diskmelts 2.1__tar.gz

diskmelts-2.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Chengyan Xie
+
+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.

diskmelts-2.1/PKG-INFO

@@ -0,0 +1,262 @@
+Metadata-Version: 2.4
+Name: diskmelts
+Version: 2.1
+Summary: Machine-learning Enabled Line fitting Tool for Spectra of protoplanetary disks
+Author: Chengyan Xie, Dingshan Deng
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/wddlx/DiskMELTS
+Project-URL: Documentation, https://diskmelts.readthedocs.io/en/latest/
+Project-URL: Repository, https://github.com/wddlx/DiskMELTS
+Project-URL: Issues, https://github.com/wddlx/DiskMELTS/issues
+Keywords: astronomy,protoplanetary disks,JWST,spectral fitting,machine learning
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: numpy<2,>=1.26; sys_platform == "darwin" and platform_machine == "x86_64"
+Requires-Dist: numpy; sys_platform != "darwin" or platform_machine != "x86_64"
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Provides-Extra: io
+Requires-Dist: astropy; extra == "io"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: myst-parser; extra == "dev"
+Requires-Dist: sphinx-design; extra == "dev"
+Requires-Dist: nbsphinx; extra == "dev"
+Requires-Dist: nbsphinx-link; extra == "dev"
+Provides-Extra: notebooks
+Requires-Dist: jupyterlab; extra == "notebooks"
+Requires-Dist: ipykernel; extra == "notebooks"
+Dynamic: license-file
+
+# DiskMELTS
+
+DiskMELTS (Machine-learning Enabled Line fitting Tool for Spectra) is a
+package for continuum subtraction and fitting molecular emission in JWST
+mid-infrared spectra of protoplanetary disks. Its fitting workflow loads
+pretrained molecular surrogate models and retrieves temperature (`T`), column
+density (`logN`), and emitting area scaling (`A`) from observed spectra.
+
+**Documentation:** [diskmelts.readthedocs.io](https://diskmelts.readthedocs.io/en/latest/)
+
+## Installation
+
+Requires Python 3.9 or newer. Once the package is published to PyPI, install
+it from any directory without cloning this repository:
+
+```bash
+python -m pip install diskmelts
+# Add [io] for FITS input, or [io,notebooks] for JupyterLab.
+```
+
+Until the first PyPI release, install directly from GitHub without a clone:
+
+```bash
+python -m pip install "diskmelts[io] @ git+https://github.com/wddlx/DiskMELTS.git"
+```
+
+The package includes the production checkpoints and continuum reference tables.
+Full slab grids for training and direct-grid fitting are separate downloads;
+pass their local path as `grid_root`. See the
+[installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html)
+for details.
+
+### Development checkout (macOS, Linux, Windows)
+
+From the repository root, use a native Python 3.10 or 3.11 interpreter to
+create a virtual environment. For FITS input and the example notebooks:
+
+```bash
+python3.11 -m venv .venv
+.venv/bin/python -m pip install -e ".[io,notebooks]"
+.venv/bin/python -c "import diskmelts; print(diskmelts.__name__)"
+```
+
+Use `python3.10` if that is the native Python available on your machine.
+For core fitting and CSV/array inputs only, replace the install command with
+`.venv/bin/python -m pip install -e .`. See the
+[installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html) for Windows commands.
+
+### Conda or Mamba
+
+The YAML files use Conda only for Python and pip; pip installs the package and
+its declared dependencies. Choose one from the repository root:
+
+| File | Contents |
+| --- | --- |
+| `environment.yaml` | Core package |
+| `environment-notebooks.yaml` | Core package, FITS support, JupyterLab |
+| `environment-dev.yaml` | Notebook environment, tests, documentation tools |
+
+For the notebook setup, run `mamba env create --file environment-notebooks.yaml`
+then `conda activate diskmelts-notebooks`. `conda env create --file` works with
+the same files when using a current Conda release. On Apple Silicon, use a
+native `osx-arm64` installation such as Miniforge; an older Intel Conda can
+still spend a long time solving even these smaller files.
+
+## Runtime dependencies
+
+| Package | Purpose |
+|---|---|
+| `torch` | Pretrained model inference |
+| `numpy` | Array operations |
+| `pandas` | CSV I/O |
+| `scipy` | L-BFGS-B optimizer, NNLS, Sobol sampling |
+| `scikit-learn` | Model scaling and PCA metadata |
+| `matplotlib` | Plotting |
+
+## Continuum subtraction
+
+Try the [continuum subtraction notebook](https://github.com/wddlx/DiskMELTS/blob/main/notebooks/Example_Consub.ipynb)
+with the included raw Upper Sco J16120505 spectrum. It demonstrates the
+five-array result and a plot; change `RAW_CSV` to another file in
+[`Realobs_data/Raw_data/`](https://github.com/wddlx/DiskMELTS/tree/main/Realobs_data/Raw_data) to process another source.
+
+For a CSV with `wave,flux,err` columns (wavelength in µm and flux/error in the
+same units):
+
+```python
+import diskmelts
+
+wav, flux, error = diskmelts.consub.read_spectrum("raw_spectrum.csv")
+wav, consub, err, cont, contOrig = diskmelts.consub.calculate(
+    wav, flux, error, preset="ttauri", exclude=[[12, 13]],
+)
+fig = diskmelts.consub.plot(
+    wav, consub, err, cont, contOrig, ranges=[(5, 12), (12, 25)], savedir=None,
+)
+```
+
+`calculate()` returns five NumPy arrays. `plot()` displays the raw spectrum,
+continuum, and residual; `savedir="figures/consub"` also writes `continuum.png`.
+Its `error` and `contOrig` inputs may be `None`.
+
+Presets are `water`, `ttauri`, `carbon_rich`, and `carbon_extended`.
+Use `preset=None, linefreefile="windows.csv"` for custom `xmin,xmax` windows.
+With `preset=None, linefreefile=None` (or `""`), fitting uses all nonexcluded
+pixels and skips the line-free correction, so `cont` equals `contOrig`.
+Reference tables are bundled; normal continuum subtraction needs no model grids.
+
+The private `0-Consub/` experiment directory is excluded from Git and is not
+required by the installed package. Its runtime code and reference tables are
+maintained under `src/diskmelts/consub/`.
+The distributed tests in `tests/` exercise the installed continuum API and
+bundled references without that private directory.
+
+Returned `err` represents measurement/noise error, not correlated continuum
+uncertainty. Broad excluded intervals require inspection. See the
+[continuum guide](https://diskmelts.readthedocs.io/en/latest/continuum.html) for presets, regional box sizes,
+special regions, FITS input, saving CSVs, and uncertainty diagnostics.
+
+## Quick fitting example
+
+```python
+from diskmelts import load_fitting_models, load_observed_spectrum, fit_stage
+
+pretrained = load_fitting_models(['H2O'])
+
+obs_wav, obs_flux = load_observed_spectrum(
+    'Realobs_data/Consub_data/j16120505_v9.0_contsub_RVcorr.csv'
+)
+
+fit = fit_stage(
+    obs_wav,
+    obs_flux,
+    molecule='H2O',
+    wavelength_range=(11.0, 19.0),
+    pretrained=pretrained,
+    fit_ranges=[(11.0, 12.0), (16.5, 18.5)],
+    distance_pc=122.5,
+    n_samples=20000,
+    n_refine=32,
+    n_top=20,
+    sigma=0.001,
+)
+
+print(fit['params'])
+```
+
+You can also read spectra with your own code. DiskMELTS only requires
+one-dimensional `obs_wav` and `obs_flux` arrays.
+
+For a complete staged fit-and-subtract workflow from a checkout, edit and run:
+
+```bash
+python examples/dev_v2_realobs.py
+```
+
+The v2 fitting API is `load_fitting_models`, `fit_stage`, `fit_observation`, and
+`plot_saved_observation`. The production checkpoints are packaged under
+`src/diskmelts/models/` and included in the wheel. Model fitting requires no
+`Model_grids/` or `Pretrain_grid/` directory. The model metadata, including
+PCA counts and network layers, are in `diskmelts.MODEL_SPECS` and checked when
+loading. The checkpoint flux convention is 1 au² at 140 pc; `distance_pc`
+sets the source distance and makes the returned emitting area physical.
+The [fitting notebook](https://github.com/wddlx/DiskMELTS/blob/main/notebooks/Example_Fitting.ipynb) requires 13C12CH2 to
+be no hotter than C2H2 and gives them the same emitting area. It ties 13CO2
+to CO2 in both temperature and area. Set
+`isotopologue_groups`, `Tshare` (`free`, `equal`, or `less`), and `Ashare` in a
+joint stage to choose those constraints. See the
+[fitting guide](https://diskmelts.readthedocs.io/en/latest/quickstart.html) for examples.
+
+For an optional fit directly from slab grids, use `fit_grid_stage` or
+`fit_observation_grids` and supply `grid_root='Model_grids'` explicitly. This
+separate method does require the full local grids. See the
+[quick start](https://diskmelts.readthedocs.io/en/latest/quickstart.html) for both workflows and saved-result
+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
+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
+under `Model_grids/<molecule>/`. The workflows create or reuse the corresponding
+pretraining CSV under `Pretrain_grid/`.
+
+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`.
+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:
+
+```bash
+DISKMELTS_MOLECULES=13C12CH2,C2HD,CO17O,CO18O python examples/dev_v2_pt_validation.py
+```
+
+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
+`run_H2O`, `run_Cmol`, and `run_rarer` switches select which groups run.
+
+## Forward model convention
+
+```text
+flux(T, logN, A, d) = A * (140 pc / d)^2 * peak(T, logN) * shape(T, logN)
+```
+
+Each molecule has two pretrained MLPs:
+
+- `net_shape`: `(T, logN)` to PCA coefficients of the peak-normalized spectral shape
+- `net_peak`: `(T, logN)` to `log10(peak flux)` in Jy
+
+The linear amplitude `A` is solved analytically with NNLS or bounded least
+squares after the nonlinear `(T, logN)` search.
+
+## Contributors
+
+- Chengyan Xie (University of Arizona)
+- Dingshan Deng (University of Arizona)

diskmelts-2.1/README.md

@@ -0,0 +1,223 @@
+# DiskMELTS
+
+DiskMELTS (Machine-learning Enabled Line fitting Tool for Spectra) is a
+package for continuum subtraction and fitting molecular emission in JWST
+mid-infrared spectra of protoplanetary disks. Its fitting workflow loads
+pretrained molecular surrogate models and retrieves temperature (`T`), column
+density (`logN`), and emitting area scaling (`A`) from observed spectra.
+
+**Documentation:** [diskmelts.readthedocs.io](https://diskmelts.readthedocs.io/en/latest/)
+
+## Installation
+
+Requires Python 3.9 or newer. Once the package is published to PyPI, install
+it from any directory without cloning this repository:
+
+```bash
+python -m pip install diskmelts
+# Add [io] for FITS input, or [io,notebooks] for JupyterLab.
+```
+
+Until the first PyPI release, install directly from GitHub without a clone:
+
+```bash
+python -m pip install "diskmelts[io] @ git+https://github.com/wddlx/DiskMELTS.git"
+```
+
+The package includes the production checkpoints and continuum reference tables.
+Full slab grids for training and direct-grid fitting are separate downloads;
+pass their local path as `grid_root`. See the
+[installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html)
+for details.
+
+### Development checkout (macOS, Linux, Windows)
+
+From the repository root, use a native Python 3.10 or 3.11 interpreter to
+create a virtual environment. For FITS input and the example notebooks:
+
+```bash
+python3.11 -m venv .venv
+.venv/bin/python -m pip install -e ".[io,notebooks]"
+.venv/bin/python -c "import diskmelts; print(diskmelts.__name__)"
+```
+
+Use `python3.10` if that is the native Python available on your machine.
+For core fitting and CSV/array inputs only, replace the install command with
+`.venv/bin/python -m pip install -e .`. See the
+[installation guide](https://diskmelts.readthedocs.io/en/latest/installation.html) for Windows commands.
+
+### Conda or Mamba
+
+The YAML files use Conda only for Python and pip; pip installs the package and
+its declared dependencies. Choose one from the repository root:
+
+| File | Contents |
+| --- | --- |
+| `environment.yaml` | Core package |
+| `environment-notebooks.yaml` | Core package, FITS support, JupyterLab |
+| `environment-dev.yaml` | Notebook environment, tests, documentation tools |
+
+For the notebook setup, run `mamba env create --file environment-notebooks.yaml`
+then `conda activate diskmelts-notebooks`. `conda env create --file` works with
+the same files when using a current Conda release. On Apple Silicon, use a
+native `osx-arm64` installation such as Miniforge; an older Intel Conda can
+still spend a long time solving even these smaller files.
+
+## Runtime dependencies
+
+| Package | Purpose |
+|---|---|
+| `torch` | Pretrained model inference |
+| `numpy` | Array operations |
+| `pandas` | CSV I/O |
+| `scipy` | L-BFGS-B optimizer, NNLS, Sobol sampling |
+| `scikit-learn` | Model scaling and PCA metadata |
+| `matplotlib` | Plotting |
+
+## Continuum subtraction
+
+Try the [continuum subtraction notebook](https://github.com/wddlx/DiskMELTS/blob/main/notebooks/Example_Consub.ipynb)
+with the included raw Upper Sco J16120505 spectrum. It demonstrates the
+five-array result and a plot; change `RAW_CSV` to another file in
+[`Realobs_data/Raw_data/`](https://github.com/wddlx/DiskMELTS/tree/main/Realobs_data/Raw_data) to process another source.
+
+For a CSV with `wave,flux,err` columns (wavelength in µm and flux/error in the
+same units):
+
+```python
+import diskmelts
+
+wav, flux, error = diskmelts.consub.read_spectrum("raw_spectrum.csv")
+wav, consub, err, cont, contOrig = diskmelts.consub.calculate(
+    wav, flux, error, preset="ttauri", exclude=[[12, 13]],
+)
+fig = diskmelts.consub.plot(
+    wav, consub, err, cont, contOrig, ranges=[(5, 12), (12, 25)], savedir=None,
+)
+```
+
+`calculate()` returns five NumPy arrays. `plot()` displays the raw spectrum,
+continuum, and residual; `savedir="figures/consub"` also writes `continuum.png`.
+Its `error` and `contOrig` inputs may be `None`.
+
+Presets are `water`, `ttauri`, `carbon_rich`, and `carbon_extended`.
+Use `preset=None, linefreefile="windows.csv"` for custom `xmin,xmax` windows.
+With `preset=None, linefreefile=None` (or `""`), fitting uses all nonexcluded
+pixels and skips the line-free correction, so `cont` equals `contOrig`.
+Reference tables are bundled; normal continuum subtraction needs no model grids.
+
+The private `0-Consub/` experiment directory is excluded from Git and is not
+required by the installed package. Its runtime code and reference tables are
+maintained under `src/diskmelts/consub/`.
+The distributed tests in `tests/` exercise the installed continuum API and
+bundled references without that private directory.
+
+Returned `err` represents measurement/noise error, not correlated continuum
+uncertainty. Broad excluded intervals require inspection. See the
+[continuum guide](https://diskmelts.readthedocs.io/en/latest/continuum.html) for presets, regional box sizes,
+special regions, FITS input, saving CSVs, and uncertainty diagnostics.
+
+## Quick fitting example
+
+```python
+from diskmelts import load_fitting_models, load_observed_spectrum, fit_stage
+
+pretrained = load_fitting_models(['H2O'])
+
+obs_wav, obs_flux = load_observed_spectrum(
+    'Realobs_data/Consub_data/j16120505_v9.0_contsub_RVcorr.csv'
+)
+
+fit = fit_stage(
+    obs_wav,
+    obs_flux,
+    molecule='H2O',
+    wavelength_range=(11.0, 19.0),
+    pretrained=pretrained,
+    fit_ranges=[(11.0, 12.0), (16.5, 18.5)],
+    distance_pc=122.5,
+    n_samples=20000,
+    n_refine=32,
+    n_top=20,
+    sigma=0.001,
+)
+
+print(fit['params'])
+```
+
+You can also read spectra with your own code. DiskMELTS only requires
+one-dimensional `obs_wav` and `obs_flux` arrays.
+
+For a complete staged fit-and-subtract workflow from a checkout, edit and run:
+
+```bash
+python examples/dev_v2_realobs.py
+```
+
+The v2 fitting API is `load_fitting_models`, `fit_stage`, `fit_observation`, and
+`plot_saved_observation`. The production checkpoints are packaged under
+`src/diskmelts/models/` and included in the wheel. Model fitting requires no
+`Model_grids/` or `Pretrain_grid/` directory. The model metadata, including
+PCA counts and network layers, are in `diskmelts.MODEL_SPECS` and checked when
+loading. The checkpoint flux convention is 1 au² at 140 pc; `distance_pc`
+sets the source distance and makes the returned emitting area physical.
+The [fitting notebook](https://github.com/wddlx/DiskMELTS/blob/main/notebooks/Example_Fitting.ipynb) requires 13C12CH2 to
+be no hotter than C2H2 and gives them the same emitting area. It ties 13CO2
+to CO2 in both temperature and area. Set
+`isotopologue_groups`, `Tshare` (`free`, `equal`, or `less`), and `Ashare` in a
+joint stage to choose those constraints. See the
+[fitting guide](https://diskmelts.readthedocs.io/en/latest/quickstart.html) for examples.
+
+For an optional fit directly from slab grids, use `fit_grid_stage` or
+`fit_observation_grids` and supply `grid_root='Model_grids'` explicitly. This
+separate method does require the full local grids. See the
+[quick start](https://diskmelts.readthedocs.io/en/latest/quickstart.html) for both workflows and saved-result
+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
+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
+under `Model_grids/<molecule>/`. The workflows create or reuse the corresponding
+pretraining CSV under `Pretrain_grid/`.
+
+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`.
+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:
+
+```bash
+DISKMELTS_MOLECULES=13C12CH2,C2HD,CO17O,CO18O python examples/dev_v2_pt_validation.py
+```
+
+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
+`run_H2O`, `run_Cmol`, and `run_rarer` switches select which groups run.
+
+## Forward model convention
+
+```text
+flux(T, logN, A, d) = A * (140 pc / d)^2 * peak(T, logN) * shape(T, logN)
+```
+
+Each molecule has two pretrained MLPs:
+
+- `net_shape`: `(T, logN)` to PCA coefficients of the peak-normalized spectral shape
+- `net_peak`: `(T, logN)` to `log10(peak flux)` in Jy
+
+The linear amplitude `A` is solved analytically with NNLS or bounded least
+squares after the nonlinear `(T, logN)` search.
+
+## Contributors
+
+- Chengyan Xie (University of Arizona)
+- Dingshan Deng (University of Arizona)

diskmelts-2.1/pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["setuptools>=77.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "diskmelts"
+version = "2.1"
+description = "Machine-learning Enabled Line fitting Tool for Spectra of protoplanetary disks"
+readme = "README.md"
+requires-python = ">=3.9"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Chengyan Xie" },
+    { name = "Dingshan Deng" },
+]
+keywords = ["astronomy", "protoplanetary disks", "JWST", "spectral fitting", "machine learning"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Astronomy",
+]
+dependencies = [
+    "torch",
+    # Intel macOS wheels stop at PyTorch 2.2, whose NumPy bridge needs NumPy 1.x.
+    "numpy>=1.26,<2; sys_platform == 'darwin' and platform_machine == 'x86_64'",
+    "numpy; sys_platform != 'darwin' or platform_machine != 'x86_64'",
+    "pandas",
+    "scipy",
+    "scikit-learn",
+    "matplotlib",
+]
+
+[project.urls]
+Homepage = "https://github.com/wddlx/DiskMELTS"
+Documentation = "https://diskmelts.readthedocs.io/en/latest/"
+Repository = "https://github.com/wddlx/DiskMELTS"
+Issues = "https://github.com/wddlx/DiskMELTS/issues"
+
+[project.optional-dependencies]
+io = ["astropy"]
+dev = ["pytest", "sphinx", "furo", "myst-parser", "sphinx-design",
+       "nbsphinx", "nbsphinx-link"]
+notebooks = ["jupyterlab", "ipykernel"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+diskmelts = ["models/Trained_model/*/*.pt", "models/Trained_model/*/*.json",
+            "consub/*.csv", "consub/regions/*.csv", "consub/regions/*.json"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

diskmelts-2.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

diskmelts-2.1/src/diskmelts/__init__.py

@@ -0,0 +1,98 @@
+"""
+diskmelts — Machine-learning Enabled Line fitting Tool for Spectra
+
+A neural surrogate-assisted framework for retrieving molecular gas parameters
+(T, logN, A) from JWST mid-IR spectra of protoplanetary disks.
+"""
+
+from diskmelts.trainmodel import (
+    load_model_grid,
+    generate_pre_training_set,
+    pretrain_forward_model,
+    train_model_bank,
+    select_grid_holdout,
+    tune_pca_components,
+)
+from diskmelts.fitting import (
+    load_models,
+    load_model_bank,
+    generate_spectrum,
+    fit_nested,
+    fit_molecules,
+    load_observed_spectrum,
+    save_fit_outputs,
+    detect_stage_molecules,
+    save_running_spectrum,
+    print_fit_params,
+    save_fitted_comparison,
+)
+from diskmelts.validation import (
+    validate_nt,
+    validate_nt_holdout,
+    validate_full,
+)
+from diskmelts.plotting import (
+    plot_fit,
+    plot_validation,
+    plot_validation_split,
+    plot_bank_reconstruction,
+)
+from diskmelts.v2_fitting import (
+    MODEL_SPECS,
+    load_fitting_models,
+    fit_stage,
+    fit_observation,
+)
+from diskmelts.v2_grid_fitting import (
+    fit_grid_stage,
+    fit_observation_grids,
+    combine_grid_uncertainty,
+)
+from diskmelts.v2_read_plot import (
+    read_stage_result,
+    plot_saved_observation,
+)
+from diskmelts.v2_paper_comparison import plot_literature_comparisons
+from diskmelts import consub
+
+__all__ = [
+    "consub",
+    "MODEL_SPECS",
+    "load_fitting_models",
+    "fit_stage",
+    "fit_observation",
+    "fit_grid_stage",
+    "fit_observation_grids",
+    "combine_grid_uncertainty",
+    "read_stage_result",
+    "plot_saved_observation",
+    "plot_literature_comparisons",
+    # trainmodel
+    "load_model_grid",
+    "generate_pre_training_set",
+    "pretrain_forward_model",
+    "train_model_bank",
+    "select_grid_holdout",
+    "tune_pca_components",
+    # fitting
+    "load_models",
+    "load_model_bank",
+    "generate_spectrum",
+    "fit_nested",
+    "fit_molecules",
+    "load_observed_spectrum",
+    "save_fit_outputs",
+    "detect_stage_molecules",
+    "save_running_spectrum",
+    "print_fit_params",
+    "save_fitted_comparison",
+    # validation
+    "validate_nt",
+    "validate_nt_holdout",
+    "validate_full",
+    # plotting
+    "plot_fit",
+    "plot_validation",
+    "plot_validation_split",
+    "plot_bank_reconstruction",
+]

diskmelts-2.1/src/diskmelts/consub/__init__.py

@@ -0,0 +1,15 @@
+"""Continuum subtraction and plotting for disk spectra.
+
+Use ``calculate`` to return five arrays and ``plot`` to display or save them.
+The diagnostic DataFrame interface remains available as ``subtract_continuum``.
+"""
+from ._core import (
+    generate_line_free_regions, load_regions, read_spectrum,
+    subtract_continuum, plot_consub, save_consub,
+)
+from ._api import calculate, plot
+
+__all__ = [
+    "calculate", "plot", "read_spectrum", "load_regions",
+    "generate_line_free_regions", "subtract_continuum", "plot_consub", "save_consub",
+]