From e7e6ca3e56208b91fa0e431f7ed599f191e02eaf Mon Sep 17 00:00:00 2001 From: RobbinBouwmeester Date: Sun, 18 Jun 2023 15:21:11 +0200 Subject: [PATCH] numpy explicit list fix --- CHANGELOG.md | 5 +++++ deeplc/deeplc.py | 20 ++++++++++---------- setup.py | 2 +- 3 files changed, 16 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f3b844f..23dff41 100644 --- 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 index 70425c8..70a750c 100644 --- 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 index 6c768fe..f61fdc7 100644 --- 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,