Merge remote-tracking branch 'origin/main' into frb20210912A

.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

@@ -4,81 +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: ['3.9','3.10']
-        deps: [current, numpy122, astropydev, numpydev, astropydev-numpydev]
-
+        python: ['3.11', '3.12']
+        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 = 1.22
-      if: "contains(matrix.deps, 'numpy122')"
-      run: |
-        python -m pip install numpy==1.22
-    - 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 -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: 3.9
-    - name: Install base dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install pycodestyle
-    - name: Check for runtime errors using pycodestyle
+        python -m pip install git+https://github.com/linetools/linetools#egg=linetools
+    - name: Test with tox
       run: |
-        pycodestyle frb --count --select=E9
+        tox -e ${{ matrix.python }}-${{ matrix.toxenv }}

.gitignore

@@ -16,6 +16,7 @@ Galaxy_DB/
 *.hdf5
 .DS_Store
 *.json
+*.npz
 
 # Tests
 ./pytest_cache

bin/frb_pz_dm → bin/frb_pzdm_mag

@@ -6,11 +6,11 @@
 
 
 """
-This script performs estimates P(z|DM)
+This script performs estimates P(z|DM) and limiting mag
 """
 
-from frb.scripts import pz_dm
+from frb.scripts import pzdm_mag
 
 if __name__ == '__main__':
-    args = pz_dm.parser()
-    pz_dm.main(args)
+    args = pzdm_mag.parser()
+    pzdm_mag.main(args)

docs/installing.rst

@@ -26,14 +26,14 @@ We recommend that you use `Anaconda <https://www.continuum.io/downloads/>`_
 to install and/or update these packages.
 
 * `python <http://www.python.org/>`_ versions 3.8 or later
-* `numpy <http://www.numpy.org/>`_ version 1.18 or later
-* `astropy <http://www.astropy.org/>`_ version 4.5 or later
-* `scipy <http://www.scipy.org/>`_ version 1.7 or later
-* `healpy <https://healpy.readthedocs.io/en/latest/index.html>`_ version 1.12 or later
-* `pandas <https://pandas.pydata.org/>`_ version 1.3 or later
+* `numpy <http://www.numpy.org/>`_ version 2.1 or later
+* `astropy <http://www.astropy.org/>`_ version 5.1 or later
+* `scipy <http://www.scipy.org/>`_ version 1.11 or later
+* `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 0.4.2 or greater
-* `matplotlib <https://matplotlib.org/>`_ version 3.3 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
 
@@ -47,7 +47,7 @@ out all the packages and their version numbers.
 The following packages are required to access surveys (e.g. SDSS, DES)
 for data that may be associated to an FRB:
 
-* `astroquery <https://astroquery.readthedocs.io/en/latest/>`_ v0.4.4 only (maybe)
+* `astroquery <https://astroquery.readthedocs.io/en/latest/>`_ v0.4.7 or later
 * `datalab-client <https://github.com/noaodatalab/datalab/>`_ v2.20 or later
 * `pyvo <https://pyvo.readthedocs.io/en/latest/>`_  version 0.9.2 or later
 
@@ -57,7 +57,8 @@ The following package(s) is/are required to access FRB galaxy spectra:
 
 The following package is required to map a slit onto a finder chart (frb.figures.finder):
 
-* `photutils <https://photutils.readthedocs.io/en/stable/>`_  version 1.2.0 or later
+* `photutils <https://photutils.readthedocs.io/en/stable/>`_  version 1.11.0 or later
+* `scikit-image <https://scikit-image.org/>`_  version 0.21.0 or later
 
 The following are required to use our KCWI datacube handling tools:
 

docs/mags_to_flux.rst

@@ -0,0 +1,33 @@
+*****************************
+Magnitudes to flux conversion
+*****************************
+
+Most public photometry tables report brightness of objects
+in terms of magnitudes as opposed to flux units (Jy or mJy).
+However, using software such as CIGALE and EAZY is made
+less ambiguous if fluxes are supplied. To enable this, we provide
+the function `frb.surveys.catalog_utils.convert_mags_to_flux`
+
+The definition for magnitude errors arises from the following
+equation:
+
+.. math::
+  
+  m\pm \delta m = ZP-2.5 \log_{10}(f\pm \delta f) 
+  \Rightarrow m = ZP-2.5 \log_{10}(f)
+  \Rightarrow \delta m = 2.5 \log_{10}(1+\delta f/f)
+
+While the math:`\delta m` formula above is exact, most photometry
+software use a first order Taylor expansion in math:`\delta f/f`
+assuming the error is typically small. i.e. 
+
+.. math::
+  
+  \delta m \approx \frac{2.5}{\log_{10}}(\delta f/f)
+
+This will obviously break down when looking at really faint objects,
+barely at the threshold of detection above the noise floor.
+`convert_mags_to_flux` explicitly assumes the catalog mag errors are
+produced using this approximation. However, if you have reason to believe
+the exact formula was used, you can set `exact_mag_err=True` to get the
+correct flux error.