sxs 2025.0.15__tar.gz → 2025.0.17__tar.gz

{sxs-2025.0.15 → sxs-2025.0.17}/CITATION.cff

@@ -16,5 +16,5 @@ authors:
 title: "The sxs package"
 license: MIT
 doi: 10.5281/zenodo.4034006
-version: 2025.0.15
-date-released: 2025-05-14
+version: 2025.0.17
+date-released: 2025-06-11

{sxs-2025.0.15 → sxs-2025.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sxs
-Version: 2025.0.15
+Version: 2025.0.17
 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-2025.0.15 → sxs-2025.0.17}/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-2025.0.15 → sxs-2025.0.17}/docs/tutorials/00-Introduction.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Introduction\n",
     "\n",
-    "This series of notebooks describes the `sxs` python package, which provides an interface to the data produced by the Simulating eXtreme Spacetimes collaboration.  All that data is hosted on [Zenodo](https://zenodo.org/communities/sxs) and [CaltechDATA](https://data.caltech.edu/).  Each simulation gets its own DOI and its own web page — like [this one](https://doi.org/10.5281/zenodo.1213436), for example.  But you want an easier way to get the data than clicking on links.  This package will do that for you.\n",
+    "This series of notebooks describes the `sxs` python package, which provides an interface to the data produced by the Simulating eXtreme Spacetimes collaboration.  All that data is hosted on [Zenodo](https://zenodo.org/communities/sxs) and [CaltechDATA](https://data.caltech.edu/).  Each simulation gets its own DOI and its own web page — like [DOI 10.26138/SXS:BBH:4001](https://doi.org/10.26138/SXS:BBH:4001), for example, which redirects to its CaltechDATA page.  But you want an easier way to get the data than clicking on links.  This package will do that for you.\n",
     "\n",
     "The documentation is [here](https://sxs.readthedocs.io/en/main/).  The github page is [here](https://github.com/sxs-collaboration/sxs/).  Please feel free to open issues to report problems, or pull requests to fix them."
    ]
@@ -251,10 +251,10 @@
     "\n",
     "It is probably best to go through these notebooks in order:\n",
     "\n",
-    "  1. [The catalog `DataFrame` interface](/tutorials/01-Catalog_Dataframe)\n",
-    "  2. [The `Simulation` interface](/tutorials/02-Simulation)\n",
-    "  3. [Data describing `Horizons`](/tutorials/03-Horizons)\n",
-    "  4. [Introduction to `WaveformModes` objects](/tutorials/04-Waveforms)"
+    "  1. [The catalog `DataFrame` interface](../01-Catalog_Dataframe)\n",
+    "  2. [The `Simulation` interface](../02-Simulation)\n",
+    "  3. [Data describing `Horizons`](../03-Horizons)\n",
+    "  4. [Introduction to `WaveformModes` objects](../04-Waveforms)"
    ]
   }
  ],

{sxs-2025.0.15 → sxs-2025.0.17}/docs/tutorials/01-Catalog_Dataframe.ipynb

@@ -3345,7 +3345,7 @@
    "source": [
     "The `simulations` object, especially when agumented with the `dataframe`, provides powerful methods for selecting the particular simulations we are interested in.  Once we have done so, we need to load and interact with the simulations.\n",
     "\n",
-    "Continue with the [introduction to the `Simulation` objects](/tutorials/02-Simulation)."
+    "Continue with the [introduction to the `Simulation` objects](../02-Simulation)."
    ]
   }
  ],

{sxs-2025.0.15 → sxs-2025.0.17}/docs/tutorials/02-Simulation.ipynb

@@ -664,8 +664,8 @@
    "source": [
     "The objects returned will be the subject of the next two notebooks in this series:\n",
     "\n",
-    "- [`Horizons`](/tutorials/03-Horizons)\n",
-    "- [`WaveformModes`](/tutorials/04-Waveforms)"
+    "- [`Horizons`](../03-Horizons)\n",
+    "- [`WaveformModes`](../04-Waveforms)"
    ]
   }
  ],

{sxs-2025.0.15 → sxs-2025.0.17}/docs/tutorials/03-Horizons.ipynb

@@ -394,7 +394,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Continue with the [introduction to waveforms](/tutorials/04-Waveforms)."
+    "Continue with the [introduction to waveforms](../04-Waveforms)."
    ]
   }
  ],

{sxs-2025.0.15 → sxs-2025.0.17}/mkdocs.yml

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

sxs-2025.0.17/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-2025.0.15 → sxs-2025.0.17}/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-2025.0.17/sxs/__version__.py

@@ -0,0 +1 @@
+__version__ = "2025.0.17"

{sxs-2025.0.15 → sxs-2025.0.17}/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-2025.0.15 → sxs-2025.0.17}/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-2025.0.15 → sxs-2025.0.17}/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-2025.0.15/sxs/__version__.py

@@ -1 +0,0 @@
-__version__ = "2025.0.15"