From e6330ca3441958863eae37fe495b6291f3b072ca Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Fri, 5 Jun 2026 09:47:27 +0200 Subject: [PATCH 1/8] refactor: replace pkg_resources with importlib.resources for example database path --- isocor/ui/isocordb.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/isocor/ui/isocordb.py b/isocor/ui/isocordb.py index 2f18ee4..380ed54 100644 --- a/isocor/ui/isocordb.py +++ b/isocor/ui/isocordb.py @@ -5,7 +5,8 @@ from decimal import Decimal import shutil import numpy as np -import pkg_resources +# import pkg_resources +import importlib.resources class EnvComputing(object): @@ -18,7 +19,8 @@ def __init__(self, home=expanduser('~')): self.home = Path(home) self.default_db = Path(self.home, 'isocordb') self.db_path = self.default_db - self.example_db = pkg_resources.resource_filename('isocor', 'data/') + # self.example_db = pkg_resources.resource_filename('isocor', 'data/') + self.example_db = importlib.resources.files('isocor') / 'data/' def initializeDB(self): # if db files don't exist, copy the example folder From 365e3c2e9b4dd04a8a9c51f74da48cad8d31dcbd Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Fri, 5 Jun 2026 10:05:15 +0200 Subject: [PATCH 2/8] refactor: update Python versions in tox.ini environment list --- tox.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index 11b14a0..e81d75d 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ [tox] env_list = - py36, py37, py38, py39, py310, py311 + py310, py11, py12, py13, py14 minversion = 4.4.8 [testenv] From 731546a92bd25c72bf50098e92a840d1b1dbd0dc Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Fri, 5 Jun 2026 10:07:11 +0200 Subject: [PATCH 3/8] bump version to 2.2.4 --- isocor/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/isocor/__init__.py b/isocor/__init__.py index 233ca47..1dd7be0 100644 --- a/isocor/__init__.py +++ b/isocor/__init__.py @@ -5,7 +5,7 @@ """ # Version number MUST be maintained here (x.y.z format) -__version__ = '2.2.3' +__version__ = '2.2.4' from isocor.mscorrectors import MetaboliteCorrectorFactory from isocor.mscorrectors import LowResMetaboliteCorrector, HighResMetaboliteCorrector From 7f9149bf9296676960b5b430e21452fcd7d90811 Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Mon, 8 Jun 2026 14:53:50 +0200 Subject: [PATCH 4/8] use joinpath() to improve readability --- isocor/ui/isocordb.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/isocor/ui/isocordb.py b/isocor/ui/isocordb.py index 380ed54..cde9e6a 100644 --- a/isocor/ui/isocordb.py +++ b/isocor/ui/isocordb.py @@ -20,7 +20,7 @@ def __init__(self, home=expanduser('~')): self.default_db = Path(self.home, 'isocordb') self.db_path = self.default_db # self.example_db = pkg_resources.resource_filename('isocor', 'data/') - self.example_db = importlib.resources.files('isocor') / 'data/' + self.example_db = importlib.resources.files('isocor').joinpath('data') def initializeDB(self): # if db files don't exist, copy the example folder From 2f674778dc010d09fc74f6a2e72dbaba484500e9 Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Mon, 8 Jun 2026 14:54:14 +0200 Subject: [PATCH 5/8] fix: update Python version format in tox.ini --- tox.ini | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index e81d75d..de965a0 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ [tox] env_list = - py310, py11, py12, py13, py14 + 3.10, 3.11, 3.12, 3.13, 3.14 minversion = 4.4.8 [testenv] From 3f2b7bea2c4ee8900ef941eb80632a3a2d52bad0 Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Thu, 11 Jun 2026 14:36:43 +0200 Subject: [PATCH 6/8] update Python version list in test configurations --- .github/workflows/test_suite.yml | 2 +- tox.ini | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml index 1147739..d0d5363 100644 --- a/.github/workflows/test_suite.yml +++ b/.github/workflows/test_suite.yml @@ -16,7 +16,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, windows-latest] - python-version: [ '3.8', '3.9', '3.10', '3.11'] + python-version: [ '3.8', '3.9', '3.10', '3.11','3.12', '3.13', '3.14' ] steps: - uses: actions/checkout@v4 diff --git a/tox.ini b/tox.ini index de965a0..bcb267a 100644 --- a/tox.ini +++ b/tox.ini @@ -1,6 +1,6 @@ [tox] env_list = - 3.10, 3.11, 3.12, 3.13, 3.14 + 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14 minversion = 4.4.8 [testenv] From 5323259bc2902347737ff57279f265539dd84f31 Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Thu, 11 Jun 2026 14:37:00 +0200 Subject: [PATCH 7/8] add support for Python 3.13 and 3.14 in classifiers --- setup.cfg | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.cfg b/setup.cfg index c7ac906..18a4732 100644 --- a/setup.cfg +++ b/setup.cfg @@ -14,6 +14,8 @@ classifiers = Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 + Programming Language :: Python :: 3.13 + Programming Language :: Python :: 3.14 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) Operating System :: OS Independent Intended Audience :: Science/Research From 20c1fac4ec2b50d102f51cfa05adec4ab39890a7 Mon Sep 17 00:00:00 2001 From: rkouakou06 Date: Thu, 11 Jun 2026 14:42:17 +0200 Subject: [PATCH 8/8] update Python version requirement to 3.7 in documentation --- doc/faq.rst | 2 +- doc/quickstart.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/faq.rst b/doc/faq.rst index 38782f8..d07819c 100644 --- a/doc/faq.rst +++ b/doc/faq.rst @@ -209,7 +209,7 @@ Please follow this simple procedure: * If it is related to your system or your Python installation, you will need to ask some help from your local system administrator or your IT department so they could guide you toward a clean installation. Tell them that you wanted "to use the graphical - user interface of IsoCor, a Python 3.5 software" and what you did so far (installation), + user interface of IsoCor, a Python 3.7 software" and what you did so far (installation), give them the traceback and a link toward the documentation. They should know what to do. * If you believe the problem is in IsoCor or that your local system administrator told you so, then you probably have found a bug! We would greatly appreciate diff --git a/doc/quickstart.rst b/doc/quickstart.rst index 9f1f78e..4b1e810 100644 --- a/doc/quickstart.rst +++ b/doc/quickstart.rst @@ -7,7 +7,7 @@ Quick start Installation ------------------------------------------------ -IsoCor requires Python 3.5 or higher. If you do not have a Python environment +IsoCor requires Python 3.7 or higher. If you do not have a Python environment configured on your computer, we recommend that you follow the instructions from `Anaconda `_.