Merge pull request #38 from MetaSys-LISBP/dev

Dev

.github/workflows/pypi_deployment.yml

@@ -7,7 +7,7 @@ on:
       - v*
 
 jobs:
-  build-n-publish:
+  build:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
     runs-on: ubuntu-latest
     steps:
@@ -29,7 +29,15 @@ jobs:
           --sdist
           --wheel
           --outdir dist/
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+  pypi-publish:
+      name: Publish distribution 📦 to PyPI
+      runs-on: ubuntu-latest
+      environment:
+        name: pypi
+        url: https://https://pypi.org/project/IsoCor/
+      permissions:
+        id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      steps:
+        # retrieve your distributions here
+        - name: Publish package distributions to PyPI
+          uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -19,7 +19,7 @@ The output of IsoCor is the isotopologue distribution of the molecule
 of isotopic substitutions of the tracer). IsoCor also calculates
 the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.
 
-It is one of the routine tools that we use at the [MetaSys team](http://www.lisbp.fr/en/research/molecular-physiology-and-metabolism/metasys.html) and [MetaToul platform](http://www.metatoul.fr) in isotopic studies of metabolic systems.
+It is one of the routine tools that we use at the [MetaSys team](https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/) and [MetaToul platform](https://www.metabohub.fr/home.html) in isotopic studies of metabolic systems.
 
 The code is open-source, and available under a GPLv3 license. Additional information can be found in [IsoCor publication](https://doi.org/10.1093/bioinformatics/btz209).
 
@@ -34,12 +34,12 @@ Check out the [Tutorials](https://isocor.readthedocs.io/en/latest/tutorials.html
 * can be applied to singly- and multiply-charged ions
 * can be used with any tracer element (having two or more isotopes)
 * account for the contribution of derivatization steps (if any),
-* generate isotopic InChIs of the tracer isotopologues,
+* generate isotopic InChIs of tracer isotopologues,
 * open-source, free and easy to install everywhere where Python 3 and pip run,
 * biologist-friendly.
 
 ## Quick-start
-IsoCor requires Python 3.5 or higher and run on all plate-forms.
+IsoCor requires Python 3.7 or higher and run on all platforms.
 Please check [the documentation](https://isocor.readthedocs.io/en/latest/quickstart.html) for complete
 installation and usage instructions.
 

doc/index.rst

@@ -18,7 +18,7 @@ The output of IsoCor is the :ref:`isotopologue distribution <isotopologue distri
 of isotopic substitutions of the tracer) of the molecule. IsoCor also calculates
 the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.
 
-It is one of the routine tools that we use at the `MetaSys team <http://www.toulouse-biotechnology-institute.fr/en/research/molecular-physiology-and-metabolism/metasys.html>`_ and `MetaToul platform <http://www.metatoul.fr>`_ in isotopic studies of metabolic systems.
+It is one of the routine tools that we use at the `MetaSys team <https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/>`_ and `MetaToul platform <https://www.metabohub.fr/home.html>`_ in isotopic studies of metabolic systems.
 
 The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/IsoCor/>`_ under a :ref:`GPLv3 license <license>`.
 

isocor/__init__.py

@@ -5,7 +5,7 @@
 """
 
 # Version number MUST be maintained here (x.y.z format)
-__version__ = '2.2.1'
+__version__ = '2.2.2'
 
 from isocor.mscorrectors import MetaboliteCorrectorFactory
 from isocor.mscorrectors import LowResMetaboliteCorrector, HighResMetaboliteCorrector

isocor/ui/isocordb.py

@@ -3,7 +3,6 @@
 from os.path import expanduser
 import isocor as hr
 from decimal import Decimal
-from distutils.dir_util import copy_tree
 import shutil
 import numpy as np
 import pkg_resources
@@ -28,7 +27,7 @@ def initializeDB(self):
                 if not Path(self.default_db, i).is_file():
                     shutil.copy(Path(self.example_db, i), self.default_db)
         else:
-            copy_tree(str(self.example_db), str(self.default_db))
+            shutil.copytree(str(self.example_db), str(self.default_db))
 
     def initializeEnv(self):
         self.home = self.home

setup.cfg

@@ -8,9 +8,12 @@ long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/MetaSys-LISBP/IsoCor/
 classifiers =
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
     Operating System :: OS Independent
     Intended Audience :: Science/Research
@@ -19,7 +22,7 @@ classifiers =
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.6
+python_requires = >=3.7
 install_requires =
     pandas >= 0.17.1,
     scipy >= 0.12.1