numpy explicit list fix

compomics · Jun 18, 2023 · e7e6ca3 · e7e6ca3
1 parent 7aa082d
commit e7e6ca3
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Showing 3 changed files with 16 additions and 11 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+# [2.2.1] - 2023-06-18
+
+### Changed
+- Fixed a bug where numpy no longer accepts dict_values, explicit list conversion
+
 # [2.2.0] - 2023-06-14
 
 ### Changed

diff --git a/deeplc/deeplc.py b/deeplc/deeplc.py
@@ -548,12 +548,12 @@ def make_preds_core(self,
             #X = self.do_f_extraction_psm_list(psm_list)
             X = self.do_f_extraction_psm_list_parallel(psm_list)
 
-            X_sum = np.stack(X["matrix_sum"].values())
-            X_global = np.concatenate((np.stack(X["matrix_all"].values()),
-                                    np.stack(X["pos_matrix"].values())),
+            X_sum = np.stack(list(X["matrix_sum"].values()))
+            X_global = np.concatenate((np.stack(list(X["matrix_all"].values())),
+                                    np.stack(list(X["pos_matrix"].values()))),
                                     axis=1)
-            X_hc = np.stack(X["matrix_hc"].values())
-            X = np.stack(X["matrix"].values())
+            X_hc = np.stack(list(X["matrix_hc"].values()))
+            X = np.stack(list(X["matrix"].values()))
         elif len(X) == 0 and len(psm_list) == 0:
             return []
 
@@ -631,12 +631,12 @@ def make_preds(self,
                 logger.debug("Extracting features for the CNN model ...")
 
             X = self.do_f_extraction_psm_list_parallel(psm_list)
-            X_sum = np.stack(X["matrix_sum"].values())
-            X_global = np.concatenate((np.stack(X["matrix_all"].values()),
-                                    np.stack(X["pos_matrix"].values())),
+            X_sum = np.stack(list(X["matrix_sum"].values()))
+            X_global = np.concatenate((np.stack(list(X["matrix_all"].values())),
+                                    np.stack(list(X["pos_matrix"].values()))),
                                     axis=1)
-            X_hc = np.stack(X["matrix_hc"].values())
-            X = np.stack(X["matrix"].values())
+            X_hc = np.stack(list(X["matrix_hc"].values()))
+            X = np.stack(list(X["matrix"].values()))
         else:
             return []
 

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='deeplc',
-    version='2.2.0',
+    version='2.2.1',
     license='apache-2.0',
     description='DeepLC: Retention time prediction for (modified) peptides using Deep Learning.',
     long_description=LONG_DESCRIPTION,