Mag vs dm

.github/ci_orig_tests.yml

@@ -0,0 +1,85 @@
+name: CI Tests
+
+on:
+  push:
+    branches:
+    - master
+    tags:
+  pull_request:
+
+env:
+  SETUP_XVFB: True  # avoid issues if mpl tries to open a GUI window
+
+jobs:
+  ci-tests:
+    name: Python-${{ matrix.python }}, deps=${{ matrix.deps }}
+    runs-on: ${{ matrix.os }}
+    if: "!(contains(github.event.head_commit.message, '[skip ci]') || contains(github.event.head_commit.message, '[ci skip]'))"
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python: ['3.11', '3.12']
+        deps: [current, numpy211, astropydev, numpydev, astropydev-numpydev]
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - name: Install base dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Test with numpy = 2.1.1
+      if: "contains(matrix.deps, 'numpy211')"
+      run: |
+        python -m pip install numpy==2.1.1
+    - name: Test with dev version of numpy
+      if: "contains(matrix.deps, 'numpydev')"
+      run: |
+        python -m pip install git+https://github.com/numpy/numpy.git#egg=numpy
+    - name: Test with dev version astropy
+      if: "contains(matrix.deps, 'astropydev')"
+      run: |
+        python -m pip install git+https://github.com/astropy/astropy.git#egg=astropy
+    - name: Install frb requirements
+      run: |
+        python -m pip install wheel scipy IPython
+        python -m pip install git+https://github.com/FRBs/ne2001.git#egg=ne2001
+        python -m pip install git+https://github.com/FRBs/astropath.git#egg=astropath
+        python -m pip install git+https://github.com/linetools/linetools#egg=linetools
+        python -m pip install -r frb/requirements.txt
+    - name: Install numba
+      run: |
+        python -m pip install numba
+    - name: Install astroquery
+      run: |
+        python -m pip install astroquery
+    - name: Print Python, pip, astropy, numpy, and setuptools versions
+      run: |
+        python -c "import sys; print(f'Python {sys.version}')"
+        python -c "import pip; print(f'pip {pip.__version__}')"
+        python -c "import astropy; print(f'astropy {astropy.__version__}')"
+        python -c "import numpy; print(f'numpy {numpy.__version__}')"
+        python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
+    - name: Run tests
+      run: tox -e ${{ matrix.python }}-${{ matrix.toxenv }} 
+
+  codestyle:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[ci skip]')"
+    steps:
+    - uses: actions/checkout@v2
+    - name: Python codestyle check
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.11
+    - name: Install base dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pycodestyle
+    - name: Check for runtime errors using pycodestyle
+      run: |
+        pycodestyle frb --count --select=E9

.github/workflows/ci_tests.yml

@@ -4,82 +4,33 @@ on:
   push:
     branches:
     - master
-    tags:
   pull_request:
 
 env:
-  SETUP_XVFB: True  # avoid issues if mpl tries to open a GUI window
+  SETUP_XVFB: True  # avoid issues if something tries to open a GUI window
 
 jobs:
   ci-tests:
-    name: Python-${{ matrix.python }}, deps=${{ matrix.deps }}
+    name: Tox env ${{ matrix.python }}-${{ matrix.toxenv }}
     runs-on: ${{ matrix.os }}
-    if: "!(contains(github.event.head_commit.message, '[skip ci]') || contains(github.event.head_commit.message, '[ci skip]'))"
-
     strategy:
       matrix:
         os: [ubuntu-latest]
         python: ['3.11', '3.12']
-        deps: [current, numpy211, astropydev, numpydev, astropydev-numpydev]
-
+        toxenv: [test, test-astropydev]
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
     - name: Install base dependencies
       run: |
-        python -m pip install --upgrade pip
-    - name: Test with numpy = 2.1.1
-      if: "contains(matrix.deps, 'numpy211')"
-      run: |
-        python -m pip install numpy==2.1.1
-    - name: Test with dev version of numpy
-      if: "contains(matrix.deps, 'numpydev')"
-      run: |
-        python -m pip install git+https://github.com/numpy/numpy.git#egg=numpy
-    - name: Test with dev version astropy
-      if: "contains(matrix.deps, 'astropydev')"
-      run: |
-        python -m pip install git+https://github.com/astropy/astropy.git#egg=astropy
-    - name: Install frb requirements
-      run: |
-        python -m pip install wheel scipy IPython
+        python -m pip install -r frb/requirements.txt --upgrade pip tox
         python -m pip install git+https://github.com/FRBs/ne2001.git#egg=ne2001
         python -m pip install git+https://github.com/FRBs/astropath.git#egg=astropath
         python -m pip install git+https://github.com/linetools/linetools#egg=linetools
-        python -m pip install -r frb/requirements.txt
-    - name: Install numba
-      run: |
-        python -m pip install numba
-    - name: Install astroquery
-      run: |
-        python -m pip install astroquery
-    - name: Print Python, pip, astropy, numpy, and setuptools versions
-      run: |
-        python -c "import sys; print(f'Python {sys.version}')"
-        python -c "import pip; print(f'pip {pip.__version__}')"
-        python -c "import astropy; print(f'astropy {astropy.__version__}')"
-        python -c "import numpy; print(f'numpy {numpy.__version__}')"
-        python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
-    - name: Run tests
-      run: python setup.py test
-
-  codestyle:
-    runs-on: ubuntu-latest
-    if: "!contains(github.event.head_commit.message, '[ci skip]')"
-    steps:
-    - uses: actions/checkout@v2
-    - name: Python codestyle check
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.11
-    - name: Install base dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install pycodestyle
-    - name: Check for runtime errors using pycodestyle
+    - name: Test with tox
       run: |
-        pycodestyle frb --count --select=E9
+        tox -e ${{ matrix.python }}-${{ matrix.toxenv }}

docs/installing.rst

@@ -32,7 +32,7 @@ to install and/or update these packages.
 * `healpy <https://healpy.readthedocs.io/en/latest/index.html>`_ version 1.15 or later
 * `pandas <https://pandas.pydata.org/>`_ version 1.5 or later
 * `requests <https://pillow.readthedocs.io/en/5.3.x/>`_  version 2.18 or later
-* `extinction <https://extinction.readthedocs.io/en/latest/>`_ version 0.4.6 or greater
+* `dust_extinction <https://dust-extinction.readthedocs.io/en/latest/>`_ 
 * `matplotlib <https://matplotlib.org/>`_ version 3.7 or greater
 * `linetools <https://github.com/linetools/linetools>`_  version 0.3 or later
 * `astropath <https://github.com/FRBs/astropath>`_  version 0.1 or later

frb/builds/build_hosts.py

@@ -26,17 +26,13 @@
 except:
     print('WARNING:  ppxf not installed')
 from frb.galaxies import nebular
+from frb.galaxies import utils as galaxy_utils
 from frb.galaxies import hosts
 from frb.galaxies import defs as galaxy_defs
 from frb.surveys import survey_utils
 from frb import utils
 import pandas
 
-try:
-    import extinction
-except ImportError:
-    print("extinction package not loaded.  Extinction corrections will fail")
-
 try:
     from frb.galaxies import cigale
 except ModuleNotFoundError:
@@ -386,14 +382,9 @@ def run(host_input:pandas.core.series.Series,
         # Correct for Galactic extinction
         ebv = float(nebular.get_ebv(Host.coord)['meanValue'])
         print(f'Correcting the spectrum for Galactic extinction with reddening E(B-V)={ebv}')
-        AV = ebv * 3.1  # RV
-        Al = extinction.ccm89(spectrum.wavelength.value, AV, 3.1)
-        # New spec
-        new_flux = spectrum.flux * 10**(Al/2.5)
-        new_sig = spectrum.sig * 10**(Al/2.5)
-        new_spec = XSpectrum1D.from_tuple((spectrum.wavelength, new_flux, new_sig))
-
-        #
+        new_spec = galaxy_utils.deredden_spec(spectrum, ebv)
+
+        # Run it
         ppxf.run(new_spec, R, host_input.z, 
                  results_file=ppxf_results_file, 
                  spec_fit=spec_file,

frb/data/DM/convert_npy_to_npz.py

@@ -0,0 +1,36 @@
+""" Simple script to convert .npy files to .npz files. """
+
+import numpy as np
+
+from frb.dm import prob_dmz
+
+def main():
+
+    npy_files = ['DSA_pzdm.npy',
+        'parkes_mb_class_I_and_II_pzdm.npy',
+        'CRAFT_class_I_and_II_pzdm.npy',
+        'CRAFT_ICS_1300_pzdm.npy',
+        'CRAFT_ICS_892_pzdm.npy',
+        'CRAFT_ICS_1632_pzdm.npy',
+        'FAST_pzdm.npy']
+
+    # Load of z, DM_EG from CHIME
+    chime_dict = prob_dmz.grab_repo_grid(prob_dmz.telescope_dict['CHIME'])
+
+    # Parse
+    z = chime_dict['z']
+    DM = chime_dict['DM']
+
+    # Loop on the files
+    for npy_file in npy_files:
+        # Load
+        pzdm = prob_dmz.grab_repo_grid(npy_file)
+        # Save
+        npz_file = npy_file.replace('.npy', '.npz')
+        np.savez(npz_file, pzdm=pzdm, z=z, DM=DM)
+        # Report
+        print(f"Wrote: {npz_file}")
+
+# Command line execution
+if __name__ == '__main__':
+    main()

frb/dm/prob_dmz.py

@@ -14,6 +14,20 @@
 
 from IPython import embed
 
+# Dict to resolve telescope/survey into the appropriate grid filename
+telescope_dict = {
+    'CHIME_repeaters': 'CHIME_pzdm_repeaters.npz',
+    'CHIME': 'CHIME_pzdm.npz',
+    'DSA': 'DSA_pzdm.npz',
+    'Parkes': 'parkes_mb_class_I_and_II_pzdm.npz',
+    'CRAFT': 'CRAFT_class_I_and_II_pzdm.npz',
+    'CRAFT_ICS_1300': 'CRAFT_ICS_1300_pzdm.npz',
+    'CRAFT_ICS_892': 'CRAFT_ICS_892_pzdm.npz',
+    'CRAFT_ICS_1632': 'CRAFT_ICS_1632_pzdm.npz',
+    'FAST': 'FAST_pzdm.npz',
+    'perfect': 'PDM_z.npz'
+}
+
 class P_DM_z(object):
     pass
 

frb/galaxies/nebular.py

@@ -12,10 +12,7 @@
 from astropy.table import Table
 from astropy import units
 
-try:
-    import extinction
-except ImportError:
-    warnings.warn("extinction package not loaded.  Extinction corrections will fail")
+import dust_extinction
 
 try:
     from linetools.lists import linelist
@@ -33,7 +30,7 @@ def calc_dust_extinct(neb_lines, method):
     """
     Estimate the Visual extinction A_V based on input nebular emission lines
 
-    Uses the Fitzpatrick & Massa (2007) extinction law
+    Uses the Gordon 2024
 
     Args:
         neb_lines (dict):  Line fluxes
@@ -71,8 +68,11 @@ def calc_dust_extinct(neb_lines, method):
         raise IOError("Not ready for this mode")
 
     # Extinction
-    a1AV = extinction.fm07(np.atleast_1d(wave1), 1.0)[0]
-    a2AV = extinction.fm07(np.atleast_1d(wave2), 1.0)[0]
+    #a1AV = extinction.fm07(np.atleast_1d(wave1), 1.0)[0]
+    #a2AV = extinction.fm07(np.atleast_1d(wave2), 1.0)[0]
+    extmod = dust_extinction.parameter_averages.G23(Rv=3.1)
+    a1AV = extmod(np.atleast_1d(wave1*units.AA))  # *units.AA)
+    a2AV = extmod(np.atleast_1d(wave2*units.AA))  # *units.AA)
 
     # Observed ratio
     fratio_obs = F1_obs/F2_obs
@@ -153,7 +153,10 @@ def calc_lum(neb_lines, line, z, cosmo, AV=None):
 
     # Dust correct?
     if AV is not None:
-        al = extinction.fm07(np.atleast_1d(wave.to('Angstrom').value), AV)[0]
+        #al = extinction.fm07(np.atleast_1d(wave.to('Angstrom').value), AV)[0]
+        extmod = dust_extinction.parameter_averages.G23(Rv=3.1)
+        AlAV = extmod(np.atleast_1d(wave)*units.AA)[0]
+        al = AlAV * AV
     else:
         al = 0.