Cycles-utils 4.0.6__tar.gz → 4.2.0__tar.gz

{cycles_utils-4.0.6 → cycles_utils-4.2.0}/Cycles_utils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Cycles-utils
-Version: 4.0.6
+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
@@ -10,21 +10,43 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pandas>=1.2.4
-Requires-Dist: geopandas>=0.9.0
 Requires-Dist: numpy>=1.19.5
-Requires-Dist: cartopy>=0.18.0
 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"
+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: scipy>=1.6.3; extra == "weather"
 Provides-Extra: soilgrids
+Requires-Dist: geopandas>=0.9.0; extra == "soilgrids"
 Requires-Dist: rioxarray>=0.5.0; extra == "soilgrids"
 Requires-Dist: owslib>=0.24.1; extra == "soilgrids"
 Requires-Dist: rasterio>=1.2.3; extra == "soilgrids"
 Requires-Dist: shapely>=1.7.1; extra == "soilgrids"
-Provides-Extra: gssurgo
-Requires-Dist: shapely>=1.7.1; extra == "gssurgo"
-Requires-Dist: fiona>=1.8.20; extra == "gssurgo"
-Provides-Extra: weather
-Requires-Dist: netCDF4>=1.5.7; extra == "weather"
-Requires-Dist: tqdm>=4.60.0; extra == "weather"
+Requires-Dist: pyproj>=3.0.1; extra == "soilgrids"
+Provides-Extra: ssurgo
+Requires-Dist: geopandas>=0.9.0; extra == "ssurgo"
+Requires-Dist: shapely>=1.7.1; extra == "ssurgo"
+Requires-Dist: fiona>=1.8.20; extra == "ssurgo"
+Provides-Extra: gadm
+Requires-Dist: geopandas>=0.9.0; extra == "gadm"
+Provides-Extra: all
+Requires-Dist: cartopy>=0.18.0; extra == "all"
+Requires-Dist: geopandas>=0.9.0; extra == "all"
+Requires-Dist: fiona>=1.8.20; extra == "all"
+Requires-Dist: shapely>=1.7.1; extra == "all"
+Requires-Dist: rioxarray>=0.5.0; extra == "all"
+Requires-Dist: owslib>=0.24.1; extra == "all"
+Requires-Dist: rasterio>=1.2.3; extra == "all"
+Requires-Dist: pyproj>=3.0.1; extra == "all"
+Requires-Dist: netCDF4>=1.5.7; extra == "all"
+Requires-Dist: tqdm>=4.60.0; extra == "all"
+Requires-Dist: scipy>=1.6.3; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
@@ -61,6 +83,8 @@ 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         |
 | 4.0.4                | 1.5.20         |

{cycles_utils-4.0.6 → cycles_utils-4.2.0}/Cycles_utils.egg-info/SOURCES.txt

@@ -8,12 +8,15 @@ 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
+cycles/cycles_tools/crop_file.py
 cycles/cycles_tools/nudge_file.py
 cycles/cycles_tools/operation_file.py
 cycles/cycles_tools/output_file.py
@@ -41,4 +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-4.2.0/Cycles_utils.egg-info/requires.txt

@@ -0,0 +1,44 @@
+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
+geopandas>=0.9.0
+fiona>=1.8.20
+shapely>=1.7.1
+rioxarray>=0.5.0
+owslib>=0.24.1
+rasterio>=1.2.3
+pyproj>=3.0.1
+netCDF4>=1.5.7
+tqdm>=4.60.0
+scipy>=1.6.3
+
+[gadm]
+geopandas>=0.9.0
+
+[plot]
+cartopy>=0.18.0
+geopandas>=0.9.0
+fiona>=1.8.20
+shapely>=1.7.1
+
+[soilgrids]
+geopandas>=0.9.0
+rioxarray>=0.5.0
+owslib>=0.24.1
+rasterio>=1.2.3
+shapely>=1.7.1
+pyproj>=3.0.1
+
+[ssurgo]
+geopandas>=0.9.0
+shapely>=1.7.1
+fiona>=1.8.20
+
+[weather]
+netCDF4>=1.5.7
+scipy>=1.6.3

{cycles_utils-4.0.6 → cycles_utils-4.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Cycles-utils
-Version: 4.0.6
+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
@@ -10,21 +10,43 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pandas>=1.2.4
-Requires-Dist: geopandas>=0.9.0
 Requires-Dist: numpy>=1.19.5
-Requires-Dist: cartopy>=0.18.0
 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"
+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: scipy>=1.6.3; extra == "weather"
 Provides-Extra: soilgrids
+Requires-Dist: geopandas>=0.9.0; extra == "soilgrids"
 Requires-Dist: rioxarray>=0.5.0; extra == "soilgrids"
 Requires-Dist: owslib>=0.24.1; extra == "soilgrids"
 Requires-Dist: rasterio>=1.2.3; extra == "soilgrids"
 Requires-Dist: shapely>=1.7.1; extra == "soilgrids"
-Provides-Extra: gssurgo
-Requires-Dist: shapely>=1.7.1; extra == "gssurgo"
-Requires-Dist: fiona>=1.8.20; extra == "gssurgo"
-Provides-Extra: weather
-Requires-Dist: netCDF4>=1.5.7; extra == "weather"
-Requires-Dist: tqdm>=4.60.0; extra == "weather"
+Requires-Dist: pyproj>=3.0.1; extra == "soilgrids"
+Provides-Extra: ssurgo
+Requires-Dist: geopandas>=0.9.0; extra == "ssurgo"
+Requires-Dist: shapely>=1.7.1; extra == "ssurgo"
+Requires-Dist: fiona>=1.8.20; extra == "ssurgo"
+Provides-Extra: gadm
+Requires-Dist: geopandas>=0.9.0; extra == "gadm"
+Provides-Extra: all
+Requires-Dist: cartopy>=0.18.0; extra == "all"
+Requires-Dist: geopandas>=0.9.0; extra == "all"
+Requires-Dist: fiona>=1.8.20; extra == "all"
+Requires-Dist: shapely>=1.7.1; extra == "all"
+Requires-Dist: rioxarray>=0.5.0; extra == "all"
+Requires-Dist: owslib>=0.24.1; extra == "all"
+Requires-Dist: rasterio>=1.2.3; extra == "all"
+Requires-Dist: pyproj>=3.0.1; extra == "all"
+Requires-Dist: netCDF4>=1.5.7; extra == "all"
+Requires-Dist: tqdm>=4.60.0; extra == "all"
+Requires-Dist: scipy>=1.6.3; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
@@ -61,6 +83,8 @@ 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         |
 | 4.0.4                | 1.5.20         |

{cycles_utils-4.0.6 → cycles_utils-4.2.0}/README.md

@@ -22,6 +22,8 @@ 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         |
 | 4.0.4                | 1.5.20         |

cycles_utils-4.2.0/cycles/__init__.py

@@ -0,0 +1,67 @@
+from .cycles import Cycles
+from .cycles_tools import generate_control_file
+from .cycles_tools import generate_nudge_file
+from .cycles_tools import generate_soil_file
+from .cycles_tools import generate_reinit_file
+from .cycles_tools import read_control_file
+from .cycles_tools import read_crop_file
+from .cycles_tools import generate_crop_file
+from .cycles_tools import read_soil_file
+from .cycles_tools import read_weather_file
+from .cycles_tools import read_output
+from .cycles_tools import read_operation_file
+from .cycles_tools import generate_operation_file
+from .cycles_tools import convert_obsolete_crop_files
+from .cycles_tools import convert_obsolete_operation_files
+from .cycles_tools import convert_obsolete_soil_files
+from .cycles_tools import SoilLayer
+from .cycles_tools import Operation, Planting, Tillage, Harvest, Kill, FixedFertilization, FixedIrrigation, AutoIrrigation
+from .cycles_runner import CyclesRunner
+from .rotation_builder import CyclesRotationBuilder, Crop, CropGroup
+
+__all__ = [
+    "Cycles",
+    "CyclesRunner",
+    "CyclesRotationBuilder",
+    "Crop",
+    "CropGroup",
+    "generate_control_file",
+    "read_control_file",
+    "generate_nudge_file",
+    "read_crop_file",
+    "generate_crop_file",
+    "read_operation_file",
+    "generate_operation_file",
+    "read_output",
+    "generate_soil_file",
+    "read_soil_file",
+    "read_weather_file",
+    "generate_reinit_file",
+    "convert_obsolete_crop_files",
+    "convert_obsolete_operation_files",
+    "convert_obsolete_soil_files",
+    "SoilLayer",
+    "Operation", "Planting", "Tillage", "Harvest", "Kill",
+    "FixedFertilization", "FixedIrrigation", "AutoIrrigation",
+    "plot_yield",
+    "plot_operations",
+    "plot_map",
+    "plot_satellite_map",
+]
+
+# Plotting helpers require the optional [plot] extra (cartopy, geopandas,
+# fiona). Import lazily so `import cycles` never requires them.
+_PLOT_ATTRS = ("plot_yield", "plot_operations", "plot_map", "plot_satellite_map")
+
+
+def __getattr__(name: str):
+    if name in _PLOT_ATTRS:
+        from . import cycles_tools
+        value = getattr(cycles_tools, name)
+        globals()[name] = value
+        return value
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __dir__():
+    return sorted(list(globals().keys()) + list(_PLOT_ATTRS))

cycles_utils-4.2.0/cycles/_base_file.py

@@ -0,0 +1,98 @@
+from __future__ import annotations
+import os
+import sys
+import types
+from dataclasses import fields
+from pathlib import Path
+from typing import Union, Any
+
+def _fmt_float(value: float, digits: int=2) -> str:
+    if value == -999.0:
+        return '-999'
+    for d in range(1, digits):
+        if value == round(value, d):
+            return f'{value:.{d}f}'
+    else:
+        return f'{value:.{digits}f}'
+
+# Convenience lambdas for metadata
+FMT_1F = lambda v: _fmt_float(v, 1)
+FMT_2F = lambda v: _fmt_float(v, 2)
+FMT_3F = lambda v: _fmt_float(v, 3)
+FMT_4F = lambda v: _fmt_float(v, 4)
+
+def _format_field(object, attribute, widths: tuple[int, int], value=None) -> str:
+    fmt = attribute.metadata.get('fmt')
+    description = attribute.metadata.get('description', '')
+
+    if value is None:
+        value = getattr(object, attribute.name)
+
+    formatted = fmt(value) if fmt is not None else str(value)
+
+    return f'{attribute.name.upper():<{widths[0]}}{formatted:<{widths[1]}}# {description}' if description else f'{attribute.name.upper():<{widths[0]}}{formatted}'
+
+
+def _format_block(label: str, object, *, widths: tuple[int, int]=(28, 8), center: bool=False, all_caps: bool=True) -> str:
+    label = label.replace("_", " ").upper() if all_caps else label.replace("_", " ").capitalize()
+
+    lines = [f' ' * (28 if center else 0) + f'## {label} ##']
+    for f in fields(object):
+        lines.append(_format_field(object, f, widths))
+    lines.append('')
+
+    return '\n'.join(lines)
+
+
+def _write_file(fn: Path, config) -> None:
+    content = '\n'.join(
+        _format_block(f.name, getattr(config, f.name))
+        for f in fields(config)
+        if getattr(config, f.name) is not None
+    )
+    fn.write_text(content)
+
+
+def _resolve_dict_values(user_dict: dict, simulation: dict[str, Any] | None) -> dict:
+    return {key: func(simulation) if callable(func) else func for key, func in user_dict.items()}
+
+
+def _extract(dc_class, resolved: dict) -> dict:
+    return {f.name: resolved[f.name] for f in fields(dc_class) if f.name in resolved}
+
+
+def _parse_value(raw: str, name: str, hint: type) -> int | float | str:
+    hint = _unwrap_optional(hint)
+    if raw.split()[0].lower() == name.lower():
+        if hint is int: return int(raw.split()[1])
+        if hint is float: return float(raw.split()[1])
+        return raw.split()[1]
+    else:
+        raise ValueError(f"Expected field name '{name}' not found in line: {raw}")
+
+
+def _unwrap_optional(t) -> type:
+    origin = getattr(t, '__origin__', None)
+    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-4.0.6 → 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
@@ -14,8 +12,6 @@ from .cycles_tools import read_weather_file as _read_weather_file
 from .cycles_tools import read_output as _read_output
 from .cycles_tools import read_operation_file as _read_operation_file
 from .cycles_tools import generate_reinit_file as _generate_reinit_file
-from .cycles_tools import plot_yield as _plot_yield
-from .cycles_tools import plot_operations as _plot_operations
 
 @dataclass
 class Output:
@@ -26,13 +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).
@@ -44,12 +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.
     """
 
-    path: Path | str
     simulation: str
-    executable: Path | str | None = None
+    path: Path | str = '.'
     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)
@@ -63,36 +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.
-        """
-        cmd = [self.executable, *(options.split() if options else []), self.simulation]
-        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)
-        return result.returncode, result.stdout
 
 
     def read_output(self, output_types: Collection) -> None:
@@ -167,6 +130,7 @@ class Cycles:
         if 'harvest' not in self.output:
             self.read_output('harvest')
 
+        from .cycles_tools import plot_yield as _plot_yield  # lazy: optional [plot] extra
         return _plot_yield(self.output['harvest'].data, ax=ax, crop_colors=crop_colors, fontsize=fontsize)
 
 
@@ -188,4 +152,5 @@ class Cycles:
 
         rotation_size = self.control.simulation_years.rotation_size
 
+        from .cycles_tools import plot_operations as _plot_operations  # lazy: optional [plot] extra
         return _plot_operations(self.operations, rotation_size, axs=axs, fontsize=fontsize)