Merge pull request #153 from biosimulators/reconcile-rbapy

remove RBApy until it can be added back via PyPI

.github/actions/setup-poetry-env/action.yml

@@ -29,14 +29,7 @@ runs:
       run: poetry config virtualenvs.in-project true
       shell: bash
 
-    - name: Load cached venv
-      id: cached-poetry-dependencies
-      uses: actions/cache@v4
-      with:
-        path: .venv
-        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }}
-
     - name: Install dependencies
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      run: poetry install --no-interaction --with bngl,cellml,lems,neuroml,sbml,simularium,escher,containers,logging,rba,smoldyn
+      run: poetry install --no-interaction --with bngl,cellml,lems,neuroml,sbml,simularium,escher,containers,logging,smoldyn
       shell: bash

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.10", "3.11" ]
       fail-fast: false
     defaults:
       run:

biosimulators_utils/_version.py

@@ -1 +1 @@
-__version__ = '0.1.189'
+__version__ = '0.2.0'

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biosimulators-utils"
-version = "0.1.188"
+version = "0.2.0"
 description = "description"
 license = "MIT"
 authors = ["Center for Reproducible Biomedical Modeling <[email protected]>"]
@@ -21,7 +21,7 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = "~3.10"
+python = "^3.10"
 appdirs = "*"
 biopython = "*"
 cement = "*"
@@ -58,7 +58,7 @@ pylems = {version = "*", optional = true}
 pyneuroml = {version = ">=0.5.18", optional = true}
 pint = {version = "*", optional = true}
 libneuroml = {version = "*", optional = true}
-rbapy = { git = "https://github.com/biosimulators/RBApy.git", rev="d82e1ade319cb503f6e28759a0cbeffccabd89e8", optional = true }
+#rbapy = { git = "https://github.com/biosimulators/RBApy.git", rev="d82e1ade319cb503f6e28759a0cbeffccabd89e8", optional = true }
 python-libsbml = {version = "*", optional = true}
 smoldyn = {version = ">=2.66", optional = true}
 simulariumio = {version = "*", optional = true}
@@ -111,18 +111,17 @@ dependencies = { pylems = "*", pyneuroml = "*", pint = "*" }
 optional = true
 dependencies = { libneuroml = "*", pyneuroml = ">=0.5.18" }
 
-[tool.poetry.group.rba]
-optional = true
-# in requirements.optional.txt, rbapy was specified as:
-#
-# [rba]
-# python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
-#
- dependencies = { rbapy = { git = "https://github.com/biosimulators/RBApy.git", rev="d82e1ade319cb503f6e28759a0cbeffccabd89e8" } }
-#
-# if using official release (not biosimulators fork), use:
-# dependencies = { rbapy = "*" }
-
+#[tool.poetry.group.rba]
+#optional = true
+## in requirements.optional.txt, rbapy was specified as:
+##
+## [rba]
+## python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
+##
+# dependencies = { rbapy = { git = "https://github.com/biosimulators/RBApy.git", rev="d82e1ade319cb503f6e28759a0cbeffccabd89e8" } }
+##
+## if using official release (not biosimulators fork), use:
+## dependencies = { rbapy = "*" }
 
 [tool.poetry.group.sbml]
 optional = true

tests/model_lang/rba/test_rba_utils.py

@@ -1,79 +1,80 @@
-from biosimulators_utils.model_lang.rba.utils import get_parameters_variables_outputs_for_simulation
-from biosimulators_utils.sedml.data_model import SteadyStateSimulation
-import math
-import os
+# from biosimulators_utils.model_lang.rba.utils import get_parameters_variables_outputs_for_simulation
+# from biosimulators_utils.sedml.data_model import SteadyStateSimulation
+# import math
+# import os
 import unittest
 
 
 class RbaUtilsTestCase(unittest.TestCase):
-    FIXTURES_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba')
-
-    def test_get_parameters_variables_for_simulation(self):
-        filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip')
-        params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation)
-
-        self.assertEqual(len(params), 1620)
-
-        param = next(param for param in params if param.id == 'parameter_amino_acid_concentration_Y_MIN')
-        self.assertEqual(param.name, 'Value of parameter "Y_MIN" of function "amino_acid_concentration"')
-        self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN')
-        self.assertEqual(param.new_value, '-inf')
-
-        self.assertEqual(len(sims), 1)
-        sim = sims[0]
-        self.assertIsInstance(sim, SteadyStateSimulation)
-        self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669')
-        self.assertEqual(sim.algorithm.changes, [])
-
-        self.assertEqual(len(vars), 15766)
-
-        self.assertEqual(vars[0].id, 'objective')
-        self.assertEqual(vars[0].name, 'Value of objective')
-        self.assertEqual(vars[0].target, 'objective')
-
-        var = next(var for var in vars if var.id == 'M_pqq_p')
-        self.assertEqual(var.name, 'Dual of constraint "M_pqq_p"')
-        self.assertEqual(var.target, 'constraints.M_pqq_p')
-
-        var = next(var for var in vars if var.id == 'test_process_2_machinery')
-        self.assertEqual(var.name, 'Primal of variable "test_process_2_machinery"')
-        self.assertEqual(var.target, 'variables.test_process_2_machinery')
-
-    def test_get_parameters_variables_for_simulation_native_ids_data_types(self):
-        filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip')
-        params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation, native_ids=True, native_data_types=True)
-
-        self.assertEqual(len(params), 1620)
-
-        param = next(param for param in params if param.id == 'amino_acid_concentration.Y_MIN')
-        self.assertEqual(param.name, None)
-        self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN')
-        self.assertEqual(param.new_value, -math.inf)
-
-        self.assertEqual(len(sims), 1)
-        sim = sims[0]
-        self.assertIsInstance(sim, SteadyStateSimulation)
-        self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669')
-        self.assertEqual(sim.algorithm.changes, [])
-
-        self.assertEqual(len(vars), 15766)
-
-        self.assertEqual(vars[0].id, None)
-        self.assertEqual(vars[0].name, None)
-        self.assertEqual(vars[0].target, 'objective')
-
-        var = next(var for var in vars if var.id == 'M_pqq_p')
-        self.assertEqual(var.name, None)
-        self.assertEqual(var.target, 'constraints.M_pqq_p')
-
-        var = next(var for var in vars if var.id == 'test_process_2_machinery')
-        self.assertEqual(var.name, None)
-        self.assertEqual(var.target, 'variables.test_process_2_machinery')
-
-    def test_get_parameters_variables_for_simulation_error_handling(self):
-        with self.assertRaises(ValueError):
-            get_parameters_variables_outputs_for_simulation(None, None, None)
-
-        filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip')
-        with self.assertRaises(NotImplementedError):
-            get_parameters_variables_outputs_for_simulation(filename, None, None)
+    pass
+    # FIXTURES_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba')
+
+    # def test_get_parameters_variables_for_simulation(self):
+    #     filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip')
+    #     params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation)
+    #
+    #     self.assertEqual(len(params), 1620)
+    #
+    #     param = next(param for param in params if param.id == 'parameter_amino_acid_concentration_Y_MIN')
+    #     self.assertEqual(param.name, 'Value of parameter "Y_MIN" of function "amino_acid_concentration"')
+    #     self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN')
+    #     self.assertEqual(param.new_value, '-inf')
+    #
+    #     self.assertEqual(len(sims), 1)
+    #     sim = sims[0]
+    #     self.assertIsInstance(sim, SteadyStateSimulation)
+    #     self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669')
+    #     self.assertEqual(sim.algorithm.changes, [])
+    #
+    #     self.assertEqual(len(vars), 15766)
+    #
+    #     self.assertEqual(vars[0].id, 'objective')
+    #     self.assertEqual(vars[0].name, 'Value of objective')
+    #     self.assertEqual(vars[0].target, 'objective')
+    #
+    #     var = next(var for var in vars if var.id == 'M_pqq_p')
+    #     self.assertEqual(var.name, 'Dual of constraint "M_pqq_p"')
+    #     self.assertEqual(var.target, 'constraints.M_pqq_p')
+    #
+    #     var = next(var for var in vars if var.id == 'test_process_2_machinery')
+    #     self.assertEqual(var.name, 'Primal of variable "test_process_2_machinery"')
+    #     self.assertEqual(var.target, 'variables.test_process_2_machinery')
+    #
+    # def test_get_parameters_variables_for_simulation_native_ids_data_types(self):
+    #     filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip')
+    #     params, sims, vars, plots = get_parameters_variables_outputs_for_simulation(filename, None, SteadyStateSimulation, native_ids=True, native_data_types=True)
+    #
+    #     self.assertEqual(len(params), 1620)
+    #
+    #     param = next(param for param in params if param.id == 'amino_acid_concentration.Y_MIN')
+    #     self.assertEqual(param.name, None)
+    #     self.assertEqual(param.target, 'parameters.functions.amino_acid_concentration.parameters.Y_MIN')
+    #     self.assertEqual(param.new_value, -math.inf)
+    #
+    #     self.assertEqual(len(sims), 1)
+    #     sim = sims[0]
+    #     self.assertIsInstance(sim, SteadyStateSimulation)
+    #     self.assertEqual(sim.algorithm.kisao_id, 'KISAO_0000669')
+    #     self.assertEqual(sim.algorithm.changes, [])
+    #
+    #     self.assertEqual(len(vars), 15766)
+    #
+    #     self.assertEqual(vars[0].id, None)
+    #     self.assertEqual(vars[0].name, None)
+    #     self.assertEqual(vars[0].target, 'objective')
+    #
+    #     var = next(var for var in vars if var.id == 'M_pqq_p')
+    #     self.assertEqual(var.name, None)
+    #     self.assertEqual(var.target, 'constraints.M_pqq_p')
+    #
+    #     var = next(var for var in vars if var.id == 'test_process_2_machinery')
+    #     self.assertEqual(var.name, None)
+    #     self.assertEqual(var.target, 'variables.test_process_2_machinery')
+    #
+    # def test_get_parameters_variables_for_simulation_error_handling(self):
+    #     with self.assertRaises(ValueError):
+    #         get_parameters_variables_outputs_for_simulation(None, None, None)
+    #
+    #     filename = os.path.join(self.FIXTURES_DIRNAME, 'Escherichia-coli-K12-WT.zip')
+    #     with self.assertRaises(NotImplementedError):
+    #         get_parameters_variables_outputs_for_simulation(filename, None, None)

tests/model_lang/rba/test_rba_validation.py

@@ -1,40 +1,41 @@
-from biosimulators_utils.model_lang.rba import validation
-from biosimulators_utils.utils.core import flatten_nested_list_of_strings
-import os
-import rba
+# from biosimulators_utils.model_lang.rba import validation
+# from biosimulators_utils.utils.core import flatten_nested_list_of_strings
+# import os
+# import rba
 import unittest
 
 
 class RbaValidationTestCase(unittest.TestCase):
-    FIXTURE_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba')
+    pass
+    # FIXTURE_DIRNAME = os.path.join(os.path.dirname(__file__), '..', '..', 'fixtures', 'rba')
 
-    def test(self):
-        filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT.zip')
-        errors, warnings, model = validation.validate_model(filename)
-        self.assertEqual(errors, [])
-        self.assertEqual(warnings, [])
-        self.assertIsInstance(model, rba.model.RbaModel)
-
-        filename = None
-        errors, warnings, model = validation.validate_model(filename)
-        self.assertIn('is not a path', flatten_nested_list_of_strings(errors))
-        self.assertEqual(warnings, [])
-        self.assertEqual(model, None)
-
-        filename = os.path.join(self.FIXTURE_DIRNAME, 'not exist.zip')
-        errors, warnings, model = validation.validate_model(filename)
-        self.assertIn('does not exist', flatten_nested_list_of_strings(errors))
-        self.assertEqual(warnings, [])
-        self.assertEqual(model, None)
-
-        filename = __file__
-        errors, warnings, model = validation.validate_model(filename)
-        self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors))
-        self.assertEqual(warnings, [])
-        self.assertEqual(model, None)
-
-        filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT-invalid.zip')
-        errors, warnings, model = validation.validate_model(filename)
-        self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors))
-        self.assertEqual(warnings, [])
-        self.assertEqual(model, None)
+    # def test(self):
+        # filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT.zip')
+        # errors, warnings, model = validation.validate_model(filename)
+        # self.assertEqual(errors, [])
+        # self.assertEqual(warnings, [])
+        # self.assertIsInstance(model, rba.model.RbaModel)
+        #
+        # filename = None
+        # errors, warnings, model = validation.validate_model(filename)
+        # self.assertIn('is not a path', flatten_nested_list_of_strings(errors))
+        # self.assertEqual(warnings, [])
+        # self.assertEqual(model, None)
+        #
+        # filename = os.path.join(self.FIXTURE_DIRNAME, 'not exist.zip')
+        # errors, warnings, model = validation.validate_model(filename)
+        # self.assertIn('does not exist', flatten_nested_list_of_strings(errors))
+        # self.assertEqual(warnings, [])
+        # self.assertEqual(model, None)
+        #
+        # filename = __file__
+        # errors, warnings, model = validation.validate_model(filename)
+        # self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors))
+        # self.assertEqual(warnings, [])
+        # self.assertEqual(model, None)
+        #
+        # filename = os.path.join(self.FIXTURE_DIRNAME, 'Escherichia-coli-K12-WT-invalid.zip')
+        # errors, warnings, model = validation.validate_model(filename)
+        # self.assertIn('is not a valid RBA', flatten_nested_list_of_strings(errors))
+        # self.assertEqual(warnings, [])
+        # self.assertEqual(model, None)