From fd03e385074915e6b74e4599839623af4b10492b Mon Sep 17 00:00:00 2001 From: Arnaud Belcour Date: Fri, 13 Jan 2023 17:34:24 +0100 Subject: [PATCH] Move to 0.8.3. Fix issue in test and with mpwt exiting when all runs are complete. Update license year. --- CHANGELOG.md | 11 +++++++++++ mpwt/__init__.py | 4 ++-- mpwt/__main__.py | 2 +- mpwt/mpwt_workflow.py | 8 +++++++- mpwt/pathologic_input.py | 2 +- mpwt/pwt_wrapper.py | 2 +- mpwt/results_check.py | 2 +- mpwt/to_pathologic.py | 2 +- mpwt/utils.py | 2 +- setup.py | 2 +- 10 files changed, 27 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dde6ada..f4f4929 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +# mpwt 0.8.3 (2023-01-13) + +## Fix: + +- issue making mpwt exits when all runs are already complete. +- issue in test (wrong argument for removing PGDBs). + +## Modify: + +- update license year. + # mpwt 0.8.2 (2022-12-16) ## Modify: diff --git a/mpwt/__init__.py b/mpwt/__init__.py index 1adf047..081a1fb 100755 --- a/mpwt/__init__.py +++ b/mpwt/__init__.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or @@ -17,4 +17,4 @@ from mpwt.utils import cleaning, cleaning_input, find_ptools_path, list_pgdb, pubmed_citations, remove_pgdbs from mpwt.to_pathologic import create_pathologic_file -__version__='0.8.2' \ No newline at end of file +__version__='0.8.3' \ No newline at end of file diff --git a/mpwt/__main__.py b/mpwt/__main__.py index 57c2684..d46c652 100755 --- a/mpwt/__main__.py +++ b/mpwt/__main__.py @@ -1,7 +1,7 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or diff --git a/mpwt/mpwt_workflow.py b/mpwt/mpwt_workflow.py index 4d8dc4f..8bee596 100755 --- a/mpwt/mpwt_workflow.py +++ b/mpwt/mpwt_workflow.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or @@ -361,6 +361,12 @@ def independent_mpwt(input_folder, output_folder=None, patho_inference=None, run_ids = [folder_id for folder_id in next(os.walk(input_folder))[1]] run_patho_flat_ids, run_flat_ids = check_input_and_existing_pgdb(run_ids, input_folder, output_folder, number_cpu_to_use) if run_patho_flat_ids is None and run_flat_ids is None: + # If all run_ids are in output folder, return as it has complete. + if output_folder: + already_present_outputs = [output_pgdb.replace('.zip', '') for output_pgdb in os.listdir(output_folder)] + if set(run_ids) == set(already_present_outputs): + return + # For other case, there is possibly an error, mpwt exits. logger.critical('/!\\ Issue during input check.') sys.exit() diff --git a/mpwt/pathologic_input.py b/mpwt/pathologic_input.py index faf1474..4f8321b 100755 --- a/mpwt/pathologic_input.py +++ b/mpwt/pathologic_input.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or diff --git a/mpwt/pwt_wrapper.py b/mpwt/pwt_wrapper.py index 5803a71..d15f1fe 100755 --- a/mpwt/pwt_wrapper.py +++ b/mpwt/pwt_wrapper.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or diff --git a/mpwt/results_check.py b/mpwt/results_check.py index 019dd9d..969a638 100755 --- a/mpwt/results_check.py +++ b/mpwt/results_check.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or diff --git a/mpwt/to_pathologic.py b/mpwt/to_pathologic.py index 310cd3e..e04d5ec 100755 --- a/mpwt/to_pathologic.py +++ b/mpwt/to_pathologic.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or diff --git a/mpwt/utils.py b/mpwt/utils.py index 7721ee5..c737e30 100755 --- a/mpwt/utils.py +++ b/mpwt/utils.py @@ -1,4 +1,4 @@ -# Copyright (C) 2018-2022 Arnaud Belcour- Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour- Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or diff --git a/setup.py b/setup.py index 2d013e2..e72ff4d 100755 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -# Copyright (C) 2018-2022 Arnaud Belcour - Inria Dyliss +# Copyright (C) 2018-2023 Arnaud Belcour - Inria Dyliss # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation, either version 3 of the License, or