowSOM is installed, otherwise use regular FlowSOM for type checking
+# Skip the entire test file if pyflowsom is not installed
+pytest.importorskip("pyFlowSOM", reason="pyflowsom is not installed")
+
 try:
     from flowsom.models.pyflowsom_estimator import PyFlowSOMEstimator
 except ImportError:
     from flowsom.models import FlowSOMEstimator as PyFlowSOMEstimator
 
 
-@pytest.importorskip("flowsom.models.pyflowsom_estimator")
 def test_clustering(X):
     fsom = PyFlowSOMEstimator(n_clusters=10)
     y_pred = fsom.fit_predict(X)
     assert y_pred.shape == (100,)
 
 
-@pytest.importorskip("flowsom.models.pyflowsom_estimator")
 def test_clustering_v_measure(X_and_y):
     som = PyFlowSOMEstimator(n_clusters=10)
     X, y_true = X_and_y
@@ -24,7 +24,6 @@ def test_clustering_v_measure(X_and_y):
     assert score > 0.7
 
 
-@pytest.importorskip("flowsom.models.pyflowsom_estimator")
 def test_reproducibility_no_seed(X):
     fsom_1 = PyFlowSOMEstimator(n_clusters=10)
     fsom_2 = PyFlowSOMEstimator(n_clusters=10)
@@ -34,7 +33,6 @@ def test_reproducibility_no_seed(X):
     assert not all(y_pred_1 == y_pred_2)
 
 
-@pytest.importorskip("flowsom.models.pyflowsom_estimator")
 def test_reproducibility_seed(X):
     fsom_1 = PyFlowSOMEstimator(n_clusters=10, seed=0)
     fsom_2 = PyFlowSOMEstimator(n_clusters=10, seed=0)