non-code files merged

Author: mssiwek

.github/workflows/publish_to_pypi.yaml

@@ -0,0 +1,73 @@
+name: Build and publish Python distributions to PyPI
+on:
+  release:
+    types: [published]
+
+jobs:
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+        with:
+          python-version: 3.11
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.16.2
+        env:
+          # Skip CPython 3.6, 3.7, 3.8, 3.12, PyPy, 32-bit, and musl
+          CIBW_SKIP: "cp36-* cp37-* cp38-* cp312-* pp* *i686 *musllinux*"
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+    - name: git checkout repository main
+      uses: actions/checkout@v3
+
+    - name: check github reference for tags
+      run: |
+        echo "github.ref = ${{ github.ref }}, github.ref_type = ${{ github.ref_type }}"
+        echo "github.repository = ${{ github.repository }}, github.event_name = ${{ github.event_name }} "
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+
+    - name: Install pypa/build
+      run: python -m pip install build --user
+
+    - name: Build a source tarball
+      run: python -m build --sdist --outdir dist/ .
+
+    - uses: actions/upload-artifact@v3
+      with:
+        path: ./dist/*.tar.gz
+
+  pypi-publish:
+    needs: ['build_wheels', 'make_sdist']
+    environment: 'publish'
+
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v3
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: artifact/

.gitignore

@@ -120,7 +120,6 @@ output/*
 docs/source/apidoc_modules
 hostfile
 readthedocs.html
-data/
 notes.md
 minos_run_gen_lib_sams.sh
 cyutils.c
@@ -141,4 +140,4 @@ run_gen_lib_sams__*
 
 # Mac Desktop Services
 .DS_Store
-.history
+.history

CHANGELOG.md

@@ -1,68 +1,100 @@
 # Change Log
 
+
 ## Future (To-Do)
+
 * General
-    - [ ] Add fit/interpolated GW spectra from Chen19 into SAM modules.
-* Structures for comprehensive binary evolution / hardening modules
-    - [ ] a class-based structure allowing for modular hardening processes to be added/removed/modified easily.
-    - [ ] structures allowing for storing host-galaxy information (e.g. based on semi-analytic models, Illustris, observations, etc) that can be used for hardening calculations
-    - [ ] accretion rate models based on semi-analytic models, Illustris, observations, etc
+    * [ ] Add fit/interpolated GW spectra from Chen19 into SAM modules.
 * Explicit evolution/hardening models for
-    - [ ] dynamical friction
-    - [ ] stellar scattering using uniform/standard stellar distributions (e.g. isotropic & isothermal)
-    - [ ] comprehensive stellar scattering using arbitrary stellar distributions
-    - [ ] circumbinary accretion mediated hardening ( inward-migration)
-    - [ ] circumbinary accretion mediated softening (outward-migration)
-    - [ ] eccentric binary evolution
-    - [ ] triple MBH interactions
-* Comparisons with observations (particularly EM) to calibrate sythesized populations
-    - [ ] accurate catalogs of 'direct' MBH mass measurements from the local universe
-    - [ ] approximate catalogs of 'indirect' MBH mass measurements from populations of AGN/quasars
-    - [ ] MBH--host-galaxy scaling relationships
-    - [ ] AGN/Quasar luminosity functions
-    - [ ] constraints on kpc--Mpc scale galaxy and AGN mergers
-    - [ ] constraints on sub-kpc separation binary AGN based on EM candidates (and upper-limits)
-* Gaussian Processes
-    - [ ] How significant are deviations in predicted spectra from Gaussians?  What produces those deviations, are they single (or single-like) sources, or are they actual "population" trends?  (Former is okay to ignore, latter is not!)
-    - [ ]
-* Testing
-  * Add sphinx docs build to github action for testing
+    * [ ] comprehensive stellar scattering using arbitrary stellar distributions
+    * [ ] eccentric binary evolution
+    * [ ] triple MBH interactions
+* Comparisons with observations (particularly EM) to calibrate synthesized populations
+    * [ ] accurate catalogs of 'direct' MBH mass measurements from the local universe
+    * [ ] approximate catalogs of 'indirect' MBH mass measurements from populations of AGN/quasars
+    * [ ] AGN/Quasar luminosity functions
+    * [ ] constraints on kpc--Mpc scale galaxy and AGN mergers
+    * [ ] constraints on sub-kpc separation binary AGN based on EM candidates (and upper-limits)
 
 
-----
-
 ## Current
 
+## v1.6 - 2024/05/01
+
+* DEPRECATIONS:
+    * `holodeck.librarian.py` ==> `holodeck.librarian.lib_tools`
+        * Rename submodule.  All components remain the same.  All `lib_tools` elements are now also imported into the `librarian` namespace.  i.e. elements like `holodeck.librarian.lib_tools._Param_Space` will now be accessible via `holodeck.librarian._Param_Space`.
+    * Library filenames:
+        * Standard library simulation files will now be saved to the 'library_sims' subdirectory, and filenames 'library__p######.npz'.  Combined library files will now be 'sam-library.hdf5'.
+        * 'Domain' simulation files will be saved to the 'domain_sims' subdirectory, and filenames 'domain__p######.npz'.  Combined domain files will now be 'sam-domain.hdf5'.
+
+* BUGS:
+    * Semi-Analytic Models
+        * `Semi_Analytic_Model._dynamic_binary_number_at_fobs_inconsistent` was not checking for systems that had already coalesced.  Only effected GW-only evolution using the python version of the calculation.
+
+* DEFAULTS:
+    * Semi-Analytic Models
+        * `Semi_Analytic_Models` instances now use galaxy merger-rates (instead of galaxy pair-fractions and merger-times) by default.  To use GPF+GMT SAMs, the user must pass in at least a GPF instance manually.
+
+* General Changes
+
+    * Semi-Analytic Models (`holodeck.sams`)
+        * Improve accuracy of dynamic binary number calculation for consistent evolution models.
+
+    * `holodeck.librarian`
+        * Added functionality to construct 'domain' sets of simulations, to explore each parameter in a parameter-space one at a time.
+        * NOTE: Standard library files will now be called "sam-library.hdf5" instead of "sam_lib.hdf5"
+
+
+## v1.5.2 - 2024/04/12
+
+* DEPRECATIONS
+    * `host_relations.py`: remove the `mamp` parameter and `MASS_AMP` attributes in the MMBulge relationships, and use `mamp_log10` and `MASS_AMP_LOG10` exclusively.
+
+
+## v1.5 - 2024/03/29
+
+* Deprecated `relations.py`.
+    * **Material from this file has mostly been moved to `host_relations.py`**.  The components for galaxy/halo density/velocity profiles have been moved to `galaxy_profiles.py`.  Stellar-mass vs. halo-mass relations are still in `host_relations.py`.
+    * All of the same material can temporarily still be accessed/imported from `relations.py`, and it will log/print a deprecation warning.
+* **M-Mbulge relations now use separate bulge-fractions.**
+    * All subclasses of `_MMBulge_Relation` now utilize separate bulge-fraction instances, implemented as subclasses of the new `holodeck.host_relations._Bulge_Frac` class.
+    * The overall API remains unchanged (users can still perform conversions from total stellar-mass `mstar` to black-hole masses `mbh`), but internally conversions from total stellar-mass to stellar bulge-mass are performed by the bulge-fraction instances, and then stellar bulge-masses are converted to black-hole masses by the M-Mbulge instances.
+    * The API for M-Mbulge relations has also been cleaned up and unified.
+    * Two `_Bulge_Frac` subclasses have been implememted:
+        * `BF_Constant` which is a single, fixed bulge-fraction value.  This maintains the behavior that was previously performed within `_MMBulge_Relation`.
+        * `BF_Sigmoid` is a new implementation that transitions from one bulge-fraction value at asymptotically low stellar-masses, up to a second bulge-fraction at and above a fixed characteristic stellar mass.  The 'width' or 'steepness' of the transition can also be varied.
 
 ----
 
+
 ## Past
 
 ### v0.2 - 2022/03/28
 
 * Binary Evolution (`evolution.py`)
-    - Now tracking hardening rates in evolution.
-    - Simple implementation of some binary hardening models, both physical and phenomenological (i.e. power-law like).
-    - Modules for Dynamical Friction, Stellar Scattering, and GW hardening.
+    * Now tracking hardening rates in evolution.
+    * Simple implementation of some binary hardening models, both physical and phenomenological (i.e. power-law like).
+    * Modules for Dynamical Friction, Stellar Scattering, and GW hardening.
 * Logistical and Internals
-    - Added submodule for logging (`log.py`)
-    - Added submodule for plotting (`plot.py`)
-    - Added submodule for observational data and relations (`observations.py`)
-    - New, and also improvements to old, notebooks for testing and demonstration purposes.  Addition of more unit tests and test scripts.
-    - Extensive additions to utility / mathematical / numerical functions (`utils.py`).
-    - Improved README.md, and started adding basics to holodeck paper manuscript.
+    * Added submodule for logging (`log.py`)
+    * Added submodule for plotting (`plot.py`)
+    * Added submodule for observational data and relations (`observations.py`)
+    * New, and also improvements to old, notebooks for testing and demonstration purposes.  Addition of more unit tests and test scripts.
+    * Extensive additions to utility / mathematical / numerical functions (`utils.py`).
+    * Improved README.md, and started adding basics to holodeck paper manuscript.
 * Populations
-    - Cleaned up of observationally-based populations (`pop_observational.py`)
-    - Unified implementation of MBH-galaxy relationships (`relations.py`)
-    - Significant cleanup and upgrades in Semi-Analytic Models based populations (`sam.py`)
-        - Developed methodology for sampling discrete binaries from continuous distributions (in coordination with `kalepy` modules)
+    * Cleaned up of observationally-based populations (`pop_observational.py`)
+    * Unified implementation of MBH-galaxy relationships (`relations.py`)
+    * Significant cleanup and upgrades in Semi-Analytic Models based populations (`sam.py`)
+        * Developed methodology for sampling discrete binaries from continuous distributions (in coordination with `kalepy` modules)
 
 ### v0.1 - 2021/08/15
 
 * Basic GW spectra can be generated using simple versions of population synthesis based on:
-    - A finite, discrete population of binaries from the Illustris simulations
-    - Continuous distributions from semi-analytic modeling
-    - Continuous distributions from semi-analytic modeling, with Illustris merger rates, calibrated to local galaxy observations.
+    * A finite, discrete population of binaries from the Illustris simulations
+    * Continuous distributions from semi-analytic modeling
+    * Continuous distributions from semi-analytic modeling, with Illustris merger rates, calibrated to local galaxy observations.
 * A class-based implementation is used in a way to facilitate subclassing (i.e. extensibility).
 * Only the simplest models for binary evolution (i.e. fixed time-delays and GW emission) are currently included.
 * Continuous population distributions can be easily interfaced with the `kalepy` package to facilitate discrete sampling.  Even without formal discrete sampling, proper GW (foreground and background) statistics can be approximated.

CONTRIBUTING.md

@@ -93,3 +93,23 @@ version 1.4, available at
 
 [homepage]: http://contributor-covenant.org
 [version]: http://contributor-covenant.org/version/1/4/
+
+
+## Contributors
+
+(List is very likely out-of-date, please bump if you notice someone/yourself missing!)
+
+Bence Becsy  
+Andrew Casey-Clyde  
+Alex Cingoranelli  
+Siyuan Chen  
+Daniel D’Orazio  
+Emiko Gardiner  
+Kayhan Gültekin  
+William Lamb  
+Luke Zoltan Kelley  
+Cayenne Matt  
+Joseph Simon  
+Magdalena Siwek  
+Jeremy Wachter  
+David Wright