sxs 2024.0.31__tar.gz → 2024.0.33__tar.gz

{sxs-2024.0.31 → sxs-2024.0.33}/CITATION.cff

@@ -10,5 +10,5 @@ authors:
 title: "The sxs package"
 license: MIT
 doi: 10.5281/zenodo.4034006
-version: 2024.0.31
-date-released: 2025-02-15
+version: 2024.0.33
+date-released: 2025-02-19

{sxs-2024.0.31 → sxs-2024.0.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sxs
-Version: 2024.0.31
+Version: 2024.0.33
 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/
@@ -42,7 +42,7 @@ Requires-Dist: numba>=0.55; implementation_name == 'cpython'
 Requires-Dist: numpy>=1.25
 Requires-Dist: pandas>=1.1.2
 Requires-Dist: pytz>=2020.1
-Requires-Dist: quaternionic>=1.0
+Requires-Dist: quaternionic>=1.0.15
 Requires-Dist: requests>=2.24.0
 Requires-Dist: scipy>=1.13
 Requires-Dist: spherical>=1.0.15

{sxs-2024.0.31 → sxs-2024.0.33}/pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
   "numpy >=1.25",
   "scipy >=1.13",
   "numba >=0.55; implementation_name == 'cpython'",
-  "quaternionic >=1.0",
+  "quaternionic >=1.0.15",
   "spherical >=1.0.15",
   "h5py >=3",
   "inflection >=0.5.1",

sxs-2024.0.33/sxs/__version__.py

@@ -0,0 +1 @@
+__version__ = "2024.0.33"

{sxs-2024.0.31 → sxs-2024.0.33}/sxs/simulations/local.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 from .. import sxs_id, Metadata, sxs_directory
 from ..utilities import sxs_identifier_re
-from ..zenodo import path_to_invenio as p2i
+from ..zenodo import path_to_invenio
 
 def file_upload_allowed(file, directory_listing):
     """Return True if the file should be uploaded
@@ -65,7 +65,7 @@ def extract_id_from_common_metadata(file, annex_dir):
     return key
 
 
-def local_simulations(annex_dir):
+def local_simulations(annex_dir, compute_md5=False):
     """
     Walk the annex directory to find and process all simulations
 
@@ -88,6 +88,9 @@ def local_simulations(annex_dir):
     ----------
     annex_dir : (str or Path)
         The path to the annex directory to be processed.
+    compute_md5 : bool, optional
+        Whether to compute the MD5 hash of each file.  Default is
+        False.
 
     Returns
     -------
@@ -95,6 +98,7 @@ def local_simulations(annex_dir):
         A dictionary containing the processed metadata.
     """
     from os import walk
+    from ..utilities import md5checksum
 
     simulations = {}
     annex_dir = Path(annex_dir).resolve()
@@ -121,8 +125,14 @@ def local_simulations(annex_dir):
             metadata = Metadata.load(dirpath / highest_lev / "metadata")
             metadata = metadata.add_standard_parameters()
 
+            metadata["directory"] = str(dirpath.relative_to(annex_dir))
+
             metadata["files"] = {
-                p2i(file.relative_to(dirpath)): {"link": str(file)}
+                path_to_invenio(file.relative_to(dirpath)): {
+                    "link": str(file),
+                    "size": file.stat().st_size,
+                    "checksum": md5checksum(file) if compute_md5 else "",
+                }
                 for file in files_to_upload(dirpath, annex_dir)
             }
 
@@ -136,6 +146,10 @@ def local_simulations(annex_dir):
 def write_local_simulations(annex_dir, output_file=None):
     """Write the local simulations to a file for use when loading `Simulations`
 
+    This function calls `local_simulations` to obtain the dictionary,
+    but also writes the dictionary to a JSON file.
+
+
     Parameters
     ----------
     annex_dir : (str or Path)
@@ -148,7 +162,8 @@ def write_local_simulations(annex_dir, output_file=None):
 
     Returns
     -------
-        None
+    dict :
+        A dictionary containing the processed metadata.
     """
     from json import dump
 
@@ -163,3 +178,5 @@ def write_local_simulations(annex_dir, output_file=None):
     output_file.parent.mkdir(parents=True, exist_ok=True)
     with output_file.open("w") as f:
         dump(simulations, f, indent=2, separators=(",", ": "), ensure_ascii=True)
+
+    return simulations

{sxs-2024.0.31 → sxs-2024.0.33}/sxs/waveforms/alignment.py

@@ -312,7 +312,7 @@ def _cost4d(δt_δso3, args):
 
     modes_A, modes_B, t_reference, normalization = args
     δt = δt_δso3[0]
-    δSO3 = np.exp(quaternionic.array.from_vector_part(δt_δso3[1:]))
+    δSpin3 = np.exp(quaternionic.array.from_vector_part(δt_δso3[1:]))
 
     modes_A_at_δt = modes_A(t_reference + δt)
     ell_max = int(np.sqrt(modes_A_at_δt.shape[1] + 4)) - 1
@@ -327,7 +327,7 @@ def _cost4d(δt_δso3, args):
         spin_weight=-2,
     )
 
-    wa_prime = wa_prime.rotate(δSO3)
+    wa_prime = wa_prime.rotate(δSpin3)
 
     # Take the sqrt because least_squares squares the inputs...
     diff = trapezoid(
@@ -479,8 +479,13 @@ def align4d(
     # Brute force over R_IG * exp(theta * z / 2) with δt_IG
     n_brute_force_δϕ = n_brute_force_δϕ or 2 * (2 * ell_max + 1)
     δt_δso3_brute_force = [
-        [δt_IG, *np.log(R_IG * np.exp(quaternionic.array([0, 0, 0, angle / 2]))).vector]
-        for angle in np.linspace(0, 2 * np.pi, num=n_brute_force_δϕ, endpoint=False)
+        [
+            δt_IG,
+            *np.log(
+                (R_IG * np.exp(quaternionic.array([0, 0, 0, angle / 2]))).canonicalized
+            ).vector
+        ]
+        for angle in np.linspace(-np.pi, np.pi, num=n_brute_force_δϕ, endpoint=False)
     ]
 
     # Remove certain modes, if requested
@@ -529,7 +534,7 @@ def align4d(
         max_nfev=50000,
     )
     δt = optimum.x[0]
-    δSO3 = np.exp(quaternionic.array.from_vector_part(optimum.x[1:]))
+    δSpin3 = np.exp(quaternionic.array.from_vector_part(optimum.x[1:]))
     
     wa_prime = WaveformModes(
         input_array=(wa_orig[:, wa_orig.index(ell_min, -ell_min) : wa_orig.index(ell_max, ell_max)+1].data),
@@ -540,6 +545,6 @@ def align4d(
         ell_max=ell_max,
         spin_weight=spin_weight,
     )
-    wa_prime = wa_prime.rotate(δSO3)
+    wa_prime = wa_prime.rotate(δSpin3)
 
     return optimum.cost, wa_prime, optimum

sxs-2024.0.31/sxs/__version__.py

@@ -1 +0,0 @@
-__version__ = "2024.0.31"