rtc-tools 2.6.0b2__py3-none-any.whl → 2.7.0__py3-none-any.whl

{rtc_tools-2.6.0b2.dist-info → rtc_tools-2.7.0.dist-info}/METADATA

@@ -1,12 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: rtc-tools
-Version: 2.6.0b2
+Version: 2.7.0
 Summary: Toolbox for control and optimization of water systems.
 Home-page: https://oss.deltares.nl/web/rtc-tools/home
+Download-URL: http://github.com/deltares/rtc-tools/
 Author: Deltares
 Maintainer: Deltares
-License: UNKNOWN
-Download-URL: http://gitlab.com/deltares/rtc-tools/
 Platform: Windows
 Platform: Linux
 Platform: Mac OS-X
@@ -24,19 +23,31 @@ Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 License-File: COPYING.LESSER
-Requires-Dist: casadi ==3.6.*,>=3.6.3
-Requires-Dist: numpy <1.26,>=1.16.0
-Requires-Dist: scipy <1.11,>=1.0.0
-Requires-Dist: pymoca ==0.9.1
-Requires-Dist: rtc-tools-channel-flow >=1.1.0
-Provides-Extra: all
-Requires-Dist: netCDF4 ; extra == 'all'
+Requires-Dist: casadi!=3.6.6,<=3.7,>=3.6.3
+Requires-Dist: numpy>=1.16.0
+Requires-Dist: scipy>=1.0.0
+Requires-Dist: pymoca==0.9.*,>=0.9.1
+Requires-Dist: rtc-tools-channel-flow>=1.2.0
+Requires-Dist: defusedxml>=0.7.0
+Requires-Dist: importlib_metadata>=5.0.0; python_version < "3.10"
 Provides-Extra: netcdf
-Requires-Dist: netCDF4 ; extra == 'netcdf'
+Requires-Dist: netCDF4; extra == "netcdf"
+Provides-Extra: all
+Requires-Dist: netCDF4; extra == "all"
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: maintainer
+Dynamic: platform
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 RTC-Tools is the Deltares toolbox for control and optimization of water systems.
 
-
-

rtc_tools-2.7.0.dist-info/RECORD

@@ -0,0 +1,50 @@
+rtc_tools-2.7.0.dist-info/licenses/COPYING.LESSER,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+rtctools/__init__.py,sha256=91hvS2-ryd2Pvw0COpsUzTwJwSnTZ035REiej-1hNI4,107
+rtctools/_version.py,sha256=GRY0UZKaQFpBKoUgttmG_1W-QGsYu3oGtZePebKhXj4,497
+rtctools/rtctoolsapp.py,sha256=2RVZI4QQUg0yC6ii4lr50yx1blEfHBFsAgUjLR5pBkA,4336
+rtctools/util.py,sha256=8IGva7xWcAH-9Xcr1LaxUpYoZjF6vbo1eqdNJ9pKgGA,9098
+rtctools/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rtctools/_internal/alias_tools.py,sha256=XuQSAhhFuVtwn0yrAObZWIKPsSF4j2axXRtEmitIFPs,5310
+rtctools/_internal/caching.py,sha256=p4gqSL7kCI7Hff-KjMEP7mhJCQSiU_lYm2MR7E18gBM,905
+rtctools/_internal/casadi_helpers.py,sha256=q8j5h9XXXkZMUgjg6wbkcFj1mcHi5_SdEi8SrkM---M,1457
+rtctools/_internal/debug_check_helpers.py,sha256=UgQTEPw4PyR7MbYLewSSWQqTwQj7xr5yUBk820O9Kk4,1084
+rtctools/data/__init__.py,sha256=EllgSmCdrlvQZSd1VilvjPaeYJGhY9ErPiQtedmuFoA,157
+rtctools/data/csv.py,sha256=hEpoTH3nhZaAvRN4r-9-nYeAjaFiNDRoiZWg8GxM3yo,5539
+rtctools/data/netcdf.py,sha256=tMs-zcSlOR0HhajUKJVbXGNoi3GeKCM3X4DjuW8FDo8,19130
+rtctools/data/pi.py,sha256=D2r9gaYu6qMpgWRqiWpWPSPJXWgqCVV0bz6ewgM78mc,46701
+rtctools/data/rtc.py,sha256=tYPOzZSFE02bAXX3lgcGR1saoQNIv6oWVWH8CS0dl5Q,9079
+rtctools/data/storage.py,sha256=67J4BRTl0AMEzlKNZ8Xdpy_4cGtwx8Lo_tL2n0G4S9w,13206
+rtctools/data/interpolation/__init__.py,sha256=GBubCIT5mFoSTV-lOk7cpwvZekNMEe5bvqSQJ9HE34M,73
+rtctools/data/interpolation/bspline.py,sha256=qevB842XWCH3fWlWMBqKMy1mw37ust-0YtSnb9PKCEc,948
+rtctools/data/interpolation/bspline1d.py,sha256=HAh7m5xLBuiFKzMzuYEqZX_GmCPChKjV7ynTS6iRZOc,6166
+rtctools/data/interpolation/bspline2d.py,sha256=ScmX0fPDxbUVtj3pbUE0L7UJocqroD_6fUT-4cvdRMc,1693
+rtctools/optimization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rtctools/optimization/collocated_integrated_optimization_problem.py,sha256=gB1RgEsOSgb745NxSosDqjBEJZI_ULtjlHZcuCcRjO4,131267
+rtctools/optimization/control_tree_mixin.py,sha256=ZMMH7Xy_qIVXeLDNtPdXQ8o_0ELRYVdM5QK2R8YulKU,9036
+rtctools/optimization/csv_lookup_table_mixin.py,sha256=TUYAT-u-mzH6HLP0iJHnLBVqV5tWnhYAqDC4Aj17MJg,17399
+rtctools/optimization/csv_mixin.py,sha256=_6iPVK_EJ8PxnukepzkhFtidceucsozRML_DDEycYik,12453
+rtctools/optimization/goal_programming_mixin.py,sha256=vdnKnz1Ov3OFN-J9KQiiAwHbrLjWH6o_PeZz2YfLz6k,33320
+rtctools/optimization/goal_programming_mixin_base.py,sha256=qJQQcJlJdio4GTcrKfuBi6Nho9u16pDuuprzK0LUyhA,43835
+rtctools/optimization/homotopy_mixin.py,sha256=Kh0kMfxB-Fo1FBGW5tPOQk24Xx_Mmw_p0YuSQotdkMU,6905
+rtctools/optimization/initial_state_estimation_mixin.py,sha256=74QYfG-VYYTNVg-kAnCG6QoY3_sUmaID0ideF7bPkkY,3116
+rtctools/optimization/io_mixin.py,sha256=AsZQ7YOUcUbWoczmjTXaSje5MUEsPNbQyZBJ6qzSjzU,11821
+rtctools/optimization/linearization_mixin.py,sha256=mG5S7uwvwDydw-eBPyQKnLyKoy08EBjQh25vu97afhY,1049
+rtctools/optimization/linearized_order_goal_programming_mixin.py,sha256=LQ2qpYt0YGLpEoerif4FJ5wwzq16q--27bsRjcqIU5A,9087
+rtctools/optimization/min_abs_goal_programming_mixin.py,sha256=WMOv9EF8cfDJgTunzXfI_cUmBSQK26u1HJB_9EAarfM,14031
+rtctools/optimization/modelica_mixin.py,sha256=b_VsEcg_VsAnODnTQybrY0GbuZUNQ3uugQmML6FlklE,18037
+rtctools/optimization/netcdf_mixin.py,sha256=-zkXh3sMYE50c3kHsrmUVGWMSFm-0cXQpGrCm0yn-Tc,7563
+rtctools/optimization/optimization_problem.py,sha256=lTk4tUBEb1xy9eyNy7-w0D6L6HxSCJ0MyvxjzrYLsR4,44824
+rtctools/optimization/pi_mixin.py,sha256=G_6RPlXO-IOjqYxNsMZGY4fmnfxVpwN-_T5Ka3rDwK4,11788
+rtctools/optimization/planning_mixin.py,sha256=O_Y74X8xZmaNZR4iYOe7BR06s9hnmcapbuHYHQTBPPQ,724
+rtctools/optimization/single_pass_goal_programming_mixin.py,sha256=Zb9szg3PGT2o6gkGsXluSfEaAswkw3TKfPQDzUrj_Y4,25784
+rtctools/optimization/timeseries.py,sha256=nCrsGCJThBMh9lvngEpbBDa834_QvklVvkxJqwX4a1M,1734
+rtctools/simulation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rtctools/simulation/csv_mixin.py,sha256=rGDUFPsqGHmF0_dWdXeWzWzMpkPmwCNweTBVrwSh31g,6704
+rtctools/simulation/io_mixin.py,sha256=WIKOQxr3fS-aNbgjet9iWoUayuD22zLIYmqlWEqxXHo,6215
+rtctools/simulation/pi_mixin.py,sha256=_TU2DrK2MQqVsyrHBD9W4SDEuot9dYmgTDNiXkDAJfk,9833
+rtctools/simulation/simulation_problem.py,sha256=v5Lk2x-yuVb5s7ne5fFgxONxGniLHTyTR0XRzYRl1fw,50005
+rtc_tools-2.7.0.dist-info/METADATA,sha256=ULtELHwTloQVwwzBsmnqDlvFMj-SMQmNO2r3ATeJRC8,1772
+rtc_tools-2.7.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rtc_tools-2.7.0.dist-info/entry_points.txt,sha256=DVS8sWf3b9ph9h8srEr6zmQ7ZKGwblwgZgGPZg-jRNQ,150
+rtc_tools-2.7.0.dist-info/top_level.txt,sha256=pnBrb58PFPd1kp1dqa-JHU7R55h3alDNJIJnF3Jf9Dw,9
+rtc_tools-2.7.0.dist-info/RECORD,,

{rtc_tools-2.6.0b2.dist-info → rtc_tools-2.7.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{rtc_tools-2.6.0b2.dist-info → rtc_tools-2.7.0.dist-info}/entry_points.txt

@@ -1,4 +1,3 @@
 [console_scripts]
 rtc-tools-copy-libraries = rtctools.rtctoolsapp:copy_libraries
 rtc-tools-download-examples = rtctools.rtctoolsapp:download_examples
-

rtctools/_internal/casadi_helpers.py

@@ -5,12 +5,12 @@ import casadi as ca
 logger = logging.getLogger("rtctools")
 
 
-def is_affine(e, v):
+def is_affine(expr, symbols):
     try:
-        Af = ca.Function("f", [v], [ca.jacobian(e, v)]).expand()
-    except RuntimeError as e:
-        if "'eval_sx' not defined for" in str(e):
-            Af = ca.Function("f", [v], [ca.jacobian(e, v)])
+        Af = ca.Function("f", [symbols], [ca.jacobian(expr, symbols)]).expand()
+    except RuntimeError as error:
+        if "'eval_sx' not defined for" in str(error):
+            Af = ca.Function("f", [symbols], [ca.jacobian(expr, symbols)])
         else:
             raise
     return Af.sparsity_jac(0, 0).nnz() == 0

rtctools/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.18) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-01-18T16:11:20+0000",
+ "date": "2025-05-23T14:56:50+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "e868661a3b37bb27f61ffcf9cdf1d53d857d5108",
- "version": "2.6.0b2"
+ "full-revisionid": "16ab781cd81009655c779d5cc5b7c4aa3e73fa85",
+ "version": "2.7.0"
 }
 '''  # END VERSION_JSON
 

rtctools/data/csv.py

@@ -1,6 +1,7 @@
 import logging
 import sys
 from datetime import datetime
+from typing import Union
 
 import numpy as np
 
@@ -41,6 +42,21 @@ def _boolean_to_nan(data, fname):
     return data
 
 
+def _string_to_datetime(string: Union[str, bytes]) -> datetime:
+    """Convert a string to a datetime object."""
+    if isinstance(string, bytes):
+        string = string.decode("utf-8")
+    return datetime.strptime(string, "%Y-%m-%d %H:%M:%S")
+
+
+def _string_to_float(string: Union[str, bytes]) -> float:
+    """Convert a string to a float."""
+    if isinstance(string, bytes):
+        string = string.decode("utf-8")
+    string = string.replace(",", ".")
+    return float(string)
+
+
 def load(fname, delimiter=",", with_time=False):
     """
     Check delimiter of csv and read contents to an array. Assumes no date-time conversion needed.
@@ -53,7 +69,7 @@ def load(fname, delimiter=",", with_time=False):
     """
     c = {}
     if with_time:
-        c.update({0: lambda str: datetime.strptime(str.decode("utf-8"), "%Y-%m-%d %H:%M:%S")})
+        c.update({0: _string_to_datetime})
 
     # Check delimiter of csv file. If semicolon, check if decimal separator is
     # a comma.
@@ -73,12 +89,7 @@ def load(fname, delimiter=",", with_time=False):
             # If commas are used as decimal separator, we need additional
             # converters.
             if n_comma_decimal:
-                c.update(
-                    {
-                        i + len(c): lambda str: float(str.decode("utf-8").replace(",", "."))
-                        for i in range(1 + n_semicolon - len(c))
-                    }
-                )
+                c.update({i + len(c): _string_to_float for i in range(1 + n_semicolon - len(c))})
 
     # Read the csv file and convert to array
     try:

rtctools/data/interpolation/bspline1d.py

@@ -55,6 +55,7 @@ class BSpline1D(BSpline):
         epsilon=1e-7,
         delta=1e-4,
         interior_pts=None,
+        ipopt_options=None,
     ):
         """
         fit() returns a tck tuple like scipy.interpolate.splrep, but adjusts
@@ -153,7 +154,10 @@ class BSpline1D(BSpline):
         nlp = {"x": c, "f": f, "g": g}
         my_solver = "ipopt"
         solver = nlpsol(
-            "solver", my_solver, nlp, {"print_time": 0, "expand": True, "ipopt": {"print_level": 0}}
+            "solver",
+            my_solver,
+            nlp,
+            {"print_time": 0, "expand": True, "ipopt": ipopt_options},
         )
         sol = solver(lbg=lbg, ubg=ubg)
         stats = solver.stats()

rtctools/data/netcdf.py

@@ -401,20 +401,21 @@ class ExportDataset:
         """
         assert len(set(variable_names)) == len(variable_names)
 
-        assert (
-            self.__time_dim is not None
-        ), "First call write_times to ensure the time dimension has been created."
-        assert (
-            self.__station_dim is not None
-        ), "First call write_station_data to ensure the station dimension has been created"
+        assert self.__time_dim is not None, (
+            "First call write_times to ensure the time dimension has been created."
+        )
+        assert self.__station_dim is not None, (
+            "First call write_station_data to ensure the station dimension has been created"
+        )
         assert (
             self.__station_id_to_index_mapping is not None
         )  # should also be created in write_station_data
 
         if ensemble_size > 1:
-            assert (
-                self.__ensemble_member_dim is not None
-            ), "First call write_ensemble_data to ensure the realization dimension has been created"
+            assert self.__ensemble_member_dim is not None, (
+                "First call write_ensemble_data to ensure "
+                "the realization dimension has been created"
+            )
 
             for variable_name in variable_names:
                 self.__dataset.createVariable(
@@ -446,15 +447,15 @@ class ExportDataset:
         :param values:        The values that are to be written to the file
         :param ensemble_size: the number of members in the ensemble
         """
-        assert (
-            self.__station_id_to_index_mapping is not None
-        ), "First call write_station_data and create_variables."
+        assert self.__station_id_to_index_mapping is not None, (
+            "First call write_station_data and create_variables."
+        )
 
         station_index = self.__station_id_to_index_mapping[station_id]
         if ensemble_size > 1:
-            self.__dataset.variables[variable_name][
-                :, station_index, ensemble_member_index
-            ] = values
+            self.__dataset.variables[variable_name][:, station_index, ensemble_member_index] = (
+                values
+            )
         else:
             self.__dataset.variables[variable_name][:, station_index] = values
 

rtctools/data/pi.py

@@ -5,6 +5,7 @@ import logging
 import os
 import xml.etree.ElementTree as ET
 
+import defusedxml.ElementTree as DefusedElementTree
 import numpy as np
 
 ns = {"fews": "http://www.wldelft.nl/fews", "pi": "http://www.wldelft.nl/fews/PI"}
@@ -30,7 +31,7 @@ class Diag:
         """
         self.__path_xml = os.path.join(folder, basename + ".xml")
 
-        self.__tree = ET.parse(self.__path_xml)
+        self.__tree = DefusedElementTree.parse(self.__path_xml)
         self.__xml_root = self.__tree.getroot()
 
     def get(self, level=ERROR_FATAL):
@@ -87,7 +88,7 @@ class DiagHandler(logging.Handler):
         self.__path_xml = os.path.join(folder, basename + ".xml")
 
         try:
-            self.__tree = ET.parse(self.__path_xml)
+            self.__tree = DefusedElementTree.parse(self.__path_xml)
             self.__xml_root = self.__tree.getroot()
         except Exception:
             self.__xml_root = ET.Element("{%s}Diag" % (ns["pi"],))
@@ -135,7 +136,7 @@ class ParameterConfig:
             basename = basename + ".xml"
         self.__path_xml = os.path.join(folder, basename)
 
-        self.__tree = ET.parse(self.__path_xml)
+        self.__tree = DefusedElementTree.parse(self.__path_xml)
         self.__xml_root = self.__tree.getroot()
 
     def get(self, group_id, parameter_id, location_id=None, model=None):
@@ -300,9 +301,8 @@ class ParameterConfig:
                 # get table contenstart_datetime
                 el_row = child.findall("pi:row", ns)
                 table = {
-                    columnId[key]: np.empty(len(el_row), columnType[key])  # initialize table
-                    for key in columnId
-                }
+                    columnId[key]: np.empty(len(el_row), columnType[key]) for key in columnId
+                }  # initialize table
 
                 i_row = 0
                 for row in el_row:
@@ -333,8 +333,11 @@ class ParameterConfig:
 
             parameters = group.findall("pi:parameter", ns)
             for parameter in parameters:
-                yield location_id, model_id, parameter.attrib["id"], self.__parse_parameter(
-                    parameter
+                yield (
+                    location_id,
+                    model_id,
+                    parameter.attrib["id"],
+                    self.__parse_parameter(parameter),
                 )
 
 
@@ -369,8 +372,6 @@ class Timeseries:
         self.__folder = folder
         self.__basename = basename
 
-        self.__path_xml = os.path.join(self.__folder, basename + ".xml")
-
         self.__internal_dtype = np.float64
         self.__pi_dtype = np.float32
 
@@ -378,7 +379,7 @@ class Timeseries:
         if self.make_new_file:
             self.__reset_xml_tree()
         else:
-            self.__tree = ET.parse(self.__path_xml)
+            self.__tree = DefusedElementTree.parse(self.path)
             self.__xml_root = self.__tree.getroot()
 
         self.__values = [{}]
@@ -801,13 +802,20 @@ class Timeseries:
         # Add series to xml
         self.__xml_root.append(series)
 
-    def write(self):
+    def write(self, output_folder=None, output_filename=None) -> None:
         """
         Writes the time series data to disk.
+
+        :param output_folder:   The folder in which the output file is located.
+                                If None, the original folder is used.
+        :param output_filename: The name of the output file without extension.
+                                If None, the original filename is used.
         """
+        xml_path = self.output_path(output_folder, output_filename)
+        binary_path = self.output_binary_path(output_folder, output_filename)
 
         if self.__binary:
-            f = io.open(self.binary_path, "wb")
+            f = io.open(binary_path, "wb")
 
         if self.make_new_file:
             # Force reinitialization in case write() is called more than once
@@ -855,7 +863,7 @@ class Timeseries:
 
                 variable = self.__data_config.variable(header)
 
-                miss_val = float(header.find("pi:missVal", ns).text)
+                miss_val = header.find("pi:missVal", ns).text
                 values = self.__values[ensemble_member][variable]
 
                 # Update the header, which may have changed
@@ -868,37 +876,34 @@ class Timeseries:
                     self.__xml_root.remove(series)
                     continue
 
-                # Replace NaN with missing value
-                nans = np.isnan(values)
-                values[nans] = miss_val
-
                 # Write output
+                nans = np.isnan(values)
                 if self.__binary:
                     f.write(values.astype(self.__pi_dtype).tobytes())
                 else:
                     events = series.findall("pi:event", ns)
 
                     t = self.__start_datetime
-                    for i in range(min(len(events), len(values))):
+                    for i, value in enumerate(values):
                         if self.dt is None:
                             t = self.times[i]
-                        # Set the date/time, so that any date/time steps that
-                        # are wrong in the placeholder file are corrected.
-                        events[i].set("date", t.strftime("%Y-%m-%d"))
-                        events[i].set("time", t.strftime("%H:%M:%S"))
 
-                        # Set the value
-                        events[i].set("value", str(values[i]))
-                        if self.dt:
-                            t += self.dt
-                    for i in range(len(events), len(values)):
-                        if self.dt is None:
-                            t = self.times[i]
-                        event = ET.Element("pi:event")
+                        if i < len(events):
+                            event = events[i]
+                        else:
+                            event = ET.Element("pi:event")
+                            series.append(event)
+
+                        # Always set the date/time, so that any date/time steps
+                        # that are wrong in the placeholder file are corrected.
                         event.set("date", t.strftime("%Y-%m-%d"))
                         event.set("time", t.strftime("%H:%M:%S"))
-                        event.set("value", str(values[i]))
-                        series.append(event)
+
+                        if nans[i]:
+                            event.set("value", miss_val)
+                        else:
+                            event.set("value", str(value))
+
                         if self.dt:
                             t += self.dt
 
@@ -907,14 +912,11 @@ class Timeseries:
                         for i in range(len(values), len(events)):
                             series.remove(events[i])
 
-                # Restore NaN
-                values[nans] = np.nan
-
         if self.__binary:
             f.close()
 
         self.format_xml_data()
-        self.__tree.write(self.__path_xml)
+        self.__tree.write(xml_path)
 
     def format_xml_data(self):
         """
@@ -1173,16 +1175,45 @@ class Timeseries:
         self.__end_datetime = end_datetime
 
     @property
-    def path(self):
-        return self.__path_xml
+    def path(self) -> str:
+        """
+        The path to the original xml file.
+        """
+        return os.path.join(self.__folder, self.__basename + ".xml")
 
     @property
-    def binary_path(self):
+    def binary_path(self) -> str:
         """
-        The path for the binary data .bin file.
+        The path to the original binary data .bin file.
         """
         return os.path.join(self.__folder, self.__basename + ".bin")
 
+    def _output_path_without_extension(self, output_folder=None, output_filename=None) -> str:
+        """
+        Get the output path without file extension.
+        """
+        if output_folder is None:
+            output_folder = self.__folder
+        if output_filename is None:
+            output_filename = self.__basename
+        return os.path.join(output_folder, output_filename)
+
+    def output_path(self, output_folder=None, output_filename=None) -> str:
+        """
+        Get the path to the output xml file.
+
+        The optional arguments are the same as in :py:method:`write`.
+        """
+        return self._output_path_without_extension(output_folder, output_filename) + ".xml"
+
+    def output_binary_path(self, output_folder=None, output_filename=None) -> str:
+        """
+        Get the path to the output binary file.
+
+        The optional arguments are the same as in :py:method:`write`.
+        """
+        return self._output_path_without_extension(output_folder, output_filename) + ".bin"
+
     def items(self, ensemble_member=0):
         """
         Returns an iterator over all timeseries IDs and value arrays for the given

rtctools/data/rtc.py

@@ -1,8 +1,9 @@
 import logging
 import os
-import xml.etree.ElementTree as ET
 from collections import namedtuple
 
+import defusedxml.ElementTree as DefusedElementTree
+
 ts_ids = namedtuple("ids", "location_id parameter_id qualifier_id")
 p_ids = namedtuple("ids", "model_id location_id parameter_id")
 
@@ -31,7 +32,7 @@ class DataConfig:
 
         path = os.path.join(folder, "rtcDataConfig.xml")
         try:
-            tree = ET.parse(path)
+            tree = DefusedElementTree.parse(path)
             root = tree.getroot()
 
             timeseriess1 = root.findall("./*/fews:timeSeries", ns)
@@ -59,9 +60,9 @@ class DataConfig:
                         logger.error(message)
                         raise Exception(message)
                     else:
-                        self.__location_parameter_ids[
-                            internal_id
-                        ] = self.__pi_location_parameter_id(pi_timeseries, "fews")
+                        self.__location_parameter_ids[internal_id] = (
+                            self.__pi_location_parameter_id(pi_timeseries, "fews")
+                        )
                         self.__variable_map[external_id] = internal_id
 
             for k in ["import", "export"]:

rtctools/optimization/collocated_integrated_optimization_problem.py

@@ -898,11 +898,11 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
                     function_options,
                 )
 
+                # Expand the residual function if possible.
                 try:
                     dae_residual_function_integrated = dae_residual_function_integrated.expand()
                 except RuntimeError as e:
-                    # We only expect to fail if the DAE was an external function
-                    if "'eval_sx' not defined for External" in str(e):
+                    if "'eval_sx' not defined for" in str(e):
                         pass
                     else:
                         raise
@@ -933,13 +933,13 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
                     [dae_residual_collocated],
                     function_options,
                 )
+                # Expand the residual function if possible.
                 try:
                     self.__dae_residual_function_collocated = (
                         self.__dae_residual_function_collocated.expand()
                     )
                 except RuntimeError as e:
-                    # We only expect to fail if the DAE was an external function
-                    if "'eval_sx' not defined for External" in str(e):
+                    if "'eval_sx' not defined for" in str(e):
                         pass
                     else:
                         raise
@@ -1028,8 +1028,8 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
             + len(self.dae_variables["constant_inputs"])
         ]
         constant_inputs_1 = accumulated_U[
-            2 * len(collocated_variables)
-            + len(self.dae_variables["constant_inputs"]) : 2 * len(collocated_variables)
+            2 * len(collocated_variables) + len(self.dae_variables["constant_inputs"]) : 2
+            * len(collocated_variables)
             + 2 * len(self.dae_variables["constant_inputs"])
         ]
 
@@ -1803,9 +1803,9 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
                     # Cast delay from DM to np.array
                     delay = delay.toarray().flatten()
 
-                    assert np.all(
-                        np.isfinite(delay)
-                    ), "Delay duration must be resolvable to real values at transcribe()"
+                    assert np.all(np.isfinite(delay)), (
+                        "Delay duration must be resolvable to real values at transcribe()"
+                    )
 
                     out_times = np.concatenate([history_times, collocation_times])
                     out_values = ca.veccat(
@@ -2043,9 +2043,7 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
     def controls(self):
         return self.__controls
 
-    def _collint_get_lbx_ubx(self, count, indices):
-        bounds = self.bounds()
-
+    def _collint_get_lbx_ubx(self, bounds, count, indices):
         lbx = np.full(count, -np.inf, dtype=np.float64)
         ubx = np.full(count, np.inf, dtype=np.float64)
 
@@ -2210,7 +2208,7 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
                 count = max(count, control_indices_stop)
 
         discrete = self._collint_get_discrete(count, indices)
-        lbx, ubx = self._collint_get_lbx_ubx(count, indices)
+        lbx, ubx = self._collint_get_lbx_ubx(bounds, count, indices)
         x0 = self._collint_get_x0(count, indices)
 
         # Return number of control variables
@@ -2326,7 +2324,7 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
                 offset += 1
 
         discrete = self._collint_get_discrete(count, indices)
-        lbx, ubx = self._collint_get_lbx_ubx(count, indices)
+        lbx, ubx = self._collint_get_lbx_ubx(bounds, count, indices)
         x0 = self._collint_get_x0(count, indices)
 
         # Return number of state variables
@@ -2869,8 +2867,7 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
 
         # Check coefficient matrix
         logger.info(
-            "Sanity check on objective and constraints Jacobian matrix"
-            "/constant coefficients values"
+            "Sanity check on objective and constraints Jacobian matrix/constant coefficients values"
         )
 
         in_var = nlp["x"]
@@ -3113,7 +3110,7 @@ class CollocatedIntegratedOptimizationProblem(OptimizationProblem, metaclass=ABC
         variable_to_all_indices = {k: set(v) for k, v in indices[0].items()}
         for ensemble_indices in indices[1:]:
             for k, v in ensemble_indices.items():
-                variable_to_all_indices[k] |= v
+                variable_to_all_indices[k] |= set(v)
 
         if len(inds_up) > 0:
             exceedences = []