diskmelts 2.1.1__tar.gz → 2.1.2__tar.gz

{diskmelts-2.1.1/src/diskmelts.egg-info → diskmelts-2.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diskmelts
-Version: 2.1.1
+Version: 2.1.2
 Summary: Machine-learning Enabled Line fitting Tool for Spectra of protoplanetary disks
 Author: Chengyan Xie, Dingshan Deng
 License-Expression: MIT
@@ -49,7 +49,8 @@ density (`logN`), and emitting area scaling (`A`) from observed spectra.
 
 ## Installation
 
-DiskMELTS 2.1.1 is available on [PyPI](https://pypi.org/project/diskmelts/).
+DiskMELTS is available on [PyPI](https://pypi.org/project/diskmelts/).
+The C6H6 and C3H4 checkpoints are included starting with version 2.1.2.
 With Python 3.9 or newer, install it from any directory. These commands use
 `python` in an activated environment; the
 [installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html)
@@ -196,9 +197,9 @@ plotting.
 
 ## Training and validation data
 
-`Model_grids/` and `Pretrain_grid/` are intentionally ignored by Git because
-they contain the full local training data. The generated checkpoint directories
-under the top-level `Trained_model/` are also optional; the package bundles
+Generated data under `Model_grids/` and `Pretrain_grid/` are intentionally
+ignored by Git because they contain the full local training data. Generated
+checkpoint directories under the top-level `Trained_model/` are also optional; the package bundles
 only the production checkpoints needed for v2 fitting. To run
 `examples/dev_v2_pt_validation.py` or
 `notebooks/Example_Training_Validation.ipynb`, place the complete model grids
@@ -209,7 +210,8 @@ The maintained v2 workflow uses a hybrid design after restricting the expanded
 IRIS grids to the intended physical domain. H2O uses five overlapping
 wavelength checkpoints covering 4.9–25.0 µm, all sharing `T=100–1400 K` and
 `logN=13–19`. Primary carbon-bearing and rarer molecules use one checkpoint
-each, the same temperature range, and `logN=13–19.5`.
+each and `logN=13–19.5`; C6H6 is limited to `T=100–675 K`, while the others
+use `T=100–1400 K`.
 The new C2HD checkpoint spans 11.5–20.5 µm to include its 19 µm band;
 CO17O and CO18O span 13–18 µm. The updated 13C12CH2 checkpoint keeps
 11.5–17 µm. To retrain these four grids, run:
@@ -218,6 +220,13 @@ CO17O and CO18O span 13–18 µm. The updated 13C12CH2 checkpoint keeps
 DISKMELTS_MOLECULES=13C12CH2,C2HD,CO17O,CO18O python examples/dev_v2_pt_validation.py
 ```
 
+C6H6 and C3H4 also have bundled fitting checkpoints. The C6H6 checkpoint
+covers 13–17 µm and 100–675 K; C3H4 covers 15–18 µm and 100–1400 K. Load
+either by name with `load_fitting_models`. Direct grid fitting
+uses the same names with local `Model_grids/C6H6/` and `Model_grids/C3H4/`
+files. See the [training guide](https://diskmelts.readthedocs.io/en/latest/training.html)
+for peak audits and retraining commands.
+
 Five to ten percent of complete `(T, logN)` grid spectra are excluded before
 PCA or neural-network training. They are used to select the PCA dimension and
 to validate spectral reconstruction and full parameter fitting. The

{diskmelts-2.1.1 → diskmelts-2.1.2}/README.md

@@ -10,7 +10,8 @@ density (`logN`), and emitting area scaling (`A`) from observed spectra.
 
 ## Installation
 
-DiskMELTS 2.1.1 is available on [PyPI](https://pypi.org/project/diskmelts/).
+DiskMELTS is available on [PyPI](https://pypi.org/project/diskmelts/).
+The C6H6 and C3H4 checkpoints are included starting with version 2.1.2.
 With Python 3.9 or newer, install it from any directory. These commands use
 `python` in an activated environment; the
 [installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html)
@@ -157,9 +158,9 @@ plotting.
 
 ## Training and validation data
 
-`Model_grids/` and `Pretrain_grid/` are intentionally ignored by Git because
-they contain the full local training data. The generated checkpoint directories
-under the top-level `Trained_model/` are also optional; the package bundles
+Generated data under `Model_grids/` and `Pretrain_grid/` are intentionally
+ignored by Git because they contain the full local training data. Generated
+checkpoint directories under the top-level `Trained_model/` are also optional; the package bundles
 only the production checkpoints needed for v2 fitting. To run
 `examples/dev_v2_pt_validation.py` or
 `notebooks/Example_Training_Validation.ipynb`, place the complete model grids
@@ -170,7 +171,8 @@ The maintained v2 workflow uses a hybrid design after restricting the expanded
 IRIS grids to the intended physical domain. H2O uses five overlapping
 wavelength checkpoints covering 4.9–25.0 µm, all sharing `T=100–1400 K` and
 `logN=13–19`. Primary carbon-bearing and rarer molecules use one checkpoint
-each, the same temperature range, and `logN=13–19.5`.
+each and `logN=13–19.5`; C6H6 is limited to `T=100–675 K`, while the others
+use `T=100–1400 K`.
 The new C2HD checkpoint spans 11.5–20.5 µm to include its 19 µm band;
 CO17O and CO18O span 13–18 µm. The updated 13C12CH2 checkpoint keeps
 11.5–17 µm. To retrain these four grids, run:
@@ -179,6 +181,13 @@ CO17O and CO18O span 13–18 µm. The updated 13C12CH2 checkpoint keeps
 DISKMELTS_MOLECULES=13C12CH2,C2HD,CO17O,CO18O python examples/dev_v2_pt_validation.py
 ```
 
+C6H6 and C3H4 also have bundled fitting checkpoints. The C6H6 checkpoint
+covers 13–17 µm and 100–675 K; C3H4 covers 15–18 µm and 100–1400 K. Load
+either by name with `load_fitting_models`. Direct grid fitting
+uses the same names with local `Model_grids/C6H6/` and `Model_grids/C3H4/`
+files. See the [training guide](https://diskmelts.readthedocs.io/en/latest/training.html)
+for peak audits and retraining commands.
+
 Five to ten percent of complete `(T, logN)` grid spectra are excluded before
 PCA or neural-network training. They are used to select the PCA dimension and
 to validate spectral reconstruction and full parameter fitting. The

{diskmelts-2.1.1 → diskmelts-2.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "diskmelts"
-version = "2.1.1"
+version = "2.1.2"
 description = "Machine-learning Enabled Line fitting Tool for Spectra of protoplanetary disks"
 readme = "README.md"
 requires-python = ">=3.9"

{diskmelts-2.1.1 → diskmelts-2.1.2}/src/diskmelts/fitting.py

@@ -1347,14 +1347,14 @@ def save_fitted_comparison(csv_path, source_name, all_fits):
 
     def _v(comp, key):
         if comp not in all_params:
-            return ''
+            return np.nan
         return round(all_params[comp][key], 4)
 
     def _e(comp, key, which):
         if comp not in all_unc:
-            return ''
+            return np.nan
         v = all_unc[comp].get(key, {}).get(which, float('nan'))
-        return round(v, 4) if np.isfinite(v) else ''
+        return round(v, 4) if np.isfinite(v) else np.nan
 
     row = {
         'Source':               source_name,

{diskmelts-2.1.1 → diskmelts-2.1.2}/src/diskmelts/plotting.py

@@ -43,6 +43,8 @@ _MOL_LABEL = {
     'C2HD':      r'C$_2$HD',
     'CO17O':     r'C$^{16}$O$^{17}$O',
     'CO18O':     r'C$^{16}$O$^{18}$O',
+    'C6H6':      r'C$_6$H$_6$',
+    'C3H4':      r'C$_3$H$_4$',
 }
 
 _MOL_COLOR = {
@@ -64,6 +66,8 @@ _MOL_COLOR = {
     'C2HD':     'teal',
     'CO17O':    'slateblue',
     'CO18O':    'goldenrod',
+    'C6H6':     'darkorange',
+    'C3H4':     'purple',
 }
 
 # ---------------------------------------------------------------------------

{diskmelts-2.1.1 → diskmelts-2.1.2}/src/diskmelts/v2_fitting.py

@@ -34,7 +34,8 @@ CARBON_RANGES = {
     'HC3N': (13.0, 18.0), 'C2H6': (9.0, 15.0),
     'C2H4': (8.0, 14.0), 'CH4': (5.0, 9.0),
     'C2HD': (11.5, 20.5), 'CO17O': (13.0, 18.0),
-    'CO18O': (13.0, 18.0),
+    'CO18O': (13.0, 18.0), 'C6H6': (13.0, 17.0),
+    'C3H4': (15.0, 18.0),
 }
 MODEL_SPECS = {
     'H2O': {
@@ -49,9 +50,9 @@ MODEL_SPECS = {
         mol: {
             'path': f'Trained_model/{mol}_single_v2/net_{mol}_forward.pt',
             'wavelength_ranges': (wav_range,),
-            'T_bounds': (100.0, 1400.0),
+            'T_bounds': (100.0, 675.0) if mol == 'C6H6' else (100.0, 1400.0),
             'logN_bounds': (13.0, 19.5),
-            'n_pca': 30,
+            'n_pca': 75 if mol == 'C3H4' else 30,
             'hidden': (64, 128, 64),
         }
         for mol, wav_range in CARBON_RANGES.items()

{diskmelts-2.1.1 → diskmelts-2.1.2/src/diskmelts.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diskmelts
-Version: 2.1.1
+Version: 2.1.2
 Summary: Machine-learning Enabled Line fitting Tool for Spectra of protoplanetary disks
 Author: Chengyan Xie, Dingshan Deng
 License-Expression: MIT
@@ -49,7 +49,8 @@ density (`logN`), and emitting area scaling (`A`) from observed spectra.
 
 ## Installation
 
-DiskMELTS 2.1.1 is available on [PyPI](https://pypi.org/project/diskmelts/).
+DiskMELTS is available on [PyPI](https://pypi.org/project/diskmelts/).
+The C6H6 and C3H4 checkpoints are included starting with version 2.1.2.
 With Python 3.9 or newer, install it from any directory. These commands use
 `python` in an activated environment; the
 [installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html)
@@ -196,9 +197,9 @@ plotting.
 
 ## Training and validation data
 
-`Model_grids/` and `Pretrain_grid/` are intentionally ignored by Git because
-they contain the full local training data. The generated checkpoint directories
-under the top-level `Trained_model/` are also optional; the package bundles
+Generated data under `Model_grids/` and `Pretrain_grid/` are intentionally
+ignored by Git because they contain the full local training data. Generated
+checkpoint directories under the top-level `Trained_model/` are also optional; the package bundles
 only the production checkpoints needed for v2 fitting. To run
 `examples/dev_v2_pt_validation.py` or
 `notebooks/Example_Training_Validation.ipynb`, place the complete model grids
@@ -209,7 +210,8 @@ The maintained v2 workflow uses a hybrid design after restricting the expanded
 IRIS grids to the intended physical domain. H2O uses five overlapping
 wavelength checkpoints covering 4.9–25.0 µm, all sharing `T=100–1400 K` and
 `logN=13–19`. Primary carbon-bearing and rarer molecules use one checkpoint
-each, the same temperature range, and `logN=13–19.5`.
+each and `logN=13–19.5`; C6H6 is limited to `T=100–675 K`, while the others
+use `T=100–1400 K`.
 The new C2HD checkpoint spans 11.5–20.5 µm to include its 19 µm band;
 CO17O and CO18O span 13–18 µm. The updated 13C12CH2 checkpoint keeps
 11.5–17 µm. To retrain these four grids, run:
@@ -218,6 +220,13 @@ CO17O and CO18O span 13–18 µm. The updated 13C12CH2 checkpoint keeps
 DISKMELTS_MOLECULES=13C12CH2,C2HD,CO17O,CO18O python examples/dev_v2_pt_validation.py
 ```
 
+C6H6 and C3H4 also have bundled fitting checkpoints. The C6H6 checkpoint
+covers 13–17 µm and 100–675 K; C3H4 covers 15–18 µm and 100–1400 K. Load
+either by name with `load_fitting_models`. Direct grid fitting
+uses the same names with local `Model_grids/C6H6/` and `Model_grids/C3H4/`
+files. See the [training guide](https://diskmelts.readthedocs.io/en/latest/training.html)
+for peak audits and retraining commands.
+
 Five to ten percent of complete `(T, logN)` grid spectra are excluded before
 PCA or neural-network training. They are used to select the PCA dimension and
 to validate spectral reconstruction and full parameter fitting. The

{diskmelts-2.1.1 → diskmelts-2.1.2}/src/diskmelts.egg-info/SOURCES.txt

@@ -34,7 +34,9 @@ src/diskmelts/models/Trained_model/C2H2_single_v2/net_C2H2_forward.pt
 src/diskmelts/models/Trained_model/C2H4_single_v2/net_C2H4_forward.pt
 src/diskmelts/models/Trained_model/C2H6_single_v2/net_C2H6_forward.pt
 src/diskmelts/models/Trained_model/C2HD_single_v2/net_C2HD_forward.pt
+src/diskmelts/models/Trained_model/C3H4_single_v2/net_C3H4_forward.pt
 src/diskmelts/models/Trained_model/C4H2_single_v2/net_C4H2_forward.pt
+src/diskmelts/models/Trained_model/C6H6_single_v2/net_C6H6_forward.pt
 src/diskmelts/models/Trained_model/CH4_single_v2/net_CH4_forward.pt
 src/diskmelts/models/Trained_model/CO17O_single_v2/net_CO17O_forward.pt
 src/diskmelts/models/Trained_model/CO18O_single_v2/net_CO18O_forward.pt

{diskmelts-2.1.1 → diskmelts-2.1.2}/tests/test_dev_v2_fitting_grids.py

@@ -14,12 +14,13 @@ from diskmelts.v2_grid_fitting import (
 )
 
 
-def _small_grid(tmp_path):
-    grid_dir = tmp_path / 'grids' / 'C2H2'
+def _small_grid(tmp_path, molecule='C2H2', wavelength_range=(11.0, 13.0)):
+    grid_dir = tmp_path / 'grids' / molecule
     grid_dir.mkdir(parents=True)
-    wav = np.linspace(11.0, 13.0, 60)
+    lo, hi = wavelength_range
+    wav = np.linspace(lo, hi, 60)
     basis = np.stack([np.exp(-((wav - center) / 0.09) ** 2)
-                      for center in (11.3, 12.0, 12.7)])
+                      for center in (lo + 0.3, (lo + hi) / 2, hi - 0.3)])
 
     def spectrum(T, logN):
         return 0.01 * (basis[0] + (1 + (T - 100) / 25) * basis[1]
@@ -33,6 +34,25 @@ def _small_grid(tmp_path):
     return wav, spectrum
 
 
+@pytest.mark.parametrize('molecule,wavelength_range', [
+    ('C6H6', (13.0, 17.0)),
+    ('C3H4', (15.0, 18.0)),
+])
+def test_new_molecules_fit_from_direct_grids(tmp_path, molecule,
+                                             wavelength_range):
+    wav, spectrum = _small_grid(tmp_path, molecule, wavelength_range)
+    observed = spectrum(113.0, 13.07)
+    fit = fit_grid_stage(
+        wav, observed, molecule, wavelength_range, wavelength_range,
+        grid_root=tmp_path / 'grids', T_bounds=(100, 150),
+        logN_bounds=(13, 13.25), sigma=1e-4,
+        maxiter=20, popsize=5, n_refine=2,
+    )
+    assert molecule in fit['params']
+    assert np.isfinite(fit['model_flux']).all()
+    assert np.linalg.norm(fit['residual']) < np.linalg.norm(observed)
+
+
 def test_grid_fit_and_saved_errors(tmp_path):
     wav, spectrum = _small_grid(tmp_path)
     distance_pc = 177.0

{diskmelts-2.1.1 → diskmelts-2.1.2}/tests/test_io.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+import warnings
+
 import numpy as np
 import pandas as pd
 import pytest
@@ -53,3 +55,26 @@ def test_save_running_spectrum(tmp_path):
     assert list(df.columns) == ["wave", "residual", "cumulative_model"]
     assert len(df) == 50
     assert df["wave"].iloc[0] == pytest.approx(11.0)
+
+
+def test_save_fitted_comparison_updates_missing_numeric_fields(tmp_path):
+    pytest.importorskip("torch")
+    from diskmelts import save_fitted_comparison
+
+    path = tmp_path / "comparison.csv"
+    water = {"water": {"params": {
+        "H2O_warm": {"logN": 17.0, "T": 400.0, "log10A": 1.0},
+    }}}
+    carbon = {"carbon": {"params": {
+        "C2H2": {"logN": 18.0, "T": 600.0, "log10A": 2.0},
+    }}}
+    save_fitted_comparison(path, "source", water)
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", FutureWarning)
+        save_fitted_comparison(path, "source", carbon)
+
+    df = pd.read_csv(path)
+    assert len(df) == 1
+    assert pd.isna(df.loc[0, "H2O_N_warm"])
+    assert pd.isna(df.loc[0, "C2H2_N_err_low"])
+    assert df.loc[0, "C2H2_N"] == pytest.approx(18.0)

{diskmelts-2.1.1 → diskmelts-2.1.2}/tests/test_v2_package_assets.py

@@ -23,3 +23,22 @@ def test_bundled_model_fit_without_grids(tmp_path, monkeypatch):
     assert fit['params']['C2H2']['logN'] == pytest.approx(16, abs=0.02)
     with pytest.raises(ValueError, match='grid_root is required'):
         fit_grid_stage(wave, flux, 'C2H2', (13.5, 14.1), (13.5, 14.1))
+
+
+@pytest.mark.parametrize('molecule,window', [
+    ('C6H6', (14.5, 15.2)),
+    ('C3H4', (15.68, 15.85)),
+])
+def test_new_bundled_molecules_fit_without_grids(tmp_path, monkeypatch,
+                                                  molecule, window):
+    monkeypatch.chdir(tmp_path)
+    models = load_fitting_models(molecule)
+    wave = np.linspace(*window, 100)
+    flux = generate_spectrum(500, 16, 1.0, models[molecule], obs_wav=wave)
+    fit = fit_stage(
+        wave, flux, molecule, window, window, models,
+        n_samples=64, n_refine=2, n_top=2, seed=4,
+    )
+    assert molecule in fit['params']
+    assert np.isfinite(fit['model_flux']).all()
+    assert np.linalg.norm(fit['residual']) < np.linalg.norm(flux)

{diskmelts-2.1.1 → diskmelts-2.1.2}/tests/test_workflows.py

@@ -30,6 +30,14 @@ def test_notebook_code_cells_compile(path):
             compile("".join(cell["source"]), f"{path.name}:cell-{index}", "exec")
 
 
+@pytest.mark.parametrize("path", [FITTING_NOTEBOOK, TRAINING_NOTEBOOK])
+def test_notebook_rejects_incompatible_sklearn(path, monkeypatch):
+    sklearn = pytest.importorskip("sklearn")
+    monkeypatch.setattr(sklearn, "__version__", "0.0")
+    with pytest.raises(RuntimeError, match="require scikit-learn 1.8.0"):
+        exec(_code_cell(_notebook(path), 1), {})
+
+
 @pytest.mark.parametrize("start_dir", [ROOT, ROOT / "notebooks"])
 def test_consub_notebook_reads_public_usco_csv(monkeypatch, start_dir):
     raw_dir = ROOT / "Realobs_data" / "Raw_data"
@@ -46,6 +54,9 @@ def test_consub_notebook_reads_public_usco_csv(monkeypatch, start_dir):
 @pytest.mark.parametrize("start_dir", [ROOT, ROOT / "notebooks"])
 def test_fitting_notebook_resolves_committed_assets(monkeypatch, start_dir):
     pytest.importorskip("torch")
+    sklearn = pytest.importorskip("sklearn")
+    # This test checks paths and stage settings; the version guard is tested above.
+    monkeypatch.setattr(sklearn, "__version__", "1.8.0")
     notebook = _notebook(FITTING_NOTEBOOK)
     namespace = {}
 
@@ -65,6 +76,8 @@ def test_fitting_notebook_resolves_committed_assets(monkeypatch, start_dir):
 @pytest.mark.parametrize("start_dir", [ROOT, ROOT / "notebooks"])
 def test_training_notebook_resolves_local_data_locations(monkeypatch, start_dir):
     pytest.importorskip("torch")
+    sklearn = pytest.importorskip("sklearn")
+    monkeypatch.setattr(sklearn, "__version__", "1.8.0")
     notebook = _notebook(TRAINING_NOTEBOOK)
     namespace = {}
 
@@ -83,11 +96,11 @@ def test_production_checkpoint_files_are_bundled():
     from diskmelts import MODEL_SPECS
     from diskmelts.v2_fitting import MODEL_ROOT
 
-    assert len(MODEL_SPECS) == 14
+    assert len(MODEL_SPECS) == 16
     for molecule, spec in MODEL_SPECS.items():
         path = MODEL_ROOT / spec['path']
         assert path.is_file(), f'missing bundled checkpoint for {molecule}: {path}'
-    assert len(list(MODEL_ROOT.rglob('*.pt'))) == 18
+    assert len(list(MODEL_ROOT.rglob('*.pt'))) == 20
 
 
 def test_new_grid_checkpoints_load_and_generate_finite_spectra():
@@ -95,7 +108,7 @@ def test_new_grid_checkpoints_load_and_generate_finite_spectra():
     from diskmelts import load_fitting_models
     from diskmelts.fitting import generate_spectrum
 
-    molecules = ('13C12CH2', 'C2HD', 'CO17O', 'CO18O')
+    molecules = ('13C12CH2', 'C2HD', 'CO17O', 'CO18O', 'C6H6', 'C3H4')
     models = load_fitting_models(molecules)
     for molecule in molecules:
         flux = generate_spectrum(400., 16., 1., models[molecule])
@@ -111,7 +124,7 @@ def test_gitignore_separates_fitting_assets_from_training_data():
         if line.strip() and not line.lstrip().startswith("#")
     }
 
-    for pattern in ('/Model_grids/', '/Pretrain_grid/', '/Trained_model/',
+    for pattern in ('/Model_grids/*', '/Pretrain_grid/', '/Trained_model/',
                     '/0-Consub/',
                     '/docs/_build/', '/realobs_results/', '/figures/*'):
         assert pattern in patterns