Merge pull request #140 from Hazboun6/linting

Merging these changes which fixed @paulthebaker concerns.

.flake8

@@ -0,0 +1,22 @@
+[flake8]
+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
+exclude =
+    .git
+    .tox
+    __pycache__
+    build
+    dist
+    docs/*
+    .enterprise_extensions/*

.github/workflows/ci_test.yml

@@ -40,16 +40,16 @@ jobs:
     - name: Install dependencies and package
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install flake8 pytest black pytest-cov
+        python -m pip install flake8 pytest pytest-cov
         NO_MKL=1 python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
         python -c "import sys; print(f'Python {sys.version}')"
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
         python -m pip freeze
-    #- name: Run lint
-    #  run: make lint
+    - name: Run lint
+      run: make lint
     - name: Test with pytest
       run: make test
     - name: Codecov

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: "3.7.7"
+    hooks:
+    - id: flake8
+      args: ["--config=.flake8"]
+- repo: https://github.com/timothycrosley/isort
+  rev: 5.6.1
+  hooks:
+    - id: isort

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2.3.1 (2021-09-30)
+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)*
 Functionality added for NANOGrav 15yr dataset analyses.
 Outlier analysis software moved into separate package.

Makefile

@@ -31,15 +31,11 @@ init:
 	@./.enterprise_extensions/bin/python3 -m pip install -U pip setuptools wheel
 	@./.enterprise_extensions/bin/python3 -m pip install -r requirements.txt -U
 	@./.enterprise_extensions/bin/python3 -m pip install -r requirements_dev.txt -U
+	@./.enterprise_extensions/bin/python3 -m pre_commit install --install-hooks --overwrite
 	@./.enterprise_extensions/bin/python3 -m pip install -e .
 	@echo "run source .enterprise_extensions/bin/activate to activate environment"
 
-
-format:
-	black .
-
 lint:
-	black --check .
 	flake8 .
 
 clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts

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 v0.9.2. https://github.com/nanograv/enterprise_extensions
+>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
 
 ```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         = {v2.2.0}
+  note         = {v2.3.1}
 }
 ```
 

docs/conf.py

@@ -20,6 +20,7 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath('..'))
 
 import enterprise_extensions

enterprise_extensions/__init__.py

@@ -1 +1 @@
-__version__ = "2.3.0"
+__version__ = "2.3.1"

enterprise_extensions/blocks.py

@@ -1,30 +1,26 @@
 # -*- coding: utf-8 -*-
-from __future__ import (absolute_import, division,
-                        print_function, unicode_literals)
-import numpy as np
+
 import types
 
-from enterprise.signals import parameter
-from enterprise.signals import selections
-from enterprise.signals import white_signals
-from enterprise.signals import gp_signals
-from enterprise.signals import utils
+import numpy as np
+from enterprise import constants as const
+from enterprise.signals import deterministic_signals
 from enterprise.signals import gp_bases as gpb
 from enterprise.signals import gp_priors as gpp
-from enterprise.signals import deterministic_signals
-from enterprise import constants as const
-from . import gp_kernels as gpk
-from . import chromatic as chrom
-from . import model_orfs
+from enterprise.signals import (gp_signals, parameter, selections, utils,
+                                white_signals)
 
 from enterprise_extensions import deterministic as ee_deterministic
 
+from . import chromatic as chrom
+from . import gp_kernels as gpk
+from . import model_orfs
+
 __all__ = ['white_noise_block',
            'red_noise_block',
            'bwm_block',
-           'bwm_sglpsr_block'
+           'bwm_sglpsr_block',
            'dm_noise_block',
-           'scattering_noise_block',
            'chromatic_noise_block',
            'common_red_noise_block',
            ]
@@ -169,7 +165,7 @@ def red_noise_block(psd='powerlaw', prior='log-uniform', Tspan=None,
             alpha_adapt = gpp.InvGamma(df/2, df/2, size=1)
             nfreq = parameter.Uniform(-0.5, 10-0.5)
             pl = gpp.t_process_adapt(log10_A=log10_A, gamma=gamma,
-                                    alphas_adapt=alpha_adapt, nfreq=nfreq)
+                                     alphas_adapt=alpha_adapt, nfreq=nfreq)
         elif psd == 'infinitepower':
             pl = gpp.infinitepower()
 
@@ -225,6 +221,7 @@ def red_noise_block(psd='powerlaw', prior='log-uniform', Tspan=None,
 
     return rn
 
+
 def bwm_block(Tmin, Tmax, amp_prior='log-uniform',
               skyloc=None, logmin=-18, logmax=-11,
               name='bwm'):
@@ -272,16 +269,16 @@ def bwm_block(Tmin, Tmax, amp_prior='log-uniform',
         costh = parameter.Constant(skyloc[0])(costh_name)
         phi = parameter.Constant(skyloc[1])(phi_name)
 
-
     # BWM signal
     bwm_wf = ee_deterministic.bwm_delay(log10_h=log10_A_bwm, t0=t0,
-                            cos_gwtheta=costh, gwphi=phi, gwpol=pol)
+                                        cos_gwtheta=costh, gwphi=phi, gwpol=pol)
     bwm = deterministic_signals.Deterministic(bwm_wf, name=name)
 
     return bwm
 
+
 def bwm_sglpsr_block(Tmin, Tmax, amp_prior='log-uniform',
-               logmin=-17, logmax=-12, name='ramp', fixed_sign=None):
+                     logmin=-17, logmax=-12, name='ramp', fixed_sign=None):
 
     if fixed_sign is None:
         sign = parameter.Uniform(-1, 1)("sign")
@@ -297,12 +294,12 @@ def bwm_sglpsr_block(Tmin, Tmax, amp_prior='log-uniform',
     t0_name = '{}_t0'.format(name)
     t0 = parameter.Uniform(Tmin, Tmax)(t0_name)
 
-
-    ramp_wf = ee_deterministic.bwm_sglpsr_delay(log10_A=log10_A_ramp, t0=t0, sign = sign)
+    ramp_wf = ee_deterministic.bwm_sglpsr_delay(log10_A=log10_A_ramp, t0=t0, sign=sign)
     ramp = deterministic_signals.Deterministic(ramp_wf, name=name)
 
     return ramp
 
+
 def dm_noise_block(gp_kernel='diag', psd='powerlaw', nondiag_kernel='periodic',
                    prior='log-uniform', dt=15, df=200,
                    Tspan=None, components=30,
@@ -361,15 +358,15 @@ def dm_noise_block(gp_kernel='diag', psd='powerlaw', nondiag_kernel='periodic',
                 df = 2
                 alphas_dm = gpp.InvGamma(df/2, df/2, size=components)
                 dm_prior = gpp.t_process(log10_A=log10_A_dm, gamma=gamma_dm,
-                                        alphas=alphas_dm)
+                                         alphas=alphas_dm)
             elif psd == 'tprocess_adapt':
                 df = 2
                 alpha_adapt_dm = gpp.InvGamma(df/2, df/2, size=1)
                 nfreq_dm = parameter.Uniform(-0.5, 10-0.5)
                 dm_prior = gpp.t_process_adapt(log10_A=log10_A_dm,
-                                              gamma=gamma_dm,
-                                              alphas_adapt=alpha_adapt_dm,
-                                              nfreq=nfreq_dm)
+                                               gamma=gamma_dm,
+                                               alphas_adapt=alpha_adapt_dm,
+                                               nfreq=nfreq_dm)
 
         if psd == 'spectrum':
             if prior == 'uniform':
@@ -559,14 +556,14 @@ def chromatic_noise_block(gp_kernel='nondiag', psd='powerlaw',
             log10_alpha_wgt = parameter.Uniform(-4, 1)
 
             chm_basis = gpk.get_tf_quantization_matrix(df=df, dt=dt*const.day,
-                                                      dm=True, dm_idx=idx)
+                                                       dm=True, dm_idx=idx)
             chm_prior = gpk.sf_kernel(log10_sigma=log10_sigma,
-                                     log10_ell=log10_ell,
-                                     log10_alpha_wgt=log10_alpha_wgt,
-                                     log10_ell2=log10_ell2)
+                                      log10_ell=log10_ell,
+                                      log10_alpha_wgt=log10_alpha_wgt,
+                                      log10_ell2=log10_ell2)
 
     cgp = gp_signals.BasisGP(chm_prior, chm_basis, name=name+'_gp',
-                              coefficients=coefficients)
+                             coefficients=coefficients)
 
     if include_quadratic:
         # quadratic piece
@@ -580,8 +577,8 @@ def chromatic_noise_block(gp_kernel='nondiag', psd='powerlaw',
 
 def common_red_noise_block(psd='powerlaw', prior='log-uniform',
                            Tspan=None, components=30,
-                           log10_A_val = None, gamma_val=None, delta_val=None,
-                           logmin = None, logmax = None,
+                           log10_A_val=None, gamma_val=None, delta_val=None,
+                           logmin=None, logmax=None,
                            orf=None, orf_ifreq=0, leg_lmax=5,
                            name='gw', coefficients=False,
                            pshift=False, pseed=None):
@@ -632,30 +629,29 @@ def common_red_noise_block(psd='powerlaw', prior='log-uniform',
 
     """
 
-
     orfs = {'crn': None, 'hd': model_orfs.hd_orf(),
             'gw_monopole': model_orfs.gw_monopole_orf(),
             'gw_dipole': model_orfs.gw_dipole_orf(),
             'st': model_orfs.st_orf(),
-            'gt': model_orfs.gt_orf(tau = parameter.Uniform(-1.5,1.5)('tau')),
+            'gt': model_orfs.gt_orf(tau=parameter.Uniform(-1.5, 1.5)('tau')),
             'dipole': model_orfs.dipole_orf(),
             'monopole': model_orfs.monopole_orf(),
-            'param_hd': model_orfs.param_hd_orf(a=parameter.Uniform(-1.5,3.0)('gw_orf_param0'),
-                                     b=parameter.Uniform(-1.0,0.5)('gw_orf_param1'),
-                                     c=parameter.Uniform(-1.0,1.0)('gw_orf_param2')),
-            'spline_orf': model_orfs.spline_orf(params=parameter.Uniform(-0.9,0.9,size=7)('gw_orf_spline')),
-            'bin_orf': model_orfs.bin_orf(params=parameter.Uniform(-1.0,1.0,size=7)('gw_orf_bin')),
+            'param_hd': model_orfs.param_hd_orf(a=parameter.Uniform(-1.5, 3.0)('gw_orf_param0'),
+                                                b=parameter.Uniform(-1.0, 0.5)('gw_orf_param1'),
+                                                c=parameter.Uniform(-1.0, 1.0)('gw_orf_param2')),
+            'spline_orf': model_orfs.spline_orf(params=parameter.Uniform(-0.9, 0.9, size=7)('gw_orf_spline')),
+            'bin_orf': model_orfs.bin_orf(params=parameter.Uniform(-1.0, 1.0, size=7)('gw_orf_bin')),
             'zero_diag_hd': model_orfs.zero_diag_hd(),
             'zero_diag_bin_orf': model_orfs.zero_diag_bin_orf(params=parameter.Uniform(
-                                -1.0,1.0,size=7)('gw_orf_bin_zero_diag')),
-            'freq_hd': model_orfs.freq_hd(params=[components,orf_ifreq]),
+                -1.0, 1.0, size=7)('gw_orf_bin_zero_diag')),
+            'freq_hd': model_orfs.freq_hd(params=[components, orf_ifreq]),
             'legendre_orf': model_orfs.legendre_orf(params=parameter.Uniform(
-                                            -1.0,1.0,size=leg_lmax+1)('gw_orf_legendre')),
+                -1.0, 1.0, size=leg_lmax+1)('gw_orf_legendre')),
             'zero_diag_legendre_orf': model_orfs.zero_diag_legendre_orf(params=parameter.Uniform(
-                                            -1.0,1.0,size=leg_lmax+1)('gw_orf_legendre_zero_diag'))}
+                -1.0, 1.0, size=leg_lmax+1)('gw_orf_legendre_zero_diag'))}
 
     # common red noise parameters
-    if psd in ['powerlaw', 'turnover', 'turnover_knee','broken_powerlaw']:
+    if psd in ['powerlaw', 'turnover', 'turnover_knee', 'broken_powerlaw']:
         amp_name = '{}_log10_A'.format(name)
         if log10_A_val is not None:
             log10_Agw = parameter.Constant(log10_A_val)(amp_name)
@@ -724,8 +720,8 @@ def common_red_noise_block(psd='powerlaw', prior='log-uniform',
             delta_gw = parameter.Uniform(-2, 0)(delta_name)
             lfk_gw = parameter.Uniform(-8, -7)(lfk_name)
             cpl = gpp.turnover_knee(log10_A=log10_Agw, gamma=gamma_gw,
-                                   lfb=lfb_gw, lfk=lfk_gw,
-                                   kappa=kappa_gw, delta=delta_gw)
+                                    lfb=lfb_gw, lfk=lfk_gw,
+                                    kappa=kappa_gw, delta=delta_gw)
 
     if psd == 'spectrum':
         rho_name = '{}_log10_rho'.format(name)
@@ -744,14 +740,14 @@ def common_red_noise_block(psd='powerlaw', prior='log-uniform',
     elif orf in orfs.keys():
         if orf == 'crn':
             crn = gp_signals.FourierBasisGP(cpl, coefficients=coefficients,
-                                        components=components, Tspan=Tspan,
-                                        name=name, pshift=pshift, pseed=pseed)
+                                            components=components, Tspan=Tspan,
+                                            name=name, pshift=pshift, pseed=pseed)
         else:
             crn = gp_signals.FourierBasisCommonGP(cpl, orfs[orf],
-                                                components=components,
-                                                Tspan=Tspan,
-                                                name=name, pshift=pshift,
-                                                pseed=pseed)
+                                                  components=components,
+                                                  Tspan=Tspan,
+                                                  name=name, pshift=pshift,
+                                                  pseed=pseed)
     elif isinstance(orf, types.FunctionType):
         crn = gp_signals.FourierBasisCommonGP(cpl, orf,
                                               components=components,

enterprise_extensions/chromatic/__init__.py

@@ -1,5 +1,3 @@
 # -*- coding: utf-8 -*-
-from __future__ import (absolute_import, division,
-                        print_function, unicode_literals)
 
-from .chromatic import *
+from .chromatic import *  # noqa: F401, F403