Cycles-utils 4.1.0__tar.gz → 4.2.0__tar.gz

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/Cycles_utils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Cycles-utils
-Version: 4.1.0
+Version: 4.2.0
 Summary: Python scripts to build Cycles input files and post-process Cycles output files
 Home-page: https://github.com/PSUmodeling/Cycles-utils
 Author: Yuning Shi
@@ -12,6 +12,8 @@ License-File: LICENSE
 Requires-Dist: pandas>=1.2.4
 Requires-Dist: numpy>=1.19.5
 Requires-Dist: matplotlib>=3.4.2
+Requires-Dist: tqdm>=4.60.0
+Requires-Dist: IPython>=7.0.0
 Provides-Extra: plot
 Requires-Dist: cartopy>=0.18.0; extra == "plot"
 Requires-Dist: geopandas>=0.9.0; extra == "plot"
@@ -19,7 +21,6 @@ Requires-Dist: fiona>=1.8.20; extra == "plot"
 Requires-Dist: shapely>=1.7.1; extra == "plot"
 Provides-Extra: weather
 Requires-Dist: netCDF4>=1.5.7; extra == "weather"
-Requires-Dist: tqdm>=4.60.0; extra == "weather"
 Requires-Dist: scipy>=1.6.3; extra == "weather"
 Provides-Extra: soilgrids
 Requires-Dist: geopandas>=0.9.0; extra == "soilgrids"
@@ -82,6 +83,7 @@ pip install Cycles-utils
 
 | Cycles-utils version | Cycles version |
 | -------------------- | -------------- |
+| 4.2.0                | 1.5.20+        |
 | 4.1.0                | 1.5.20+        |
 | 4.0.6                | 1.5.20         |
 | 4.0.5                | 1.5.20         |

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/Cycles_utils.egg-info/SOURCES.txt

@@ -8,11 +8,11 @@ Cycles_utils.egg-info/dependency_links.txt
 Cycles_utils.egg-info/requires.txt
 Cycles_utils.egg-info/top_level.txt
 cycles/__init__.py
+cycles/_base_file.py
 cycles/cycles.py
 cycles/cycles_runner.py
 cycles/rotation_builder.py
 cycles/cycles_tools/__init__.py
-cycles/cycles_tools/_base_file.py
 cycles/cycles_tools/_geo_file.py
 cycles/cycles_tools/control_file.py
 cycles/cycles_tools/converter.py
@@ -44,4 +44,5 @@ cycles/soilgrids/soilgrids.py
 cycles/ssurgo/__init__.py
 cycles/ssurgo/ssurgo.py
 cycles/weather/__init__.py
-cycles/weather/weather.py
+cycles/weather/weather.py
+test/test_runner.py

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/Cycles_utils.egg-info/requires.txt

@@ -1,6 +1,8 @@
 pandas>=1.2.4
 numpy>=1.19.5
 matplotlib>=3.4.2
+tqdm>=4.60.0
+IPython>=7.0.0
 
 [all]
 cartopy>=0.18.0
@@ -39,5 +41,4 @@ fiona>=1.8.20
 
 [weather]
 netCDF4>=1.5.7
-tqdm>=4.60.0
 scipy>=1.6.3

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Cycles-utils
-Version: 4.1.0
+Version: 4.2.0
 Summary: Python scripts to build Cycles input files and post-process Cycles output files
 Home-page: https://github.com/PSUmodeling/Cycles-utils
 Author: Yuning Shi
@@ -12,6 +12,8 @@ License-File: LICENSE
 Requires-Dist: pandas>=1.2.4
 Requires-Dist: numpy>=1.19.5
 Requires-Dist: matplotlib>=3.4.2
+Requires-Dist: tqdm>=4.60.0
+Requires-Dist: IPython>=7.0.0
 Provides-Extra: plot
 Requires-Dist: cartopy>=0.18.0; extra == "plot"
 Requires-Dist: geopandas>=0.9.0; extra == "plot"
@@ -19,7 +21,6 @@ Requires-Dist: fiona>=1.8.20; extra == "plot"
 Requires-Dist: shapely>=1.7.1; extra == "plot"
 Provides-Extra: weather
 Requires-Dist: netCDF4>=1.5.7; extra == "weather"
-Requires-Dist: tqdm>=4.60.0; extra == "weather"
 Requires-Dist: scipy>=1.6.3; extra == "weather"
 Provides-Extra: soilgrids
 Requires-Dist: geopandas>=0.9.0; extra == "soilgrids"
@@ -82,6 +83,7 @@ pip install Cycles-utils
 
 | Cycles-utils version | Cycles version |
 | -------------------- | -------------- |
+| 4.2.0                | 1.5.20+        |
 | 4.1.0                | 1.5.20+        |
 | 4.0.6                | 1.5.20         |
 | 4.0.5                | 1.5.20         |

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/README.md

@@ -22,6 +22,7 @@ pip install Cycles-utils
 
 | Cycles-utils version | Cycles version |
 | -------------------- | -------------- |
+| 4.2.0                | 1.5.20+        |
 | 4.1.0                | 1.5.20+        |
 | 4.0.6                | 1.5.20         |
 | 4.0.5                | 1.5.20         |

{cycles_utils-4.1.0/cycles/cycles_tools → cycles_utils-4.2.0/cycles}/_base_file.py

@@ -1,4 +1,6 @@
 from __future__ import annotations
+import os
+import sys
 import types
 from dataclasses import fields
 from pathlib import Path
@@ -74,3 +76,23 @@ def _unwrap_optional(t) -> type:
     if origin is Union or origin is types.UnionType or isinstance(t, types.UnionType):
         return next(arg for arg in t.__args__ if arg is not type(None))
     return t
+
+
+def _if_ipython() -> bool:
+    try:
+        from IPython import get_ipython     # type: ignore
+        shell = get_ipython()
+        return shell is not None and shell.__class__.__name__ == 'ZMQInteractiveShell'
+    except ImportError:
+        return False
+
+
+def _disable_progress_bar() -> bool:
+    if _if_ipython():
+        return False
+    if os.environ.get('SLURM_JOB_ID') is not None:
+        return True
+    try:
+        return not sys.stderr.isatty()
+    except AttributeError:
+        return True

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles.py

@@ -1,8 +1,6 @@
 from __future__ import annotations
 import numpy as np
-import os
 import pandas as pd
-import subprocess
 from collections.abc import Collection
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -24,13 +22,12 @@ class Output:
 class Cycles:
     """Interface for executing one Cycles simulation and reading its files.
 
-    Provides methods to run simulations, read outputs, and inspect soil/weather/operation configurations. Automatically
-    loads the control file upon initialization.
+    Provides methods to read outputs, and inspect soil/weather/operation configurations. Automatically loads the control
+    file upon initialization.
 
     Args:
         path: Path to the simulation directory (containing input/ and output/ subdirs).
         simulation: Name of the simulation (base name of control file without extension).
-        executable: Optional absolute path to the Cycles executable binary. This is required to run simulations using the `run` method.
 
     Attributes:
         path: Path to the simulation directory (containing input/ and output/ subdirs).
@@ -42,12 +39,10 @@ class Cycles:
         curve_number: Runoff curve number for hydrologic calculations.
         slope: Land slope used in erosion and runoff models.
         weather: DataFrame of weather forcing data (temperature, precipitation, etc.).
-        executable: Absolute path to the Cycles executable binary.
     """
 
     simulation: str
     path: Path | str = '.'
-    executable: Path | str | None = None
     output: dict[str, Output] = field(init=False, default_factory=dict[str, Output])
     control: ControlConfig | None = field(init=False, default=None)
     operations: list | None = field(init=False, default=None)
@@ -61,42 +56,6 @@ class Cycles:
         self.path = Path(self.path)
         assert isinstance(self.path, Path)
         self.control = _read_control_file(self.path / 'input' / f'{self.simulation}.ctrl')
-        if self.executable is not None:
-            self.executable = str(Path(self.executable).resolve())
-
-
-    def run(self, options: str, silence: bool=False) -> tuple[int, str]:
-        """Run the Cycles executable for this simulation.
-
-        To use the `run` method, the `executable` attribute must be set to the path of the Cycles executable. The
-        `options` string is passed directly to the command line when invoking Cycles, allowing you to specify any
-        command-line options supported by Cycles (e.g., `-s` for spin-up, etc.).
-
-        Args:
-            options: Command-line options passed to Cycles.
-            silence: If True, suppress stdout and stderr printing.
-
-        Returns:
-            A tuple with process return code and stdout text.
-        """
-        cwd = os.getcwd()
-        cmd = [self.executable, *(options.split() if options else []), self.simulation]
-
-        os.chdir(self.path)
-        result = subprocess.run(
-            cmd,
-            shell=os.name == 'nt',
-            capture_output=True,
-            text=True,
-        )
-        if not silence:
-            print(result.stdout)
-        if result.stderr:
-            print(result.stderr)
-
-        os.chdir(cwd)
-
-        return result.returncode, result.stdout
 
 
     def read_output(self, output_types: Collection) -> None:

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles_runner.py

@@ -3,15 +3,20 @@ import os
 import pandas as pd
 import shutil
 import subprocess
+import warnings
+from collections.abc import Sequence
 from dataclasses import dataclass
 from pathlib import Path
 from string import Template
 from typing import Any
 from .cycles import Cycles
 from .cycles_tools import generate_control_file, generate_nudge_file
-from .cycles_tools._base_file import _resolve_dict_values
+from .cycles_tools.control_file import DEFAULT_CROP_FILE
+from ._base_file import _resolve_dict_values, _if_ipython, _disable_progress_bar
+if _if_ipython(): from tqdm.notebook import tqdm
+else: from tqdm import tqdm
 
-SimulationConfig = list[dict] | pd.DataFrame
+SimulationConfig = list[dict] | pd.DataFrame | list[None] | None
 
 INPUT_DIR: str = 'input'
 OUTPUT_DIR: str = 'output'
@@ -33,8 +38,10 @@ OUTPUT_CONTROL_FLAGS: dict = {
 class SimulationContext:
     name: str
     control_dict: dict
+    crop_dict: dict | None
     operation_dict: dict | None
     calibration_dict: dict | None
+    crop_fn: Path
     operation_fn: Path
 
 
@@ -57,20 +64,28 @@ class CyclesRunner:
         self.path = Path(self.path)
 
 
-    def run(self, simulations: SimulationConfig, control_dict: dict[str, Any], *,
-        summary: str | dict[str, str] | None=None,
-        operation_template: Path | str | None=None, operation_dict: dict[str, Any] | None=None,
-        calibration_dict: dict[str, Any] | None=None,
-        options: str='', rm_input: bool=False, rm_output: bool=False, rm_steady_state_soil: bool=True, silence: bool=True, user_comment: str='') -> None:
+    def run(self, *, control_dict: dict[str, Any], simulations: SimulationConfig=None,
+            summary: Sequence[str] | None=None,
+            summary_prefix: str | None=None,
+            operation_template: Path | str | None=None, operation_dict: dict[str, Any] | None=None,
+            crop_template: Path | str | None=None, crop_dict: dict[str, Any] | None=None,
+            calibration_dict: dict[str, Any] | None=None,
+            options: str='', rm_input: bool=False, rm_output: bool=False, rm_steady_state_soil: bool=True, silence: bool=True, user_comment: str='',
+            _progress_bar: tqdm | None=None) -> None:   # type: ignore
         """Execute a batch of simulations and write a consolidated summary.
 
         Args:
             simulations: Simulation configurations as list of dicts or a DataFrame. Each dict or DataFrame row should be
                 corresponding to a single simulation and contain values to support the control, operation, and
-                calibration dictionaries.
+                calibration dictionaries. If None, a single simulation is run directly from `control_dict`/
+                `operation_dict` (no per-row substitution). In this single-run mode, the summary CSV is **not**
+                written and `rm_input`/`rm_output`/`rm_steady_state_soil` are **not** applied, regardless of how
+                those flags are set -- the full input/output is always left in place for inspection.
             control_dict: Control-file values or callables evaluated per simulation.
-            summary: Summary CSV name for the summary harvest file written under summary directory. If a dictionary is provided, the keys are output file types and the values are
-                summary CSV names. If None, only the harvest summary is written into `summary/summary.csv`.
+            summary: List or tuple of output file types to be summarized/aggregated. If None, only the harvest summary is written into `summary/harvest.csv`.
+            summary_prefix: Prefix for the summary CSV files. If None, no prefix is added.
+            crop_template: Template file for generated crop files.
+            crop_dict: Substitutions used with crop template.
             operation_template: Template file for generated operation files.
             operation_dict: Substitutions used with operation template.
             calibration_dict: Nudge-file values or callables per simulation.
@@ -81,6 +96,10 @@ class CyclesRunner:
             silence: If True, suppress simulation screen output.
             user_comment: Optional text prefixed to summary header comments.
 
+        In batch mode (`simulations` is a list/DataFrame), a simulation that fails (non-zero exit code) is skipped --
+        its summary row is not written -- but does not abort the remaining batch; cleanup (`rm_input`/`rm_output`)
+        still runs for the failed row if requested.
+
         The following fields are required in `control_dict`:
 
         - `simulation_name`
@@ -139,8 +158,9 @@ class CyclesRunner:
         }
         ```
 
-        The operation dictionary should work with a template operation file to generate the appropriate operation files for each simulation. In the template operation file, use
-        placeholders for planting `DOY`, `END_DOY`, and `CROP` like below:
+        The operation dictionary should work with a template operation file to generate the appropriate operation files
+        for each simulation. In the template operation file, use placeholders for planting `DOY`, `END_DOY`, and `CROP`
+        like below:
 
         ```
         DOY         $PD1
@@ -148,7 +168,8 @@ class CyclesRunner:
         CROP        $CROP
         ```
 
-        Then define the operation dictionary to substitute the placeholders with values from the simulation configurations:
+        Then define the operation dictionary to substitute the placeholders with values from the simulation
+        configurations:
 
         ```python
         operation_dict: dict = {
@@ -166,60 +187,65 @@ class CyclesRunner:
             control_dict=control_dict,
             operation_template='path/to/template.operation',
             operation_dict=operation_dict,
-            summary='summary.csv',
             options='-s',
         )
         ```
 
-        The `-s` option enables spin-up for the simulations. The results will be consolidated into `summary/summary.csv`.
+        The `-s` option enables spin-up for the simulations. The results will be consolidated into `summary/harvest.csv`.
         """
-        if isinstance(simulations, pd.DataFrame):
-            simulations = simulations.to_dict(orient='records')
-        assert isinstance(simulations, list)
+        if calibration_dict is not None and 'n' not in options:
+            warnings.warn('Nudge parameters are provided but Cycles is not running in nudge mode.', UserWarning)
 
-        if (operation_template is None) != (operation_dict is None):
-            raise ValueError(
-                "operation_template and operation_dict must be provided together or not at all. "
-                f"Got operation_template={'None' if operation_template is None else repr(operation_template)}, "
-                f"operation_dict={'None' if operation_dict is None else '...'}"
-            )
+        _check_template_and_dict('crop', crop_template, crop_dict)
+        _check_template_and_dict('operation', operation_template, operation_dict)
 
+        crop_template = Path(crop_template) if crop_template is not None else None
         operation_template = Path(operation_template) if operation_template is not None else None
-        if user_comment:
-            user_comment = f'# {user_comment.lstrip("# ").rstrip()}\n'
+        user_comment = f'# {user_comment.lstrip("# ").rstrip()}\n' if user_comment else ''
         comment = user_comment + _generate_comment(self.executable, options)
         first_run = True
 
         if summary is None:
-            summary = {'harvest': 'summary.csv'}
-        elif isinstance(summary, str):
-            summary = {'harvest': summary}
-        assert isinstance(summary, dict)
+            summary = ['harvest']
+        else:
+            summary = list(set(summary) | {'harvest'})
 
-        for key in summary.keys():
-            if key == 'harvest': continue
-            control_dict[OUTPUT_CONTROL_FLAGS[key]] = 1
+        for s in summary:
+            if s == 'harvest': continue
+            control_dict[OUTPUT_CONTROL_FLAGS[s]] = 1
 
         assert isinstance(self.path, Path)
         (self.path / SUMMARY_DIR).mkdir(exist_ok=True)
 
+        simulations = _prepare_simulations(simulations)
+
+        owns_progress = _progress_bar is None and silence and len(simulations) > 1
+        progress = tqdm(simulations, unit='simulation', disable=_disable_progress_bar()) if owns_progress else _progress_bar
+
+        def _report(message: str) -> None:
+            tqdm.write(message) if progress is not None else print(message)
+
+        assert simulations is not None
         for s in simulations:
-            cxt: SimulationContext = self._resolve(s, control_dict, operation_dict, calibration_dict)
-            print(f'{cxt.name} - ', end='')
+            cxt: SimulationContext = self._resolve(s, control_dict, crop_dict, operation_dict, calibration_dict)
+            if owns_progress and progress is not None:
+                progress.set_description(f'Running {cxt.name}')
 
-            self._write_inputs(cxt, operation_template)
+            self._write_inputs(cxt, crop_template, operation_template)
 
-            cycles = Cycles(simulation=cxt.name, path=self.path, executable=self.executable)
+            code, _ = _run_cycles_simulation(self.path, self.executable, cxt.name, options, silence)
+            if code != 0:
+                _report(f'{cxt.name} - Fail (exit code {code})')
+            if progress is not None:
+                progress.update()
 
-            code, _ = cycles.run(options=options, silence=silence)
+            if s is None:
+                return
 
             if code == 0:
-                self._write_summary(cycles, summary, header=first_run, comment=comment)
+                cycles = Cycles(simulation=cxt.name, path=self.path)
+                _write_summary(self.path, cycles, summary, summary_prefix, header=first_run, comment=comment)
                 first_run = False
-                print('Success')
-            elif code == 1:
-                print('Fail')
-
             if rm_input:
                 self._remove_inputs(cxt)
             if rm_output:
@@ -229,21 +255,30 @@ class CyclesRunner:
                 # If using an existing steady-state soil file, it should not be removed.
                 (self.path / INPUT_DIR / f'{cxt.name}_ss.soil').unlink(missing_ok=True)
 
+        if owns_progress and progress is not None:
+            progress.set_description('Done')
+
 
-    def _resolve(self, simulation: dict[str, Any], control_dict: dict[str, Any], operation_dict: dict[str, Any] | None, calibration_dict: dict[str, Any] | None) -> SimulationContext:
+    def _resolve(self, simulation: dict[str, Any] | None, control_dict: dict[str, Any], crop_dict: dict[str, Any] | None, operation_dict: dict[str, Any] | None,
+                 calibration_dict: dict[str, Any] | None) -> SimulationContext:
         control = _resolve_dict_values(control_dict, simulation)
         assert isinstance(self.path, Path)
         return SimulationContext(
             name=control['simulation_name'],
             control_dict=control,
+            crop_dict=_resolve_dict_values(crop_dict, simulation) if crop_dict is not None else None,
             operation_dict=_resolve_dict_values(operation_dict, simulation) if operation_dict is not None else None,
             calibration_dict=_resolve_dict_values(calibration_dict, simulation) if calibration_dict is not None else None,
             operation_fn=self.path / INPUT_DIR / control['operation_file'],
+            crop_fn=self.path / INPUT_DIR / control.get('crop_file', DEFAULT_CROP_FILE),
         )
 
 
-    def _write_inputs(self, cxt: SimulationContext, operation_template: Path | None) -> None:
+    def _write_inputs(self, cxt: SimulationContext, crop_template: Path | None, operation_template: Path | None) -> None:
         assert isinstance(self.path, Path)
+        if crop_template is not None:
+            assert cxt.crop_dict is not None
+            _render_template(crop_template, cxt.crop_fn, cxt.crop_dict)
         if operation_template is not None:
             assert cxt.operation_dict is not None
             _render_template(operation_template, cxt.operation_fn, cxt.operation_dict)
@@ -256,21 +291,31 @@ class CyclesRunner:
         assert isinstance(self.path, Path)
         (self.path / INPUT_DIR / f'{cxt.name}.ctrl').unlink(missing_ok=True)
         (self.path / INPUT_DIR / f'{cxt.name}.nudge').unlink(missing_ok=True)
+        if cxt.crop_dict is not None:
+            cxt.crop_fn.unlink(missing_ok=True)
         if cxt.operation_dict is not None:
             cxt.operation_fn.unlink(missing_ok=True)
 
 
-    def _write_summary(self, cycles: Cycles, summary: dict, *, header: bool, comment: str) -> None:
-        assert isinstance(self.path, Path)
-        cycles.read_output(summary.keys())
-        for key, fn in summary.items():
-            cycles.output[key].data.insert(0, 'simulation', cycles.simulation)
+def _write_summary(path: Path, cycles: Cycles, summary: list[str], summary_prefix: str | None, *, header: bool, comment: str) -> None:
+    cycles.read_output(summary)
+    for s in summary:
+        cycles.output[s].data.insert(0, 'simulation', cycles.simulation)
+
+        mode = 'w' if header else 'a'
+        with open(path / SUMMARY_DIR / (f'{summary_prefix}_{s}.csv' if summary_prefix else f'{s}.csv'), mode) as f:
+            if header:
+                f.write(comment)
+            cycles.output[s].data.to_csv(f, header=header, index=False)
+
 
-            mode = 'w' if header else 'a'
-            with open(self.path / SUMMARY_DIR / fn, mode) as f:
-                if header:
-                    f.write(comment)
-                cycles.output[key].data.to_csv(f, header=header, index=False)
+def _check_template_and_dict(input_type: str, template_name: Path | str | None, dict_name: dict | None):
+    if (template_name is None) != (dict_name is None):
+        raise ValueError(
+            f"{input_type}_template and {input_type}_dict must be provided together or not at all. "
+            f"Got {input_type}_template={'None' if template_name is None else repr(template_name)}, "
+            f"{input_type}_dict={'None' if dict_name is None else '...'}"
+        )
 
 
 def _render_template(template_fn: Path, dest_fn: Path, substitutions: dict) -> None:
@@ -293,3 +338,33 @@ def _generate_comment(executable: str, options: str) -> str:
         'dynamically reduced fertilization rates' if 'x' in options else None,
     ]
     return ', '.join(p for p in parts if p) + '\n'
+
+
+def _run_cycles_simulation(path: Path, executable: str, simulation: str, options: str, silence: bool) -> tuple[int, str]:
+    cwd = os.getcwd()
+    cmd = [executable, *(options.split() if options else []), simulation]
+
+    os.chdir(path)
+    result = subprocess.run(
+        cmd,
+        shell=os.name == 'nt',
+        capture_output=True,
+        text=True,
+    )
+    if not silence:
+        print(result.stdout)
+    if result.stderr:
+        print(result.stderr)
+
+    os.chdir(cwd)
+
+    return result.returncode, result.stdout
+
+
+def _prepare_simulations(simulations: SimulationConfig) -> list:
+    if simulations is None:
+        simulations = [None]
+    if isinstance(simulations, pd.DataFrame):
+        simulations = simulations.to_dict(orient='records')
+
+    return simulations

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles_tools/control_file.py

@@ -3,7 +3,9 @@ import warnings
 from dataclasses import dataclass, field, fields
 from pathlib import Path
 from typing import Any, get_type_hints
-from ._base_file import _write_file, _resolve_dict_values, _extract, _parse_value, _unwrap_optional, FMT_1F
+from .._base_file import _write_file, _resolve_dict_values, _extract, _parse_value, _unwrap_optional, FMT_1F
+
+DEFAULT_CROP_FILE = 'GenericCrops.crop'
 
 @dataclass(kw_only=True)
 class SimulationYears:
@@ -13,7 +15,7 @@ class SimulationYears:
 
 @dataclass(kw_only=True)
 class InputFiles:
-    crop_file: str = 'GenericCrops.crop'
+    crop_file: str = DEFAULT_CROP_FILE
     operation_file: str
     soil_file: str
     weather_file: str

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles_tools/converter.py

@@ -1,7 +1,7 @@
 from dataclasses import dataclass, field, fields
 from pathlib import Path
 from typing import get_type_hints, Any
-from ._base_file import _unwrap_optional, _format_field, FMT_1F, FMT_2F, FMT_3F
+from .._base_file import _unwrap_optional, _format_field, FMT_1F, FMT_2F, FMT_3F
 from .operation_file import Planting, Tillage, FixedFertilization
 from .operation_file import generate_operation_file
 from .crop_file import Crop, generate_crop_file

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles_tools/crop_file.py

@@ -2,8 +2,8 @@ from __future__ import annotations
 from dataclasses import dataclass, field, fields
 from pathlib import Path
 from typing import Any, get_type_hints, Protocol
-from ._base_file import _write_file, _resolve_dict_values, _extract, _parse_value, _unwrap_optional, _format_block
-from ._base_file import FMT_1F, FMT_2F, FMT_3F, FMT_4F
+from .._base_file import _write_file, _resolve_dict_values, _extract, _parse_value, _unwrap_optional, _format_block
+from .._base_file import FMT_1F, FMT_2F, FMT_3F, FMT_4F
 
 @dataclass(kw_only=True)
 class Phenology:

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles_tools/nudge_file.py

@@ -2,8 +2,8 @@ from __future__ import annotations
 from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Any
-from ._base_file import _write_file, _resolve_dict_values, _extract
-from ._base_file import FMT_2F
+from .._base_file import _write_file, _resolve_dict_values, _extract
+from .._base_file import FMT_2F
 
 @dataclass(kw_only=True)
 class CalibrationMultipliers:
@@ -18,6 +18,7 @@ class CalibrationMultipliers:
     nitrif_rate: float = field(default=1.0, metadata={'description': 'nitrification rate', 'fmt': FMT_2F})
     pot_denitrif_rate: float = field(default=1.0, metadata={'description': 'potential denitrification rate', 'fmt': FMT_2F})
     denitrif_half_rate: float = field(default=1.0, metadata={'description': 'half saturation constant for denitrification', 'fmt': FMT_2F})
+    n2o_respiration_factor: float = field(default=1.0, metadata={'description': 'respiration factor that modulates proportion of N2O from denitrification', 'fmt': FMT_2F})
     decomp_half_resp: float = field(default=1.0, metadata={'description': 'decomposition half response to saturation (default 0.22)', 'fmt': FMT_2F})
     decomp_resp_power: float = field(default=1.0, metadata={'description': 'decomposition exponential response to saturation (default 3.0)', 'fmt': FMT_2F})
     root_progression: float = field(default=1.0, metadata={'description': 'rooting depth progression rate', 'fmt': FMT_2F})

{cycles_utils-4.1.0 → cycles_utils-4.2.0}/cycles/cycles_tools/operation_file.py

@@ -3,7 +3,7 @@ import re
 from pathlib import Path
 from dataclasses import dataclass, field, fields
 from typing import get_type_hints, Protocol, Any
-from ._base_file import _parse_value, FMT_1F, FMT_2F, _format_field
+from .._base_file import _parse_value, FMT_1F, FMT_2F, _format_field
 
 class Operation(Protocol):
     year: int | None