From e10b132a1f3a5abee1959e5f1c1b248ad3607b04 Mon Sep 17 00:00:00 2001
From: LucianaMartins26 <lucianacmartins8@gmail.com>
Date: Mon, 11 Nov 2024 18:07:20 +0000
Subject: [PATCH] [MODIFY] requirements.txt and setup.cfg files so that the
 only package that needs to be installed in the environment is cobra. There is
 no version specified so that the latest version compatible with each python
 version used is installed + [FIX] integration DFA tests to skip this in
 continuous integration since this are post-processing tests

---
 requirements.txt                           | 8 +-------
 setup.cfg                                  | 6 ------
 tests/integration_tests/test_dfa.py        | 4 ++++
 tests/integration_tests/test_dfa_tomato.py | 3 +++
 4 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 1f43a05..766f65f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1 @@
-cobra~=0.26.2
-pandas~=1.5.3
-statsmodels~=0.13.5
-matplotlib>=3.7.1
-numpy>=1.22
-scipy>=1.10
-setuptools>=65.6.3
\ No newline at end of file
+cobra
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index ccc9ccf..3c01cc0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -27,12 +27,6 @@ zip_safe = False
 include_package_data = True
 install_requires =
     cobra
-    numpy
-    pandas
-    statsmodels
-    matplotlib
-    scipy
-    setuptools
 
 
 [options.packages.find]
diff --git a/tests/integration_tests/test_dfa.py b/tests/integration_tests/test_dfa.py
index ee5efac..38291f9 100644
--- a/tests/integration_tests/test_dfa.py
+++ b/tests/integration_tests/test_dfa.py
@@ -1,4 +1,5 @@
 import os
+import unittest
 from unittest import TestCase
 
 import cobra.io
@@ -24,6 +25,7 @@ def setUp(self) -> None:
                                                                      'results_troppo', self.dataset_id,
                                                                      'reconstructed_models', 'Diel_Model.xml'))
 
+    @unittest.skip
     def test_sampling(self) -> None:
         day_sampling, night_sampling = self.dfa.sampling(thinning=100, n_samples=1000)
 
@@ -58,6 +60,7 @@ def test_sampling(self) -> None:
             expected_file = os.path.join(self.results_folder, '%s_sampling.csv' % modelname)
             self.assertTrue(os.path.exists(expected_file))
 
+    @unittest.skip
     def test_ktest(self) -> None:
 
         self.dfa.sampling()
@@ -78,6 +81,7 @@ def test_ktest(self) -> None:
         expected_columns = ['Reaction', 'Pvalue', 'Padj', 'Reject', 'FC']
         self.assertListEqual(list(result_df.columns), expected_columns)
 
+    @unittest.skip
     def test_pathways(self) -> None:
 
         self.dfa.sampling()
diff --git a/tests/integration_tests/test_dfa_tomato.py b/tests/integration_tests/test_dfa_tomato.py
index bf09a44..ac5da2d 100644
--- a/tests/integration_tests/test_dfa_tomato.py
+++ b/tests/integration_tests/test_dfa_tomato.py
@@ -1,4 +1,5 @@
 import os
+import unittest
 from unittest import TestCase
 
 import cobra.io
@@ -23,6 +24,7 @@ def setUp(self) -> None:
                                                                      self.dataset_id, 'reconstructed_models',
                                                                      'Tomato_Diel_Model.xml'))
 
+    @unittest.skip
     def test_sampling(self) -> None:
         day_sampling, night_sampling = self.dfa.sampling(thinning=100, n_samples=1000)
 
@@ -57,6 +59,7 @@ def test_sampling(self) -> None:
             expected_file = os.path.join(self.results_folder, '%s_sampling.csv' % modelname)
             self.assertTrue(os.path.exists(expected_file))
 
+    @unittest.skip
     def test_ktest(self) -> None:
 
         self.dfa.sampling()