V239 changes (#5031)

* Save statmap significance fits information (#4951) * Report significance fit info in sngls_findtrigs * Report significance calculation info in statmap jobs * Fix typo, fix test * TD comments, some tidying up * neaten comments * comment fix --------- Co-authored-by: Thomas Dent <[email protected]> * index issue (#5018) * Bump to v2.3.9 * Updating pegasus_sites * Ensure v2.3.8 pycbc_inspiral * Missing " in updating singularity image * Fix [hopefully] documentation failure (#4901) * try macos latest version (#4922) * try macos latest version * move to update macos on build as well * Fix mac tests with conda (#4946) * tox: fix tox integration with conda use setup-miniconda github action and specify more packages in conda_deps for each testenv * tox: install ligo-segments and python-ligo-lw with conda these packages don't install cleanly with pypi, but the conda packages have patches * test: use numpy.longdouble instead of float128 float128 isn't available on macOS ARM64 * tox: clean up duplicate package lists * ci: unpin tox * tox: further simplify duplicate configuration * Use old stashcp * Undo hardcode singularity image * Issue in rebasing(?) * Don't run on 3.8 * Used the wrong version ... somehow * Don't build for 3.12 * Try not building mac wheels * Don't try and support BBHx * CHange optimization * Avoid lalsuite 7.25 --------- Co-authored-by: Gareth S Cabourn Davies <[email protected]> Co-authored-by: Thomas Dent <[email protected]> Co-authored-by: Alex Nitz <[email protected]> Co-authored-by: Duncan Macleod <[email protected]>
gwastro · Feb 11, 2025 · 5593465 · 5593465
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diff --git a/.github/workflows/basic-tests.yml b/.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']
         test-type: [unittest, search, docs]
     steps:
     - uses: actions/checkout@v4
@@ -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* git-lfs graphviz
-        pip install "tox<4.0.0" pip setuptools --upgrade
+        pip install tox pip setuptools --upgrade
     - name: installing auxiliary data files
       run: |
         GIT_CLONE_PROTECTION_ACTIVE=false GIT_LFS_SKIP_SMUDGE=1 git clone https://git.ligo.org/lscsoft/lalsuite-extra

diff --git a/.github/workflows/distribution.yml b/.github/workflows/distribution.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-12]
+        os: [ubuntu-20.04]
 
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/mac-test.yml b/.github/workflows/mac-test.yml
@@ -12,18 +12,46 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        os: [macos-12]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        os: [macos-latest]
+        python-version:
+          - '3.10'
+          - '3.11'
+
+    # this is needed for conda environments to activate automatically
+    defaults:
+      run:
+        shell: bash -el {0}
+
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+
+    - name: Cache conda packages
+      uses: actions/cache@v4
+      env:
+        # increment to reset cache
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-conda-${{ matrix.python-version}}-${{ env.CACHE_NUMBER }}
+
+    - name: Configure conda
+      uses: conda-incubator/setup-miniconda@v3
       with:
+        activate-environment: test
+        channels: conda-forge
+        miniforge-version: latest
         python-version: ${{ matrix.python-version }}
-    - run: |
-        brew install fftw openssl gsl
-        pip install --upgrade pip setuptools "tox<4.0.0"
-    - name: run basic pycbc test suite
+
+    - name: Conda info
+      run: conda info --all
+
+    - name: Install tox
+      run: |
+        conda install \
+            pip \
+            setuptools \
+            tox
+
+    - name: Run basic pycbc test suite
       run: |
-        sudo chmod -R 777 /usr/local/miniconda/
         tox -e py-unittest
diff --git a/Dockerfile b/Dockerfile
@@ -10,8 +10,8 @@ ADD docker/etc/cvmfs/config-osg.opensciencegrid.org.conf /etc/cvmfs/config-osg.o
 RUN dnf -y install https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest.noarch.rpm && dnf -y install cvmfs cvmfs-config-default && dnf clean all && dnf makecache && \
     dnf -y groupinstall "Development Tools" \
                         "Scientific Support" && \
-    rpm -e --nodeps git perl-Git && dnf -y install @python39 rsync zlib-devel libpng-devel libjpeg-devel sqlite-devel openssl-devel fftw-libs-single fftw-devel fftw fftw-libs-long fftw-libs fftw-libs-double gsl gsl-devel hdf5 hdf5-devel python39-devel swig which osg-ca-certs && python3.9 -m pip install --upgrade pip setuptools wheel cython && python3.9 -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 && dnf clean all
+    rpm -e --nodeps git perl-Git && dnf -y install @python39 rsync zlib-devel libpng-devel libjpeg-devel sqlite-devel openssl-devel fftw-libs-single fftw-devel fftw fftw-libs-long fftw-libs fftw-libs-double gsl gsl-devel hdf5 hdf5-devel python39-devel swig which osg-ca-certs && python3.9 -m pip install --upgrade pip setuptools wheel cython && python3.9 -m pip install mkl ipython jupyter jupyterhub jupyterlab lalsuite==7.24 && \
+    dnf -y install https://repo.opensciencegrid.org/osg/3.5/el8/testing/x86_64/osg-wn-client-3.5-5.osg35.el8.noarch.rpm && dnf -y install pelican-osdf-compat-7.10.11-1.x86_64 && dnf -y install pelican-7.10.11-1.x86_64 && dnf clean all
 
 # set up environment
 RUN cd / && \

diff --git a/bin/all_sky_search/pycbc_add_statmap b/bin/all_sky_search/pycbc_add_statmap
@@ -310,14 +310,14 @@ if injection_style:
     for bg_fname in args.background_files:
         bg_f = h5py.File(bg_fname, 'r')
         ifo_combo_key = bg_f.attrs['ifos'].replace(' ','')
-        _, far[ifo_combo_key] = significance.get_far(
+        _, far[ifo_combo_key], _ = significance.get_far(
                 bg_f['background/stat'][:],
                 f['foreground/stat'][:],
                 bg_f['background/decimation_factor'][:],
                 bg_f.attrs['background_time'],
                 **significance_dict[ifo_combo_key])
 
-        _, far_exc[ifo_combo_key] = \
+        _, far_exc[ifo_combo_key], _ = \
             significance.get_far(
                 bg_f['background_exc/stat'][:],
                 f['foreground/stat'][:],
@@ -329,15 +329,15 @@ else:
     # background included
     for f_in in files:
         ifo_combo_key = get_ifo_string(f_in).replace(' ','')
-        _, far[ifo_combo_key] = \
+        _, far[ifo_combo_key], _ = \
             significance.get_far(
                 f_in['background/stat'][:],
                 f['foreground/stat'][:],
                 f_in['background/decimation_factor'][:],
                 f_in.attrs['background_time'],
                 **significance_dict[ifo_combo_key])
 
-        _, far_exc[ifo_combo_key] = \
+        _, far_exc[ifo_combo_key], _ = \
             significance.get_far(
                 f_in['background_exc/stat'][:],
                 f['foreground/stat'][:],
@@ -608,7 +608,7 @@ while True:
         fg_time_ct[key] -= args.cluster_window
         bg_t_y = conv.sec_to_year(bg_time_ct[key])
         fg_t_y = conv.sec_to_year(fg_time_ct[key])
-        bg_far, fg_far = significance.get_far(
+        bg_far, fg_far, _ = significance.get_far(
             sep_bg_data[key].data['stat'],
             sep_fg_data[key].data['stat'],
             sep_bg_data[key].data['decimation_factor'],
@@ -632,7 +632,7 @@ while True:
 
     logging.info("Recalculating combined IFARs")
     for key in all_ifo_combos:
-        _, far[key] = significance.get_far(
+        _, far[key], _ = significance.get_far(
             sep_bg_data[key].data['stat'],
             combined_fg_data.data['stat'],
             sep_bg_data[key].data['decimation_factor'],

diff --git a/bin/all_sky_search/pycbc_coinc_findtrigs b/bin/all_sky_search/pycbc_coinc_findtrigs
@@ -411,7 +411,7 @@ def process_template(tnum):
             # with any trigger in the fixed network
             tidx = len(threshes)
             for i in range(1, len(threshes)):
-                if pivot_stat[-1] >= pivot_lower[kidx]:
+                if pivot_stat[-1] >= pivot_lower[i]:
                     tidx = i
                     break
 

diff --git a/bin/all_sky_search/pycbc_coinc_statmap b/bin/all_sky_search/pycbc_coinc_statmap
@@ -241,7 +241,7 @@ fore_stat = all_trigs.stat[fore_locs]
 
 # Cumulative array of inclusive background triggers and the number of
 # inclusive background triggers louder than each foreground trigger
-bg_far, fg_far = significance.get_far(
+bg_far, fg_far, sig_info = significance.get_far(
     back_stat,
     fore_stat,
     all_trigs.decimation_factor[back_locs],
@@ -250,7 +250,7 @@ bg_far, fg_far = significance.get_far(
 
 # Cumulative array of exclusive background triggers and the number
 # of exclusive background triggers louder than each foreground trigger
-bg_far_exc, fg_far_exc = significance.get_far(
+bg_far_exc, fg_far_exc, exc_sig_info = significance.get_far(
     exc_zero_trigs.stat,
     fore_stat,
     exc_zero_trigs.decimation_factor,
@@ -288,10 +288,14 @@ if fore_locs.sum() > 0:
     fap = 1 - numpy.exp(- coinc_time / ifar)
     f['foreground/ifar'] = conv.sec_to_year(ifar)
     f['foreground/fap'] = fap
+    for key, value in sig_info.items():
+        f['foreground'].attrs[key] = value
     ifar_exc = 1. / fg_far_exc
     fap_exc = 1 - numpy.exp(- coinc_time_exc / ifar_exc)
     f['foreground/ifar_exc'] = conv.sec_to_year(ifar_exc)
     f['foreground/fap_exc'] = fap_exc
+    for key, value in exc_sig_info.items():
+        f['foreground'].attrs[key + '_exc'] = value
 else:
     f['foreground/ifar'] = numpy.array([])
     f['foreground/fap'] = numpy.array([])
@@ -425,7 +429,7 @@ while numpy.any(ifar_foreground >= background_time):
     logging.info("Calculating FAN from background statistic values")
     back_stat = all_trigs.stat[back_locs]
     fore_stat = all_trigs.stat[fore_locs]
-    bg_far, fg_far = significance.get_far(
+    bg_far, fg_far, sig_info = significance.get_far(
         back_stat,
         fore_stat,
         all_trigs.decimation_factor[back_locs],
@@ -452,7 +456,7 @@ while numpy.any(ifar_foreground >= background_time):
     # Exclusive background doesn't change when removing foreground triggers.
     # So we don't have to take background ifar, just repopulate ifar_foreground
     else :
-        _, fg_far_exc = significance.get_far(
+        _, fg_far_exc, _ = significance.get_far(
             exc_zero_trigs.stat,
             fore_stat,
             exc_zero_trigs.decimation_factor,
@@ -479,6 +483,8 @@ while numpy.any(ifar_foreground >= background_time):
         fap = 1 - numpy.exp(- coinc_time / ifar)
         f['foreground_h%s/ifar' % h_iterations] = conv.sec_to_year(ifar)
         f['foreground_h%s/fap' % h_iterations] = fap
+        for key, value in sig_info.items():
+            f['foreground_h%' % h_iterations].attrs[key] = value
 
         # Update ifar and fap for other foreground triggers
         for i in range(len(ifar)):

diff --git a/bin/all_sky_search/pycbc_coinc_statmap_inj b/bin/all_sky_search/pycbc_coinc_statmap_inj
@@ -91,7 +91,7 @@ f.attrs['foreground_time'] = coinc_time
 
 if len(zdata) > 0:
 
-    _, fg_far_exc = significance.get_far(
+    _, fg_far_exc, exc_sig_info = significance.get_far(
         back_stat,
         zdata.stat,
         dec_fac,
@@ -108,6 +108,8 @@ if len(zdata) > 0:
     fap_exc = 1 - numpy.exp(- coinc_time / ifar_exc)
     f['foreground/ifar_exc'] = conv.sec_to_year(ifar_exc)
     f['foreground/fap_exc'] = fap_exc
+    for key, value in exc_sig_info.items():
+        f['foreground'].attrs[key + '_exc'] = value
 
 else:
     f['foreground/ifar_exc'] = numpy.array([])

diff --git a/bin/all_sky_search/pycbc_exclude_zerolag b/bin/all_sky_search/pycbc_exclude_zerolag
@@ -94,7 +94,7 @@ for k in filtered_trigs.data:
     f_out['background_exc/%s' % k] = filtered_trigs.data[k]
 
 logging.info('Recalculating IFARs')
-bg_far, fg_far = significance.get_far(
+bg_far, fg_far, sig_info = significance.get_far(
     filtered_trigs.data['stat'],
     f_in['foreground/stat'][:],
     filtered_trigs.data['decimation_factor'],
@@ -110,6 +110,8 @@ bg_ifar_exc = 1. / bg_far
 logging.info('Writing updated ifars to file')
 f_out['foreground/ifar_exc'][:] = conv.sec_to_year(fg_ifar_exc)
 f_out['background_exc/ifar'][:] = conv.sec_to_year(bg_ifar_exc)
+for key, value in sig_info.items():
+    f_out['foreground'].attrs[key + '_exc'] = value
 
 fg_time_exc = conv.sec_to_year(f_in.attrs['foreground_time_exc'])
 f_out['foreground/fap_exc'][:] = 1 - np.exp(-fg_time_exc / fg_ifar_exc)

diff --git a/bin/all_sky_search/pycbc_sngls_statmap b/bin/all_sky_search/pycbc_sngls_statmap
@@ -109,6 +109,7 @@ assert ifo + '/time' in all_trigs.data
 logging.info("We have %s triggers" % len(all_trigs.stat))
 logging.info("Clustering triggers")
 all_trigs = all_trigs.cluster(args.cluster_window)
+logging.info("%s triggers remain" % len(all_trigs.stat))
 
 fg_time = float(all_trigs.attrs['foreground_time'])
 
@@ -139,12 +140,13 @@ significance_dict = significance.digest_significance_options([ifo], args)
 
 # Cumulative array of inclusive background triggers and the number of
 # inclusive background triggers louder than each foreground trigger
-bg_far, fg_far = significance.get_far(
+bg_far, fg_far, sig_info = significance.get_far(
     back_stat,
     fore_stat,
     bkg_dec_facs,
     fg_time,
-    **significance_dict[ifo])
+    **significance_dict[ifo]
+)
 
 fg_far = significance.apply_far_limit(
     fg_far,
@@ -192,7 +194,7 @@ back_exc_locs = back_exc_locs[to_keep]
 
 # Cumulative array of exclusive background triggers and the number
 # of exclusive background triggers louder than each foreground trigger
-bg_far_exc, fg_far_exc = significance.get_far(
+bg_far_exc, fg_far_exc, exc_sig_info = significance.get_far(
     back_stat_exc,
     fore_stat,
     bkg_exc_dec_facs,
@@ -231,6 +233,10 @@ f['foreground/fap'] = fap
 fap_exc = 1 - numpy.exp(- fg_time_exc / fg_ifar_exc)
 f['foreground/ifar_exc'] = conv.sec_to_year(fg_ifar_exc)
 f['foreground/fap_exc'] = fap_exc
+for key, value in sig_info.items():
+    f['foreground'].attrs[key] = value
+for key, value in exc_sig_info.items():
+    f['foreground'].attrs[f'{key}_exc'] = value
 
 if 'name' in all_trigs.attrs:
     f.attrs['name'] = all_trigs.attrs['name']
@@ -290,6 +296,10 @@ while numpy.any(ifar_louder > hier_ifar_thresh_s):
         f['foreground_h%s/ifar' % h_iterations] = conv.sec_to_year(fg_ifar)
         f['foreground_h%s/ifar_exc' % h_iterations] = conv.sec_to_year(fg_ifar_exc)
         f['foreground_h%s/fap' % h_iterations] = fap
+        for key, value in sig_info.items():
+            f['foreground_h%s' % h_iterations].attrs[key] = value
+        for key, value in exc_sig_info.items():
+            f['foreground_h%s' % h_iterations].attrs[key + "_exc"] = value
         for k in all_trigs.data:
             f['foreground_h%s/' % h_iterations + k] = all_trigs.data[k]
     # Add the iteration number of hierarchical removals done.
@@ -342,7 +352,7 @@ while numpy.any(ifar_louder > hier_ifar_thresh_s):
     logging.info("Calculating FAN from background statistic values")
     back_stat = fore_stat = all_trigs.stat
 
-    bg_far, fg_far = significance.get_far(
+    bg_far, fg_far, sig_info = significance.get_far(
         back_stat,
         fore_stat,
         numpy.ones_like(back_stat),
@@ -368,11 +378,12 @@ while numpy.any(ifar_louder > hier_ifar_thresh_s):
     # triggers are being removed via inclusive or exclusive background.
     if is_bkg_inc:
         ifar_louder = fg_ifar
+        exc_sig_info = {}
 
     # Exclusive background doesn't change when removing foreground triggers.
     # So we don't have to take bg_far_exc, just repopulate fg_ifar_exc
     else:
-        _, fg_far_exc = significance.get_far(
+        _, fg_far_exc, exc_sig_info = significance.get_far(
             back_stat_exc,
             fore_stat,
             numpy.ones_like(back_stat_exc),
@@ -400,6 +411,10 @@ while numpy.any(ifar_louder > hier_ifar_thresh_s):
         # Write ranking statistic to file just for downstream plotting code
         f['foreground_h%s/stat' % h_iterations] = fore_stat
 
+        for key, value in sig_info.items():
+            f['foreground_h%s' % h_iterations].attrs[key] = value
+        for key, value in exc_sig_info.items():
+            f['foreground_h%s' % h_iterations].attrs[key + "_exc"] = value
         fap = 1 - numpy.exp(- fg_time / fg_ifar)
         f['foreground_h%s/ifar' % h_iterations] = conv.sec_to_year(fg_ifar)
         f['foreground_h%s/fap' % h_iterations] = fap

diff --git a/bin/all_sky_search/pycbc_sngls_statmap_inj b/bin/all_sky_search/pycbc_sngls_statmap_inj
@@ -110,7 +110,7 @@ significance_dict = significance.digest_significance_options([ifo], args)
 
 # Cumulative array of exclusive background triggers and the number
 # of exclusive background triggers louder than each foreground trigger
-bg_far_exc, fg_far_exc = significance.get_far(
+bg_far_exc, fg_far_exc, sig_info = significance.get_far(
     back_stat_exc,
     fore_stat,
     bkg_exc_dec_facs,
@@ -137,6 +137,9 @@ fap_exc = 1 - numpy.exp(- fg_time_exc / fg_ifar_exc)
 f['foreground/ifar_exc'] = conv.sec_to_year(fg_ifar_exc)
 f['foreground/fap_exc'] = fap_exc
 
+for key, value in sig_info.items():
+    f['foreground'].attrs[key + '_exc'] = value
+
 if 'name' in all_trigs.attrs:
     f.attrs['name'] = all_trigs.attrs['name']
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -108,7 +108,6 @@
 # a list of builtin themes.
 import sphinx_rtd_theme
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -117,9 +116,6 @@
                       'logo_only':True,
                       }
 
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
 html_context = {
     'display_github': True,
     'github_user': 'gwastro',