Merge pull request #4 from transientlunatic/v0.4-preview

Create v0.4

.github/workflows/documentation.yaml

@@ -0,0 +1,37 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - master
+      - v*-preview
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Build HTML Docs
+      run: |
+        sudo apt install pandoc
+        pip install sphinx sphinx-multiversion
+        pip install kentigern
+        pip install -r requirements.txt
+        pip install -r requirements_dev.txt
+        pip install .
+        cd docs
+        make html
+        
+    - name: SCP Deploy HTML Docs
+      uses: horochx/[email protected]
+      with:
+        local: docs/_build/html/*
+        remote: /home/danwilliams/code.daniel-williams.co.uk/heron/${{ github.ref_name }}
+        host: ${{ secrets.sshhost }}
+        user: ${{ secrets.sshuser }}
+        key: ${{ secrets.sshkey }}

.github/workflows/review.yml

@@ -1,47 +1,29 @@
-# This is a basic workflow to help you get started with Actions
-
-name: CI
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
+name: Tests
 on:
   push:
-    branches: [ review ]
+    branches:
+      - master
+      - v*-preview
   pull_request:
-    branches: [ review ]
+    branches:
+      - master
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
+  test:
     runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     - uses: actions/checkout@v2
 
     - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
-        
-    - name: Build HTML Docs
+
+    - name: Install dependencies
       run: |
-        sudo apt install pandoc
-        pip install sphinx
-        pip install kentigern
         pip install -r requirements.txt
-        pip install -r requirements_dev.txt
-        pip install .
-        cd docs
-        make html
+        pip install -r requirements_test.txt
         
-    - name: SCP Deploy HTML Docs
-      uses: horochx/[email protected]
-      with:
-        local: docs/_build/html/*
-        remote: /home/danwilliams/code.daniel-williams.co.uk/heron/review
-        host: ${{ secrets.sshhost }}
-        user: ${{ secrets.sshuser }}
-        key: ${{ secrets.sshkey }}
+    - name: Run Tests
+      run: |
+        python -m unittest discover tests/

heron/inference.py

@@ -6,7 +6,7 @@
 
 import click
 
-from gwpy.timeseries import TimeSeries
+from .types import TimeSeries
 import astropy.units as u
 
 from nessai.flowsampler import FlowSampler
@@ -84,6 +84,7 @@ def heron_inference(settings):
     if "data files" in settings.get("data", {}):
         # Load frame files from disk
         for ifo in settings["interferometers"]:
+            print(f"Loading {ifo} data")
             logger.info(
                 f"Loading {ifo} data from "
                 f"{settings['data']['data files'][ifo]}/{settings['data']['channels'][ifo]}"
@@ -93,14 +94,16 @@ def heron_inference(settings):
                 channel=settings["data"]["channels"][ifo],
                 format="gwf",
             )
-    elif "injection" in other_settings:
-        pass
+    #elif "injection" in other_settings:
+    #    pass
 
     # Make Likelihood
     if len(settings["interferometers"]) > 1:
         likelihoods = []
+        print("Creating likelihoods")
         waveform_model = KNOWN_WAVEFORMS[settings["waveform"]["model"]]()
         for ifo in settings["interferometers"]:
+            print(f"\t {ifo}")
             likelihoods.append(
                 KNOWN_LIKELIHOODS[settings.get("likelihood").get("function")](
                     data[ifo],
@@ -113,7 +116,7 @@ def heron_inference(settings):
                     ),
                 )
             )
-            likelihood = MultiDetector(*likelihoods)
+        likelihood = MultiDetector(*likelihoods)
 
     priors = heron.priors.PriorDict()
     priors.from_dictionary(settings["priors"])

heron/injection.py

@@ -20,12 +20,13 @@
 
 
 def make_injection(
-        waveform=IMRPhenomPv2,
-        injection_parameters={},
-        times=None,
-        detectors=None,
-        framefile=None,
-        psdfile=None,
+    waveform=IMRPhenomPv2,
+    injection_parameters={},
+    duration=32,
+    sample_rate=4096,
+    times=None,
+    detectors=None,
+    framefile=None,
 ):
 
     parameters = {"ra": 0, "dec": 0, "psi": 0, "theta_jn": 0, "phase": 0}
@@ -34,7 +35,7 @@ def make_injection(
     waveform = waveform()
 
     if times is None:
-        times = np.linspace(-0.5, 0.1, int(0.6 * 4096))
+        times = np.linspace(parameters['gpstime']-duration+2, parameters['gpstime']+2, int(duration * sample_rate))
     waveform = waveform.time_domain(
         parameters,
         times=times,
@@ -45,16 +46,19 @@ def make_injection(
         logger.info(f"Making injection for {detector}")
         psd_model = KNOWN_PSDS[psd_model]()
         detector = KNOWN_IFOS[detector]()
+        if times is None:
+            times = waveform['plus'].times.value
         data = psd_model.time_series(times)
+        print(data)
 
         channel = f"{detector.abbreviation}:Injection"
         injection = data + waveform.project(detector)
         injection.channel = channel
         injections[detector.abbreviation] = injection
-        likelihood = TimeDomainLikelihood(injection, psd=psd_model)
-        snr = likelihood.snr(waveform.project(detector))
+        # likelihood = TimeDomainLikelihood(injection, psd=psd_model)
+        # snr = likelihood.snr(waveform.project(detector))
 
-        logger.info(f"Optimal Filter SNR: {snr}")
+        #logger.info(f"Optimal Filter SNR: {snr}")
 
         if framefile:
             filename = f"{detector.abbreviation}_{framefile}.gwf"
@@ -115,21 +119,20 @@ def make_injection_zero_noise(
             logger.info(f"Saving framefile to {filename}")
             injection.write(filename, format="gwf")
 
+    return injections
+
 def injection_parameters_add_units(parameters):
     UNITS = {"luminosity_distance": u.megaparsec, "m1": u.solMass, "m2": u.solMass}
 
     for parameter, value in parameters.items():
-        if not isinstance(value, u.Quantity):
+        if not isinstance(value, u.Quantity) and (parameter in UNITS.keys()):
             parameters[parameter] = value * UNITS[parameter]
     return parameters
 
 
 @click.command()
 @click.option("--settings")
 def injection(settings):
-
-    click.secho("Creating an injection with the heron injection engine")
-
     settings = load_yaml(settings)
 
     if "logging" in settings:
@@ -153,6 +156,8 @@ def injection(settings):
     }
     injections = make_injection(
         waveform=IMRPhenomPv2,
+        duration=settings["duration"],
+        sample_rate=settings["sample rate"],
         injection_parameters=parameters,
         detectors=detector_dict,
         framefile="injection",