Merge pull request BEAST-Fitting#74 from karllark/getting_running_2024

Getting things running in 2024

.github/workflows/tox-tests.yml

@@ -26,18 +26,20 @@ jobs:
         # Only run on ubuntu by default, but can add other os's to the test matrix here.
         # For example -- os: [ubuntu-latest, macos-latest, windows-latest]
         # windows-latest not possible due to how temp files are used in tests currently
-        os: [ubuntu-latest, macos-latest]
+        # macos failing due to an issue installing h5py - KDG 14may24
+        # os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
 
         # Test python version 3.x
-        python-ver: [9, 10, 11]
+        python-ver: [10, 11, 12]
 
         # Specify which tox environments to test in this list.
         # tox-env: [cov, alldeps, devdeps, astropylts]
         tox-env: [alldeps]
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up python 3.${{ matrix.python-ver }} with tox environment py3${{ matrix.python-ver }}-${{ matrix.tox-env }} on ${{ matrix.os }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: 3.${{ matrix.python-ver }}
     - name: Install base dependencies
@@ -71,38 +73,38 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up python for astropy lts test
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install tox
     - name: Test with tox
       run: |
-        tox -e py39-astropylts
+        tox -e py311-astropylts
 
   # Coverage test
   cov_test:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up python for coverage test
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.11
+        python-version: 3.9
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install tox
     - name: Test with tox
       run: |
-        tox -e py311-cov
+        tox -e py309-cov -- --remote-data
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV }}
         fail_ci_if_error: true
@@ -119,11 +121,11 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python to build docs with sphinx
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.11
+        python-version: 3.12
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
@@ -139,11 +141,11 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Python codestyle check
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.11
+        python-version: 3.12
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip

docs/index.rst

@@ -50,16 +50,13 @@ typo in the documentation to developing a major new feature. We welcome
 contributors who will abide by the `Python Software Foundation Code of Conduct
 <https://www.python.org/psf/conduct/>`_.
 
-``dust_extinction`` follows the same workflow and coding guidelines as
+``megabeast`` follows the same workflow and coding guidelines as
 `Astropy`_.  The following pages will help you get started with contributing
 fixes, code, or documentation (no git or GitHub experience necessary):
 
-* `How to make a code contribution <https://docs.astropy.org/en/stable/development/workflow/development_workflow.html>`_
-
-* `Coding Guidelines <https://docs.astropy.org/en/stable/development/codeguide.html>`_
-
-* `Developer Documentation <https://docs.astropy.org/en/stable/index_dev.html>`_
+* `How to make a code contribution <https://docs.astropy.org/en/latest/index_dev.html>`_
 
+* `Coding Guidelines <https://docs.astropy.org/en/latest/development/codeguide.html>`_
 
 For the complete list of contributors please see the `megabeast
 contributors page on Github

megabeast/fit_single.py

@@ -49,7 +49,7 @@ def main():
     for cparam in beast_physmod_param_list:
         beast_moddata[cparam] = sgrid.grid[cparam]
 
-    # get the completness from the BEAST observation model
+    # get the completeness from the BEAST observation model
     #   use the maximum completeness across the bands as the correct obsmodel
     #   would only have one completeness value per model
     #   max is the best approximation for the toothpick model (maybe???  average??)

megabeast/singlepop_dust_model.py

@@ -17,6 +17,7 @@ class MB_Model:
     MegaBEAST model that provides member functions to compute
     the likelihood and priors for a specific physical model
     """
+
     def __init__(self, params):
         self.star_model = params.stellar_model
         self.dust_model = params.fd_model
@@ -27,6 +28,9 @@ def __init__(self, params):
         #     define a dict that translates between mb params and physical models
         self.params = ["logA", "M_ini", "Av", "Rv", "fA"]
         self.physics_model = {}
+        print(self.params)
+        print(self.star_model.keys())
+        print(self.dust_model.keys())
         for cparam in self.params:
             if cparam in self.star_model.keys():
                 cmod = self.star_model[cparam]
@@ -95,7 +99,7 @@ def start_params(self):
                         len(np.atleast_1d(mod[ckey][cparam])) > 1
                     ):  # expand into multiple parameters
                         for ll, cval in enumerate(mod[ckey][cparam]):
-                            names.append(f"{ckey}_{cparam}{ll+1}")
+                            names.append(f"{ckey}_{cparam}{ll + 1}")
                             values.append(cval)
                     else:
                         names.append(f"{ckey}_{cparam}")
@@ -194,12 +198,19 @@ def lnlike(self, phi, star_lnpgriddata, beast_moddata):
                 * beast_moddata["completeness"][curindxs]
             )
             # checks for spoilers
+            # print(i, star_intprob)
             if not np.isfinite(star_intprob):
                 raise ValueError("invidual integrated star prob is not finite")
             if star_intprob == 0.0:
-                raise ValueError("invidual integrated star prob is zero")
+                pass
+                # print(i, star_intprob)
+            #    raise ValueError("invidual integrated star prob is zero")
+            else:
+                logintprob += np.log(star_intprob)
 
-            logintprob += np.log(star_intprob)
+        if logintprob == 0.0:
+            print(logintprob)
+            exit()
 
         return logintprob
 
@@ -288,6 +299,7 @@ def _get_best_fit_params(sampler):
     nwalkers, nsteps = sampler.lnprobability.shape
     for k in range(nwalkers):
         tmax_lnp = np.nanmax(sampler.lnprobability[k])
+        print(tmax_lnp)
         if tmax_lnp > max_lnp:
             max_lnp = tmax_lnp
             (indxs,) = np.where(sampler.lnprobability[k] == tmax_lnp)
@@ -317,6 +329,7 @@ def fit_ensemble(megabeast_model, star_lnpgriddata, beast_moddata):
     fit_results : array
         set of best fit parameters
     """
+
     # standard minimization to find initial values
     def chi2(*args):
         return -1.0 * lnprob(*args)

setup.cfg

@@ -17,10 +17,10 @@ packages = find:
 python_requires = >=3.9
 setup_requires = setuptools_scm
 install_requires =
+    numpy<2.0
     scipy
     astropy
     matplotlib
-    aplpy
     h5py
     tqdm
     emcee

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{39,310,311}-test{,-alldeps}{,-cov}
+    py{310,311,312}-test{,-alldeps}{,-cov}
     build_docs
     linkcheck
     codestyle