phytkit 0.1.0__cp39-abi3-win_amd64.whl

phytkit/__init__.py

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+"""phytkit: plant physiology model fitting.
+
+The commands run the same Rust code as the `pk` command line and return the same
+structure as its JSON output, as dicts::
+
+    import phytkit as pk
+    fit = pk.fit("photosynthesis", "leaf1.csv", model="fvcb")
+    fit["params"]["Vcmax25"]
+
+For data already in memory, use `fit_arrays`, `fit_many` (parallel) and `predict`.
+"""
+from __future__ import annotations
+
+import os
+from typing import Any, Iterable, Mapping
+
+from ._phytkit import PhytKitError, __version__, fit_arrays, fit_many, models, predict, run
+
+__all__ = [
+    "PhytKitError", "__version__", "concat", "describe", "fit", "fit_arrays", "fit_many",
+    "li600_correct", "li600_estimate", "models", "predict", "run",
+]
+
+
+def _flags(options: Mapping[str, Any]) -> list[str]:
+    """Keyword arguments to `pk` flags: max_iter=400 -> --max-iter 400, fix=["gm"] -> --fix gm,
+    set={"gm": 1e6} -> --set gm=1000000, predicted=True -> --predicted. None is skipped."""
+    out: list[str] = []
+    for key, value in options.items():
+        if value is None or value is False:
+            continue
+        flag = "--" + key.rstrip("_").replace("_", "-")
+        if value is True:
+            out.append(flag)
+        elif isinstance(value, Mapping):
+            for k, v in value.items():
+                out += [flag, f"{k}={v!r}" if isinstance(v, float) else f"{k}={v}"]
+        elif isinstance(value, (list, tuple)):
+            # Repeatable flags (--survey, --no-constraint) take one value each.
+            for v in value:
+                out += [flag, os.fspath(v) if isinstance(v, os.PathLike) else str(v)]
+        else:
+            out += [flag, os.fspath(value) if isinstance(value, os.PathLike) else str(value)]
+    return out
+
+
+def _paths(files: Iterable[str | os.PathLike]) -> list[str]:
+    return [os.fspath(f) for f in files]
+
+
+def describe(model: str | None = None) -> dict:
+    """Tools, models, parameters and constraints; or one model's details."""
+    return run(["describe"] + ([model] if model else []))
+
+
+def fit(tool: str, *files: str | os.PathLike, **options: Any) -> dict | str:
+    """Fit a tool's model to one or more files (`pk fit`).
+
+    tool: "photosynthesis", "stomatal", "hydraulics" or "soil".
+    options: model, fit=[...], fix=[...], set={...}, no_constraint=[...], constraints="none",
+    weight={...}, units, max_iter, group_by, survey=[...], stat, ref_ci, predicted, format.
+    One file returns that fit; several (or group_by) return a batch summary.
+    """
+    for name in ("fit", "fix"):
+        if isinstance(options.get(name), (list, tuple)):
+            options[name] = ",".join(options[name])
+    return run(["fit", tool, *_paths(files), *_flags(options)])
+
+
+def li600_correct(file: str | os.PathLike, **options: Any) -> dict | str:
+    """LI-600 energy-balance gsw correction (`pk li600 correct`).
+    options: sidedness, thermal_conductance, rows, out, format."""
+    return run(["li600", "correct", os.fspath(file), *_flags(options)])
+
+
+def li600_estimate(file: str | os.PathLike, **options: Any) -> dict | str:
+    """A, Ci and Cc from LI-600 gsw and photosynthesis parameters (`pk li600 estimate`).
+    options: model, params (a file), set={...}, ca, absorptance, min_gsw, rows, out, format."""
+    return run(["li600", "estimate", os.fspath(file), *_flags(options)])
+
+
+def concat(*files: str | os.PathLike, **options: Any) -> dict | str:
+    """Merge LI-6800 logs or CSVs under one header with a CurveID per file (`pk concat`).
+    options: out, format. Returns the merged CSV text unless out or format="json" is given."""
+    return run(["concat", *_paths(files), *_flags(options)])

phytkit/__main__.py

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+"""`pk` from the Python package: the same command line, output and exit codes as the `pk` binary."""
+import sys
+
+from ._phytkit import main as _main
+
+
+def main() -> int:
+    text, code = _main(sys.argv[1:])
+    # Write UTF-8 bytes, like the binary. sys.stdout.write would encode with the console's
+    # code page on Windows (cp1252), which can't encode the Greek letters and dashes in
+    # `pk describe` and --help, and would also turn \n into \r\n.
+    sys.stdout.flush()
+    sys.stdout.buffer.write(text.encode("utf-8"))
+    sys.stdout.buffer.flush()
+    return code
+
+
+if __name__ == "__main__":
+    sys.exit(main())

phytkit-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: phytkit
+Version: 0.1.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+License-File: LICENSE
+Summary: Plant physiology model fitting: photosynthesis, stomatal conductance, hydraulics and soil water retention.
+Keywords: plant physiology,photosynthesis,FvCB,stomatal conductance,curve fitting,LI-6800,LI-600
+Author: PlantSimulationLab
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Documentation, https://plantsimulationlab.github.io/PhytKit/
+Project-URL: Issues, https://github.com/PlantSimulationLab/PhytKit/issues
+Project-URL: Source, https://github.com/PlantSimulationLab/PhytKit
+
+# PhytKit
+
+Plant physiology model fitting, written in Rust: photosynthesis (FvCB C3 and C4, empirical light
+response), stomatal conductance (BTA, Medlyn), xylem vulnerability, pressure–volume curves, soil
+water retention, and LI-600 porometer tools.
+
+```bash
+pip install phytkit
+```
+
+This installs the `phytkit` Python package and the `pk` command-line tool. Both return the same
+JSON.
+
+```bash
+pk describe fvcb
+pk fit photosynthesis leaf.csv --model fvcb
+pk fit soil soil.csv --group-by sample --units kPa
+pk li600 correct porometer.csv --sidedness 1.5
+```
+
+```python
+import phytkit as pk
+
+pk.fit("photosynthesis", "leaf.csv", model="fvcb", fix=["gm"], max_iter=400)  # same as `pk fit`
+pk.fit_arrays("fvcb", {"Ci": ci, "Q": q, "T": t_kelvin}, a)                   # data in memory
+pk.fit_many("fvcb", [(x1, y1), (x2, y2)], threads=8)                        # parallel batch
+pk.predict("fvcb", {"Vcmax25": 90}, {"Ci": ci, "Q": q, "T": t_kelvin})
+```
+
+Failures raise `phytkit.PhytKitError`, with a stable `.code` and a `.hint`.
+
+- Documentation: <https://plantsimulationlab.github.io/PhytKit/>
+- Source and issues: <https://github.com/PlantSimulationLab/PhytKit>
+
+MIT licensed.
+

phytkit-0.1.0.dist-info/RECORD

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+phytkit-0.1.0.dist-info/METADATA,sha256=PDJWyTHOJEwSjyIUbBdtecxNplVgy6hyp-Lb-APc75A,2193
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+phytkit-0.1.0.dist-info/licenses/LICENSE,sha256=xVDAVzdPRTqQ4_zcI0pQxM3YFhX7GXg6w80z3Ehu-P8,1096
+phytkit-0.1.0.dist-info/sboms/phytkit-py.cyclonedx.json,sha256=V9TR6RVi98jzH2xhE-jmdRjW1On34vW90HUOCyKH2_M,72574
+phytkit-0.1.0.dist-info/RECORD,,

phytkit-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.16.0)
+Root-Is-Purelib: false
+Tag: cp39-abi3-win_amd64

phytkit-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+pk=phytkit.__main__:main

phytkit-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 PlantSimulationLab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.