Move to 0.5.2.

Replace setup files by pyproject.toml.

Author: ArnaudBelcour

.github/workflows/python-publish.yml

@@ -28,5 +28,5 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+# Padmet 5.0.2 (2024-10-30)
+
+## Fix
+
+* Bug in `--enhance` functionality from pgdb_to_padmet, reaction IDs were put in dicOfNode instead of reactant IDs (issue #12). Add a test to check this.
+
+## Modification
+
+* Replace `setup.py` and `setup.cfg` by `pyproject.toml`.
+
 # Padmet 5.0.1 (2020-10-26)
 
 ## Fix

padmet/__init__.py

@@ -15,4 +15,4 @@
 along with padmet. If not, see <http://www.gnu.org/licenses/>.
 """
 
-__version__='5.0.1'
+__version__='5.0.2'

pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "padmet"
+dynamic = ["version"]
+authors = [{name = "AuReMe", email = "[email protected]"}]
+readme = "README.md"
+description = "The PADMet package allows conciliating genomics and metabolic network information used to produce a genome-scale constraint-based metabolic model within a database that traces all the reconstruction process steps. It allows representing the metabolic model in the form of a Wiki containing all the used/traced information. Other standard outputs are made available with the package."
+license = {text = "GPL-3.0-or-later"}
+
+dependencies = ['docopt>=0.6.2',
+  'python-libsbml>=5.18.0',
+  'cobra>=0.17.1',
+  'biopython>=1.78',
+  'lxml>=4.3.4'
+  ]
+
+[project.scripts]
+padmet = "padmet.__main__:main"
+
+[project.urls]
+Homepage = "https://github.com/AuReMe/padmet"
+Changelog = "https://github.com/AuReMe/padmet/blob/main/CHANGELOG.md"
+
+
+[tool.setuptools]
+packages = ['padmet', 'padmet.classes', 'padmet.utils', 'padmet.utils.connection', 'padmet.utils.exploration', 'padmet.utils.management']
+package-dir = {'padmet' = 'padmet', 'padmet.classes' = 'padmet/classes' , 'padmet.utils' = 'padmet/utils', 'padmet.utils.connection' = 'padmet/utils/connection', 'padmet.utils.exploration' = 'padmet/utils/exploration', 'padmet.utils.management' = 'padmet/utils/management'}
+
+[tool.setuptools.dynamic]
+version = { attr = "padmet.__version__" }
+dependencies = {file = ["requirements.txt"]}

setup.cfg

@@ -33,16 +33,6 @@
             'ETF-Reduced', 'WATER', 'PROTON', 'CPD66-39', 'CO-A', 'ATP', 'PPI', 'AMP', 'ACETYL-COA',
             '3-KETOACYL-COA', 'NAD', 'NADH']
 
-FABO_REACTANTS = ['D-3-HYDROXYACYL-COA', 'L-3-HYDROXYACYL-COA', 'TRANS-D2-ENOYL-COA',
-            'CIS-DELTA3-ENOYL-COA', 'Saturated-Fatty-Acyl-CoA', 'ETF-Oxidized',
-            'ETF-Reduced', 'WATER', 'PROTON', 'CPD66-39', 'CO-A', 'ATP', 'PPI', 'AMP', 'ACETYL-COA',
-            '3-KETOACYL-COA', 'NAD', 'NADH']
-
-FABO_PRODUCTS = ['D-3-HYDROXYACYL-COA', 'L-3-HYDROXYACYL-COA', 'TRANS-D2-ENOYL-COA',
-            'CIS-DELTA3-ENOYL-COA', 'Saturated-Fatty-Acyl-CoA', 'ETF-Oxidized',
-            'ETF-Reduced', 'WATER', 'PROTON', 'CPD66-39', 'CO-A', 'ATP', 'PPI', 'AMP', 'ACETYL-COA',
-            '3-KETOACYL-COA', 'NAD', 'NADH']
-
 FABO_GENES = ['b2341', 'b0221', 'b1805', 'b1701', 'b2342', 'b3845', 'b3846']