Merge pull request #71 from swryan/poem_integ

Simulate PR 3214

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.32.1-dev
+current_version = 3.33.1-dev
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -23,7 +23,7 @@ body:
     attributes:
       label: OpenMDAO Version
       description: What version of OpenMDAO is being used.
-      placeholder: "3.32.1-dev"
+      placeholder: "3.33.1-dev"
     validations:
       required: true
   - type: textarea

.github/scripts/get_poem_id.py

@@ -30,13 +30,18 @@ def get_poem_id(repository, pull_id):
     print(f"Checking Pull Request #{pull_id} for associated issue...")
     print("-------------------------------------------------------------------------------")
     try:
-        pull_json = subprocess.check_output(["gh", "--repo", repository,
-                                             "issue", "view", "--json", "body", pull_id])
+        p = subprocess.run(["gh", "--repo", repository, "issue", "view", "--json", "body", pull_id],
+                            stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except subprocess.CalledProcessError as err:
         print(f"Unable to access pull request #{pull_id}:\nrc={err.returncode}")
+        print(f"stdout:\n------\n{p.stdout}")
+        print(f"stderr:\n------\n{p.stderr}")
         return ERROR
 
-    pull_body = json.loads(pull_json)["body"]
+    print(f"stdout:\n------\n{p.stdout}")
+    print(f"stderr:\n------\n{p.stderr}")
+
+    pull_body = json.loads(p.stdout)["body"]
 
     issue_id = ""
 
@@ -58,14 +63,20 @@ def get_poem_id(repository, pull_id):
     print(f"Checking Issue #{issue_id} for associated POEM...")
     print("-------------------------------------------------------------------------------")
 
+    repository = repository.replace('swryan', 'OpenMDAO')
     try:
-        issue_json = subprocess.check_output(["gh", "--repo", repository,
-                                              "issue", "view", "--json", "body", issue_id])
+        p = subprocess.run(["gh", "--repo", repository, "issue", "view", "--json", "body", issue_id],
+                            stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except subprocess.CalledProcessError as err:
         print(f"Unable to access issue  #{issue_id}:\nrc={err.returncode}")
+        print(f"stdout:\n------\n{p.stdout}")
+        print(f"stderr:\n------\n{p.stderr}")
         return ERROR
 
-    issue_body = json.loads(issue_json)["body"]
+    print(f"stdout:\n------\n{p.stdout}")
+    print(f"stderr:\n------\n{p.stderr}")
+
+    issue_body = json.loads(p.stdout)["body"]
 
     poem_id = ""
 

.github/workflows/openmdao_latest_workflow.yml

@@ -56,6 +56,7 @@ jobs:
             PETSc: True
             PYOPTSPARSE: true
             SNOPT: true
+            BANDIT: true
             BUILD_DOCS: true
 
           # test latest versions on ubuntu
@@ -352,6 +353,28 @@ jobs:
 
           grep '^0 unique deprecation warnings' $RPT_FILE
 
+      - name: Scan for security issues
+        if: matrix.BANDIT
+        id: bandit
+        continue-on-error: true
+        run: |
+          python -m pip install bandit
+          echo "============================================================="
+          echo "Run bandit scan for high/medium severity issues"
+          echo "============================================================="
+          cd ${{ github.workspace }}
+          python -m bandit -c bandit.yml -ll -r openmdao
+
+      - name: Slack security issue
+        if: steps.bandit.outcome == 'failure'
+        uses: act10ns/[email protected]
+        with:
+          webhook-url: ${{ secrets.SLACK_WEBHOOK_URL }}
+          status: 'warning'
+          message:
+            Security issue found on `${{ matrix.NAME }}` build.
+            ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
       - name: Slack env change
         if: steps.env_info.outputs.errors != ''
         uses: act10ns/[email protected]

.github/workflows/openmdao_test_workflow.yml

@@ -726,7 +726,6 @@ jobs:
       - name: Scan for security issues
         if: matrix.BANDIT
         id: bandit
-        continue-on-error: true
         run: |
           python -m pip install bandit
           echo "============================================================="
@@ -735,16 +734,6 @@ jobs:
           cd ${{ github.workspace }}
           python -m bandit -c bandit.yml -ll -r openmdao
 
-      - name: Slack security issue
-        if: steps.bandit.outcome == 'failure'
-        uses: act10ns/[email protected]
-        with:
-          webhook-url: ${{ secrets.SLACK_WEBHOOK_URL }}
-          status: ${{ steps.bandit.outcome }}
-          message:
-            Security issue found on `${{ matrix.NAME }}` build.
-            ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
-
 
   coveralls:
     name: Finish coverage

.github/workflows/openmdao_update_poem.yml

@@ -5,15 +5,15 @@ name: Update Associated POEM
 
 on:
   pull_request:
-    types: [ opened, reopened, closed ]
+    types: [ opened, reopened, closed, synchronize ]
     branches: [ master ]
 
-permissions: {}
+# permissions: {}
 
 jobs:
 
   check_for_poem:
-    if: github.event.action == 'opened' || github.event.action == 'reopened' || github.event.pull_request.merged
+    if: github.event.action == 'opened' || github.event.action == 'reopened' || github.event.action == 'synchronize' || github.event.pull_request.merged
 
     runs-on: ubuntu-latest
 
@@ -51,7 +51,7 @@ jobs:
           fi
 
       - name: Comment on PR
-        if: (github.event.action == 'opened' || github.event.action == 'reopened') && steps.check_for_poem.outputs.POEM_ID != ''
+        if: (github.event.action == 'opened' || github.event.action == 'reopened' || github.event.action == 'synchronize') && steps.check_for_poem.outputs.POEM_ID != ''
         env:
           POEM_ID: ${{ steps.check_for_poem.outputs.POEM_ID }}
           POEM_URL: ${{ github.server_url }}/${{ github.repository_owner }}/POEMs/blob/master/POEM_${{ steps.check_for_poem.outputs.POEM_ID }}.md

README.md

@@ -3,6 +3,7 @@
 [![PyPI version][10]][11]
 [![PyPI Monthly Downloads][12]][11]
 
+
 # [OpenMDAO][0]
 
 OpenMDAO is an open-source high-performance computing platform for

openmdao/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '3.32.1-dev'
+__version__ = '3.33.1-dev'
 
 INF_BOUND = 1.0E30

openmdao/components/ks_comp.py

@@ -159,8 +159,13 @@ def initialize(self):
         self.options.declare('width', types=int, default=1, desc='Width of constraint vector.')
         self.options.declare('vec_size', types=int, default=1,
                              desc='The number of rows to independently aggregate.')
+        self.options.declare('minimum', types=bool, default=False,
+                             desc='Return the minimum instead of the maximum by multiplying both '
+                                  'the inputs and output by -1. It is not recommended to use both '
+                                  'this option and the lower_flag option (it will return the '
+                                  'negative of the aggregated max.)')
         self.options.declare('lower_flag', types=bool, default=False,
-                             desc="Set to True to reverse sign of input constraints.")
+                             desc='Set to True to reverse sign of input constraints.')
         self.options.declare('rho', 50.0, desc="Constraint Aggregation Factor.")
         self.options.declare('upper', 0.0, desc="Upper bound for constraint, default is zero.")
         self.options.declare('add_constraint', types=bool, default=False,
@@ -229,8 +234,15 @@ def compute(self, inputs, outputs):
         con_val = inputs['g'] - opt['upper']
         if opt['lower_flag']:
             con_val = -con_val
+        if opt['minimum']:
+            con_val = -con_val
+
+        ks_val = KSfunction.compute(con_val, opt['rho'])
 
-        outputs['KS'] = KSfunction.compute(con_val, opt['rho'])
+        if opt['minimum']:
+            ks_val = -ks_val
+
+        outputs['KS'] = ks_val
 
     def compute_partials(self, inputs, partials):
         """
@@ -244,11 +256,12 @@ def compute_partials(self, inputs, partials):
             Sub-jac components written to partials[output_name, input_name].
         """
         opt = self.options
-        width = opt['width']
 
         con_val = inputs['g'] - opt['upper']
         if opt['lower_flag']:
             con_val = -con_val
+        if opt['minimum']:
+            con_val = -con_val
 
         derivs = KSfunction.derivatives(con_val, opt['rho'])[0]
 

openmdao/components/tests/test_ks_comp.py

@@ -6,7 +6,7 @@
 import openmdao.api as om
 from openmdao.test_suite.components.simple_comps import DoubleArrayComp
 from openmdao.test_suite.test_examples.beam_optimization.multipoint_beam_stress import MultipointBeamGroup
-from openmdao.utils.assert_utils import assert_near_equal
+from openmdao.utils.assert_utils import assert_near_equal, assert_check_partials
 from openmdao.utils.testing_utils import force_check_partials
 
 
@@ -320,6 +320,67 @@ def test_units(self):
 
         assert_near_equal(prob.get_val('ks.KS', indices=0), np.amax(prob.get_val('x')), tolerance=1e-8)
 
+    def test_minimum(self):
+
+        n = 10
+
+        model = om.Group()
+
+        model.add_subsystem('ks', om.KSComp(width=n, minimum=True), promotes_inputs=[('g', 'x')])
+        model.set_input_defaults('x', range(n))
+
+        prob = om.Problem(model=model)
+        prob.setup()
+        prob.run_model()
+
+        assert_near_equal(prob.get_val('ks.KS', indices=0), np.amin(prob.get_val('x')), tolerance=1e-8)
+
+    def test_minimum_partials(self):
+
+        n = 10
+
+        model = om.Group()
+
+        model.add_subsystem('ks', om.KSComp(width=n, minimum=True), promotes_inputs=[('g', 'x')])
+        model.set_input_defaults('x', range(n))
+
+        prob = om.Problem(model=model)
+        prob.setup(force_alloc_complex=True)
+        prob.run_model()
+
+        partials = force_check_partials(prob, includes=['ks'], out_stream=None, method="cs", step=1e-200)
+        assert_check_partials(partials)
+
+    def test_minimum_and_lower_flag(self):
+
+        n = 10
+
+        model = om.Group()
+
+        model.add_subsystem('ks', om.KSComp(width=n, minimum=True, lower_flag=True), promotes_inputs=[('g', 'x')])
+        model.set_input_defaults('x', range(n))
+
+        prob = om.Problem(model=model)
+        prob.setup()
+        prob.run_model()
+
+        assert_near_equal(prob.get_val('ks.KS', indices=0), -np.amax(prob.get_val('x')), tolerance=1e-8)
+
+    def test_minimum_and_lower_flag_partials(self):
+
+        n = 10
+
+        model = om.Group()
+
+        model.add_subsystem('ks', om.KSComp(width=n, minimum=True, lower_flag=True), promotes_inputs=[('g', 'x')])
+        model.set_input_defaults('x', range(n))
+
+        prob = om.Problem(model=model)
+        prob.setup(force_alloc_complex=True)
+        prob.run_model()
+
+        partials = force_check_partials(prob, includes=['ks'], out_stream=None, method="cs", step=1e-200)
+        assert_check_partials(partials)
 
 if __name__ == "__main__":
     unittest.main()

openmdao/docs/openmdao_book/features/core_features/adding_desvars_cons_objs/modifying_desvars_cons_obj.ipynb

@@ -143,7 +143,6 @@
     "# modify the constraint and run again\n",
     "\n",
     "model.set_constraint_options(name='con1', upper=-1.0)\n",
-    "prob.setup()\n",
     "prob.run_driver()\n",
     "print(f\"con1 = {prob.get_val('con1')}\")"
    ]

openmdao/utils/code_utils.py

@@ -440,7 +440,7 @@ def __setstate__(self, state):
             The state of this object.
         """
         self.__dict__.update(state)
-        self._func = eval(state['_func'])
+        self._func = eval(state['_func'])  # nosec
 
     def _getsrc(self):
         if self._src is None:

openmdao/utils/relevance.py

@@ -798,6 +798,8 @@ def is_relevant_system(self, name):
         """
         Return True if the given named system is relevant.
 
+        Returns False if system has no subsystems with outputs.
+
         Parameters
         ----------
         name : str
@@ -811,7 +813,10 @@ def is_relevant_system(self, name):
         if not self._active:
             return True
 
-        return self._current_rel_sarray[self._sys2idx[name]]
+        try:
+            return self._current_rel_sarray[self._sys2idx[name]]
+        except KeyError:
+            return False
 
     def filter(self, systems, relevant=True):
         """

openmdao/utils/tests/test_relevance.py

@@ -43,3 +43,23 @@ def compute_jacvec_product(self, inputs, d_inputs, d_outputs, mode):
         prob.run_model()
         chk = prob.check_totals(of='b', wrt='a', show_only_incorrect=True)
         assert_check_totals(chk)
+
+class TestRelevanceEmptyGroups(unittest.TestCase):
+    def test_emptygroup(self):
+        '''Tests that relevance checks do not error if empty groups are present'''
+        prob = om.Problem()
+        model = prob.model
+
+        model.add_subsystem('empy_group', om.Group(), promotes=['*'])
+        grp2: om.Group = model.add_subsystem('non_empty_group', om.Group(), promotes=['*'])
+        grp2.add_subsystem('idv', om.IndepVarComp('x', val=1), promotes=['*'])
+        grp2.add_subsystem('comp', om.ExecComp('y=2*x**2'), promotes=['*'])
+        model.add_design_var('x')
+        model.add_objective('y')
+
+        prob.driver = om.ScipyOptimizeDriver()
+
+        prob.setup(force_alloc_complex=True)
+        prob.run_driver()
+
+        assert_check_totals(prob.check_totals(method='cs', out_stream=None))