Update supported Python versions in CI (#228)

* add missing CHANGELOG.rst * fix missing 3.9 * now windows wheels for 3.9 * make nosetests and coverage work correctly * update release notes Co-authored-by: Moritz E. Beber <[email protected]>
opencobra · Mar 16, 2021 · e7728cd · e7728cd
1 parent a7c02b2
commit e7728cd
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Showing 6 changed files with 44 additions and 63 deletions.
diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -20,11 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
-        exclude:
-        # Lacking swiglpk wheels for this combination.
-        - os: macos-latest
-          python-version: '3.5'
+        python-version: [2.7, 3.6, 3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -35,14 +31,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tox tox-gh-actions codecov
+        python -m pip install tox tox-gh-actions
     - name: Test with tox
-      run: tox -- --cov-report=xml
+      run: tox -- --cover-xml
     - name: Report coverage
-      run: codecov
-#      uses: codecov/codecov-action@v1
-#      with:
-#        fail_ci_if_error: true
+      shell: bash
+      run: bash <(curl -s https://codecov.io/bash)
 
   release:
     needs: test

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,13 @@
+=======
+
+Next Release
+------------
+* removed support for Python 3.5
+* added support for Python 3.9
+* enabled code coverage in tox
+* support symengine 0.7.0
+
+1.4.7
+-----
+* fix: except AttributeError when setting tolerance on cloned Configuration
+* enable cloning models between solver interfaces that do not support the same set of tolerance parameters
diff --git a/src/optlang/expression_parsing.py b/src/optlang/expression_parsing.py
@@ -72,6 +72,7 @@ def _parse_linear_expression(expression, expanded=False, **kwargs):
     """
     offset = 0
     constant = None
+    expression = expression.expand()
 
     if expression.is_Add:
         coefficients = expression.as_coefficients_dict()
@@ -108,6 +109,7 @@ def _parse_quadratic_expression(expression, expanded=False):
     linear_coefficients = {}
     quadratic_coefficients = {}
     offset = 0
+    expression = expression.expand()
 
     if expression.is_Number:  # Constant expression, no coefficients
         return float(expression), linear_coefficients, quadratic_coefficients

diff --git a/src/optlang/tests/abstract_test_cases.py b/src/optlang/tests/abstract_test_cases.py
@@ -604,15 +604,15 @@ def test_change_constraint_bounds(self):
 
     def test_initial_objective(self):
         self.assertEqual(self.model.objective.expression, 1.0 * self.model.variables["R_Biomass_Ecoli_core_w_GAM"])
-        
+
     def test_set_objective_in_constructor(self):
         var = self.interface.Variable("x", ub=5)
         obj = self.interface.Objective(var, direction="max")
         model = self.interface.Model(objective=obj, variables=[var])
         model.optimize()
         self.assertIs(model.objective, obj)
         self.assertAlmostEqual(model.objective.value, 5)
-        
+
 
     def test_optimize(self):
         self.model.optimize()
@@ -752,6 +752,8 @@ def test_clone_model_without_json(self):
         self.assertEquals(len(cloned_model.variables), len(self.model.variables))
         self.assertEquals(len(cloned_model.constraints), len(self.model.constraints))
         cloned_model.optimize()
+        print(cloned_model.objective.expression)
+        print(cloned_model.objective.value)
         self.assertAlmostEqual(cloned_model.objective.value, opt)
 
     def test_remove_variable_not_in_model_raises(self):
@@ -961,7 +963,7 @@ def test_implicitly_convert_milp_to_lp(self):
         model.remove(var3)
         model.optimize()
         self.assertAlmostEqual(model.reduced_costs["x"], 0)
-        
+
     def test_change_constraint_name(self):
         model = self.model
         const = model.constraints[0]

diff --git a/tox.ini b/tox.ini
@@ -1,13 +1,13 @@
 [tox]
-envlist = isort, black, flake8, safety, docs, py27, py3{5,6,7,8}-symengine
+envlist = isort, black, flake8, safety, docs, py27, py3{6,7,8,9}-symengine
 
 [gh-actions]
 python =
      2.7: safety, py27
-     3.5: safety, py35, py35-symengine
      3.6: safety, py36, py36-symengine
      3.7: safety, py37, py37-symengine
      3.8: safety, py38, py38-symengine
+     3.9: safety, py39, py39-symengine
 
 ;[testenv]
 ;deps =
@@ -30,7 +30,7 @@ deps =
      symengine: symengine
 passenv = CI
 commands =
-     nosetests src/optlang/tests -vv
+     nosetests -c tox.ini src/optlang/tests {posargs}
 
 [testenv:isort]
 skip_install = True
@@ -93,25 +93,29 @@ markers =
 ;     src/optlang
 ;     */site-packages/optlang
 
-;[coverage:run]
-;branch = true
-;parallel = true
-;omit =
-;     src/optlang/_version.py
+[coverage:run]
+branch = true
+parallel = true
+omit =
+     src/optlang/_version.py
+     src/optlang/tests/*
 
-;[coverage:report]
-;exclude_lines =
-;# Have to re-enable the standard pragma
-;     pragma: no cover
-;precision = 2
-;omit =
-;     src/optlang/_version.py
+[coverage:report]
+exclude_lines =
+# Have to re-enable the standard pragma
+     pragma: no cover
+precision = 2
+omit =
+     src/optlang/_version.py
+     src/optlang/tests/*
 
 [flake8]
 max-line-length = 130
 exclude =
      __init__.py
      _version.py
+     gurobi_interface.py
+     cplex_interface.py
      src/optlang/tests/*
 # The following conflict with `black` which is the more pedantic.
 ignore =