Fix dependencies

.github/workflows/tests.yml

@@ -26,8 +26,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install flake8 pytest 'sxs==2025.0.9' romspline pycbc requests bs4
+        pip install -r requirements.txt
+        pip install flake8 pytest
+        pip install -e .
+    - name: Apply pycbc numpy 2.x compatibility patch
+      run: |
+        python scripts/patch_pycbc_numpy2.py
     #- name: Lint with flake8
     #  run: |
         # stop the build if there are Python syntax errors or undefined names

PyART/__init__.py

@@ -1,7 +1,4 @@
 #!/usr/bin/env python
-from __future__ import absolute_import
-
-__import__("pkg_resources").declare_namespace(__name__)
 
 from . import analysis
 from . import analytic

PyART/analysis/__init__.py

@@ -1,3 +1 @@
-from __future__ import absolute_import
 
-__import__("pkg_resources").declare_namespace(__name__)

PyART/analytic/__init__.py

@@ -1,3 +1 @@
-from __future__ import absolute_import
 
-__import__("pkg_resources").declare_namespace(__name__)

PyART/catalogs/__init__.py

@@ -1,3 +1 @@
-from __future__ import absolute_import
 
-__import__("pkg_resources").declare_namespace(__name__)

PyART/models/__init__.py

@@ -1,3 +1 @@
-from __future__ import absolute_import
 
-__import__("pkg_resources").declare_namespace(__name__)

PyART/numerical/__init__.py

@@ -1,3 +1 @@
-from __future__ import absolute_import
 
-__import__("pkg_resources").declare_namespace(__name__)

PyART/utils/__init__.py

@@ -1,3 +1 @@
-from __future__ import absolute_import
 
-__import__("pkg_resources").declare_namespace(__name__)

PyART/utils/convert_sxs_to_lvc.py

@@ -731,7 +731,7 @@ def convert_simulation(
     The option resolution is an integer labeling the resolution of the
     converted waveform. Modes is an array of the format
     [[l1, m1], [l2, m2], ...] listing the l,m modes to convert. This function
-    outputs a file in LVC format named SXS_BBH_\#\#\#\#_Res\#.h5
+    outputs a file in LVC format named SXS_BBH_####_Res#.h5
     in out_path."""
     horizons = h5py.File(sxs_data_path + "/Horizons.h5", "r")
     rhOverM = h5py.File(sxs_data_path + "/rhOverM_Asymptotic_GeometricUnits_CoM.h5")

README.md

@@ -25,6 +25,14 @@ Install with
 pip install .
 ```
 
+> **Note:** PyART depends on `pycbc`, which currently has two incompatibilities with numpy 2.x.
+> After installing, apply the one-time patch:
+> ```
+> python scripts/patch_pycbc_numpy2.py
+> ```
+> This patches `pycbc`'s `events/threshold_cpu.py` and `filter/matchedfilter.py`
+> in-place. It is idempotent and safe to re-run after pycbc upgrades.
+
 ## For developers
 
 If you are a developer:

examples/match_sxs.py

@@ -5,6 +5,9 @@
 from PyART.models import teob
 from PyART.analysis.match import Matcher
 from PyART.utils import utils as ut
+from PyART.logging_config import setup_logging
+
+setup_logging(level="INFO")
 
 matplotlib.rc("text", usetex=True)
 
@@ -39,7 +42,13 @@
 # load (or download) SXS data
 sxs_id = f"{args.sxs_id:04}"  # e.g.0180
 nr = sxs.Waveform_SXS(
-    path=sxs_path, download=True, ID=sxs_id, order="Extrapolated_N3.dir", ellmax=7
+    path=sxs_path,
+    download=True,
+    ID=sxs_id,
+    ellmax=7,
+    ignore_deprecation=True,
+    downloads=["hlm", "metadata", "horizons"],
+    load=["hlm", "metadata", "horizons"],
 )
 nr.cut(300)
 # nr.compute_hphc()

requirements.txt

@@ -1,5 +1,8 @@
 # Requirements for most basic library
-numpy>=1.16.0,<2.0,!=1.19.0
+# Note: pycbc>=2.4.0 uses np.array(..., copy=False) which changed semantics in
+# numpy 2.x. After installing, apply the one-time patch:
+#     python scripts/patch_pycbc_numpy2.py
+numpy>=2.0
 scipy>=1.13.0
 rich>=13.7.0
 matplotlib>=3.7.3
@@ -8,11 +11,15 @@ astropy>=5.0.0
 setuptools
 
 # GW package dependencies
-# pycbc>=2.4.0
+pycbc>=2.4.0
 # teobresums>=4.4.0
 # gw-eccentricity>=1.0.4
 # mayawaves>=2024.4.25
-# lalsuite>=7.22
+lalsuite>=7.22
+
+# SXS catalog support (optional; needed for downloading SXS simulations)
+sxs>=2025.0
+romspline
 
 # Documentation
 sphinx>=4.2.0

scripts/patch_pycbc_numpy2.py

@@ -0,0 +1,96 @@
+"""
+Patch pycbc for numpy 2.x compatibility.
+
+pycbc <= 2.10.0 has two numpy 2.x incompatibilities:
+
+  1. events/threshold_cpu.py: np.array(..., copy=False) raises ValueError in
+     numpy 2.x when a copy is required; numpy.asarray() preserves the original
+     numpy 1.x semantics (copy only if necessary, silently).
+
+  2. filter/matchedfilter.py: numpy.real(x) / numpy.imag(x) dispatch via
+     x.real / x.imag. On pycbc Array objects these are plain methods, not
+     properties, so numpy.real() returns the bound method instead of the data.
+     Replacing with numpy.asarray(x).real / .imag forces conversion via
+     Array.__array__ first, which is safe and localized to the affected calls.
+
+Run once after installing pycbc:
+    python scripts/patch_pycbc_numpy2.py
+"""
+
+import inspect
+import re
+import shutil
+import sys
+from pathlib import Path
+
+
+def _clear_cache(path):
+    cache_dir = path.parent / "__pycache__"
+    if cache_dir.exists():
+        shutil.rmtree(cache_dir)
+        print(f"  Cleared __pycache__ in {cache_dir.parent.name}/")
+
+
+def patch_threshold_cpu():
+    try:
+        import pycbc.events.threshold_cpu as mod
+    except ImportError:
+        print("pycbc not found – nothing to patch.", file=sys.stderr)
+        sys.exit(1)
+
+    path = Path(inspect.getfile(mod))
+    src = path.read_text()
+    original = src
+
+    src = src.replace(
+        "numpy.array(series.data, copy=False, dtype=numpy.complex64)",
+        "numpy.asarray(series.data, dtype=numpy.complex64)",
+    )
+    src = re.sub(
+        r"numpy\.array\(series\.data,\s*copy=False,\s*\n(\s*)dtype=numpy\.complex64\)",
+        r"numpy.asarray(series.data,\n\1dtype=numpy.complex64)",
+        src,
+    )
+
+    if src == original:
+        print("threshold_cpu.py: already patched or pattern not found, skipping.")
+    else:
+        path.write_text(src)
+        _clear_cache(path)
+        print("threshold_cpu.py: patched (copy=False → asarray).")
+
+
+def patch_matchedfilter():
+    try:
+        import pycbc.filter.matchedfilter as mod
+    except ImportError:
+        print("pycbc not found – nothing to patch.", file=sys.stderr)
+        sys.exit(1)
+
+    path = Path(inspect.getfile(mod))
+    src = path.read_text()
+    original = src
+
+    replacements = [
+        ("numpy.real(hplus)", "numpy.asarray(hplus).real"),
+        ("numpy.real(hcross)", "numpy.asarray(hcross).real"),
+        ("numpy.imag(hplus)", "numpy.asarray(hplus).imag"),
+        ("numpy.imag(hcross)", "numpy.asarray(hcross).imag"),
+        ("numpy.real(hphccorr)", "numpy.asarray(hphccorr).real"),
+        ("numpy.real(hplus_cross_corr)", "numpy.asarray(hplus_cross_corr).real"),
+    ]
+    for old, new in replacements:
+        src = src.replace(old, new)
+
+    if src == original:
+        print("matchedfilter.py: already patched or pattern not found, skipping.")
+    else:
+        path.write_text(src)
+        _clear_cache(path)
+        n = sum(1 for a, b in zip(original.splitlines(), src.splitlines()) if a != b)
+        print(f"matchedfilter.py: patched ({n} lines changed).")
+
+
+if __name__ == "__main__":
+    patch_threshold_cpu()
+    patch_matchedfilter()

setup.cfg

@@ -16,6 +16,7 @@ classifiers =
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Topic :: Scientific/Engineering :: Astronomy
     Topic :: Scientific/Engineering :: Physics
     Natural Language :: English
@@ -24,4 +25,4 @@ classifiers =
 [options]
 packages = find:
 install_requires = file: requirements.txt
-python_requires = >=3.9
+python_requires = >=3.9,<3.13

setup.py

@@ -3,9 +3,34 @@
 setup.py file for GWforge package
 """
 
-from setuptools import setup, find_packages
+from setuptools import setup, find_packages, Command
+from setuptools.command.install import install
+from setuptools.command.develop import develop
 import os
 
+PATCH_MESSAGE = """
+============================================================
+  PyART post-install step required
+------------------------------------------------------------
+  pycbc <= 2.10.0 is incompatible with numpy 2.x.
+  Run the following command once to patch pycbc in-place:
+
+      python scripts/patch_pycbc_numpy2.py
+
+  The patch is idempotent and safe to re-run after pycbc
+  upgrades.
+============================================================
+"""
+
+
+def print_patch_notice(command_cls):
+    class Patched(command_cls):
+        def run(self):
+            super().run()
+            print(PATCH_MESSAGE)
+
+    return Patched
+
 
 def find_files(
     dirname,
@@ -52,6 +77,10 @@ def find_paths(directory):
 ignore_files = [".DS_Store", "*.pyc", "Thumbs.db", "*.sqlite", "*.swp", "*.env", ".env"]
 
 setup(
+    cmdclass={
+        "install": print_patch_notice(install),
+        "develop": print_patch_notice(develop),
+    },
     scripts=find_files(
         "bin/", relpath="./", ignore_dirs=ignore_dirs, ignore_files=ignore_files
     ),

tests/test_gra.py

@@ -19,6 +19,7 @@ def test_gra():
         res="128",
         downloads=["hlm", "metadata"],
         ext="CCE",
+        r_ext="50.00",
     )
     # check attributes
     assert wf.ID == "0001"