upstream merge

Author: dangunter

.coveragerc

@@ -7,8 +7,6 @@ omit =
     /opt/*
     # skip test directories
     */tests/*
-    # skip DMF's CLI
-    idaes/dmf/commands.py
     # skip plugins
     *_plugin.py
 

.github/CODEOWNERS

@@ -2,17 +2,19 @@
 # for developmental and contributed code
 
 # Overall (non-specific)
-* @lbianchi-lbl @ksbeattie
+* @sufikaur @ksbeattie
 # packaging
-setup.py @lbianchi-lbl @ksbeattie
-requirements*.txt @lbianchi-lbl @ksbeattie 
+setup.py @sufikaur @ksbeattie
+requirements*.txt @sufikaur @ksbeattie 
 
 # CI infra
-.github/ @lbianchi-lbl @ksbeattie 
+.github/ @sufikaur @ksbeattie 
+# spellchecker configuration
+.github/workflows/typos.toml @bpaul4 @sufikaur
 
 # testing
-pytest*.ini @lbianchi-lbl
-conftest.py @lbianchi-lbl
+pytest*.ini @sufikaur @ksbeattie
+conftest.py @sufikaur @ksbeattie
 
 # Docs
 /docs @dangunter @bpaul4
@@ -21,13 +23,14 @@ conftest.py @lbianchi-lbl
 /idaes/commands/ @dangunter
 
 # Core
-/idaes/core/ @andrewlee94 @dallan-keylogic @lbianchi-lbl
+/idaes/core/ @agarciadiego @dallan-keylogic
 /idaes/core/dmf/ @dangunter
-/idaes/core/surrogate/ @andrewlee94 @bpaul4 @avdudchenko @rundxdi
+/idaes/core/surrogate/ @bpaul4 @avdudchenko @rundxdi
 /idaes/core/ui/ @dangunter
 
 # Models
-/idaes/models/ @andrewlee94 @bpaul4
+/idaes/models/ @agarciadiego @bpaul4
+/idaes/models/properties/ @agarciadiego @dallan-keylogic 
 
 # Apps - each package needs a maintainer
 /idaes/apps/caprese/ @Robbybp

.github/actions/run-examples/action.yml

@@ -31,6 +31,16 @@ inputs:
     required: false
     default: ''
 
+  run-notebooks:
+    description: "Run notebook tests (via nbmake)"
+    required: false
+    default: 'true'
+
+  run-pyfiles:
+    description: "Run Python *.py tests (test_*.py, *_test.py)"
+    required: false
+    default: 'true'
+
 runs:
   using: composite
   steps:
@@ -63,6 +73,8 @@ runs:
       shell: bash -l {0}
       env:
         PYTHONPATH: ${{ github.action_path }}
+        EXAMPLES_RUN_NOTEBOOKS: ${{ inputs.run-notebooks }}
+        EXAMPLES_RUN_PYFILES: ${{ inputs.run-pyfiles }}
         PYTEST_ADDOPTS: >-
           --color=yes
           --durations=0

.github/actions/run-examples/examples_for_idaes_ci.py

@@ -3,9 +3,7 @@
 """
 
 from contextlib import contextmanager
-from dataclasses import dataclass, field
 import fnmatch
-import logging
 import os
 from pathlib import Path
 import sys
@@ -17,35 +15,29 @@
 from idaes_examples import notebooks
 from idaes_examples import build
 
-
 matchmarker = pytest.StashKey()
 marked = pytest.StashKey()
 
+# Environment triggers for use either locally
+# or in GitHub Action
+_ENV_TRUE = {"1", "true", "yes", "on"}
+RUN_NOTEBOOKS = str(os.getenv("EXAMPLES_RUN_NOTEBOOKS", "1")).lower() in _ENV_TRUE
+RUN_PYFILES = str(os.getenv("EXAMPLES_RUN_PYFILES", "1")).lower() in _ENV_TRUE
+
 
 def _matches_pattern(item: pytest.Item, pattern: str) -> bool:
     to_match = os.fspath(item.path)
     return fnmatch.fnmatch(to_match, pattern)
 
 
 def pytest_configure(config: pytest.Config):
-    tensorflow_py311_win = pytest.mark.xfail(
-        condition=sys.version_info > (3, 11),
-        run=True,
-        strict=False,
-        reason="tensorflow ImportError on 3.11+ on Windows (cannot import name 'formatargspec' from 'inspect')",
-    )
     config.stash[matchmarker] = {
         "*/held/*": pytest.mark.xfail(run=False, reason="notebook has 'held' status"),
         "*/archive/*": pytest.mark.skip(reason="notebook is archived"),
-        # TODO: Need to fix this once the Python 3.11 issue is resolved in tensorflow
-        "*/surrogates/best_practices_optimization*": tensorflow_py311_win,
-        "*/surrogates/omlt/keras_flowsheet_optimization*": tensorflow_py311_win,
         "*/surrogates/sco2/alamo/*": pytest.mark.xfail(
             run=False,
             reason="notebooks require ALAMO to run",
         ),
-        "*/surrogates/sco2/omlt/keras_training*": tensorflow_py311_win,
-        "*/surrogates/sco2/omlt/flowsheet_optimization*": tensorflow_py311_win,
     }
     config.stash[marked] = []
 
@@ -55,16 +47,31 @@ def pytest_sessionstart(session: pytest.Session):
 
 
 def pytest_ignore_collect(collection_path: Path, config: pytest.Config):
+    """Control what gets collected. By default, notebooks and tests; ignore other files."""
     if "_dev" in collection_path.parts:
         return True
     if not collection_path.is_file():
         return
-    if collection_path.suffix == ".py":
-        # specifically ignore python files
-        return True
-    if not collection_path.match("**/*_test.ipynb"):
+
+    suffix = collection_path.suffix
+    # Notebook tests (only *_test.ipynb)
+    if suffix == ".ipynb":
+        if not RUN_NOTEBOOKS:
+            return True
+        return not collection_path.match("**/*_test.ipynb")
+
+    # Python tests (only test_*.py or *_test.py)
+    if suffix == ".py":
+        if not RUN_PYFILES:
+            return True
+        name = collection_path.name
+        if fnmatch.fnmatch(name, "test_*.py") or fnmatch.fnmatch(name, "*_test.py"):
+            return False
         return True
 
+    # Ignore everything else
+    return True
+
 
 def pytest_collection_modifyitems(config: pytest.Config, items):
     for item in items:
@@ -113,7 +120,7 @@ def run_pytest(
         empty_file_for_ignoring.write_text("")
         args += ["-c", empty_file_for_ignoring]
 
-    with _temp_cwd(rootdir) as p:
+    with _temp_cwd(rootdir):
         res = pytest.main(
             args,
             **kwargs,
@@ -125,6 +132,7 @@ def run_pytest(
 def main(args):
     rootdir = Path(idaes_examples.__path__[0])
 
+    # Always include --nbmake, but notebook collection can be disabled by env
     res = run_pytest(
         rootdir,
         [

.github/actions/setup-idaes/action.yml

@@ -46,6 +46,23 @@ runs:
         echo '::group::Output of "idaes get-extensions" command'
         idaes get-extensions --extra petsc --verbose
         echo '::endgroup::'
+
+        # extra dependencies must be installed on Ubuntu 24.04
+        if [ -f "/etc/os-release" ]; then
+          . /etc/os-release
+          if [ "$ID" = "ubuntu" ] && [ "$VERSION_ID" = "24.04" ]; then
+          echo '::group::Output of "apt install" for required OS packages'
+          sudo apt install libgfortran5 libgomp1 liblapack3 libblas3
+          echo '::endgroup::'
+          fi
+        fi
+
+        echo '::group::Output of test commands for IDAES binaries'
+        echo 'List IDAES binaries directory'
+        ls -l "$(idaes bin-directory)"
+        echo 'Try to run ipopt'
+        "$(idaes bin-directory)"/ipopt -v
+        echo '::endgroup::'
     - name: Install AMPL SCIP (${{ inputs.ampl-scip-pip-target }})
       if: inputs.ampl-scip-pip-target
       shell: bash -l {0}

.github/workflows/core.yml

@@ -4,10 +4,10 @@ on:
   push:
     branches:
       - main
-      - '*_rel'
+      - "*_rel"
   schedule:
     # run daily at 5:00 am UTC (12 am ET/9 pm PT)
-    - cron: '0 5 * * *'
+    - cron: "0 5 * * *"
   repository_dispatch:
     # to run this, send a POST API call at repos/IDAES/idaes-pse/dispatches with the specified event_type
     # e.g. `gh repos/IDAES/idaes-pse/dispatches -F event_type=ci_run_tests`
@@ -38,7 +38,7 @@ concurrency:
 
 env:
   # default Python version to use for checks that do not require multiple versions
-  DEFAULT_PYTHON_VERSION: '3.10'
+  DEFAULT_PYTHON_VERSION: "3.10"
   IDAES_CONDA_ENV_NAME_DEV: idaes-pse-dev
   PYTEST_ADDOPTS: "--color=yes"
 
@@ -54,6 +54,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ env.DEFAULT_PYTHON_VERSION }}
@@ -67,17 +68,18 @@ jobs:
           pip --no-cache-dir install --progress-bar off "$black_requirement"
       - name: Run Black to verify that the committed code is formatted
         run: |
-          black --check .
+          black --check --diff .
 
   spell-check:
     name: Check Spelling
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
         uses: actions/checkout@v4
+
       - name: Run Spell Checker
-        uses: crate-ci/typos@master
-        with: 
+        uses: crate-ci/typos@v1.24.5
+        with:
           config: ./.github/workflows/typos.toml
 
   pytest:
@@ -88,27 +90,29 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         os:
           - linux
           - win64
         include:
           - os: linux
-            runner-image: ubuntu-20.04
+            runner-image: ubuntu-24.04
           - os: win64
             runner-image: windows-2022
-          - python-version: '3.11'
+          - python-version: "3.11"
             # only generate coverage report for a single python version in the matrix
             # to avoid overloading Codecov
             cov-report: true
+
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: ./.github/actions/display-debug-info
       - name: Set up Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.IDAES_CONDA_ENV_NAME_DEV }}
           python-version: ${{ matrix.python-version }}
+          miniforge-version: latest
       - name: Set up idaes
         uses: ./.github/actions/setup-idaes
         with:
@@ -117,6 +121,8 @@ jobs:
         if: matrix.cov-report
         run: |
           echo PYTEST_ADDOPTS="$PYTEST_ADDOPTS --cov --cov-report=xml" >> "$GITHUB_ENV"
+      - name: Install pandoc
+        run: conda install -c conda-forge pandoc
       - name: Run pytest (not integration)
         run: |
           pytest --pyargs idaes -m "not integration"
@@ -139,6 +145,7 @@ jobs:
     steps:
       # the checkout step is needed to have access to codecov.yml
       - uses: actions/checkout@v4
+
       - uses: actions/download-artifact@v4
         with:
           name: coverage-report-${{ matrix.report-variant }}
@@ -152,18 +159,25 @@ jobs:
           # but does require token for other workflows e.g. merge to `main`
           # see https://github.com/codecov/codecov-action/issues/1274#issuecomment-1934437359
           token: ${{ secrets.CODECOV_TOKEN }}
+          # pinning version after v0.7.0 broke tokenless upload
+          # see codecov/codecov-action#1487
+          version: v0.7.1
 
   build-docs:
     name: Build Sphinx docs
     runs-on: ubuntu-latest
     needs: [code-formatting, spell-check]
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.IDAES_CONDA_ENV_NAME_DEV }}
           python-version: ${{ env.DEFAULT_PYTHON_VERSION }}
+          miniforge-version: latest
+      - name: Install pandoc
+        run: conda install -c conda-forge pandoc
       - name: Set up idaes
         uses: ./.github/actions/setup-idaes
         with:
@@ -193,11 +207,13 @@ jobs:
       # NOTE: using Conda instead of actions/setup-python in this job is not strictly necessary
       # as it doesn't need to run on Windows or use the setup-idaes local action,
       # but we do it for consistency with the other jobs
+
       - name: Set up Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.IDAES_CONDA_ENV_NAME_DEV }}
           python-version: ${{ env.DEFAULT_PYTHON_VERSION }}
+          miniforge-version: latest
       - name: Set up idaes
         uses: ./.github/actions/setup-idaes
         with:
@@ -222,14 +238,16 @@ jobs:
 
   compat:
     name: Compatibility tests
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.IDAES_CONDA_ENV_NAME_DEV }}
           python-version: ${{ env.DEFAULT_PYTHON_VERSION }}
+          miniforge-version: latest
       - name: Set up idaes
         uses: ./.github/actions/setup-idaes
         with: