bokeh timeseries plots now comply with OpenMDAO's placement of recorder files.

.github/workflows/dymos_docs_workflow.yml

@@ -31,7 +31,7 @@ jobs:
             SCIPY: '1.13'
             PETSc: '3.19'
             PYOPTSPARSE: 'v2.11.0'
-            OPENMDAO: 'latest'
+            OPENMDAO: 'dev'
             OPTIONAL: '[docs]'
             JAX: '0.4.28'
             PUBLISH_DOCS: 1

.github/workflows/dymos_tests_workflow.yml

@@ -305,13 +305,15 @@ jobs:
           pipdeptree
 
       - name: 'Upload environment artifact'
+        if: env.RUN_BUILD
         uses: actions/upload-artifact@v3
         with:
           name: ${{ matrix.NAME }}_environment
           path: ${{ matrix.NAME }}_environment.yml
           retention-days: 5
 
       - name: Check NumPy 2.0 Compatibility
+        if: env.RUN_BUILD
         run: |
           echo "============================================================="
           echo "Check Dymos code for NumPy 2.0 compatibility"
@@ -321,7 +323,7 @@ jobs:
           ruff check . --select NPY201
 
       - name: Perform linting with Ruff
-        if: ${{ matrix.NAME == 'baseline' }}
+        if: env.RUN_BUILD && matrix.NAME == 'baseline'
         run: |
           echo "============================================================="
           echo "Lint Dymos code per settings in pyproject.toml"

.pre-commit-config.yaml

@@ -6,3 +6,11 @@ repos:
     # Run the linter.
     - id: ruff
       types_or: [ python, pyi, jupyter ]
+-   repo: local
+    hooks:
+    - id: check-notebook-outputs
+      name: Check that notebooks have no output cells.
+      description: Verifies that documentation notebooks contain no output cells.
+      language: python
+      pass_filenames: false
+      entry: python ./docs/clean_notebooks.py --dryrun ./docs

benchmark/benchmark_balanced_field.py

@@ -262,8 +262,8 @@ def benchmark_gausslobatto_timeseries_nosim_nosolveseg(self):
                                            solvesegs=False)
 
     def benchmark_radau_timeseries_nosim_nosolveseg(self):
-            _run_balanced_field_length_problem(tx=dm.Radau, timeseries=True, sim=False,
-                                               solvesegs=False)
+        _run_balanced_field_length_problem(tx=dm.Radau, timeseries=True, sim=False,
+                                           solvesegs=False)
 
     def benchmark_radau_notimeseries_nosim_solveseg(self):
         _run_balanced_field_length_problem(tx=dm.Radau, timeseries=False, sim=False,

benchmark/benchmark_brachistochrone.py

@@ -14,7 +14,7 @@ def brachistochrone_min_time(transcription='gauss-lobatto', num_segments=8, tran
     p = om.Problem(model=om.Group())
 
     p.driver = om.pyOptSparseDriver()
-    OPT, OPTIMIZER = set_pyoptsparse_opt(optimizer, fallback=True)
+    _, OPTIMIZER = set_pyoptsparse_opt(optimizer, fallback=True)
     p.driver.options['optimizer'] = OPTIMIZER
 
     if simul_derivs:

benchmark/benchmark_racecar.py

@@ -7,7 +7,6 @@
 import dymos as dm
 
 from dymos.examples.racecar.combinedODE import CombinedODE
-from dymos.examples.racecar.spline import get_spline, get_track_points
 from dymos.examples.racecar.tracks import ovaltrack  # track curvature imports
 
 
@@ -17,10 +16,7 @@ def _run_racecar_problem(transcription, timeseries=False, make_plots=False):
 
     # generate nodes along the centerline for curvature calculation (different
     # than collocation nodes)
-    points = get_track_points(track)
 
-    # fit the centerline spline.
-    finespline, gates, gatesd, curv, slope = get_spline(points, s=0.0)
     # by default 10000 points
     s_final = track.get_total_length()
 

docs/build_source_docs.py

@@ -15,7 +15,6 @@
     'transcriptions.common',
     'transcriptions.explicit_shooting',
     'transcriptions.pseudospectral',
-    'transcriptions.solve_ivp',
     'utils',
 ]
 

docs/clean_notebooks.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import pathlib
+import subprocess
+
+
+EXCLUDE_DIRS = ('_build', '.ipynb_checkpoints')
+
+
+class bcolors:
+    FILE = '\033[96m'  # blue
+    CYAN = '\033[96m'
+    GREEN = '\033[92m'
+    WARNING = '\033[93m'
+    FAIL = '\033[91m'
+    ENDC = '\033[0m'
+    BOLD = '\033[1m'
+    UNDERLINE = '\033[4m'
+
+
+def _clear_notebook_outputs(path=os.getcwd(), dry_run=True):
+
+    # Find all the notebooks
+    notebooks = []
+    if pathlib.Path(path).is_dir():
+        for dirpath, dirs, files in os.walk(path, topdown=True):
+            dirs[:] = [d for d in dirs if d not in EXCLUDE_DIRS]
+            notebooks.extend(pathlib.Path(dirpath).glob('*.ipynb'))
+        if not notebooks:
+            print(f'{bcolors.FAIL}No notebooks found.{bcolors.ENDC}')
+            return
+    elif path.endswith('.ipynb'):
+        notebooks.append(path)
+    else:
+        print(f'{bcolors.FILE}{path}{bcolors.ENDC}{bcolors.FAIL} is not a notebook file.{bcolors.ENDC}')
+        return
+
+    num_cleaned = 0
+    for file in notebooks:
+        with open(file) as f:
+            json_data = json.load(f)
+            for i in json_data['cells']:
+                if 'execution_count' in i and i['execution_count'] is not None:
+                    break
+            else:
+                # Notebook clean, process next notebook.
+                continue
+        num_cleaned += 1
+        if dry_run:
+            print(f'Would clear outputs from {bcolors.FILE}{file}{bcolors.ENDC}. '
+                  f'{bcolors.WARNING}(dryrun = True){bcolors.ENDC}')
+        else:
+            print(f'Clearing {bcolors.FILE}{file}{bcolors.ENDC}...', end='')
+            subprocess.Popen(f"jupyter nbconvert --clear-output --inplace {file}",
+                             shell=True,
+                             stdout=subprocess.DEVNULL,
+                             stderr=subprocess.STDOUT).wait()
+            print('done')
+
+    if num_cleaned == 0:
+        print('No unclean notebooks found.')
+
+    return num_cleaned
+
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Clear notebook outputs in place.')
+    parser.add_argument('path', nargs='?', default='.', help='The or directory path to clean.')
+    parser.add_argument('-d', '--dryrun', action='store_true',
+                        help='Print notebooks with outputs but do not clean them.')
+    args = parser.parse_args()
+    num_cleaned = _clear_notebook_outputs(path=args.path, dry_run=args.dryrun)
+    if num_cleaned >0 and  args.dryrun:
+        exit(1)

docs/dymos_book/examples/balanced_field/balanced_field.ipynb

@@ -720,7 +720,8 @@
    },
    "outputs": [],
    "source": [
-    "sim_case = om.CaseReader('dymos_simulation.db').get_case('final')\n",
+    "sim_prob = traj.sim_prob\n",
+    "sim_case = om.CaseReader(sim_prob.get_outputs_dir() / 'dymos_simulation.db').get_case('final')\n",
     "\n",
     "fig, axes = plt.subplots(2, 1, sharex=True, gridspec_kw={'top': 0.92}, figsize=(12,6))\n",
     "for phase in ['br_to_v1', 'rto', 'v1_to_vr', 'rotate', 'climb']:\n",
@@ -813,7 +814,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

docs/dymos_book/examples/balanced_field/balanced_field_funccomp.ipynb

@@ -458,13 +458,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim_case = om.CaseReader('dymos_solution.db').get_case('final')\n",
+    "sol_case = om.CaseReader(p.get_outputs_dir() / 'dymos_solution.db').get_case('final')\n",
     "\n",
     "fig, axes = plt.subplots(2, 1, sharex=True, gridspec_kw={'top': 0.92}, figsize=(12, 6))\n",
     "for phase in ['br_to_v1', 'rto', 'v1_to_vr', 'rotate', 'climb']:\n",
-    "    r = sim_case.get_val(f'traj.{phase}.timeseries.r', units='ft')\n",
-    "    v = sim_case.get_val(f'traj.{phase}.timeseries.v', units='kn')\n",
-    "    t = sim_case.get_val(f'traj.{phase}.timeseries.time', units='s')\n",
+    "    r = sol_case.get_val(f'traj.{phase}.timeseries.r', units='ft')\n",
+    "    v = sol_case.get_val(f'traj.{phase}.timeseries.v', units='kn')\n",
+    "    t = sol_case.get_val(f'traj.{phase}.timeseries.time', units='s')\n",
     "    axes[0].plot(t, r, '-', label=phase)\n",
     "    axes[1].plot(t, v, '-', label=phase)\n",
     "fig.suptitle('Balanced Field Length')\n",
@@ -474,11 +474,11 @@
     "axes[0].grid(True)\n",
     "axes[1].grid(True)\n",
     "\n",
-    "tv1 = sim_case.get_val('traj.br_to_v1.timeseries.time', units='s')[-1, 0]\n",
-    "v1 = sim_case.get_val('traj.br_to_v1.timeseries.v', units='kn')[-1, 0]\n",
+    "tv1 = sol_case.get_val('traj.br_to_v1.timeseries.time', units='s')[-1, 0]\n",
+    "v1 = sol_case.get_val('traj.br_to_v1.timeseries.v', units='kn')[-1, 0]\n",
     "\n",
-    "tf_rto = sim_case.get_val('traj.rto.timeseries.time', units='s')[-1, 0]\n",
-    "rf_rto = sim_case.get_val('traj.rto.timeseries.r', units='ft')[-1, 0]\n",
+    "tf_rto = sol_case.get_val('traj.rto.timeseries.time', units='s')[-1, 0]\n",
+    "rf_rto = sol_case.get_val('traj.rto.timeseries.r', units='ft')[-1, 0]\n",
     "\n",
     "axes[0].annotate(f'field length = {r[-1, 0]:5.1f} ft', xy=(t[-1, 0], r[-1, 0]),\n",
     "                 xycoords='data', xytext=(0.7, 0.5),\n",
@@ -551,7 +551,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

docs/dymos_book/examples/brachistochrone/brachistochrone_tandem_phases.ipynb

@@ -320,7 +320,11 @@
     "i = np.array(0)\n",
     "legend_contents = []\n",
     "\n",
-    "sol_case = om.CaseReader('dymos_solution.db').get_case('final')\n",
+    "print(p.get_outputs_dir())\n",
+    "import os\n",
+    "print(os.listdir(os.getcwd()))\n",
+    "\n",
+    "sol_case = om.CaseReader(p.get_outputs_dir() / 'dymos_solution.db').get_case('final')\n",
     "\n",
     "sol_x = sol_case.get_val('phase0.timeseries.x')\n",
     "sol_y = sol_case.get_val('phase0.timeseries.y')\n",
@@ -363,13 +367,6 @@
     "\n",
     "HTML(html_with_custom_height)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

docs/dymos_book/examples/brachistochrone/brachistochrone_upstream_controls.ipynb

@@ -77,19 +77,19 @@
    ]
   },
   {
-    "cell_type": "code",
-    "execution_count": null,
-    "metadata": {
-     "tags": [
-      "active-ipynb",
-      "remove-input",
-      "remove-output"
-     ]
-    },
-    "outputs": [],
-    "source": [
-     "%matplotlib inline"
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "active-ipynb",
+     "remove-input",
+     "remove-output"
     ]
+   },
+   "outputs": [],
+   "source": [
+    "%matplotlib inline"
+   ]
   },
   {
    "cell_type": "code",
@@ -193,8 +193,7 @@
     "# Test the results\n",
     "print(p.get_val('traj.phase0.timeseries.time')[-1])\n",
     "\n",
-    "# Check the validity of our results by using scipy.integrate.solve_ivp to\n",
-    "# integrate the solution.\n",
+    "# Check the validity of our results.\n",
     "sim_out = traj.simulate()\n",
     "\n",
     "# Plot the results\n",
@@ -273,7 +272,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.4"
   },
   "orphan": true
  },

docs/dymos_book/examples/brachistochrone/brachistochrone_upstream_init_duration_states.ipynb

@@ -61,19 +61,19 @@
    ]
   },
   {
-    "cell_type": "code",
-    "execution_count": null,
-    "metadata": {
-     "tags": [
-      "active-ipynb",
-      "remove-input",
-      "remove-output"
-     ]
-    },
-    "outputs": [],
-    "source": [
-     "%matplotlib inline"
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "active-ipynb",
+     "remove-input",
+     "remove-output"
     ]
+   },
+   "outputs": [],
+   "source": [
+    "%matplotlib inline"
+   ]
   },
   {
    "cell_type": "code",
@@ -195,10 +195,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Check the validity of our results by using scipy.integrate.solve_ivp to\n",
-    "# integrate the solution.\n",
-    "sol = om.CaseReader('dymos_solution.db').get_case('final')\n",
-    "sim = om.CaseReader('dymos_simulation.db').get_case('final')\n",
+    "# Check the validity of our results.\n",
+    "sol = om.CaseReader(p.get_outputs_dir() / 'dymos_solution.db').get_case('final')\n",
+    "sim = om.CaseReader(traj.sim_prob.get_outputs_dir() / 'dymos_simulation.db').get_case('final')\n",
     "\n",
     "# Plot the results\n",
     "fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(12, 4.5))\n",
@@ -259,7 +258,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,

docs/dymos_book/examples/bryson_denham/bryson_denham.ipynb

@@ -461,8 +461,8 @@
    },
    "outputs": [],
    "source": [
-    "sol = om.CaseReader('dymos_solution.db').get_case('final')\n",
-    "sim = om.CaseReader('dymos_simulation.db').get_case('final')\n",
+    "sol = om.CaseReader(p.get_outputs_dir() / 'dymos_solution.db').get_case('final')\n",
+    "sim = om.CaseReader(traj.sim_prob.get_outputs_dir() / 'dymos_simulation.db').get_case('final')\n",
     "\n",
     "t = sol.get_val('traj.phase0.timeseries.time')\n",
     "x = sol.get_val('traj.phase0.timeseries.x')\n",

docs/dymos_book/examples/cart_pole/cart_pole.ipynb

@@ -329,8 +329,8 @@
     "print('objective value:', obj)\n",
     "\n",
     "# get optimization solution and simulation (time integration) results\n",
-    "sol = om.CaseReader('dymos_solution.db').get_case('final')\n",
-    "sim = om.CaseReader('dymos_simulation.db').get_case('final')\n",
+    "sol = om.CaseReader(p.get_outputs_dir() / 'dymos_solution.db').get_case('final')\n",
+    "sim = om.CaseReader(traj.sim_prob.get_outputs_dir() / 'dymos_simulation.db').get_case('final')\n",
     "\n",
     "# plot time histories of x, x_dot, theta, theta_dot\n",
     "plot_results([('traj.phase.timeseries.time', 'traj.phase.timeseries.x', 'time (s)', 'x (m)'),\n",