Changes for v2.3.13 release (#5126)

spxiwh · titodalcanton · ahnitz · web-flow · commit f1208f1ff4ac · 2025-05-12T14:24:39.000+01:00
* Update PyPI publish action (#5097) * Workaround for git.ligo.org authentication change (#5119) * Workaround for git.ligo.org auth change * Workaround for git.ligo.org auth change * Forgot args * Fix error * Two possible URL schemes * Fix regex * Don't miss this bit! * Address ci deprecations (#5076) * Update CI to Ubuntu 24.04 * Use Python 3.11 for distribution CI * Try ubuntu-22 for basic tests * updated for depcreated fillcolor value (#5123) * Update cibuildwheel to v311 * Pin cython version * Bump pegasus versions to 5.0.8 * Fix strange usage of pycbc.version.release (#5033) * Fix usage of release flag in Pegasus sites code (#5098) --------- Co-authored-by: Tito Dal Canton <tito.dalcanton@ijclab.in2p3.fr> Co-authored-by: Alex Nitz <alex.nitz@gmail.com>
diff --git a/.github/workflows/bank-compress-workflow.yml b/.github/workflows/bank-compress-workflow.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 90
     steps:
     - uses: actions/checkout@v1
diff --git a/.github/workflows/basic-tests.yml b/.github/workflows/basic-tests.yml
@@ -12,8 +12,8 @@ jobs:
     strategy:
       max-parallel: 60
       matrix:
-        os: [ubuntu-20.04]
-        python-version: [3.9, '3.10', '3.11']
+        os: [ubuntu-22.04]
+        python-version: ['3.9', '3.10', '3.11']
         test-type: [unittest, search, docs]
     steps:
     - uses: actions/checkout@v4
diff --git a/.github/workflows/build_venv.yml b/.github/workflows/build_venv.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       -
         uses: actions/checkout@v1
diff --git a/.github/workflows/distribution.yml b/.github/workflows/distribution.yml
@@ -12,15 +12,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-24.04]
 
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
       - name: Build wheels
@@ -36,7 +36,7 @@ jobs:
           path: ./wheelhouse/*.whl
   deploy_pypi:
     name: Package and publish to PyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     needs: build_wheels
     steps:
     - uses: actions/checkout@v4
@@ -57,6 +57,6 @@ jobs:
         ls -lh dist
     - name: Publish to PyPI
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4
       with:
         password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       -
         uses: actions/checkout@v1
diff --git a/.github/workflows/inference-workflow.yml b/.github/workflows/inference-workflow.yml
@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
@@ -25,7 +25,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
diff --git a/.github/workflows/search-workflow.yml b/.github/workflows/search-workflow.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 90
     steps:
     - uses: actions/checkout@v1
@@ -30,7 +30,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
diff --git a/.github/workflows/tmpltbank-workflow.yml b/.github/workflows/tmpltbank-workflow.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
@@ -29,7 +29,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
diff --git a/.github/workflows/tut-test.yml b/.github/workflows/tut-test.yml
@@ -12,8 +12,8 @@ jobs:
     strategy:
       max-parallel: 60
       matrix:
-        os: [ubuntu-20.04]
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        os: [ubuntu-24.04]
+        python-version: ['3.10', '3.11']
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
diff --git a/.github/workflows/workflow-tests.yml b/.github/workflows/workflow-tests.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       max-parallel: 60
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-24.04]
         test-type: [simple_subworkflow_data, multilevel_subworkflow_data]
     steps:
     - uses: actions/checkout@v1
@@ -34,7 +34,7 @@ jobs:
         wget -qO - https://download.pegasus.isi.edu/pegasus/gpg.txt | sudo apt-key add -
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.6-1+ubuntu18
+        sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.8-1+ubuntu18
     - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
diff --git a/pycbc/results/scatter_histograms.py b/pycbc/results/scatter_histograms.py
@@ -383,6 +383,7 @@ def create_marginalized_hist(ax, values, label, percentiles=None,
     """
     if fillcolor is None:
         htype = 'step'
+        fillcolor = 'none'
     else:
         htype = 'stepfilled'
     if rotated:
diff --git a/pycbc/results/versioning.py b/pycbc/results/versioning.py
@@ -90,9 +90,11 @@ def add_info_new_version(info_dct, curr_module, extra_str):
 
     pycbcinfo = {}
     pycbcinfo['Name'] = 'PyCBC'
-    pycbcinfo['ID'] = pycbc.version.version
+    pycbcinfo['ID'] = pycbc.version.git_hash
     pycbcinfo['Status'] = pycbc.version.git_status
-    pycbcinfo['Version'] = pycbc.version.release or ''
+    pycbcinfo['Version'] = pycbc.version.version
+    if pycbc.version.release:
+        pycbcinfo['Version'] += ' (release)'
     pycbcinfo['Tag'] = pycbc.version.git_tag
     pycbcinfo['Author'] = pycbc.version.git_author
     pycbcinfo['Builder'] = pycbc.version.git_builder
diff --git a/pycbc/workflow/configuration.py b/pycbc/workflow/configuration.py
@@ -27,14 +27,14 @@
 https://ldas-jobs.ligo.caltech.edu/~cbc/docs/pycbc/ahope/initialization_inifile.html
 """
 
+import re
 import os
 import logging
 import stat
 import shutil
 import subprocess
 from shutil import which
 import urllib.parse
-from urllib.parse import urlparse
 
 from pycbc.types.config import InterpolatingConfigParser
 
@@ -45,6 +45,69 @@
 urllib.parse.uses_netloc.append('osdf')
 
 
+def resolve_url_http(url, u, filename):
+    """Helper function used by `resolve_url()` to handle HTTP and HTTPS URLs.
+    """
+
+    # Would like to move ciecplib import to top using import_optional, but
+    # it needs to be available when documentation runs in the CI, and I
+    # can't get it to install in the GitHub CI
+    import ciecplib
+
+    headers = None
+
+    if u.netloc == 'git.ligo.org':
+        # We need to do two ugly special things to download a file from
+        # git.ligo.org. First, we need to pass a per-user GitLab Personal Access
+        # Token via the headers. Second, we need to translate the raw-download
+        # URL scheme to a different scheme that uses GitLab's REST API.
+        re_match = re.match(
+            'https://git.ligo.org/([^ ]+(?<!/-))/(?:-/)?raw/([^ /]+)/(.+)', url
+        )
+        assert re_match, f'Failed to parse URL {url} for git.ligo.org special case'
+        project = re_match.group(1)
+        ref = re_match.group(2)
+        file_path = re_match.group(3)
+        logging.info(
+            'Special-case download from git.ligo.org: '
+            'file %s from ref %s of project %s',
+            file_path,
+            ref,
+            project
+        )
+        project = urllib.parse.quote(project, safe='')
+        ref = urllib.parse.quote(ref, safe='')
+        # GitLab's REST API does not seem to like double slashes
+        file_path = os.path.normpath(file_path)
+        file_path = urllib.parse.quote(file_path, safe='')
+        # FIXME This code will break once GitLab changes their mind about the
+        # URL format. As a different approach, we could rely on the gitlab
+        # Python module to (arguably) make this more robust. For now I prefer
+        # to avoid adding one more dependency, and stick with ciecplib.
+        url = f'https://git.ligo.org/api/v4/projects/{project}/repository/files/{file_path}/raw?ref={ref}'
+        # Get the user's Personal Access Token and pass it as a header
+        xdg_config_home = (
+            os.environ.get('XDG_CONFIG_HOME') or os.path.expanduser('~/.config')
+        )
+        with open(f'{xdg_config_home}/pycbc/git-ligo-org.pat', 'rb') as pat_fh:
+            headers = {
+                'PRIVATE-TOKEN': pat_fh.read().decode('ascii').strip()
+            }
+
+    # Make the scitokens logger a little quieter
+    # (it is called through ciecpclib)
+    curr_level = logging.getLogger().level
+    logging.getLogger('scitokens').setLevel(curr_level + 10)
+
+    with ciecplib.Session() as s:
+        r = s.get(url, allow_redirects=True, headers=headers)
+        r.raise_for_status()
+    content = r.content
+
+    with open(filename, "wb") as output_fp:
+        output_fp.write(r.content)
+
+
 def resolve_url(url, directory=None, permissions=None, copy_to_cwd=True):
     """Resolves a URL to a local file, and returns the path to that file.
 
@@ -54,7 +117,7 @@ def resolve_url(url, directory=None, permissions=None, copy_to_cwd=True):
     (the default).
     """
 
-    u = urlparse(url)
+    u = urllib.parse.urlparse(url)
 
     # determine whether the file exists locally
     islocal = u.scheme == "" or u.scheme == "file"
@@ -83,24 +146,8 @@ def resolve_url(url, directory=None, permissions=None, copy_to_cwd=True):
             else:
                 shutil.copy(u.path, filename)
 
-    elif u.scheme == "http" or u.scheme == "https":
-        # Would like to move ciecplib import to top using import_optional, but
-        # it needs to be available when documentation runs in the CI, and I
-        # can't get it to install in the GitHub CI
-        import ciecplib
-        # Make the scitokens logger a little quieter
-        # (it is called through ciecpclib)
-        logging.getLogger('scitokens').setLevel(logging.root.level + 10)
-        with ciecplib.Session() as s:
-            if u.netloc in ("git.ligo.org", "code.pycbc.phy.syr.edu"):
-                # authenticate with git.ligo.org using callback
-                s.get("https://git.ligo.org/users/auth/shibboleth/callback")
-            r = s.get(url, allow_redirects=True)
-            r.raise_for_status()
-
-        output_fp = open(filename, "wb")
-        output_fp.write(r.content)
-        output_fp.close()
+    elif u.scheme in ("http", "https"):
+        resolve_url_http(url, u, filename)
 
     elif u.scheme == "osdf":
         # OSDF will require a scitoken to be present and stashcp to be
diff --git a/pycbc/workflow/pegasus_sites.py b/pycbc/workflow/pegasus_sites.py
@@ -23,7 +23,8 @@
 
 from pycbc.version import last_release, version, release  # noqa
 
-if release == 'True':
+
+if release:
     sing_version = version
 else:
     sing_version = last_release
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [build-system]
 requires = ["setuptools",
             "wheel",
-            "cython>=3.0.0",
+            "cython>=3.0.0,<3.1.0",
             "numpy==1.16.0; python_version <= '3.7'",
             "numpy==1.17.3; python_version == '3.8'",
             "numpy==1.19.3; python_version == '3.9'",
diff --git a/requirements.txt b/requirements.txt
@@ -11,7 +11,7 @@ h5py>=3.0.0,!=3.7.0
 jinja2
 mpld3>=0.3
 beautifulsoup4>=4.6.0
-cython
+cython<3.1.0
 lalsuite!=7.2,<7.25
 lscsoft-glue>=1.59.3
 ligo-segments
diff --git a/setup.py b/setup.py
@@ -33,7 +33,7 @@
 requires = []
 setup_requires = ['numpy>=1.16.0']
 install_requires = setup_requires + [
-    'cython>=0.29',
+    'cython>=0.29,<3.1.0',
     'numpy>=1.16.0,!=1.19.0,<2.0.0',
     'scipy>=0.16.0,<1.14.0',
     'astropy>=2.0.3,!=4.2.1,!=4.0.5',
@@ -119,16 +119,16 @@ def __getattr__(self, attr):
         vinfo = _version_helper.generate_git_version_info()
     except:
         vinfo = vdummy()
-        vinfo.version = '2.3.12'
-        vinfo.release = 'True'
+        vinfo.version = '2.3.13'
+        vinfo.release = True
 
     version_script = f"""# coding: utf-8
 # Generated by setup.py for PyCBC on {vinfo.build_date}.
 
 # general info
 version = '{vinfo.version}'
 date = '{vinfo.date}'
-release = '{vinfo.release}'
+release = {vinfo.release}
 last_release = '{vinfo.last_release}'
 
 # git info

Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@ concurrency:`
`8`	`8`
`9`	`9`	`jobs:`
`10`	`10`	`build:`
`11`		`- runs-on: ubuntu-20.04`
	`11`	`+ runs-on: ubuntu-24.04`
`12`	`12`	`steps:`
`13`	`13`	`-`
`14`	`14`	`uses: actions/checkout@v1`