Changes for release 0.0.6 (#565)

* Docstring fix

* Update main README

* Update main README

* Bump maximum jaxlib/jax version

* Bump minimum jaxlib/jax version

* Bump max flax version

* Add warning about GPU requirement for astra 3d projections

* Fix markup

* Set release version number and date

* Fix manifest

CHANGES.rst

@@ -3,7 +3,7 @@ SCICO Release Notes
 ===================
 
 
-Version 0.0.6   (unreleased)
+Version 0.0.6   (2024-10-25)
 ----------------------------
 
 • Significant changes to ``linop.xray.astra`` API.
@@ -20,8 +20,8 @@ Version 0.0.6   (unreleased)
 • Rename ``scico.flax.save_weights`` and ``scico.flax.load_weights`` to
   ``scico.flax.save_variables`` and ``scico.flax.load_variables``
   respectively.
-• Support ``jaxlib`` and ``jax`` versions 0.4.3 to 0.4.34.
-• Support ``flax`` versions 0.8.0 to 0.9.0.
+• Support ``jaxlib`` and ``jax`` versions 0.4.13 to 0.4.35.
+• Support ``flax`` versions 0.8.0 to 0.10.0.
 
 
 

MANIFEST.in

@@ -8,10 +8,10 @@ include pyproject.toml
 include pytest.ini
 include requirements.txt
 include dev_requirements.txt
-include examples/scriptcheck.sh
 include docs/docs_requirements.txt
 
 recursive-include scico *.py
-recursive-include scico/data *.png *.npz
-recursive-include docs Makefile *.py *.ipynb *.rst *.bib *.css *.svg *.ico
-recursive-include examples *_requirements.txt *.txt *.rst *.py
+recursive-include scico/data *.png *.mpk *.rst
+recursive-include docs Makefile *.py *.ipynb *.rst *.bib *.css *.svg *.png *.ico
+recursive-include examples *_requirements.txt *.txt *.rst *.py *.sh
+recursive-include misc *.py *.sh *.rst

README.md

@@ -32,11 +32,12 @@ this software for published work, please cite the corresponding [JOSS
 Paper](https://doi.org/10.21105/joss.04722) (see bibtex entry
 `balke-2022-scico` in `docs/source/references.bib`).
 
+
 # Installation
 
-See the [online
-documentation](https://scico.rtfd.io/en/latest/install.html) for
-installation instructions.
+The online documentation includes detailed
+[installation instructions](https://scico.rtfd.io/en/latest/install.html).
+
 
 # Usage Examples
 
@@ -47,8 +48,11 @@ Jupyter Notebooks are provided in the
 to `examples/notebooks`. They are also viewable on
 [GitHub](https://github.com/lanl/scico-data/tree/main/notebooks) or
 [nbviewer](https://nbviewer.jupyter.org/github/lanl/scico-data/tree/main/notebooks/index.ipynb),
-or can be run online by
-[binder](https://mybinder.org/v2/gh/lanl/scico-data/binder?labpath=notebooks%2Findex.ipynb).
+and can be run online on
+[binder](https://mybinder.org/v2/gh/lanl/scico-data/binder?labpath=notebooks%2Findex.ipynb)
+or
+[google colab](https://colab.research.google.com/github/lanl/scico-data/blob/colab/notebooks/index.ipynb).
+
 
 # License
 

examples/scripts/ct_astra_3d_tv_padmm.py

@@ -56,7 +56,7 @@
 y = C @ tangle  # sinogram
 
 
-"""
+r"""
 Set up problem and solver. We want to minimize the functional
 
   $$\mathrm{argmin}_{\mathbf{x}} \; (1/2) \| \mathbf{y} - C \mathbf{x}

requirements.txt

@@ -4,8 +4,8 @@ scipy>=1.6.0
 imageio>=2.17
 tifffile
 matplotlib
-jaxlib>=0.4.3,<=0.4.34
-jax>=0.4.3,<=0.4.34
+jaxlib>=0.4.13,<=0.4.35
+jax>=0.4.13,<=0.4.35
 orbax-checkpoint>=0.5.0
-flax>=0.8.0,<=0.9.0
+flax>=0.8.0,<=0.10.0
 pyabel>=0.9.0

scico/__init__.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2021-2023 by SCICO Developers
+# Copyright (C) 2021-2024 by SCICO Developers
 # All rights reserved. BSD 3-clause License.
 # This file is part of the SCICO package. Details of the copyright and
 # user license can be found in the 'LICENSE' file distributed with the
@@ -8,22 +8,15 @@
 solving the inverse problems that arise in scientific imaging applications.
 """
 
-__version__ = "0.0.6.dev0"
+__version__ = "0.0.6"
 
 import logging
 import sys
 
 # isort: off
 
 # Suppress jax device warning. See https://github.com/google/jax/issues/6805
-# This only works for jax>0.3.23; for earlier versions, the getLogger
-# argument should be "absl". Two filters are included here due to a change
-# in jax between versions 0.4.2 and 0.4.8, both of which are supported by
-# scico.
-logging.getLogger("jax._src.lib.xla_bridge").addFilter(  # jax 0.4.2
-    logging.Filter("No GPU/TPU found, falling back to CPU.")
-)
-logging.getLogger("jax._src.xla_bridge").addFilter(  # jax 0.4.8
+logging.getLogger("jax._src.xla_bridge").addFilter(  # jax 0.4.8 and later
     logging.Filter("No GPU/TPU found, falling back to CPU.")
 )
 

scico/linop/xray/astra.py

@@ -462,6 +462,9 @@ class XRayTransform3D(LinearOperator):  # pragma: no cover
     `ASTRA toolbox <https://github.com/astra-toolbox/astra-toolbox>`_.
     The `3D geometries <https://astra-toolbox.com/docs/geom3d.html#projection-geometries>`__
     "parallel3d" and "parallel3d_vec" are supported by this interface.
+    **NB:** A GPU is required for the primary functionality of this
+    class; if no GPU is available, projections and back projections will
+    fail with an "Unknown algorithm type" error.
 
     The volume is fixed with respect to the coordinate system, centered
     at the origin, as illustrated below: