Merge pull request #17 from cfrioux/15-filter-the-presence-of-seeds-i…

…n-the-scope-by-removing-seeds-absent-from-the-network

15 filter the presence of seeds in the scope by removing seeds absent from the network

.github/workflows/pythonpublish.yml

@@ -21,12 +21,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install setuptools wheel twine build
         pip install -r requirements.txt
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERS }}
         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
 
+# MeneTools v3.4.0 (2024-02-28)
+
+## Modify
+
+* Filter the presence of seeds in the scope by removing seeds absent from the network (issue #15)
+* Modify if statement that will be deprecated in the future
+* Replace use of pkg_resources that will become deprecated
+* Move from `setup.py`/`setup.cfg` to `pyproject.toml`
+* Update license year
+
 # MeneTools v3.3.0 (2023-01-05)
 
 ## Add

README.md

@@ -140,6 +140,14 @@ from menetools import run_menescope
 model = run_menescope(draft_sbml='required',seeds_sbml='required',output='optional')
 ```
 
+The outputs for menecope are
+
+- As a control: seeds that were provided but do not appear in the metabolic network.
+- The _scope_ i.e. compounds that are in the seeds and those that are produced from the seeds
+- Two subsets to distinguish seed status
+  - those that can be produced by the metabolic network. For such seeds, the organism would have the metabolic capability to renew the production in addition to what was available in the environement. 
+  - those that cannot be produced by the metabolic network. For such seeds, there is no alternative other than relying on the environmental composition.
+
 ### MENEACTI
 
 Meneacti is a python3 tool that retrieve the activable reactions from
@@ -304,4 +312,3 @@ model = run_menescope_inc(draft_sbml='required',seeds_sbml='required',targets_sb
 Many thanks to
 * [@Aluriak](https://github.com/Aluriak) for his awesome work with [Clyngor](https://github.com/Aluriak/clyngor).
 * [@mablt](https://github.com/mablt) for his contribution to MeneSeed.
-

menetools/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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
@@ -22,6 +22,6 @@
 from menetools.menescope_inc import run_menescope_inc
 
 
-__version__="3.3.0"
+__version__="3.4.0"
 """Define the version of the package.
 """

menetools/__main__.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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
@@ -14,9 +14,7 @@
 
 import argparse
 import logging
-import pkg_resources
 import sys
-import time
 
 logger = logging.getLogger('menetools')
 logger.setLevel(logging.DEBUG)
@@ -26,6 +24,7 @@
 logger.addHandler(out_hdlr)
 logger.propagate = True
 
+from menetools import __version__ as VERSION
 from menetools.menescope import run_menescope
 from menetools.meneacti import run_meneacti
 from menetools.menecheck import run_menecheck
@@ -36,7 +35,6 @@
 from menetools.menescope_inc import run_menescope_inc
 from shutil import which
 
-VERSION = pkg_resources.get_distribution("menetools").version
 LICENSE = """Copyright (C) Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 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
@@ -217,7 +215,7 @@ def main():
 
     scope_parser = subparsers.add_parser(
         "scope",
-        help="Get producible metabolites in a metabolic network, starting from seeds.",
+        help="Get producible metabolites in a metabolic network, starting from seeds. The outputs for menecope are (i) As a control: seeds that were provided but do not appear in the metabolic network., (ii) The _scope_ i.e. compounds that are in the seeds and those that are produced from the seeds, (iii) Two subsets to distinguish seed status. (iii-a) those that can be produced by the metabolic network. For such seeds, the organism would have the metabolic capability to renew the production in addition to what was available in the environement. (iii-b) those that cannot be produced by the metabolic network. For such seeds, there is no alternative other than relying on the environmental composition.",
         parents=[
             parent_parser_d, parent_parser_s, parent_parser_o
         ]

menetools/encodings/get_scope.lp

@@ -10,12 +10,18 @@
 % You should have received a copy of the GNU Lesser General Public License
 % along with this program.  If not, see <http://www.gnu.org/licenses/>
 
+% filter seeds by removing those that never occur in the metabolic network
+true_seed(M) :- seed(M), reactant(M, _).
+true_seed(M) :- seed(M), product(M, _).
+
+absent_seed(M) :- seed(M), not true_seed(M).
+
 % scope of the seeds in the metabolic network
 dscope(M) :- product(M,R), dreaction(R),
                 dscope(M2) : reactant(M2,R).
     dscope(M) :- reactant(M,R), dreaction(R), reversible(R),
                 dscope(M2) : product(M2,R).
-    dscope(M) :- seed(M).
+    dscope(M) :- true_seed(M).
 
 % activated reactions in the metabolic network
 activated(R) :- dreaction(R),
@@ -24,8 +30,14 @@ activated(R) :- dreaction(R), reversible(R),
             dscope(M2) : product(M2,R).
 
 % seeds that can also be produced
-produced_seed(M):- product(M,R), dreaction(R), activated(R), seed(M).
-produced_seed(M):- reactant(M,R), dreaction(R), activated(R), reversible(R), seed(M).
+produced_seed(M):- product(M,R), dreaction(R), activated(R), true_seed(M).
+produced_seed(M):- reactant(M,R), dreaction(R), activated(R), reversible(R), true_seed(M).
+
+non_produced_seed(M):- true_seed(M), not produced_seed(M).
+
 
 #show dscope/1.
 #show produced_seed/1.
+#show non_produced_seed/1.
+#show absent_seed/1.
+#show activated/1.

menetools/meneacti.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/menecheck.py

@@ -1,7 +1,7 @@
 #!python
 # -*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/menecof.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python
 #-*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/menedead.py

@@ -1,7 +1,7 @@
 #!python
 # -*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/menepath.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/menescope.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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
@@ -62,17 +62,31 @@ def run_menescope(draft_sbml,seeds_sbml,output=None):
     model = query.get_scope(draftnet, seeds)
     scope = []
     produced_seeds = []
+    non_produced_seeds = []
+    absent_seeds = []
     for pred in model:
         if pred == 'dscope':
             for a in model[pred, 1]:
                 scope.append(a[0])
         if pred == 'produced_seed':
             for a in model[pred, 1]:
                 produced_seeds.append(a[0])
+        if pred == 'non_produced_seed':
+            for a in model[pred, 1]:
+                non_produced_seeds.append(a[0])
+        if pred == 'absent_seed':
+            for a in model[pred, 1]:
+                absent_seeds.append(a[0])
     logger.info(' ' + str(len(scope)) + ' compounds on scope:')
     logger.info('\n'.join(scope))
+    logger.info(' ' + str(len(produced_seeds)) + ' seeds are producible:')
+    logger.info('\n'.join(produced_seeds))
+    logger.info(' ' + str(len(non_produced_seeds)) + ' seeds are not producible:')
+    logger.info('\n'.join(non_produced_seeds))
+    logger.info(' ' + str(len(absent_seeds)) + ' seeds that were provided as input are absent from the network:')
+    logger.info('\n'.join(absent_seeds))
 
-    results = {'scope': scope, 'produced_seeds': produced_seeds}
+    results = {'scope': scope, 'produced_seeds': produced_seeds, 'non_produced_seeds': non_produced_seeds, 'absent_seeds': absent_seeds}
     if output:
         with open(output, "w") as output_file:
             json.dump(results, output_file, indent=True, sort_keys=True)

menetools/menescope_inc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 #-*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/meneseed.py

@@ -1,7 +1,7 @@
 #!python
 # -*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/query.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

menetools/sbml.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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
@@ -245,7 +245,7 @@ def readSBMLspecies_clyngor(filename, speciestype) :
     model = get_model(sbml)
 
     listOfSpecies = get_listOfSpecies(model)
-    if listOfSpecies:
+    if listOfSpecies is not None:
         for e in listOfSpecies:
             if e.tag[0] == "{":
                 uri, tag = e.tag[1:].split("}")

menetools/utils.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2023 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
+# Copyright (C) 2017-2024 Clémence Frioux & Arnaud Belcour - Inria Dyliss - Pleiade
 # 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

pyproject.toml

@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "MeneTools"
+dynamic = ["version"]
+authors = [{name = "Clemence Frioux", email = "clemence.frioux@inria.fr"}]
+readme = "README.md"
+description = "Metabolic Network Topology Analysis Tools"
+license = {text = "LGPL-3.0-or-later"}
+dependencies = [
+  'clyngor_with_clingo',
+  'clyngor'
+]
+
+classifiers =[
+  'Programming Language :: Python :: 3.6',
+  'Programming Language :: Python :: 3.7',
+  'Programming Language :: Python :: 3.8',
+  'Operating System :: MacOS :: MacOS X',
+  'Operating System :: Unix',
+]
+
+[project.scripts]
+mene = "menetools.__main__:main"
+
+[project.urls]
+Homepage = "https://github.com/cfrioux/MeneTools"
+Changelog = "https://github.com/cfrioux/MeneTools/blob/main/CHANGELOG.md"
+
+[tool.setuptools]
+packages = ['menetools']
+package-dir = {'menetools' = 'menetools'}
+package-data = {'menetools' = ['encodings/*.lp']}
+
+[tool.setuptools.dynamic]
+version = { attr = "menetools.__version__" }
+dependencies = {file = ["requirements.txt"]}