Merge branch 'gwastro:master' into master

.github/workflows/basic-tests.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         test-type: [unittest, search, docs]
     steps:
     - uses: actions/checkout@v3
@@ -50,7 +50,7 @@ jobs:
         export LAL_DATA_PATH=$PWD
         tox -e py-inference
     - name: store documentation page
-      if: matrix.test-type == 'docs' && matrix.python-version == '3.8'
+      if: matrix.test-type == 'docs' && matrix.python-version == '3.12'
       uses: actions/upload-artifact@v2
       with:
         name: documentation-page

.github/workflows/distribution.yml

@@ -20,13 +20,13 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
+          CIBW_BUILD: cp39-* cp310-* cp311-* cp312-*
           CIBW_SKIP: "*musllinux*"
           CIBW_ARCHS_MACOS: x86_64 arm64
       - uses: actions/upload-artifact@v2
@@ -40,10 +40,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - uses: actions/download-artifact@v2
       with:
         path: ./

.github/workflows/inference-workflow.yml

@@ -10,7 +10,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

.github/workflows/mac-test.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 4
       matrix:
         os: [macos-12]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -25,5 +25,4 @@ jobs:
         pip install --upgrade pip setuptools "tox<4.0.0"
     - name: run basic pycbc test suite
       run: |
-        sudo chmod -R 777 /usr/local/miniconda/
         tox -e py-unittest

.github/workflows/search-workflow.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

.github/workflows/tmpltbank-workflow.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

.github/workflows/tut-test.yml

@@ -13,7 +13,7 @@ jobs:
       max-parallel: 60
       matrix:
         os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/workflow-tests.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: install condor
       run: |
         wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -

bin/all_sky_search/pycbc_cut_merge_triggers_to_tmpltbank

@@ -21,12 +21,12 @@ Reduce a MERGE triggers file to a reduced template bank
 """
 
 import logging
-import imp
 import argparse
 import numpy
 import h5py
 import pycbc
 from pycbc.io import HFile
+from pycbc import load_source
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
@@ -50,7 +50,7 @@ pycbc.init_logging(opt.verbose)
 
 bank_fd = HFile(opt.full_template_bank, 'r')
 
-modl = imp.load_source('filter_func', opt.filter_func_file)
+modl = load_source('filter_func', opt.filter_func_file)
 func = modl.filter_tmpltbank
 bool_arr = func(bank_fd)
 

bin/all_sky_search/pycbc_fit_sngls_by_template

@@ -352,6 +352,9 @@ sigma_regions = trigf[args.ifo + '/sigmasq_template'][:]
 median_sigma = []
 for reg in sigma_regions:
     strigs = trigf[args.ifo + '/sigmasq'][reg]
+    if len(strigs) == 0:
+        median_sigma.append(np.nan)
+        continue
     median_sigma.append(np.median(strigs) ** 0.5)
 
 outfile = HFile(args.output, 'w')

bin/all_sky_search/pycbc_fit_sngls_over_multiparam

@@ -342,14 +342,20 @@ if len(args.template_fit_file) > 1:
     nasum = nabove[tidsort].cumsum()
     invsum = invalphan[tidsort].cumsum()
     ntsum = ntotal[tidsort].cumsum()
-    mssum = median_sigma[tidsort].cumsum()
     num = right - left
 
     tid = tid_unique
     nabove = (nasum[right] - nasum[left]) / num
     invalphan = (invsum[right] - invsum[left]) / num
     ntotal = (ntsum[right] - ntsum[left]) / num
-    median_sigma = (mssum[right] - mssum[left]) / num
+    if median_sigma is not None:
+        # Median sigma is a special one - we need to make sure that
+        # we do not mess things up when nan values are given, so we
+        # can't use the special cumsum fast option
+        median_sigma = [
+            numpy.nanmean(median_sigma[tidsort[l:r]])
+            for l, r in zip(left, right)
+        ]
 
 if args.output_fits_by_template:
     # Store fit_by_template values for output file

bin/all_sky_search/pycbc_reduce_template_bank

@@ -23,10 +23,10 @@ Reduce a template bank using some input parameter cuts
 
 import numpy
 import logging
-import imp
 import argparse
 import pycbc
 from pycbc.io import HFile
+from pycbc import load_source
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
@@ -48,7 +48,7 @@ pycbc.init_logging(opt.verbose)
 
 bank_fd = HFile(opt.input_bank, 'r')
 
-modl = imp.load_source('filter_func', opt.filter_func_file)
+modl = load_source('filter_func', opt.filter_func_file)
 func = modl.filter_tmpltbank
 bool_arr = func(bank_fd)
 

bin/live/pycbc_live_plot_single_significance_fits

@@ -131,10 +131,10 @@ for ifo in all_ifos:
         continue
 
     # Keep track of some maxima for use in setting the plot limits
-    maxstat = stats[ifo].max()
+    maxstat = np.nanmax(stats[ifo])
     max_rate = 0
 
-    statrange = maxstat - max(stats[ifo].min(), fit_threshold[ifo])
+    statrange = maxstat - max(np.nanmin(stats[ifo]), fit_threshold[ifo])
     plotmax = maxstat + statrange * 0.05
 
     plotbins = np.linspace(fit_threshold[ifo], plotmax, 400)

bin/live/pycbc_live_single_significance_fits

@@ -98,13 +98,6 @@ args.trigger_cuts = args.trigger_cuts or []
 args.trigger_cuts.append(f"end_time:{args.gps_start_time}:lower_inc")
 args.trigger_cuts.append(f"end_time:{args.gps_end_time}:upper_inc")
 
-# Efficiency saving: add SNR cut before any others as sngl_ranking can
-# only be less than SNR.
-args.trigger_cuts.insert(0, f"snr:{args.fit_threshold}:lower_inc")
-
-# Cut triggers with sngl-ranking below threshold
-args.trigger_cuts.append(f"{args.sngl_ranking}:{args.fit_threshold}:lower_inc")
-
 trigger_cut_dict, template_cut_dict = cuts.ingest_cuts_option_group(args)
 
 logging.info("Setting up duration bins")