Implement cue+prospectorv2

.github/workflows/release.yml

@@ -0,0 +1,64 @@
+name: Release
+on:
+  release:
+    types: [created]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_wheels:
+    name: Build wheel for ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - "ubuntu-22.04"
+          - "macos-14"
+    steps:
+      - uses: pypa/cibuildwheel@v2.16.5
+      - uses: actions/upload-artifact@v4
+        with:
+          name: binary-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+            python -m pip install -U pip
+            python -m pip install -U build twine
+      - name: Build sdist
+        run: |
+          python -m pip install -U pip
+          python -m build --sdist .
+      - uses: actions/upload-artifact@v4
+        with:
+          path: dist/*.tar.gz
+
+  publish:
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fsps
+    permissions:
+      id-token: write
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@v1.8.12

.github/workflows/tests.yml

@@ -1,9 +1,9 @@
 name: Tests
 on:
   push:
-    branches: [main]
+    branches: [main, v2.0]
   pull_request:
-    branches: [main]
+    branches: [main, v2.0]
 
 jobs:
   tests:
@@ -12,29 +12,30 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.9", "3.11"]
         os: [ubuntu-latest, macos-latest]
     steps:
       - name: Clone the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Clone fsps
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: cconroy20/fsps
           path: fsps
       - name: Install dependencies
         run: |
           python -m pip install -U pip pytest
           python -m pip install -U fsps astro-sedpy astropy
-          python -m pip install -U six dynesty
+          python -m pip install -U scipy
+          python -m pip install -U dynesty
           python -m pip install .
         env:
           SPS_HOME: ${{ github.workspace }}/fsps
       - name: Run tests
-        run: python -m pytest --durations=0 --maxfail=1 -vs tests/
+        run: python -m pytest --durations=0 --maxfail=1 -W ignore::DeprecationWarning --ignore tests/misc/ -vs tests/
         env:
           SPS_HOME: ${{ github.workspace }}/fsps

.readthedocs.yaml

@@ -1,8 +1,14 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 sphinx:
    configuration: doc/conf.py
 
 python:
-  version: 3.7
   install:
     - requirements: doc/requirements.txt
     - method: pip

AUTHORS.rst

@@ -1,26 +1 @@
-Author:
-
-- `Ben Johnson (Harvard) <https://github.com/bd-j>`_
-
-Direct contributions to the code base:
-
-- `Gabe Brammer <https://github.com/gbrammer>`_
-- `James Guillochon <https://github.com/guillochon>`_
-- `Joel Leja <https://github.com/jrleja>`_
-- `John Moustakas <https://github.com/moustakas>`_
-- `Josh Speagle <https://github.com/joshspeagle>`_
-
-Comments, corrections & suggestions:
-
-- Antara Basu-Zych
-- Kevin Bundy
-- Phill Cargile
-- Charlie Conroy
-- Johnny Greco
-- Song Huang
-- Gourav Khullar
-- Sidney Lower
-- Dylan Nelson
-- Imad Pasha
-- Dan Weisz
-- Tom Zick
+The list of contributors can be found `on GitHub <https://github.com/bd-j/prospector/graphs/contributors>`_.

CHANGELOG.rst

@@ -1,5 +1,26 @@
 .. :changelog:
 
+v1.4.0 (2024-07-06)
++++++++++++++++++++
+- Adds the stochastic SFH hyper-prior courtesy @jwan22
+- Adds an explicit check of any provided emission line names and fixes a bug
+  when multiple emission lines are ignored
+
+Last release before v2.0
+
+`Full Changelog <https://github.com/bd-j/prospector/compare/v1.3.0...v1.4.0>`_
+
+
+v1.3.0 (2024-03-27)
++++++++++++++++++++
+- Adds the prospector-beta SFH priors and documentation courtesy @wangbingjie
+- Bugfixes in emission line masking, polynomial regularization, sfr_ratio
+  clipping (h/t @mjastro, @wangbingjie, @davidjsetton)
+- Documentation updates
+
+`Full Changelog <https://github.com/bd-j/prospector/compare/v1.2.0...v1.3.0>`_
+
+
 v1.2.0 (2022-12-31)
 +++++++++++++++++++
 
@@ -10,7 +31,7 @@ v1.2.0 (2022-12-31)
 - Fixes to the dynesty interface for dynesty >= 2.0 (h/t @mjastro)
 - Fix sign error in Powell minimization (h/t @blanton144)
 - Fix bugs in parameter template for emission line fitting.
-- numeropus documentation updates including nebular emission details.
+- numerous documentation updates including nebular emission details.
 
 
 v1.1.0 (2022-02-20)

README.md

@@ -1,21 +1,122 @@
 <img src="doc/_static/logo_name_kh.png" height=75/>  <!-- . -->
 ==========
 
+Version 2.0! (in progress)
+--------------------------
+
+This is a major refactor to allow for multiple datasets (i.e. multiple spectra)
+with different noise models and instrument parameters to constrain a single
+galaxy model.  Other updates may include cleaner stored outputs, interfaces with
+additional nested samplers, and improved tretments of smoothing.
+
+Work to do includes:
+
+- [x] Convert to/from old style observation dictionaries
+- [x] Put responsibility for Noise Models including outlier modeling in individual Observation instances
+- [x] Make predictions even when there is no fittable data (e.g. model spectra when fitting photometry only)
+- [x] Store Observation objects in HDF5, FITS, etc as structured arrays with metadata
+- [x] Catch (and handle) emission line marginalization if spectra overlap.
+- [x] Structured ndarray for output chains and lnlikehoods
+- [x] Update docs
+- [x] Update demo scripts
+- [x] Account for undersampled spectra via explicit rebinning.
+- [ ] Account for undersampled spectra via a square convolution in pixel space.
+- [x] Implement UltraNest and Nautilus backends
+- [x] Test i/o with structured arrays
+- [ ] Structured ndarray for derived parameters
+- [ ] Store samples of spectra, photometry, and mfrac (blobs)
+- [ ] Update notebooks
+- [ ] Update plotting module
+- [ ] Test multi-spectral calibration, smoothing, and noise modeling
+- [ ] Test smoothing accounting for library, instrumental & physical smoothing
+- [ ] Implement an emulator-based SpecModel class
+
+Nebular emission is computed using [`cuejax`](https://github.com/efburnham/cue), a jax-compatible version of [`cue`](https://github.com/yi-jia-li/cue) ([Li et al. 2024](https://ui.adsabs.harvard.edu/abs/2025ApJ...986....9L/abstract)). 
+
+To install the `cuejax` version adapted to work with this branch of `prospector`:
+```bash
+git clone https://github.com/yi-jia-li/cue.git
+cd cue
+git checkout cuejax
+pip install .
+```
+
+The ionizing spectrum that powers the nebular emission can either be modeled as a 4-segment power-law or fixed to the spectrum of stellar populations ([example](https://github.com/yi-jia-li/prospector/tree/add_cue/demo/prospector+cue.ipynb)):
+```py
+from prospect.models.templates import TemplateLibrary
+TemplateLibrary["cue_nebular"] # Uses a power-law ionizing spectrum
+TemplateLibrary["cue_stellar_nebular"] # Uses the stellar ionizing spectrum
+```
+**Note:** Dust emission is not yet fully implemented for compatibility with nebular emission.
+
+Migration from < v2.0
+---------------------
+
+For many users the primary difference from v1.X will be that the data to predict
+and fit a model to is now specified as a list of
+`prospect.observation.Observation()` instances, instead of a single 'obs'
+dictionary.  There is a new convenience method to convert from the old 'obs'
+dictionary format to the new specification. This can be used with existing
+scripts as follows:
+
+```py
+# old build_obs function giving a dictionary
+obs_dict = build_obs(**run_params)
+# get convenience method
+from prospect.observation import from_oldstyle
+# make a new list of Observation instances from the dictionary
+observations = from_oldstyle(obs_dict)
+# verify and prepare for fitting; similar to 'obsutils.fix_obs()'
+[obs.rectify() for obs in observations]
+print(observations)
+```
+
+It is recommended to do the conversion within the `build_obs()` method, if
+possible. This list of observations is then supplied to `fit_model`.  Because
+noise models are now attached explicitly to each observation, they do not need
+to be generated separately or supplied to `fit_model()`, which no longer accepts
+a `noise=` argument.  For outlier models, the the noise model should be
+instantiated with names for the outlier model that correspond to fixed or free
+parameters of the model.
+
+```py
+from prospect.fitting import fit_model
+output = fit_model(observations, model, sps, **config)
+```
+
+Another change is that spectral response functions (i.e. calibration vectors)
+are now handled by specialized sub-classes of these `Observation` classes.  See
+the [spectroscopy docs](doc/spectra.rst) for details.
+
+The interface to `write_model` has been changed and simplified.  See
+[usage](doc/usage.rst) for details.
+
+Finally, the output chain or samples is now stored as a structured array, where
+each row corresponds to a sample, and each column is a parameter (possibly
+multidimensional).  Additional information (such as sample weights, likelihoods,
+and poster probabilities) are stored as additional datasets in the output.  The
+`unstructured_chain` dataset of the output contains an old-style simple
+`numpy.ndarray` of shape `(nsample, ndim)`
+
+
+Purpose
+-------
+
 [![Docs](https://readthedocs.org/projects/prospect/badge/?version=latest)](https://readthedocs.org/projects/prospect/badge/?version=latest)
+[![Tests](https://github.com/bd-j/prospector/workflows/Tests/badge.svg)](https://github.com/bd-j/prospector/actions?query=workflow%3ATests)
 [![arXiv](https://img.shields.io/badge/arXiv-2012.01426-b31b1b.svg)](https://arxiv.org/abs/2012.01426)
 [![LICENSE](https://img.shields.io/badge/license-MIT-blue.svg?style=flat)](https://github.com/bd-j/prospector/blob/main/LICENSE)
 
-Purpose
--------
+
 Conduct principled inference of stellar population properties from photometric
 and/or spectroscopic data.  Prospector allows you to:
 
 * Infer high-dimensional stellar population properties using parametric or
   highly flexible SFHs (with nested or ensemble Monte Carlo sampling)
 
-* Combine photometric and spectroscopic data from the UV to Far-IR rigorously
-  using a flexible spectroscopic calibration model and forward modeling many
-  aspects of spectroscopic data analysis.
+* Combine multiple photometric, spectroscopic, and/or line flux datasets from
+  the UV to Far-IR rigorously using a flexible spectroscopic calibration model
+  and forward modeling many aspects of spectroscopic data analysis.
 
 Read the [documentation](http://prospect.readthedocs.io/en/latest/) and the
 code [paper](https://ui.adsabs.harvard.edu/abs/2021ApJS..254...22J/abstract).

conda_install.sh

@@ -9,10 +9,9 @@ cd $CODEDIR
 git clone https://github.com/cconroy20/fsps.git
 export SPS_HOME="$PWD/fsps"
 
-# Create and activate environment (named 'prospector')
 git clone https://github.com/bd-j/prospector.git
 cd prospector
-conda env create -f environment.yml
+conda env create -f environment.yml -n prospector
 conda activate prospector
 python -m pip install .