Prepare for release 2.8.6

.github/workflows/bank-compress-workflow.yml

@@ -34,7 +34,7 @@ jobs:
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
-        python -m pip install --upgrade pip setuptools
+        python -m pip install --upgrade pip "setuptools<82.0.0"
         pip install GitPython # This shouldn't really be needed!
         pip install -r requirements.txt
         pip install .

.github/workflows/basic-tests.yml

@@ -25,7 +25,7 @@ jobs:
       run: |
         sudo apt-get -o Acquire::Retries=3 update
         sudo apt-get -o Acquire::Retries=3 install *fftw3* mpi intel-mkl* graphviz
-        pip install tox pip setuptools --upgrade
+        pip install tox pip "setuptools<82.0.0" --upgrade
     - name: Cache LAL auxiliary data files
       id: cache-lal-aux-data
       uses: actions/cache@v4
@@ -41,6 +41,23 @@ jobs:
           --remote-name https://zenodo.org/records/14999310/files/SEOBNRv4ROM_v2.0.hdf5 \
           --remote-name https://zenodo.org/records/14999310/files/SEOBNRv4ROM_v3.0.hdf5
         popd
+    - name: Cache example GW data
+      id: cache-example-gw-data
+      uses: actions/cache@v4
+      with:
+        key: example-gw-data
+        path: |
+          docs/_include/*_TDI_v2.gwf
+          docs/_include/*_GWOSC_4KHZ_R1-1126257415-4096.gwf
+          docs/_include/*_LOSC_CLN_4_V1-1187007040-2048.gwf
+          examples/inference/lisa_smbhb_ldc/*_psd.txt
+          examples/inference/lisa_smbhb_ldc/*_TDI_v2.gwf
+          examples/inference/lisa_smbhb_ldc/MBHB_params_v2_LISA_frame.pkl
+          examples/inference/margtime/*.gwf
+          examples/inference/multisignal/*.gwf
+          examples/inference/relative/*.gwf
+          examples/inference/relmarg/*.gwf
+          examples/inference/single/*.gwf
     - name: run pycbc test suite
       run: |
         export LAL_DATA_PATH=$HOME/lal_aux_data

.github/workflows/inference-workflow.yml

@@ -29,7 +29,7 @@ jobs:
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
-        python -m pip install --upgrade pip setuptools
+        python -m pip install --upgrade pip "setuptools<82.0.0"
         pip install GitPython # This shouldn't really be needed!
         pip install -r requirements.txt
         pip install .

.github/workflows/mac-test.yml

@@ -50,7 +50,7 @@ jobs:
       run: |
         conda install \
             pip \
-            setuptools \
+            "setuptools<82.0.0" \
             tox
 
     - name: Run basic pycbc test suite

.github/workflows/search-workflow.yml

@@ -34,7 +34,7 @@ jobs:
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
-        python -m pip install --upgrade pip setuptools
+        python -m pip install --upgrade pip "setuptools<82.0.0"
         pip install GitPython # This shouldn't really be needed!
         pip install -r requirements.txt
         pip install .

.github/workflows/tmpltbank-workflow.yml

@@ -33,7 +33,7 @@ jobs:
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
-        python -m pip install --upgrade pip setuptools
+        python -m pip install --upgrade pip "setuptools<82.0.0"
         pip install GitPython # This shouldn't really be needed!
         pip install -r requirements.txt
         pip install sbank

.github/workflows/tut-test.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         sudo apt-get -o Acquire::Retries=3 update
         sudo apt-get -o Acquire::Retries=3 install *fftw3* mpi intel-mkl*
-        pip install tox pip setuptools notebook --upgrade
+        pip install tox pip "setuptools<82.0.0" notebook --upgrade
         pip install .
     - name: retrieving pycbc tutorials
       run: |

.github/workflows/workflow-tests.yml

@@ -38,7 +38,7 @@ jobs:
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
-        python -m pip install --upgrade pip setuptools
+        python -m pip install --upgrade pip "setuptools<82.0.0"
         pip install GitPython # This shouldn't really be needed!
         pip install -r requirements.txt
         pip install .

Dockerfile

@@ -8,7 +8,7 @@ ADD docker/etc/cvmfs/config-osg.opensciencegrid.org.conf /etc/cvmfs/config-osg.o
 
 # Set up extra repositories
 RUN <<EOF
-dnf -y install https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest.noarch.rpm
+dnf -y install https://cvmrepo.s3.cern.ch/cvmrepo/yum/cvmfs-release-latest.noarch.rpm
 dnf -y install cvmfs cvmfs-config-default
 dnf makecache
 dnf -y groupinstall "Development Tools" "Scientific Support"
@@ -36,7 +36,7 @@ dnf -y install \
     which \
     zlib-devel
 alternatives --set python /usr/bin/python3.9
-python -m pip install --upgrade pip setuptools wheel cython
+python -m pip install --upgrade pip "setuptools<82.0.0" wheel cython
 python -m pip install mkl ipython jupyter jupyterhub jupyterlab lalsuite
 dnf -y install https://repo.opensciencegrid.org/osg/3.5/el8/testing/x86_64/osg-wn-client-3.5-5.osg35.el8.noarch.rpm
 # force old version of stashcp as a workaround to

bin/pygrb/pycbc_pygrb_minifollowups

@@ -27,6 +27,7 @@ import os
 import argparse
 import logging
 
+from igwn_segments import segmentlist
 import pycbc.workflow as wf
 from pycbc.workflow.core import FileList, resolve_url_to_file
 import pycbc.workflow.minifollowups as mini
@@ -181,11 +182,17 @@ if veto_file:
     veto_file = os.path.join(start_rundir, args.veto_file)
     veto_file = wf.resolve_url_to_file(veto_file)
 
+seg_file_abs_paths = [os.path.join(start_rundir, f) for f in args.seg_files]
+
 # Convert the segments files to a FileList
-seg_files = wf.FileList([
-    wf.resolve_url_to_file(os.path.join(start_rundir, f))
-    for f in args.seg_files
-])
+seg_files = wf.FileList(
+    [wf.resolve_url_to_file(f) for f in seg_file_abs_paths]
+)
+
+# The Q-scan jobs need to be told the valid science segments to deal with
+# triggers near the boundaries correctly. We use the offsource segment as a
+# proxy for the valid science segments, and ignore vetoed time inside it.
+valid_segs = segmentlist([ppu._read_seg_files(seg_file_abs_paths)['off']])
 
 # (Loudest) off/on-source events are on time-slid data so the
 # try will succeed, as it finds the time shift columns.
@@ -220,7 +227,8 @@ for num_event in range(num_events):
         for ifo in ifos:
             files += mini.make_qscan_plot(workflow, ifo, gps_time,
                                           args.output_dir,
-                                          tags=tags)
+                                          tags=tags,
+                                          data_segments=valid_segs)
     # Handle off/on-source loudest triggers follow-up (which may be on slid
     # data in the case of the off-source)
     else:
@@ -235,7 +243,8 @@ for num_event in range(num_events):
                                           tags=tags)
             files += mini.make_qscan_plot(workflow, ifo, ifo_time,
                                           args.output_dir,
-                                          tags=tags)
+                                          tags=tags,
+                                          data_segments=valid_segs)
 
     layouts += list(layout.grouper(files, 2))
 

bin/pygrb/pycbc_pygrb_page_tables

@@ -579,7 +579,7 @@ if onsource_file:
 
     # Table data: assemble human readable message when no trigger is recovered
     if not loud_on_bestnr_trigs:
-        td = [list("-" * len(format_strings))]
+        td = [["-"] for _ in format_strings]
         td[0][0] = "There are no events"
     td = [np.asarray(d) for d in td]
     html_table = pycbc.results.html_table(td, th,

bin/pygrb/pycbc_pygrb_plot_stats_distribution

@@ -51,7 +51,7 @@ parser = ppu.pygrb_initialize_plot_parser(description=__doc__)
 parser.add_argument("-F", "--trig-file", action="store", required=True,
                     help="Location of off-source trigger file")
 parser.add_argument("-x", "--x-variable", required=True,
-                    choices=["bestnr", "snr", "snruncut"],
+                    choices=["bestnr", "snr", "snraftercuts"],
                     help="Quantity to plot on the horizontal axis.")
 ppu.pygrb_add_bestnr_cut_opt(parser)
 ppu.pygrb_add_slide_opts(parser)
@@ -114,13 +114,13 @@ trig_data = ppu.extract_trig_properties(
 # Calculate SNR and BestNR values and maxima
 time_veto_max_snr = {}
 time_veto_max_bestnr = {}
-time_veto_max_snr_uncut = {}
+time_veto_max_snr_aftercuts = {}
 
 for slide_id in slide_dict:
     num_slide_segs = len(trial_dict[slide_id])
     time_veto_max_snr[slide_id] = np.zeros(num_slide_segs)
     time_veto_max_bestnr[slide_id] = np.zeros(num_slide_segs)
-    time_veto_max_snr_uncut[slide_id] = np.zeros(num_slide_segs)
+    time_veto_max_snr_aftercuts[slide_id] = np.zeros(num_slide_segs)
 
 for slide_id in slide_dict:
     for j, trial in enumerate(trial_dict[slide_id]):
@@ -134,25 +134,25 @@ for slide_id in slide_dict:
         # Max BestNR
         time_veto_max_bestnr[slide_id][j] = \
             max(trig_data[keys[2]][slide_id][trial_cut])
-        # Max SNR for triggers passing SBVs
-        sbv_cut = trig_data[keys[2]][slide_id][:] != 0
+        # Max SNR for triggers passing the cut on reweighted SNR
+        sbv_cut = trig_data[keys[2]][slide_id][:] >= opts.newsnr_threshold
         if not (trial_cut & sbv_cut).any():
             continue
-        time_veto_max_snr_uncut[slide_id][j] =\
+        time_veto_max_snr_aftercuts[slide_id][j] =\
             max(trig_data[keys[1]][slide_id][trial_cut & sbv_cut])
 
 # This is the data that will be plotted
 full_time_veto_max_snr = ppu.sort_stat(time_veto_max_snr)
-full_time_veto_max_snr_uncut = ppu.sort_stat(time_veto_max_snr_uncut)
+full_time_veto_max_snr_aftercuts = ppu.sort_stat(time_veto_max_snr_aftercuts)
 _, _, full_time_veto_max_bestnr = \
     ppu.max_median_stat(slide_dict, time_veto_max_bestnr, trig_data[keys[2]],
                         total_trials)
 # The 0.'s here force the histograms to start at (0, 1) if no trial
 # returned a no-event (i.e., BestNR = 0)
 if full_time_veto_max_bestnr[0] != 0.:
     full_time_veto_max_snr = np.concatenate(([0.], full_time_veto_max_snr))
-    full_time_veto_max_snr_uncut = \
-        np.concatenate(([0.], full_time_veto_max_snr_uncut))
+    full_time_veto_max_snr_aftercuts = \
+        np.concatenate(([0.], full_time_veto_max_snr_aftercuts))
     full_time_veto_max_bestnr = \
         np.concatenate(([0.], full_time_veto_max_bestnr))
 
@@ -164,10 +164,10 @@ logging.info("SNR and bestNR maxima calculated.")
 # =========
 x_label_dict = {"bestnr": "BestNR",
                 "snr": "SNR",
-                "snruncut": "SNR after signal based vetoes"}
+                "snraftercuts": "SNR after signal based vetoes"}
 data_dict = {"bestnr": full_time_veto_max_bestnr,
              "snr": full_time_veto_max_snr,
-             "snruncut": full_time_veto_max_snr_uncut}
+             "snraftercuts": full_time_veto_max_snr_aftercuts}
 fig = plt.figure()
 ax = fig.gca()
 ax.grid(True)

examples/inference/lisa_smbhb_ldc/get.sh

@@ -1,16 +1,24 @@
 set -e
 
+download_if_absent() {
+    local URL="$1"
+    local FILENAME=$(basename "$URL")
+    if [ ! -f "$FILENAME" ]; then
+        echo "Downloading $FILENAME"
+        curl -O -L --show-error --silent "$URL"
+    else
+        echo "File $FILENAME already exists, download skipped"
+    fi
+}
+
 for channel in A E T
 do
     strain_file=${channel}_TDI_v2.gwf
-    test -f ${strain_file} && continue
-    curl -LO --show-error --silent https://zenodo.org/record/7497853/files/${strain_file}
+    download_if_absent https://zenodo.org/record/7497853/files/${strain_file}
 
     psd_file=${channel}_psd.txt
-    test -f ${psd_file} && continue
-    curl -LO --show-error --silent https://zenodo.org/record/7497853/files/${psd_file}
+    download_if_absent https://zenodo.org/record/7497853/files/${psd_file}
 done
 
 params_file=MBHB_params_v2_LISA_frame.pkl 
-test -f ${params_file} && continue
-curl -LO --show-error --silent https://zenodo.org/record/7497853/files/${params_file}
+download_if_absent https://zenodo.org/record/7497853/files/${params_file}

examples/inference/margtime/get.sh

@@ -5,5 +5,5 @@ do
     file=${ifo}_GWOSC_4KHZ_R1-1126257415-4096.gwf
     test -f ${file} && continue
     curl -O -L --show-error --silent \
-        https://www.gwosc.org/eventapi/html/GWTC-1-confident/GW150914/v3/${ifo}_GWOSC_4KHZ_R1-1126257415-4096.gwf
+        https://www.gwosc.org/eventapi/html/GWTC-1-confident/GW150914/v3/${file}
 done

examples/inference/multisignal/get.sh

@@ -4,5 +4,5 @@ for ifo in H-H1 L-L1 V-V1
 do
     file=${ifo}_LOSC_CLN_4_V1-1187007040-2048.gwf
     test -f ${file} && continue
-    curl -O --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
+    curl -O -L --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
 done

examples/inference/relative/get.sh

@@ -4,5 +4,5 @@ for ifo in H-H1 L-L1 V-V1
 do
     file=${ifo}_LOSC_CLN_4_V1-1187007040-2048.gwf
     test -f ${file} && continue
-    curl -O --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
+    curl -O -L --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
 done

examples/inference/relmarg/get.sh

@@ -2,5 +2,5 @@ for ifo in H-H1 L-L1 V-V1
 do
     file=${ifo}_LOSC_CLN_4_V1-1187007040-2048.gwf
     test -f ${file} && continue
-    curl -O --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
+    curl -O -L --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
 done

examples/inference/single/get.sh

@@ -4,5 +4,5 @@ for ifo in H-H1 L-L1 V-V1
 do
     file=${ifo}_LOSC_CLN_4_V1-1187007040-2048.gwf
     test -f ${file} && continue
-    curl -O --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
+    curl -O -L --show-error --silent https://dcc.ligo.org/public/0146/P1700349/001/${file}
 done