Merge branch 'v1.1.0' into restructure

.pre-commit-config.yaml

@@ -2,10 +2,10 @@ default_language_version:
     python: python3
 repos:
 -   repo: https://github.com/ambv/black
-    rev: 22.3.0
+    rev: 22.6.0
     hooks:
     - id: black
-      language_version: python3
+      language_version: python3.8
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:

CHANGELOG.md

 # All notable changes will be documented in this file
 
+## v1.1.0 : 2022-09-07
+- remove convert_to_flat_in_component_mass (!118)
+-  make compatible with bilby==1.1.5 (!112)
+-  Calculate `log_prior` when constructing result posterior (!111)
+-  refactor CI workflows (!107)
+
 ## v1.0.1 : 2021-05-24
 - Adjust input parsing to handle sampling seed (!102)
 - Normalise string-formats to f-strings (!101)
@@ -13,7 +19,7 @@
 - Resolve "Matplotlib use 'agg' backend" (!89)
 - Make checkpoint backup before overwriting (!90)
 - Update docs with new install instructions and citations (1709d04d)
-- Add Conda badge (!87) 
+- Add Conda badge (!87)
 
 ## v1.0.0 : 2020-11-25
 - Update GW examples + add tutorial notebooks (e59e7068)

docs/examples.rst

@@ -75,6 +75,7 @@ To analyse GW170817 with Parallel Bilby you may use the following :code:`ini` fi
     :code: INI
 
 In this example we require the user to manually download the data for analysis.
+
 The priors are contained in a separate :code:`prior` file for this analysis:
 
 .. include:: ../examples/GW170817_IMRPhenomPv2_NRTidal/GW170817.prior

docs/installation.rst

@@ -14,7 +14,7 @@ Alternatively, you can install :code:`Parallel Bilby` with :code:`conda`
 
 .. code-block:: console
 
-    $ conda install -c conda-forge parallel_bilby
+    $ conda install -c conda-forge parallel-bilby
 
 
 Dependencies

parallel_bilby/parser.py

@@ -126,7 +126,7 @@ def _add_dynesty_settings_to_parser(parser):
     )
     dynesty_group.add_argument(
         "--max-its",
-        default=10 ** 10,
+        default=10**10,
         type=int,
         help="Maximum number of iterations to sample for (default=1.e10)",
     )

parallel_bilby/utils.py

@@ -4,6 +4,7 @@ import sys
 import timeit
 
 import bilby
+from dynesty.results import get_print_fn_args
 
 logger = bilby.core.utils.logger
 
@@ -55,3 +56,16 @@ def stopwatch(method):
         return result
 
     return timed
+
+
+def dynesty_print_fn_fallback(**kwargs):
+    """Logs will look like:
+    #:282|eff(%):26.406|logl*:-inf<-160.2<inf|logz:-165.5+/-0.1|dlogz:1038.1>0.1
+    """
+    # copied from dynesty
+    # https://github.com/joshspeagle/dynesty/blob/master/py/dynesty/results.py
+    niter, short_str, mid_str, long_str = get_print_fn_args(**kwargs)
+    custom_str = [f"#: {niter:d}"] + mid_str
+    custom_str = "|".join(custom_str).replace(" ", "")
+    sys.stdout.write("\033[K" + custom_str + "\r")
+    sys.stdout.flush()

setup.py

@@ -101,6 +101,7 @@ setup(
         "mpi4py>3.0.0",
         "jinja2",
     ],
+    extras_require={"test": ["mock", "pytest-cov"]},
     entry_points={
         "console_scripts": [
             "parallel_bilby_generation=parallel_bilby.generation:main",

tests/test_files/out_GW150914/data/GW150914_prior.json

@@ -9,7 +9,7 @@
       "name": "mass_ratio",
       "latex_label": "$q$",
       "unit": null,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "chirp_mass": {
@@ -21,8 +21,8 @@
       "maximum": 31,
       "name": "chirp_mass",
       "latex_label": "$\\mathcal{M}$",
-      "unit": "$M_{\\odot}$",
-      "boundary": "reflective"
+      "unit": null,
+      "boundary": null
     }
   },
   "mass_1": {
@@ -59,7 +59,7 @@
       "name": "a_1",
       "latex_label": "$a_1$",
       "unit": null,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "a_2": {
@@ -72,7 +72,7 @@
       "name": "a_2",
       "latex_label": "$a_2$",
       "unit": null,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "tilt_1": {
@@ -80,12 +80,12 @@
     "__module__": "bilby.core.prior.analytical",
     "__name__": "Sine",
     "kwargs": {
+      "minimum": 0,
+      "maximum": 3.141592653589793,
       "name": "tilt_1",
       "latex_label": "$\\theta_1$",
       "unit": null,
-      "minimum": 0,
-      "maximum": 3.141592653589793,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "tilt_2": {
@@ -93,12 +93,12 @@
     "__module__": "bilby.core.prior.analytical",
     "__name__": "Sine",
     "kwargs": {
+      "minimum": 0,
+      "maximum": 3.141592653589793,
       "name": "tilt_2",
       "latex_label": "$\\theta_2$",
       "unit": null,
-      "minimum": 0,
-      "maximum": 3.141592653589793,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "phi_12": {
@@ -137,7 +137,7 @@
       "maximum": 2000,
       "name": "luminosity_distance",
       "latex_label": "$d_L$",
-      "unit": "Mpc",
+      "unit": null,
       "boundary": null
     }
   },
@@ -146,12 +146,12 @@
     "__module__": "bilby.core.prior.analytical",
     "__name__": "Cosine",
     "kwargs": {
+      "minimum": -1.5707963267948966,
+      "maximum": 1.5707963267948966,
       "name": "dec",
       "latex_label": "$\\mathrm{DEC}$",
       "unit": null,
-      "minimum": -1.5707963267948966,
-      "maximum": 1.5707963267948966,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "ra": {
@@ -172,12 +172,12 @@
     "__module__": "bilby.core.prior.analytical",
     "__name__": "Sine",
     "kwargs": {
+      "minimum": 0,
+      "maximum": 3.141592653589793,
       "name": "theta_jn",
       "latex_label": "$\\theta_{JN}$",
       "unit": null,
-      "minimum": 0,
-      "maximum": 3.141592653589793,
-      "boundary": "reflective"
+      "boundary": null
     }
   },
   "psi": {