Merge remote-tracking branch 'upstream/master'

.flake8

@@ -2,21 +2,30 @@
 max-line-length = 120
 max-complexity = 45
 ignore =
-  E203
-  E225      # missing whitespace around operator
-  E226      # missing whitespace around arithmetic operator
-  W503      # line break before binary operator; conflicts with black
-  W504      # Don't want to change with code frozen...
-  E722      # bare except ok
-  E731      # lambda expressions ok
-  E266      # block comments
-  E741      # ambiguous variable names
-  E501      # lines
+  E203,
+  # missing whitespace around operator
+  E225,
+  # missing whitespace around arithmetic operator
+  E226,
+  # line break before binary operator; conflicts with black
+  W503,
+  # Don't want to change with code frozen...
+  W504,
+  # bare except ok
+  E722,
+  # lambda expressions ok
+  E731,
+  # block comments
+  E266,
+  # ambiguous variable names
+  E741,
+  # lines
+  E501
 exclude =
-    .git
-    .tox
-    __pycache__
-    build
-    dist
-    docs/*
+    .git,
+    .tox,
+    __pycache__,
+    build,
+    dist,
+    docs/*,
     .enterprise_extensions/*

.github/workflows/ci_test.yml

@@ -17,13 +17,13 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, '3.10']
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install non-python dependencies on mac
@@ -53,7 +53,7 @@ jobs:
     - name: Test with pytest
       run: make test
     - name: Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       #with:
       #  fail_ci_if_error: true
 
@@ -65,11 +65,11 @@ jobs:
     if: github.event_name == 'release'
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: "3.8"
+        python-version: "3.10"
     - name: Install non-python dependencies on linux
       run: |
         sudo apt-get install libsuitesparse-dev
@@ -111,11 +111,11 @@ jobs:
    runs-on: ubuntu-latest
    if: github.event_name == 'release'
    steps:
-   - uses: actions/checkout@v2
+   - uses: actions/checkout@v3
    - name: Set up Python
-     uses: actions/setup-python@v2
+     uses: actions/setup-python@v4
      with:
-       python-version: '3.8'
+       python-version: '3.10'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip

CONTRIBUTING.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
+3. The pull request should work for Python 3.7, 3.8, 3.9, and 3.10, and for PyPy. Check
    https://travis-ci.org/stevertaylor/enterprise_extensions/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

HISTORY.rst

@@ -1,6 +1,16 @@
 =======
 History
 =======
+
+2.4.3 (2023-27-06)
+Update Zenodo entry.
+
+2.4.2 (2022-28-12)
+Fix HyperModel to support newer versions of numpy.
+
+2.4.1 (2022-02-10)
+Add support for new noise definitions in WidebandTimingModel.
+
 2.4.0 (2022-02-10)
 Use Timing Package (Tempo,Tempo2,Pint) definition of EQUAD. Enterprise has
 broken backwards compatibility, and here we use the `tnequad` flag to switch on
@@ -19,7 +29,7 @@ Fix bug in HyperModel when using save_runtime_info.
 Fix bugs associated with recent function additions. Added linting and mild PEP8
 rules. Also removed older Python functionality which is no longer supported.
 
-2.3.0 (2021-09-15)*
+2.3.0 (2021-09-15)
 Functionality added for NANOGrav 15yr dataset analyses.
 Outlier analysis software moved into separate package.
 

README.md

@@ -16,15 +16,15 @@ You can also install it by cloning the repo and running `pip install .` in the `
 Did you use `enterprise_extensions`?
 Remember to cite it as:
 
->Taylor, S. R., Baker, P. T., Hazboun, J. S., Simon, J., & Vigeland, S. J. (2021). enterprise_extensions v2.3.1. https://github.com/nanograv/enterprise_extensions
+>Taylor, S. R., Baker, P. T., Hazboun, J. S., Simon, J., & Vigeland, S. J. (2021). enterprise_extensions v2.4.3. https://github.com/nanograv/enterprise_extensions
 
 ```latex
 @misc{enterprise,
   author       = {Stephen R. Taylor and Paul T. Baker and Jeffrey S. Hazboun and Joseph Simon and Sarah J. Vigeland},
   title        = {enterprise_extensions},
   year         = {2021},
   url          = {https://github.com/nanograv/enterprise_extensions},
-  note         = {v2.3.3}
+  note         = {v2.4.3}
 }
 ```
 

enterprise_extensions/__init__.py

@@ -1 +1 @@
-__version__ = "2.4.0"
+__version__ = "2.4.3"

enterprise_extensions/blocks.py

@@ -37,7 +37,7 @@ def channelized_backends(backend_flags):
 
 
 def white_noise_block(vary=False, inc_ecorr=False, gp_ecorr=False,
-                      efac1=False, select='backend', tnequad=False, name=None):
+                      efac1=False, select='backend', tnequad=False, name=None, ng_twg_setup=False, wb_efac_sigma=0.25):
     """
     Returns the white noise block of the model:
 
@@ -74,6 +74,8 @@ def white_noise_block(vary=False, inc_ecorr=False, gp_ecorr=False,
     if vary:
         if efac1:
             efac = parameter.Normal(1.0, 0.1)
+        elif ng_twg_setup:
+            efac = parameter.Normal(1.0, wb_efac_sigma)
         else:
             efac = parameter.Uniform(0.01, 10.0)
         equad = parameter.Uniform(-8.5, -5)
@@ -772,23 +774,23 @@ def common_red_noise_block(psd='powerlaw', prior='log-uniform',
         cpl = gpp.free_spectrum(log10_rho=log10_rho_gw)
 
     if orf is None:
-        crn = gp_signals.FourierBasisGP(cpl, coefficients=coefficients,
+        crn = gp_signals.FourierBasisGP(cpl, coefficients=coefficients, combine=combine,
                                         components=components, Tspan=Tspan,
                                         name=name, pshift=pshift, pseed=pseed)
     elif orf in orfs.keys():
         if orf == 'crn':
-            crn = gp_signals.FourierBasisGP(cpl, coefficients=coefficients,
+            crn = gp_signals.FourierBasisGP(cpl, coefficients=coefficients, combine=combine,
                                             components=components, Tspan=Tspan,
                                             name=name, pshift=pshift, pseed=pseed)
         else:
             crn = gp_signals.FourierBasisCommonGP(cpl, orfs[orf],
-                                                  components=components,
+                                                  components=components, combine=combine,
                                                   Tspan=Tspan,
                                                   name=name, pshift=pshift,
                                                   pseed=pseed)
     elif isinstance(orf, types.FunctionType):
         crn = gp_signals.FourierBasisCommonGP(cpl, orf,
-                                              components=components,
+                                              components=components, combine=combine,
                                               Tspan=Tspan,
                                               name=name, pshift=pshift,
                                               pseed=pseed)

enterprise_extensions/empirical_distr.py

@@ -227,6 +227,7 @@ def make_empirical_distributions(pta, paramlist, params, chain,
 
         if len(pl) == 1:
             idx = pta.param_names.index(pl[0])
+
             prior_min = pta.params[idx].prior._defaults['pmin']
             prior_max = pta.params[idx].prior._defaults['pmax']