Migrate SPISEA to synphot

.cursor/rules/spisea-synphot-conda.mdc

@@ -0,0 +1,12 @@
+---
+description: Use the spisea-synphot conda environment for all Python, pip, and tests
+alwaysApply: true
+---
+
+# Conda environment: `spisea-synphot`
+
+For this repository, use the **`spisea-synphot`** conda environment for every shell command that needs Python, `pip`, `pytest`, or project tooling.
+
+- Prefer: `conda run -n spisea-synphot <command>` (e.g. `conda run -n spisea-synphot python -m pytest ...`) so the correct interpreter is used even in non-interactive shells.
+- Alternatively: `source "$(conda info --base)/etc/profile.d/conda.sh" && conda activate spisea-synphot` then run commands as usual.
+- Do not assume `python` or `pip` on `PATH` without activating that environment; do not use other envs (e.g. a generic `astro` env) for SPISEA work unless the user says otherwise.

Dockerfile

@@ -4,13 +4,14 @@ RUN apt-get update && apt-get upgrade -y && apt-get clean
 
 RUN apt-get install -y curl python3 python3-dev python3-distutils python3-pip git wget
 
-RUN pip3 install astropy pysynphot scipy numpy matplotlib 
+# synphot + stsynphot replace deprecated pysynphot; set PYSYN_CDBS to your CDBS tree (see below).
+RUN pip3 install astropy synphot stsynphot scipy numpy matplotlib
 
 RUN ln -s /usr/bin/python3 /usr/bin/python
 
 RUN export PYTHONPATH=$PYTHONPATH:/SPISEA
 
-RUN cd / && git clone https://github.com/astropy/SPISEA.git
+RUN git clone https://github.com/MovingUniverseLab/spisea.git /SPISEA
 
 ENV PYTHONPATH "${PYTHONPATH}:/SPISEA/"
 
@@ -32,6 +33,7 @@ WORKDIR /cdbs/models
 RUN wget http://astro.berkeley.edu/~jlu/spisea/spisea_models.tar.gz && wget http://astro.berkeley.edu/~jlu/spisea/spisea_cdbs.tar.gz
 RUN tar -xvf spisea_cdbs.tar.gz && tar -xvf spisea_models.tar.gz && rm spisea_cdbs.tar.gz && rm spisea_models.tar.gz
 
+# stsynphot reads throughput/model grids from this path (same convention as legacy pysynphot).
 ENV PYSYN_CDBS /cdbs/models/cdbs/
 ENV SPISEA_MODELS /cdbs/models
 

README.md

@@ -20,10 +20,10 @@ Here is a brief list of things that SPISEA can do:
 * make a star cluster at any age with an unusual IMF and unresolved multiplicity
 * make a spectrum of a star cluster in integrated light
 
-See [documentation](https://spisea.readthedocs.io/en/latest/) for
+See [documentation](https://github.com/MovingUniverseLab/spisea/tree/main/docs) for
 details on installing and running SPISEA. We also provide jupyter notebooks with a 
-[quick-start tutorial](https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb)
-and [additional examples](https://github.com/astropy/SPISEA/tree/main/docs/paper_examples)
+[quick-start tutorial](https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb)
+and [additional examples](https://github.com/MovingUniverseLab/spisea/tree/main/docs/paper_examples)
 demonstrating how to use SPISEA.
 
 If you use SPISEA in your research, please cite [Hosek et al. (2020)](https://ui.adsabs.harvard.edu/abs/2020arXiv200606691H/abstract).
@@ -32,7 +32,7 @@ If you use SPISEA in your research, please cite [Hosek et al. (2020)](https://ui
 SPISEA is actively supported and is growing in functionality, and
 subsequently has had several updates since its
 initial release. See the
-[main documentation page](https://spisea.readthedocs.io/en/latest/)
+[main documentation page](https://github.com/MovingUniverseLab/spisea/blob/main/docs/index.rst)
 for the change log describing the updates in each release.
 
 ## Contributions
@@ -42,7 +42,7 @@ own fork of the repository, make their changes, and then submit a pull
 request to the "dev" branch.
 
 All contributions will be acknowledged on the
-[contributors page](https://spisea.readthedocs.io/en/dev/contributors.html#contributors) (with permission).
+[contributors page](https://github.com/MovingUniverseLab/spisea/blob/main/docs/contributors.rst) (with permission).
 Contributors with features used in code releases will be co-authors in future SPISEA software papers.
 
 ## License

docs/Quick_Start_Make_Cluster_w_BDs.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This is a quick start guide to making a synthetic cluster using the SPISEA package, with the recent addition of brown dwarf capabilities. The cluster is constructed using a user-specified isochrone and initial mass function (IMF). Detailed documentation is provided in the ReadtheDocs page (https://spisea.readthedocs.io/en/latest/index.html).\n",
+    "This is a quick start guide to making a synthetic cluster using the SPISEA package, with the recent addition of brown dwarf capabilities. The cluster is constructed using a user-specified isochrone and initial mass function (IMF). Detailed documentation is available at https://github.com/MovingUniverseLab/spisea/tree/main/docs.\n",
     "\n",
     "Before starting this tutorial, it is assumed that SPISEA has been installed and the user's python path has been altered to include the SPISEA top-level directory"
    ]

docs/add_atmo_models.rst

@@ -3,7 +3,7 @@
 ========================================
 Adding Atmosphere Models
 ========================================
-Stellar atmosphere grids are implemented in SPISEA using STSci's `pysynphot <https://pysynphot.readthedocs.io/en/latest/index.html>`_ and CDBS infrastructure.
+Stellar atmosphere grids are implemented in SPISEA using STSci's `stsynphot <https://stsynphot.readthedocs.io/>`_ / `synphot <https://synphot.readthedocs.io/>`_ stack and CDBS infrastructure.
 Adding a new atmosphere grid involves saving the models in a new
 sub-directory under your ``PYSYN_CDBS`` directory and creating a new
 function in ``atmospheres.py`` to access those files.
@@ -33,9 +33,9 @@ a template for how to make a new one. Some general notes:
   reflected in the 'INDEX' column of catalog.fits.
 
 * For the atmospheres, use units of angstroms for the wavelength and
-  "FLAM" for flux ([erg/s/cm^2/A]; see `pysynphot docs
-  <https://pysynphot.readthedocs.io/en/latest/units.html>`_)
+  "FLAM" for flux ([erg/s/cm^2/A]; see `synphot docs
+  <https://synphot.readthedocs.io/en/latest/synphot/units.html>`_)
 
 More detailed documentation on this is coming soon. In the meantime, let us know on the  Github `issue tracker
-<https://github.com/astropy/SPISEA/issues>`_ if you'd like to
+<https://github.com/MovingUniverseLab/spisea/issues>`_ if you'd like to
 implement a new atmospheric model grid.

docs/add_evo_models.rst

@@ -9,7 +9,7 @@ below, you can implement your own evolution models into the SPISEA
 framework.
 
 If you have questions or run into problems, please raise an issue on
-our Github `issue tracker <https://github.com/astropy/SPISEA/issues>`_. If you are willing to
+our Github `issue tracker <https://github.com/MovingUniverseLab/spisea/issues>`_. If you are willing to
 have the new models you add be added to the SPISEA package and made
 available to the community, please fork or branch off of the
 development repository and then submit merge requests to add your
@@ -104,7 +104,7 @@ new models (e.g., new metallicities, etc).
 
 If the user needs to change the available age range for an existing
 model grid, please let us know via the  Github `issue tracker
-<https://github.com/astropy/SPISEA/issues>`_. 
+<https://github.com/MovingUniverseLab/spisea/issues>`_.
 
 
 Creating a New Model Grid
@@ -114,5 +114,5 @@ To create an entirely new model set, the user needs to define a new
 the appropriate directory structure in the
 ``$SPISEA_MODELS/evolution`` directory. Detailed documentation on
 this is coming soon. In the meantime, let us know on the  Github `issue tracker
-<https://github.com/astropy/SPISEA/issues>`_ if you'd like to
+<https://github.com/MovingUniverseLab/spisea/issues>`_ if you'd like to
 implement a new model set. 

docs/add_filters.rst

@@ -18,5 +18,5 @@ If the user wants to add new photometric filters to SPISEA, there are 4 main ste
      ensure the filter can be loaded properly.
 
 Additional documentation on this is coming soon. In the meantime, let us know on the  Github `issue tracker
-<https://github.com/astropy/SPISEA/issues>`_ if you'd like to
+<https://github.com/MovingUniverseLab/spisea/issues>`_ if you'd like to
 implement new photometric filters.

docs/atmo_models.rst

@@ -13,16 +13,16 @@ To call an atmosphere for a particular star, user must define the
 metallicity ([Z]), temperature (in K), and gravity (in cgs)::
 
   spectrum = atmo(metallicity=0, temperature=5800, gravity=4)
-  wave = spectrum.wave # Wavelength in Angstroms
-  flux = spectrum.flux # Flux in ergs s^-1 cm^-2 Angstrom^-1
-  (pysynphot Flam units)
+  from astropy import units
+  wave = spectrum.waveset.to(units.AA).value   # Wavelength in Angstroms
+  flux = spectrum(spectrum.waveset)  # Flux (synphot Quantity; typically FLAM)
 
 The atmosphere function is an input for the :ref:`isochrone_objects`,
 and will automatically be used to define the
 spectrum of each star in the isochrone model.
 
-PopStar uses the pysynphot framework to extract the model atmosphere,
-and the the output spectrum is a `pysynphot.Icat object <https://pysynphot.readthedocs.io/en/latest/ref_api.html#pysynphot.catalog.Icat>`_.
+PopStar uses the stsynphot/synphot stack to extract the model atmosphere,
+and the output spectrum is a synphot ``SourceSpectrum`` built from the CDBS grid via ``stsynphot.grid_to_spec``.
 
 Below is a table of atmosphere model grids currently supported by
 SPISEA. Note that the resolution column reports the original

docs/extinction.rst

@@ -8,14 +8,14 @@ The extinction law can be defined using the classes in ``spisea/reddening.py``.
   from spisea import reddening
   red_law = reddening.<redlaw_name>()
 
-SPISEA uses the pysynphot framework to define the extinction law.
-The output is a `pysynphot.reddening.CustomRedLaw
-<https://pysynphot.readthedocs.io/en/latest/ref_api.html#module-pysynphot.extinction>`_
-oject.
+SPISEA uses tabulated :math:`A_\lambda/A_{Ks}` curves. Reddening law classes inherit from
+``reddening.RedLawBase``, which subclasses synphot's ``ExtinctionCurve`` at :math:`A_{Ks}=1` mag
+(see ``synphot.reddening.etau_madau``). For arbitrary :math:`A_{Ks}` and wavelength sampling,
+use ``red_law.extinction_at`` (or ``reddening.RedLawBase.ExtinctionAtAKs``).
 The reddening law is reported in terms of A_lambda / A_Ks, and thus is normalized to A_Ks = 1.
 
 The red_law object is passed into the :ref:`isochrone_objects` in order to
-define the extinction for the stars. See the `Quick Start <https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
+define the extinction for the stars. See the `Quick Start <https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
 for an example.
 
 Available extinction laws:

docs/filters.rst

@@ -143,8 +143,8 @@ Example: ``'hipparcos,Hp'``
 
 **Hubble Space Telescope**
 
-HST filters are defined by their `pysynphot OBSMODE strings
-<https://pysynphot.readthedocs.io/en/latest/appendixb.html#pysynphot-appendixb>`_. These
+HST filters are defined by their `stsynphot / legacy OBSMODE strings
+<https://stsynphot.readthedocs.io/en/latest/stsynphot/obsmode.html>`_. These
 are defined in the ``cdbs/mtab/`` and ``cdbs/comp/`` directories.
 
 Example: ``'wfc3,ir,f125w'``
@@ -240,9 +240,9 @@ Example: ``'ps1, g'``
 
 **Roman Space Telescope**
 
-Roman Space Telescope WFI filters are defined by their `pysynphot
-OBSMODE strings
-<https://pysynphot.readthedocs.io/en/latest/appendixb.html#non-hst-filter-systems>`_.
+Roman Space Telescope WFI filters are defined by their stsynphot-style
+`OBSMODE strings
+<https://stsynphot.readthedocs.io/en/latest/stsynphot/obsmode.html>`_.
 These are defined in the ``cdbs/mtab/`` and ``cdbs/comp/``
 directories. Note that the 2021-07-16 version of these directories
 must be downloaded from from the `STScI reference atlases

docs/getting_started.rst

@@ -10,10 +10,10 @@ If you are downloading the code from scratch, please follow the
 instructions below. If you had already downloaded version 1 of the
 code and are switching to version 2, please see :ref:`version`. 
 
-SPISEA is hosted on `GitHub <https://github.com/astropy/SPISEA>`_.
+SPISEA is hosted on `GitHub <https://github.com/MovingUniverseLab/spisea>`_.
 To begin, clone the git repository in your desired code directory::
 
-   git clone https://github.com/astropy/SPISEA.git
+   git clone https://github.com/MovingUniverseLab/spisea.git
 
 The ``main`` branch contains the current release,
 while the ``dev`` branch is for code development.
@@ -28,7 +28,8 @@ Other dependencies:
 
 * python (>=3.7, < 3.12)
 * astropy
-* pysynphot
+* synphot
+* stsynphot
 * scipy
 * numpy (>= 1.17, < 2.0)
 * matplotlib
@@ -176,7 +177,7 @@ However, these can be safely ignored since SPISEA doesn't use those functionalit
 
 To further test your SPISEA install, try running the `Quick Start
 notebook
-<https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_.
+<https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_.
 It is also located in ``SPISEA/docs``.
 
 To test the full range of
@@ -223,8 +224,8 @@ Installation
 
 To create the container image, clone this repository and build the container::
 
-    git clone https://github.com/astropy/SPISEA.git
-    cd SPISEA
+    git clone https://github.com/MovingUniverseLab/spisea.git
+    cd spisea
     docker build -t spisea .
 
 Usage

docs/ifmr.rst

@@ -21,7 +21,7 @@ Compact objects are included in the output tables produced by
 * BH: phase = 103
 
 See `Quick Start Example
-<https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
+<https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
 for more examples of how to interact with the :ref:`cluster_objects`
 output.
 

docs/index.rst

@@ -29,7 +29,7 @@ Here is a brief list of things that SPISEA can do:
 
 * make a spectrum of a star cluster in integrated light
 
-SPISEA can be downloaded from `Github <https://github.com/astropy/SPISEA>`_. Please cite `Hosek et al. (2020) <https://ui.adsabs.harvard.edu/abs/2020arXiv200606691H/abstract>`_  if you use SPISEA in
+SPISEA can be downloaded from `Github <https://github.com/MovingUniverseLab/spisea>`_. Please cite `Hosek et al. (2020) <https://ui.adsabs.harvard.edu/abs/2020arXiv200606691H/abstract>`_  if you use SPISEA in
 your research. 
 
 Getting Started
@@ -164,9 +164,9 @@ Change Log
     operating system used
 
 2.1.10 (2023-06-01)
-  * Added support for Roman Space Telescope filters (via pysynphot)
+  * Added support for Roman Space Telescope filters (via stsynphot)
 
-    * Note: this requires the pysynphot ``cdbs/mtab`` and
+    * Note: this requires the ``cdbs/mtab`` and
       ``cdbs/comp/`` directories to be at least the 2021-07-16 version or later. See :ref:`getting_started` for how to download these files
 
 2.1.9 (2023-01-10)

docs/make_cluster.rst

@@ -51,7 +51,7 @@ has already been created::
 
 
 See `Quick Start Example
-<https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
+<https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
 for a detailed example for how to make different
 cluster sub-classes and interact with the resulting output.
 Here is a table from Hosek et al. 2020 that describes

docs/make_isochrone.rst

@@ -49,7 +49,7 @@ An example of making an IsochronePhot object::
 			    iso_dir=iso_dir)
 
 See `Quick Start Example
-<https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
+<https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
 for a detailed example showing how to interact with the isochrone
 object output. Here is a table from Hosek et al. 2020 that describes
 the values in the isochrone output table:

docs/more_examples.rst

@@ -6,7 +6,7 @@ Further Examples
 Additional Jupyter notebooks with tutorials to produce the plots shown
 in the SPISEA paper (`Hosek et al. (2020)
 <https://ui.adsabs.harvard.edu/abs/2020arXiv200606691H/abstract>`_) can be found `here
-<https://github.com/astropy/SPISEA/tree/main/docs/paper_examples>`_.
+<https://github.com/MovingUniverseLab/spisea/tree/main/docs/paper_examples>`_.
 
 Figure 2: HR-Diagrams with Different Evolution Models; CMDs with different Extinction Laws
 --------------------------------------------------------------------------------------------------------

docs/multiplicity.rst

@@ -30,7 +30,7 @@ represents the combined photometry of all stars within a given system.
 For most selected evolution models, the multiples are evolved as single stars.
 To evolve binaries (does not support higher order multiples), you should use one of the ``MultiplicityResolved`` classes
 and the ``COSMIC`` evolution model. 
-See the example jupyter notebook `Cluster_w_COSMIC.ipynb <https://github.com/astropy/SPISEA/blob/main/docs/Cluster_w_COSMIC.ipynb>`_ for an example.
+See the example jupyter notebook `Cluster_w_COSMIC.ipynb <https://github.com/MovingUniverseLab/spisea/blob/main/docs/Cluster_w_COSMIC.ipynb>`_ for an example.
 Note that currently COSMIC due to being external evolution is significantly slower than the other evolution options.
 
 

docs/quick_start.rst

@@ -5,7 +5,7 @@ Quick Start Guide
 ===================
 
 We provide a `jupyter notebook
-<https://github.com/astropy/SPISEA/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
+<https://github.com/MovingUniverseLab/spisea/blob/main/docs/Quick_Start_Make_Cluster.ipynb>`_
 as a Quick-Start Guide to demonstrate the steps required to simulate a cluster and interact
 with the resulting output. This guide shows you how to:
 

docs/requirements.txt

@@ -2,7 +2,8 @@ matplotlib
 numpy <= 1.24.4
 numpydoc
 astropy
-pysynphot
+synphot>=1.5
+stsynphot>=1.4
 scipy
 pandas
 setuptools<=81.0