sxs 2025.0.16__tar.gz → 2025.0.18__tar.gz

{sxs-2025.0.16 → sxs-2025.0.18}/.github/workflows/build.yml

@@ -52,7 +52,7 @@ jobs:
         if: ${{ env.skipping_build_and_test_replicate != 'true' }}
         uses: actions/cache@v4
         with:
-          key: sxs-${{ runner.os }}-2 # Increment this number whenever the cached files should change
+          key: sxs-${{ runner.os }}-3 # Increment this number whenever the cached files should change
           path: |
             ${{ runner.os == 'Linux' && '/home/runner/.cache/sxs' || runner.os == 'Windows' && 'C:\Users\runneradmin\.sxs\cache' || '/Users/runner/.sxs/cache' }}
 
@@ -83,6 +83,8 @@ jobs:
       - name: Run tests
         if: ${{ env.skipping_build_and_test_replicate != 'true' }}
         shell: bash
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           hatch run test --durations=0
 

{sxs-2025.0.16 → sxs-2025.0.18}/CITATION.cff

@@ -16,5 +16,5 @@ authors:
 title: "The sxs package"
 license: MIT
 doi: 10.5281/zenodo.4034006
-version: 2025.0.16
-date-released: 2025-05-29
+version: 2025.0.18
+date-released: 2025-07-21

{sxs-2025.0.16 → sxs-2025.0.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sxs
-Version: 2025.0.16
+Version: 2025.0.18
 Summary: Interface to data produced by the Simulating eXtreme Spacetimes collaboration
 Project-URL: Homepage, https://github.com/sxs-collaboration/sxs
 Project-URL: Documentation, https://sxs.readthedocs.io/
@@ -83,6 +83,14 @@ Description-Content-Type: text/markdown
 
 # Simulating eXtreme Spacetimes package
 
+> [!NOTE]
+> As described in our [latest paper](https://arxiv.org/abs/2505.13378), our
+> waveforms now include memory effects.  Specifically, when using any
+> simulation with version 3 or greater, you should expect to see memory effects,
+> most visible in the $(\ell, 0)$ modes, and generally resulting in ringdowns
+> that do not approach 0 at late times.
+
+
 The `sxs` python package provides a high-level interface for using data
 produced by the SXS collaboration.  In particular, the function `sxs.load` can
 automatically find, download, and load data, returning objects that provide

{sxs-2025.0.16 → sxs-2025.0.18}/README.md

@@ -8,6 +8,14 @@
 
 # Simulating eXtreme Spacetimes package
 
+> [!NOTE]
+> As described in our [latest paper](https://arxiv.org/abs/2505.13378), our
+> waveforms now include memory effects.  Specifically, when using any
+> simulation with version 3 or greater, you should expect to see memory effects,
+> most visible in the $(\ell, 0)$ modes, and generally resulting in ringdowns
+> that do not approach 0 at late times.
+
+
 The `sxs` python package provides a high-level interface for using data
 produced by the SXS collaboration.  In particular, the function `sxs.load` can
 automatically find, download, and load data, returning objects that provide

{sxs-2025.0.16 → sxs-2025.0.18}/mkdocs.yml

@@ -12,6 +12,7 @@ plugins:
           options:
             docstring_style: numpy
             show_source: true
+  - admonitions_translation
 
 nav:
   - Home: "index.md"

sxs-2025.0.18/mkdocs_preprocess.py

@@ -0,0 +1,33 @@
+import re
+import difflib
+from mkdocs.plugins import BasePlugin
+
+
+class AdmonitionTranslationPlugin(BasePlugin):
+    """
+    Convert GitHub-flavored admonitions to MkDocs numpy-style admonitions.
+    """
+
+    def on_page_markdown(self, markdown, page, config, files):
+        lines = markdown.splitlines(keepends=True)
+        out = []
+        i = 0
+        while i < len(lines):
+            m = re.match(r'> \[\!(?P<tag>\w+)\]\s*$', lines[i])
+            if m:
+                tag = m.group('tag').lower()
+                # emit the MkDocs admonition start
+                out.append(f"!!! {tag}\n")
+                i += 1
+                # consume all the > … lines as the body
+                while i < len(lines) and lines[i].startswith('>'):
+                    # strip leading "> " (or just ">") and rstrip newline
+                    body = lines[i].lstrip('> ').rstrip('\n')
+                    out.append(f"    {body}\n")
+                    i += 1
+                continue
+            # otherwise, copy line verbatim
+            out.append(lines[i])
+            i += 1
+
+        return "".join(out)

{sxs-2025.0.16 → sxs-2025.0.18}/pyproject.toml

@@ -64,6 +64,9 @@ ecosystem = [
 Homepage = "https://github.com/sxs-collaboration/sxs"
 Documentation = "https://sxs.readthedocs.io/"
 
+[project.entry-points."mkdocs.plugins"]
+admonitions_translation = "mkdocs_preprocess:AdmonitionTranslationPlugin"
+
 
 [build-system]
 requires = ["hatchling"]

sxs-2025.0.18/sxs/__version__.py

@@ -0,0 +1 @@
+__version__ = "2025.0.18"

{sxs-2025.0.16 → sxs-2025.0.18}/sxs/catalog/catalog.py

@@ -6,7 +6,7 @@ import functools
 # noinspection SpellCheckingInspection
 class Catalog(object):
     """Container interface to the SXS catalog"""
-    url = "https://data.black-holes.org/catalog.json"
+    url = "https://data.black-holes.org/catalog.zip"
 
     def __init__(self, catalog=None, **kwargs):
         from .. import Metadata
@@ -60,6 +60,9 @@ class Catalog(object):
         which, as of `sxs` version 2024.0.0, has been deprecated in
         favor of the `Simulations` interface.  See the documentation
         for more information.
+
+        THIS CAN ONLY PROVIDE OLD DATA!
+
         """
         warn(deprecation_notice)
 
@@ -73,36 +76,12 @@ class Catalog(object):
             if_newer = False
 
         if download or download is None:
-            # 1. Download the full json file (zipped in flight, but auto-decompressed on arrival)
-            # 2. Zip to a temporary file (using bzip2, which is better than the in-flight compression)
-            # 3. Replace the original catalog.zip with the temporary zip file
-            # 4. Remove the full json file
-            # 5. Make sure the temporary zip file is gone too
-            temp_json = cache_path.with_suffix(".temp.json")
-            temp_zip = cache_path.with_suffix(".temp.zip")
             try:
-                try:
-                    download_file(cls.url, temp_json, progress=progress, if_newer=if_newer)
-                except Exception as e:
-                    if download:
-                        raise RuntimeError(f"Failed to download '{cls.url}'; try setting `download=False`") from e
-                    download_failed = e  # We'll try the cache
-                else:
-                    download_failed = False
-                    if temp_json.exists():
-                        with zipfile.ZipFile(temp_zip, "w", compression=zipfile.ZIP_BZIP2) as catalog_zip:
-                            catalog_zip.write(temp_json, arcname="catalog.json")
-                        temp_zip.replace(cache_path)
-            finally:
-                # The `missing_ok` argument to `unlink` would be much nicer, but was added in python 3.8
-                try:
-                    temp_json.unlink()
-                except FileNotFoundError as e:
-                    pass
-                try:
-                    temp_zip.unlink()
-                except FileNotFoundError as e:
-                    pass
+                download_file(cls.url, cache_path, progress=progress, if_newer=if_newer)
+            except Exception as e:
+                if download:
+                    raise RuntimeError(f"Failed to download '{cls.url}'; try setting `download=False`") from e
+                download_failed = e  # We'll try the cache
 
         if not cache_path.exists():
             if download is False:  # Test if it literally *is* False, rather than just casts to False

{sxs-2025.0.16 → sxs-2025.0.18}/sxs/simulations/simulation.py

@@ -782,6 +782,7 @@ class SimulationBase:
         strain = self.load_waveform(
             *self.strain_path,
             transform_to_inertial=False,
+            drop_times_before=kwargs.pop("drop_times_before", 0)
         )
         return to_lvc_conventions(strain, self.horizons, **kwargs)
 
@@ -933,7 +934,7 @@ class Simulation_v2(SimulationBase):
             download_file(json_location, json_truepath)
         return load(
             h5_location, truepath=h5_truepath, group=group, metadata=self.metadata,
-            transform_to_inertial=transform_to_inertial
+            transform_to_inertial=transform_to_inertial, drop_times_before=0,
         )
 
 

{sxs-2025.0.16 → sxs-2025.0.18}/sxs/waveforms/format_handlers/rotating_paired_diff_multishuffle_bzip2.py

@@ -387,9 +387,8 @@ def load(
         a string is given, the corresponding time will be used.  The
         "begin" option represents the earliest time in the data, so no
         data will be dropped; "reference" is the `reference_time`
-        reported in the metadata.  If `None`, the default, t=0 will be
-        used if present in the data, and the first time step
-        otherwise.
+        reported in the metadata.  If no argument is given, all times
+        will be used ("begin").
     metadata : Metadata, optional
         If given, this metadata will be used instead of attempting to
         load the metadata from an accompanying file.
@@ -582,7 +581,7 @@ def load(
         except ValueError as e:
             invalid(f"\n{e},\nbut one is expected for this data format.")
 
-    dtb = kwargs.pop("drop_times_before", 0)
+    dtb = kwargs.pop("drop_times_before", "begin")
     if dtb=="begin":
         i0 = 0
     elif dtb==0:

{sxs-2025.0.16 → sxs-2025.0.18}/tests/conftest.py

@@ -1,4 +1,5 @@
 import os
+import time
 import functools
 import pytest
 import numpy as np
@@ -36,7 +37,6 @@ if GITHUB_ACTIONS_MACOS:
 else:
     skip_macOS_GH_actions_downloads = lambda f: f
 
-
 def pytest_addoption(parser):
     parser.addoption("--ell_max", action="store", type=int, default=ell_max_default,
                      help="Maximum ell value to test")

{sxs-2025.0.16 → sxs-2025.0.18}/tests/test_simulation.py

@@ -36,6 +36,7 @@ def test_sxs_load_v2():
     s.Horizons
     s.psi4
     s.Psi4
+    assert s.h.t[0] >= 0
 
 
 @skip_macOS_GH_actions_downloads
@@ -63,6 +64,7 @@ def test_sxs_load_v2_levs():
         s.Strain
         s.horizons
         s.Horizons
+        assert s.h.t[0] >= 0
 
 
 @skip_macOS_GH_actions_downloads
@@ -81,6 +83,7 @@ def test_sxs_load_v3():
     s.Horizons
     s.psi4
     s.Psi4
+    assert s.h.t[0] >= 0
 
 
 @skip_macOS_GH_actions_downloads
@@ -108,6 +111,7 @@ def test_sxs_load_v3_levs():
         s.Strain
         s.horizons
         s.Horizons
+        assert s.h.t[0] >= 0
     # Check that Lev-1 and Lev0 work and are not the same as the highest Lev
     s = sxs.load(f"SXS:BBH:1132v3.0", ignore_deprecation=True)
     sm1 = sxs.load(f"SXS:BBH:1132v3.0/Lev-1", ignore_deprecation=True)
@@ -144,6 +148,7 @@ def test_sxs_load_v3_catalog():
     # at each Lev with each extrapolation order, but doesn't download
     # any data
     from pathlib import Path
+    from tqdm.auto import tqdm
 
     def fake_load_metadata(self):
         metadata_path = self.metadata_path
@@ -186,7 +191,7 @@ def test_sxs_load_v3_catalog():
     simulations = sxs.load("simulations")
 
     success = True
-    for sxs_id, metadata in simulations.items():
+    for sxs_id, metadata in tqdm(simulations.items()):
         if "NSNS" in sxs_id or "BHNS" in sxs_id:
             continue
 
@@ -263,3 +268,25 @@ def test_superseding(loader):
     # Version, ignore_deprecation, auto_supersede
     s = loader(f"{simulation}v2.0", ignore_deprecation=True, auto_supersede=True)
     assert s.sxs_id_stem == simulation
+
+
+def test_issue_116():
+    import tempfile
+    import contextlib
+    # Test that loading the strain as a user normally would drops
+    # times before 0
+    h = sxs.load("SXS:BBH:4000v3.0").h
+    assert h.t[0] >= 0
+    # Test that loading that same file directly *keeps* times before 0
+    h2 = sxs.load(h.__file__, metadata={})
+    assert h2.t[0] < 0
+    # Test that manually changing the time array and round-tripping
+    # through RPDMB preserves times
+    h3 = h.copy()
+    h3.t -= h3.max_norm_time()
+    with tempfile.TemporaryDirectory() as temp_dir:
+        with contextlib.redirect_stdout(None):
+            sxs.rpdmb.save(h3, f"{temp_dir}/test")
+            h4 = sxs.load(f"{temp_dir}/test", metadata={})
+    assert h4.t.size == h3.t.size == h.t.size
+    assert h4.t[0] == h3.t[0]

sxs-2025.0.16/sxs/__version__.py

@@ -1 +0,0 @@
-__version__ = "2025.0.16"