chemparseplot 1.9.7__tar.gz → 1.9.8__tar.gz

{chemparseplot-1.9.7 → chemparseplot-1.9.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 1.9.7
+Version: 1.9.8
 Summary: Parsers and plotting tools for computational chemistry
 Project-URL: Documentation, https://chemparseplot.rgoswami.me
 Project-URL: Issues, https://github.com/HaoZeke/chemparseplot/issues
@@ -115,6 +115,18 @@ publication-quality plots.
 ## Installation
 
     pip install chemparseplot
+
+Suite config (shared with rgpycrumbs — **no** `~/.config/chemparseplot`):
+
+    # ~/.config/rgpkgs/config.toml  or  ./rgpkgs.toml
+    # [pins] lock = "uv.lock"
+    # [pins.packages] …
+
+Feature extras (`plot`, `neb`, …) are *transitional* install convenience. Target
+is the same on-demand uv / `ensure_import` design as the rgpycrumbs hub; prefer
+bare install + suite pins for new work.
+
+    # transitional:
     # With plotting support
     pip install "chemparseplot[plot]"
     # Everything

{chemparseplot-1.9.7 → chemparseplot-1.9.8}/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.9.7'
-__version_tuple__ = version_tuple = (1, 9, 7)
+__version__ = version = '1.9.8'
+__version_tuple__ = version_tuple = (1, 9, 8)
 
 __commit_id__ = commit_id = None

chemparseplot-1.9.8/chemparseplot/api.py

@@ -0,0 +1,91 @@
+# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
+#
+# SPDX-License-Identifier: MIT
+"""Stable public library entry points for chemparseplot.
+
+Prefer this module for new consumers (cookbooks, wailord, notebooks).
+
+**Representative in-process path (parse → typed result):**
+
+.. code-block:: python
+
+    from chemparseplot.api import extract_orca_geomscan_energy
+
+    dist_bohr, energy_Eh = extract_orca_geomscan_energy(orca_out_text, "Actual Energy")
+    # dist_bohr, energy_Eh are pint Quantities (bohr, hartree)
+
+Heavy plot stacks still live under ``chemparseplot.plot`` (optional deps /
+transitional extras until suite uv design fully covers them).
+
+Suite pins/config: use ``rgpycrumbs.api`` (shared rgpkgs TOML) — this package
+does **not** invent ``~/.config/chemparseplot``.
+
+.. versionadded:: 1.9.8
+.. versionchanged:: 1.9.9
+   Expose ORCA geomscan energy parse as the stable library path.
+"""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from chemparseplot.parse.orca.geomscan import extract_energy_data
+from chemparseplot.units import (
+    ENERGY_UNITS,
+    convert_energy_magnitude,
+    energy_quantity,
+    normalize_energy_unit,
+)
+
+if TYPE_CHECKING:
+    from chemparseplot.units import Q_
+
+__all__ = [
+    "ENERGY_UNITS",
+    "convert_energy_magnitude",
+    "energy_quantity",
+    "extract_orca_geomscan_energy",
+    "normalize_energy_unit",
+    "suite_pins",
+]
+
+
+def extract_orca_geomscan_energy(
+    data: str, energy_type: str = "Actual Energy"
+) -> tuple[Q_, Q_]:
+    """Parse ORCA geometry-scan surface energies from output text.
+
+    In-process library path: text → typed ``(distance, energy)`` pint Quantities
+    in Bohr and Hartree (ORCA defaults).
+
+    Parameters
+    ----------
+    data:
+        Blob of ORCA output containing ``Calculated Surface`` blocks.
+    energy_type:
+        ``\"Actual Energy\"`` or ``\"SCF energy\"`` (substring match in the block).
+
+    Returns
+    -------
+    tuple[Q_, Q_]
+        Distances (bohr) and energies (hartree). Empty quantities if no match.
+    """
+    return extract_energy_data(data, energy_type)
+
+
+def suite_pins() -> dict[str, str]:
+    """Return suite package pins from rgpkgs config + env (soft on old hub).
+
+    Empty dict if rgpycrumbs is missing or too old.
+    """
+    try:
+        from rgpycrumbs.api import load_config, pins_from_env
+    except ImportError:
+        return {}
+    pins = dict(pins_from_env())
+    try:
+        cfg = load_config()
+        pins.update(cfg.merged_package_pins_normalized())
+    except Exception:  # noqa: BLE001 — soft fail for consumers
+        pass
+    return pins

{chemparseplot-1.9.7 → chemparseplot-1.9.8}/readme.md

@@ -45,6 +45,18 @@ publication-quality plots.
 ## Installation
 
     pip install chemparseplot
+
+Suite config (shared with rgpycrumbs — **no** `~/.config/chemparseplot`):
+
+    # ~/.config/rgpkgs/config.toml  or  ./rgpkgs.toml
+    # [pins] lock = "uv.lock"
+    # [pins.packages] …
+
+Feature extras (`plot`, `neb`, …) are *transitional* install convenience. Target
+is the same on-demand uv / `ensure_import` design as the rgpycrumbs hub; prefer
+bare install + suite pins for new work.
+
+    # transitional:
     # With plotting support
     pip install "chemparseplot[plot]"
     # Everything

chemparseplot-1.9.8/tests/fixtures_geomscan_snippet.txt

@@ -0,0 +1,9 @@
+The Calculated Surface using the 'Actual Energy'
+   7.55890395  -0.74239862
+   7.32930292  -0.74349939
+   7.09970189  -0.74467446
+
+The Calculated Surface using the SCF energy
+   7.55890395  -0.74239862
+   7.32930292  -0.74349939
+   7.09970189  -0.74467446

chemparseplot-1.9.8/tests/test_public_api.py

@@ -0,0 +1,72 @@
+# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
+#
+# SPDX-License-Identifier: MIT
+"""Drive shipped chemparseplot.api entry points (parse → typed result)."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+from chemparseplot.api import (
+    convert_energy_magnitude,
+    extract_orca_geomscan_energy,
+    normalize_energy_unit,
+    suite_pins,
+)
+
+# Inline fixture (same content as tests/fixtures_geomscan_snippet.txt)
+_GEOMSCAN_SNIPPET = """
+The Calculated Surface using the 'Actual Energy'
+   7.55890395  -0.74239862
+   7.32930292  -0.74349939
+   7.09970189  -0.74467446
+
+The Calculated Surface using the SCF energy
+   7.55890395  -0.74239862
+   7.32930292  -0.74349939
+   7.09970189  -0.74467446
+"""
+
+FIXTURE_FILE = Path(__file__).parent / "fixtures_geomscan_snippet.txt"
+
+
+def test_normalize_and_convert_energy_library_path():
+    assert normalize_energy_unit("ev") == "eV"
+    kcal = convert_energy_magnitude(1.0, "kcal/mol")
+    val = float(np.asarray(kcal).reshape(-1)[0])
+    assert 20.0 < val < 25.0
+    back = float(np.asarray(convert_energy_magnitude(val, "eV", source_unit="kcal/mol")))
+    assert abs(back - 1.0) < 1e-6
+
+
+def test_extract_orca_geomscan_energy_typed_nonempty():
+    """Public parse path: ORCA geomscan text → pint Quantities with data."""
+    dist, energy = extract_orca_geomscan_energy(_GEOMSCAN_SNIPPET, "Actual Energy")
+    assert dist.size == 3
+    assert energy.size == 3
+    assert str(dist.units) == "bohr"
+    assert str(energy.units) == "hartree"
+    np.testing.assert_allclose(
+        dist.magnitude,
+        [7.55890395, 7.32930292, 7.09970189],
+    )
+    np.testing.assert_allclose(
+        energy.magnitude,
+        [-0.74239862, -0.74349939, -0.74467446],
+    )
+
+
+def test_extract_orca_geomscan_energy_from_fixture_file():
+    text = FIXTURE_FILE.read_text(encoding="utf-8")
+    dist, energy = extract_orca_geomscan_energy(text, "SCF energy")
+    assert dist.size >= 1
+    assert energy.size == dist.size
+    assert dist.size == 3
+
+
+def test_suite_pins_returns_dict():
+    pins = suite_pins()
+    assert isinstance(pins, dict)