Merge branch 'main' into add-prescient

.github/actions/run-examples/build-config-for-idaes-ci.yml

@@ -14,7 +14,6 @@ notebook:
       - source: Examples/Advanced/CustomUnitModels
       - source: Examples/Advanced/DataRecon
       - source: Examples/MatOpt
-      - source: Examples/SurrMod/ALAMO
       - source: Examples/SurrMod/Helmet
       - source: Examples/SurrMod/PySMO
       - source: Examples/Tools

.github/workflows/core.yml

@@ -101,7 +101,7 @@ jobs:
         run: |
           which python
           cd docs/
-          python build.py
+          python build.py --timeout 600
       - name: Publish built docs
         uses: actions/upload-artifact@v2
         with:

.github/workflows/integration.yml

@@ -193,7 +193,7 @@ jobs:
           cat *errors.txt || echo "No error logs found"
 
   pytest-site-packages:
-    name: Run tests from site-packages (non-editable) installation
+    name: Run tests from site-packages (non-editable) installation (${{ matrix.install-mode }})
     # NOTE: using ubuntu-latest (20.04) instead of 18.04 results in failures in power_generation/carbon_capture/mea_solvent_system/unit_models/tests/test_column.py
     runs-on: ubuntu-18.04
     needs: [precheck]
@@ -203,6 +203,21 @@ jobs:
         || needs.precheck.outputs.workflow-trigger == 'not_pr'
         || needs.precheck.outputs.workflow-trigger == 'approved_pr'
       )
+    strategy:
+      fail-fast: false
+      matrix:
+        install-mode:
+          - pip-default
+          - pip-optional
+          - conda-like
+        include:
+          - install-mode: pip-default
+            pip-install-target: '.'
+          - install-mode: pip-optional
+            pip-install-target: .[optional]
+          - install-mode: conda-like
+            pip-install-target: '.'
+            dependencies-to-uninstall: omlt
     steps:
       - uses: actions/checkout@v2
       - name: Set up Conda environment
@@ -213,13 +228,18 @@ jobs:
       - name: Set up idaes (non-editable installation)
         uses: ./.github/actions/setup-idaes
         with:
-          install-target: '.[optional]'
-      - name: Install test dependencies and run pytest in empty directory
+          install-target: ${{ matrix.pip-install-target }}
+      - name: Remove dependencies installable with pip but not with conda
+        # NOTE some dependencies that are installed by default with pip are not available through conda
+        # so they're not installed if IDAES is installed with `conda -c conda-forge -c IDAES-PSE idaes-pse`
+        # to ensure this scenario is handled properly, since we don't have (yet) the conda-build process integrated with the CI,
+        # we manually remove the "pip-but-not-conda" dependencies after installing with pip
+        # as an approximation of the enviroment that we'd get from `conda install`
+        if: matrix.dependencies-to-uninstall
+        run: |
+          pip uninstall --yes ${{ matrix.dependencies-to-uninstall }}
+      - name: Install and run pytest in empty directory
         run: |
           pushd "$(mktemp -d)"
-          # TODO this could be an optional [testing] dependency
-          pip install pytest addheader
-          # TODO downloading pytest.ini is still needed for the tests to pass
-          # eventually it will be moved to the root conftest.py so that is installed as Python code
-          wget https://raw.githubusercontent.com/IDAES/idaes-pse/main/pytest.ini 
-          pytest --pyargs idaes
+          pip install pytest
+          pytest --pyargs idaes -W ignore -rs

.pylint/idaes_transform.py

@@ -4,13 +4,15 @@
 
 See #1159 for more information.
 """
+from dataclasses import dataclass
 import sys
 import functools
 import logging
 import time
 import typing
 
 import astroid
+import pylint
 from astroid.builder import extract_node, parse
 
 
@@ -21,21 +23,53 @@
 _display = _notify = lambda *a, **kw: None
 
 
-REFERENCE_PYLINT_VERSION = '2.8.3'
+def _suppress_inference_errors(max_inferred=500) -> None:
+    """
+    Increasing this number to suppress inference errors causing false-positives in e.g. pandas.read_csv().
+    The value 500 is a sufficiently high number but otherwise arbitrary.
+    See https://github.com/PyCQA/pylint/issues/4577 for more information.
+    """
+    astroid.context.InferenceContext.max_inferred = int(max_inferred)
 
 
-def _check_version_compatibility():
+_suppress_inference_errors()
 
-    from pylint import __version__
-    if __version__ != REFERENCE_PYLINT_VERSION:
-        cmd_to_install = f"pip install pylint=={REFERENCE_PYLINT_VERSION}"
-        msg = (
-            f"WARNING: this plugin's reference version is {REFERENCE_PYLINT_VERSION}, "
-            f"but the currently installed pylint version is {__version__}. "
-            "This is not necessarily a problem; "
-            f"however, in case of issues, try installing the reference version using {cmd_to_install}"
+
+@dataclass
+class VersionCompat:
+    distr_name: str
+    expected: str
+    actual: str
+
+    @property
+    def cmd_to_install(self) -> str:
+        return f"pip install {self.distr_name}=={self.expected}"
+
+
+def _check_version_compatibility() -> None:
+
+    to_check = [
+        VersionCompat(
+            distr_name="pylint",
+            expected="2.12.2",
+            actual=pylint.__version__,
+        ),
+        VersionCompat(
+            distr_name="astroid",
+            expected="2.9.3",
+            actual=astroid.__version__,
         )
-        print(msg, file=sys.stderr)
+    ]
+
+    for v in to_check:
+        if v.actual != v.expected:
+            msg = (
+                f"WARNING: this plugin's reference version for {v.distr_name} is {v.expected}, "
+                f"but the currently installed version for is {v.actual}. "
+                "This is not necessarily a problem; "
+                f"however, in case of issues, try installing the reference version using {v.cmd_to_install}"
+            )
+            print(msg, file=sys.stderr)
 
 
 def has_declare_block_class_decorator(cls_node, decorator_name="declare_process_block_class"):
@@ -56,7 +90,16 @@ def has_declare_block_class_decorator(cls_node, decorator_name="declare_process_
 @functools.lru_cache(maxsize=1)
 def get_base_class_node():
     _notify('Getting base class node')
-    import_node = extract_node('from idaes.core.process_block import ProcessBlock; ProcessBlock')
+    pb_def = """
+        import idaes.core.base.process_block.ProcessBlock
+        class ProcessBlock(idaes.core.base.process_block.ProcessBlock):
+            # creating a stub for the __getitem__() method returning the uninferable object
+            # causes pylint to stop further checks on objects returned when calling [] on a derived class
+            # see e.g. https://github.com/PyCQA/astroid/blob/main/astroid/brain/brain_numpy_ndarray.py
+            # for another example of how this can be extended to create "uninferability stubs" for other methods
+            def __getitem__(self, *args): return uninferable
+    """
+    import_node = astroid.extract_node(pb_def)
     cls_node = next(import_node.infer())
     return cls_node
 

.pylint/pylintrc

@@ -2,6 +2,7 @@
 init-hook="import sys; sys.path.append('.pylint')"
 load-plugins=idaes_transform
 ignore-patterns=test_.*
+ignore-paths=^idaes/apps/.*$,
 
 [MESSAGES CONTROL]
 disable=no-self-argument,

docs/build.py

@@ -100,28 +100,23 @@ def run_html(clean=True, vb=0, timeout=0, dry_run=False, nprocs=1, **kwargs):
                 shutil.rmtree(build_dir)
         if os.path.exists(output_file):
             os.unlink(output_file)
-    # run
-    if vb > 0:
-        verbosity = "-" + "v" * vb
-    else:
-        verbosity = "-q"
-    if nprocs <= 0:
-        nprocs_arg = "-j auto"
-    elif nprocs == 1:
-        nprocs_arg = ""
-    else:
-        nprocs_arg = f"-j {nprocs}"
     args = [
         "sphinx-build",
-        "-M",
-        "html",
+        "-M", "html",
         ".",
         build_dir,
-        "-w",
-        output_file,
-        nprocs_arg,
-        verbosity,
+        "-w", output_file
     ]
+    # run
+    verbosity = "-q" if vb <= 0 else "-" + "v" * vb
+    args.append(verbosity)
+
+    if nprocs <= 0:
+        args.append("-j auto")
+    elif nprocs > 1:
+        args.append(f"-j {nprocs}")
+    # if nprocs == 1, do not specify "-j" args and fall back to sphinx-build's default
+
     print_status(f"Run: {' '.join(args)}")
     _run("html", args, timeout, dry_run)
     if dry_run:
@@ -153,14 +148,16 @@ def _run(what, args, timeout, not_really):
         return
     _log.debug(f"command={command_line}")
     try:
-        proc = subprocess.Popen(args)
+        res = subprocess.run(args, check=True, timeout=timeout)
+    except subprocess.TimeoutExpired:
+        raise CommandError(what, f"Timed out after {timeout} seconds")
+    except subprocess.CalledProcessError as e:
+        raise CommandError(what, f"Exited with nonzero exit code {e.returncode}")
     except Exception as err:
         exe = args[0]
         raise CommandError(what, f"Could not run '{exe}':\n{err}")
-    try:
-        proc.wait(timeout)
-    except subprocess.TimeoutExpired:
-        raise CommandError(what, f"Timed out after {timeout} seconds")
+    else:
+        print_status(f"{what} completed with exit code {res.returncode}")
 
 
 def print_header(msg: str, first: bool = False):

docs/explanations/components/property_package/general/eos/cubic.rst

@@ -50,7 +50,7 @@ When using the general cubic equation of state module, users must specify the ty
 
 .. code-block:: python
 
-    from idaes.generic_models.properties.core.eos.ceos import Cubic, CubicType
+    from idaes.models.properties.core.eos.ceos import Cubic, CubicType
 
     configuration = {
         "phases": {

docs/explanations/components/property_package/general_reactions/rate_rxns.rst

@@ -39,7 +39,7 @@ The `stoichiometry` configuration argument is used to define which components ta
 Concentration Form
 ^^^^^^^^^^^^^^^^^^
 
-Many common rate forms can be written using a number of different bases, such as molarity, molality or partial pressure. The `concentration_form` configuration argument is used in these cases to determine what basis to use for the concentration terms in the rate form and automatically write the correct expression (and determine units for the associated parameters. The `concentration_form` configuration argument must be an instance of a `ConcentrationForm` `Enum` (imported from idaes.generic_models.properties.core.generic.utility), and the following forms are currently available:
+Many common rate forms can be written using a number of different bases, such as molarity, molality or partial pressure. The `concentration_form` configuration argument is used in these cases to determine what basis to use for the concentration terms in the rate form and automatically write the correct expression (and determine units for the associated parameters. The `concentration_form` configuration argument must be an instance of a `ConcentrationForm` `Enum` (imported from idaes.models.properties.core.generic.utility), and the following forms are currently available:
 
 * molarity: ConcentrationForm.molarity
 * activity: ConcentrationForm.activity

docs/reference_guides/core/process_block.rst

@@ -81,14 +81,14 @@ The core part of any IDAES Block is the build method, which contains the instruc
 ProcessBlock Class
 ------------------
 
-.. module:: idaes.core.process_block
+.. module:: idaes.core.base.process_block
 
 .. autofunction:: declare_process_block_class
 
 .. autoclass:: ProcessBlock
     :members:
 
-.. module:: idaes.core.process_base
+.. module:: idaes.core.base.process_base
 
 .. autoclass:: ProcessBlockData
     :members:

docs/reference_guides/core/solvers.rst

@@ -84,28 +84,9 @@ Installing PETSc
 ~~~~~~~~~~~~~~~~
 
 The PETSc solver is an extra binary package, and not installed by default.  If
-you are using a supported Linux distribution, you can use the command
+you are using a supported platform, you can use the command
 ``idaes get-extensions --extra petsc`` to install it.
 
-There is no precompiled PETSc solver for Windows, but here are two options for
-Windows installation. The easiest option is to run the available precompiled
-Linux version via the WSL
-(see :ref:`binary installation <tutorials/getting_started/binaries:Using the WSL>`
-for details). Expert users may wish to compile their own solver. Source code is
-available in the `idaes-ext repo <https://github.com/IDAES/idaes-ext/tree/main/petsc>`_.
-If you can compile PETSc for Windows, compiling the interface is trivial (see
-`PETSc's windows installation documentation <https://petsc.org/main/install/windows/>`_).
-
-The IDAES PETSc package also includes Python modules for reading binary data
-written by the PETSc solver.  On Windows, some manual installation of the Python
-modules is required.  If you are using the WSL method to run PETSc, copy the
-``petscpy`` directory from the Linux package you are using to the IDAES binary
-directory.  You can find the IDAES binary directory by running the command
-``idaes bin-directory`` in the OS command shell (e.g. Bash, Windows CMD,
-PowerShell).  If IDAES is installed in a Python environment, the environment
-must be active. The primary use for these Python modules is to read trajectory
-files saved by the TS solver.
-
 Registered Solvers
 ~~~~~~~~~~~~~~~~~~
 
@@ -192,6 +173,12 @@ The following function can be used to solve the DAE.
 
 .. autofunction:: idaes.core.solvers.petsc.petsc_dae_by_time_element
 
+Derivative values aren't returned by the PETSc solver, but they can be calculated
+from the discretization equations written by Pyomo.DAE. The following function can
+be used to calculate time derivatives.
+
+.. autofunction:: idaes.core.solvers.petsc.calculate_time_derivatives
+
 Reading Trajectory Data
 """""""""""""""""""""""
 

docs/reference_guides/core/util/unit_costing.rst

@@ -57,9 +57,9 @@ Below is a simple example of how to add cost correlations to a flowsheet includi
     from pyomo.environ import (ConcreteModel, SolverFactory)
     from pyomo.util.calc_var_value import calculate_variable_from_constraint
     from idaes.core import FlowsheetBlock
-    from idaes.generic_models.unit_models.heat_exchanger import \
+    from idaes.models.unit_models.heat_exchanger import \
         (HeatExchanger, HeatExchangerFlowPattern)
-    from idaes.generic_models.properties import iapws95
+    from idaes.models.properties import iapws95
     from idaes.core.util.model_statistics import degrees_of_freedom
     
     m = ConcreteModel()

docs/reference_guides/model_libraries/generic/control/pid.rst

@@ -2,9 +2,9 @@ Proportional-Integral-Derivative (PID) Controller
 =================================================
 
 .. index::
-   pair: idaes.generic_models.control.controller; Proportional-Integral-Derivative (PID) Controller
+   pair: idaes.models.control.controller; Proportional-Integral-Derivative (PID) Controller
 
-.. currentmodule:: idaes.generic_models.control.controller
+.. currentmodule:: idaes.models.control.controller
 
 The IDAES framework contains a basic PID control implementation, which is described
 in this section.
@@ -25,10 +25,10 @@ file "pid_steam_tank_pressure.pdf."
   import pyomo.environ as pyo
   from pyomo.network import Arc
   from idaes.core import FlowsheetBlock, MaterialBalanceType
-  from idaes.generic_models.unit_models import Heater, Valve
-  from idaes.generic_models.properties import iapws95
+  from idaes.models.unit_models import Heater, Valve
+  from idaes.models.properties import iapws95
   from idaes.core.util.initialization import propagate_state
-  from idaes.generic_models.control.controller import (
+  from idaes.models.control.controller import (
       PIDController,
       ControllerType,
       ControllerMVBoundType

docs/reference_guides/model_libraries/generic/property_models/activity_coefficient.rst

@@ -231,7 +231,7 @@ Initialization
 
 Config Block Documentation
 --------------------------
-.. module:: idaes.generic_models.properties.activity_coeff_models.activity_coeff_prop_pack
+.. module:: idaes.models.properties.activity_coeff_models.activity_coeff_prop_pack
 
 .. autoclass:: ActivityCoeffParameterBlock
    :members:

docs/reference_guides/model_libraries/generic/property_models/ceos.rst

@@ -212,7 +212,7 @@ List of Parameters
 
 Config Block Documentation
 --------------------------
-.. module:: idaes.generic_models.properties.cubic_eos.cubic_prop_pack
+.. module:: idaes.models.properties.cubic_eos.cubic_prop_pack
 
 .. autoclass:: CubicParameterData
    :members:

docs/reference_guides/model_libraries/generic/property_models/helmholtz.rst

@@ -2,9 +2,9 @@ Pure Component Helmholtz EoS
 ============================
 
 .. index::
-  pair: idaes.generic_models.properties.helmholtz.helmholtz; HelmholtzStateBlock
+  pair: idaes.models.properties.helmholtz.helmholtz; HelmholtzStateBlock
 
-.. module:: idaes.generic_models.properties.helmholtz.helmholtz
+.. module:: idaes.models.properties.helmholtz.helmholtz
 
 The Helmholtz Equation of State (EoS) classes serve as a common core for pure
 component property packages where very accurate and thermodynamically consistent