autoarray 2026.5.1.4__tar.gz → 2026.5.8.2__tar.gz

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/MANIFEST.in

@@ -1,6 +1,6 @@
 # MANIFEST.in
 exclude .gitignore
-include README.rst
+include README.md
 include setup.cfg
 include CITATIONS.rst
 include LICENSE

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: autoarray
-Version: 2026.5.1.4
+Version: 2026.5.8.2
 Summary: PyAuto Data Structures
 Author-email: James Nightingale <James.Nightingale@newcastle.ac.uk>, Richard Hayes <richard@rghsoftware.co.uk>
 License: MIT
@@ -16,9 +16,9 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.9
-Description-Content-Type: text/x-rst
+Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: autoconf==2026.5.1.4
+Requires-Dist: autoconf==2026.5.8.2
 Requires-Dist: astropy<=7.2.0,>=5.0
 Requires-Dist: decorator>=4.0.0
 Requires-Dist: dill>=0.3.1.1
@@ -44,4 +44,5 @@ Requires-Dist: pynufft==2022.2.2; extra == "dev"
 Dynamic: license-file
 
 # PyAutoArray
+
 A library for manipulating arrays within the PyAuto software framework

autoarray-2026.5.1.4/README.rst → autoarray-2026.5.8.2/README.md

@@ -1,2 +1,3 @@
-# PyAutoArray
-A library for manipulating arrays within the PyAuto software framework
+# PyAutoArray
+
+A library for manipulating arrays within the PyAuto software framework

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray/__init__.py

@@ -101,4 +101,4 @@ from autoconf.fitsable import hdu_list_for_output_from
 
 conf.instance.register(__file__)
 
-__version__ = "2026.5.1.4"
+__version__ = "2026.5.8.2"

autoarray-2026.5.8.2/autoarray/config/README.md

@@ -0,0 +1,13 @@
+The `config` folder contains configuration files which customize default **PyAutoLens**.
+
+# Folders
+
+- `priors`: Configs defining default priors assumed on every model component and set of parameters.
+- `visualize`: Configs defining what images are output by a lens model fit.
+
+# Files
+
+- `general.yaml`: Customizes general **PyAutoLens** settings.
+- `grids.yaml`: Customize default behaviour of grids when used for calculations.
+- `logging.yaml`: Customizes the logging behaviour.
+- `notation.yaml`: Configs defining labels and formatting of model parameters when used for visualization.

autoarray-2026.5.8.2/autoarray/config/visualize/README.md

@@ -0,0 +1,10 @@
+The `config` folder contains configuration files which customize default **PyAutoLens**.
+
+# Files
+
+- `general.yaml`: Customizes general visualization settings (e.g. the matplotlib backend).
+- `include.yaml`: Customize features that appears on plotted images by default (e.g. a mask, a grid).
+- `plots.yaml`: Customize which figures are output during a model-fit.
+- `mat_wrap.yaml`: Specify the default matplotlib settings when figures and subplots are plotted.
+- `mat_wrap_1d.yaml`: Specify the default matplotlib settings when 1D figures and subplots are plotted.
+- `mat_wrap_2d.yaml`: Specify the default matplotlib settings when 2D figures and subplots are plotted.

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray/dataset/imaging/dataset.py

@@ -203,13 +203,17 @@ class Imaging(AbstractDataset):
             passed into the calculations performed in the `inversion` module.
         """
 
+        from autoarray.util.dataset_util import cap_array_2d_for_small_datasets
+
         data = Array2D.from_fits(
             file_path=data_path, hdu=data_hdu, pixel_scales=pixel_scales
         )
+        data, pixel_scales = cap_array_2d_for_small_datasets(data, pixel_scales)
 
         noise_map = Array2D.from_fits(
             file_path=noise_map_path, hdu=noise_map_hdu, pixel_scales=pixel_scales
         )
+        noise_map, pixel_scales = cap_array_2d_for_small_datasets(noise_map, pixel_scales)
 
         if psf_path is not None:
             kernel = Array2D.from_fits(

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray/inversion/inversion/imaging_numba/inversion_imaging_numba_util.py

@@ -310,9 +310,24 @@ def psf_precision_value_from(
 
     for k0_y in range(kernel_native.shape[0]):
         for k0_x in range(kernel_native.shape[1]):
-            value = value_native[
-                ip0_y + k0_y + kernel_shift_y, ip0_x + k0_x + kernel_shift_x
-            ]
+            iy = ip0_y + k0_y + kernel_shift_y
+            ix = ip0_x + k0_x + kernel_shift_x
+
+            # numba @jit() does not bounds-check array reads. Without this
+            # guard, a kernel position that lands off the noise-map array
+            # (e.g. a mask pixel within `kernel_shift` of the array edge)
+            # silently reads uninitialized memory, producing astronomical
+            # or non-finite contributions that poison the entire
+            # psf_precision_operator and downstream curvature matrix.
+            if (
+                iy < 0
+                or iy >= value_native.shape[0]
+                or ix < 0
+                or ix >= value_native.shape[1]
+            ):
+                continue
+
+            value = value_native[iy, ix]
 
             if value > 0.0:
                 k1_y = k0_y + ip_y_offset

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray/inversion/plot/inversion_plots.py

@@ -60,8 +60,13 @@ def subplot_of_mapper(
 
     # panel 0: data subtracted
     try:
+        array = inversion.data_subtracted_dict[mapper]
+        from autoarray.structures.visibilities import Visibilities
+
+        if isinstance(array, Visibilities):
+            array = inversion.transformer.image_from(visibilities=array)
         plot_array(
-            inversion.data_subtracted_dict[mapper],
+            array,
             ax=axes[0],
             title=_pf("Data Subtracted"),
             colormap=colormap,
@@ -286,8 +291,13 @@ def subplot_mappings(
 
     # panel 0: data subtracted
     try:
+        array = inversion.data_subtracted_dict[mapper]
+        from autoarray.structures.visibilities import Visibilities
+
+        if isinstance(array, Visibilities):
+            array = inversion.transformer.image_from(visibilities=array)
         plot_array(
-            inversion.data_subtracted_dict[mapper],
+            array,
             ax=axes[0],
             title="Data Subtracted",
             colormap=colormap,

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray/plot/output.py

@@ -1,6 +1,6 @@
 import logging
-from os import path
 import os
+from pathlib import Path
 from typing import Union, List, Optional
 
 from autoarray.structures.abstract_structure import Structure
@@ -100,7 +100,7 @@ class Output:
             return None
 
         if self.format_folder:
-            output_path = path.join(self.path, format)
+            output_path = str(Path(self.path) / format)
         else:
             output_path = self.path
 
@@ -156,7 +156,7 @@ class Output:
 
         try:
             plt.savefig(
-                path.join(output_path, f"{filename}.{format}"),
+                str(Path(output_path) / f"{filename}.{format}"),
                 bbox_inches=self.bbox_inches,
                 pad_inches=0.1,
             )
@@ -257,9 +257,9 @@ class Output:
 
         import sys
 
-        script_name = path.split(sys.argv[0])[-1].replace(".py", "")
+        script_name = Path(sys.argv[0]).name.replace(".py", "")
 
-        output_path = path.join(os.getcwd(), "output_mode", script_name)
+        output_path = str(Path(os.getcwd()) / "output_mode" / script_name)
         os.makedirs(output_path, exist_ok=True)
 
         self.savefig(f"{COUNT}_{filename}", output_path, "png")

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray/plot/utils.py

@@ -4,6 +4,7 @@ Shared utilities for the direct-matplotlib plot functions.
 
 import logging
 import os
+from pathlib import Path
 from typing import List, Optional, Tuple
 
 import numpy as np
@@ -310,8 +311,8 @@ def _output_mode_save(fig, filename):
 
     import sys
 
-    script_name = os.path.splitext(os.path.basename(sys.argv[0]))[0]
-    output_path = os.path.join(os.getcwd(), "output_mode", script_name)
+    script_name = Path(sys.argv[0]).stem
+    output_path = str(Path(os.getcwd()) / "output_mode" / script_name)
     os.makedirs(output_path, exist_ok=True)
 
     count = getattr(_output_mode_save, "_count", -1) + 1
@@ -319,7 +320,7 @@ def _output_mode_save(fig, filename):
 
     try:
         fig.savefig(
-            os.path.join(output_path, f"{count}_{filename}.png"),
+            str(Path(output_path) / f"{count}_{filename}.png"),
             dpi=150,
             bbox_inches="tight",
             pad_inches=0.1,
@@ -371,7 +372,7 @@ def subplot_save(fig, output_path, output_filename, output_format=None):
         os.makedirs(output_path, exist_ok=True)
         try:
             fig.savefig(
-                os.path.join(output_path, f"{output_filename}.{output_format}"),
+                str(Path(output_path) / f"{output_filename}.{output_format}"),
                 bbox_inches="tight",
                 pad_inches=0.1,
             )
@@ -552,7 +553,7 @@ def save_figure(
                 continue
             try:
                 fig.savefig(
-                    os.path.join(path, f"{filename}.{fmt}"),
+                    str(Path(path) / f"{filename}.{fmt}"),
                     dpi=dpi,
                     bbox_inches="tight",
                     pad_inches=0.1,

autoarray-2026.5.8.2/autoarray/util/dataset_util.py

@@ -0,0 +1,73 @@
+import os
+import shutil
+from pathlib import Path
+
+
+SMALL_DATASETS_SHAPE_NATIVE = (15, 15)
+SMALL_DATASETS_PIXEL_SCALES = 0.6
+
+
+def cap_array_2d_for_small_datasets(array_2d, pixel_scales):
+    """
+    Center-crop a 2D autoarray to the small-datasets cap when
+    ``PYAUTO_SMALL_DATASETS=1`` is active.
+
+    Returns ``(array_2d, pixel_scales)`` unchanged in any of these cases:
+
+    - ``PYAUTO_SMALL_DATASETS`` is not set to ``"1"``.
+    - ``array_2d.shape_native`` is already at-or-below the cap (15, 15).
+
+    When the env var is set and the input shape exceeds (15, 15), returns a
+    new ``Array2D`` center-cropped to (15, 15) with ``pixel_scales`` overridden
+    to 0.6 — matching the convention used by ``Mask2D.circular`` and
+    ``Grid2D.uniform`` so the loaded dataset stays shape-consistent with masks
+    and grids built under the same env var.
+
+    The same env var is honoured for shape construction in
+    ``Mask2D.circular`` and ``Grid2D.uniform`` (and by ``should_simulate``
+    for on-disk regeneration). This helper closes the gap for FITS loaders
+    that read pre-committed datasets larger than the cap, which would
+    otherwise broadcast-mismatch against capped masks/grids.
+
+    Center-cropping (rather than downsampling/resampling) is intentional:
+    smoke-mode tests don't require numerical correctness, and the simpler
+    op avoids interpolation artifacts and a scipy dependency at this layer.
+    """
+    if os.environ.get("PYAUTO_SMALL_DATASETS") != "1":
+        return array_2d, pixel_scales
+
+    h, w = array_2d.shape_native
+    cap_h, cap_w = SMALL_DATASETS_SHAPE_NATIVE
+    if h <= cap_h and w <= cap_w:
+        return array_2d, pixel_scales
+
+    from autoarray.structures.arrays.uniform_2d import Array2D
+
+    h0, w0 = (h - cap_h) // 2, (w - cap_w) // 2
+    cropped = array_2d.native.array[h0:h0 + cap_h, w0:w0 + cap_w]
+    return (
+        Array2D.no_mask(values=cropped, pixel_scales=SMALL_DATASETS_PIXEL_SCALES),
+        SMALL_DATASETS_PIXEL_SCALES,
+    )
+
+
+def should_simulate(dataset_path):
+    """
+    Returns True if the dataset at ``dataset_path`` needs to be simulated.
+
+    When ``PYAUTO_SMALL_DATASETS=1`` is active, any existing dataset
+    is deleted so the simulator re-creates it at the reduced resolution.  This
+    avoids shape mismatches between full-resolution FITS files on disk and the
+    15x15 mask/grid cap applied by the env var.
+
+    Use this as a drop-in replacement for ``not path.exists(dataset_path)`` in
+    the workspace auto-simulation pattern::
+
+        if aa.util.dataset.should_simulate(dataset_path):
+            subprocess.run([sys.executable, "scripts/.../simulator.py"], check=True)
+    """
+    if os.environ.get("PYAUTO_SMALL_DATASETS") == "1":
+        if Path(dataset_path).exists():
+            shutil.rmtree(dataset_path)
+
+    return not Path(dataset_path).exists()

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/autoarray.egg-info/SOURCES.txt

@@ -4,7 +4,7 @@ CONTRIBUTING.md
 LICENSE
 MANIFEST.in
 PLAN.md
-README.rst
+README.md
 eden.ini
 pyproject.toml
 readthedocs.yml
@@ -23,10 +23,10 @@ autoarray/numba_util.py
 autoarray/settings.py
 autoarray/type.py
 autoarray/config/.gitignore
-autoarray/config/README.rst
+autoarray/config/README.md
 autoarray/config/general.yaml
 autoarray/config/logging.yaml
-autoarray/config/visualize/README.rst
+autoarray/config/visualize/README.md
 autoarray/config/visualize/general.yaml
 autoarray/config/visualize/plots.yaml
 autoarray/dataset/__init__.py
@@ -235,7 +235,7 @@ autoarray/util/fnnls.py
 autoarray/util/misc_util.py
 docs/Makefile
 docs/conf.py
-docs/index.rst
+docs/index.md
 docs/make.bat
 files/eden.ini
 files/release.sh

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/docs/conf.py

@@ -10,11 +10,11 @@ import datetime
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+# documentation root, use Path(...).resolve() to make it absolute, like shown here.
 #
-# import os
 # import sys
-# sys.path.insert(0, os.path.abspath('.'))
+# from pathlib import Path
+# sys.path.insert(0, str(Path(".").resolve()))
 
 # -- Project information -----------------------------------------------------
 
@@ -39,6 +39,7 @@ extensions = [
     "sphinx.ext.napoleon",
     "sphinx.ext.extlinks",
     "numpydoc",
+    "myst_parser",
 ]
 
 ## Generate autodoc stubs with summaries from code

autoarray-2026.5.8.2/docs/index.md

@@ -0,0 +1,2 @@
+```{include} ../README.md
+```

{autoarray-2026.5.1.4 → autoarray-2026.5.8.2}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "autoarray"
 dynamic = ["version"]
   description="PyAuto Data Structures"
-readme = { file = "README.rst", content-type = "text/x-rst" }
+readme = { file = "README.md", content-type = "text/markdown" }
 license = { text = "MIT" }
 requires-python = ">=3.9"
 authors = [
@@ -26,7 +26,7 @@ classifiers = [
 ]
 keywords = ["cli"]
 dependencies = [
-    "autoconf==2026.5.1.4",
+    "autoconf==2026.5.8.2",
     "astropy>=5.0,<=7.2.0",
     "decorator>=4.0.0",
     "dill>=0.3.1.1",

autoarray-2026.5.1.4/autoarray/config/README.rst

@@ -1,16 +0,0 @@
-The ``config`` folder contains configuration files which customize default **PyAutoLens**.
-
-Folders
--------
-
-- ``priors``: Configs defining default priors assumed on every model component and set of parameters.
-- ``visualize``: Configs defining what images are output by a lens model fit.
-
-Files
------
-
-- ``general.yaml``: Customizes general **PyAutoLens** settings.
-- ``grids.yaml``: Customize default behaviour of grids when used for calculations.
-- ``logging.yaml``: Customizes the logging behaviour.
-- ``notation.yaml``: Configs defining labels and formatting of model parameters when used for visualization.
-

autoarray-2026.5.1.4/autoarray/config/visualize/README.rst

@@ -1,11 +0,0 @@
-The ``config`` folder contains configuration files which customize default **PyAutoLens**.
-
-Files
------
-
-- ``general.yaml``: Customizes general visualization settings (e.g. the matplotlib backend).
-- ``include.yaml``: Customize features that appears on plotted images by default (e.g. a mask, a grid).
-- ``plots.yaml``: Customize which figures are output during a model-fit.
-- ``mat_wrap.yaml``: Specify the default matplotlib settings when figures and subplots are plotted.
-- ``mat_wrap_1d.yaml``: Specify the default matplotlib settings when 1D figures and subplots are plotted.
-- ``mat_wrap_2d.yaml``: Specify the default matplotlib settings when 2D figures and subplots are plotted.

autoarray-2026.5.1.4/autoarray/util/dataset_util.py

@@ -1,24 +0,0 @@
-import os
-import shutil
-
-
-def should_simulate(dataset_path):
-    """
-    Returns True if the dataset at ``dataset_path`` needs to be simulated.
-
-    When ``PYAUTO_SMALL_DATASETS=1`` is active, any existing dataset
-    is deleted so the simulator re-creates it at the reduced resolution.  This
-    avoids shape mismatches between full-resolution FITS files on disk and the
-    15x15 mask/grid cap applied by the env var.
-
-    Use this as a drop-in replacement for ``not path.exists(dataset_path)`` in
-    the workspace auto-simulation pattern::
-
-        if aa.util.dataset.should_simulate(dataset_path):
-            subprocess.run([sys.executable, "scripts/.../simulator.py"], check=True)
-    """
-    if os.environ.get("PYAUTO_SMALL_DATASETS") == "1":
-        if os.path.exists(dataset_path):
-            shutil.rmtree(dataset_path)
-
-    return not os.path.exists(dataset_path)

autoarray-2026.5.1.4/docs/index.rst

@@ -1 +0,0 @@
-.. include:: ../README.rst