Update to pty-chi 1.1 (#110)

- Update to pty-chi v1.1 api
- Enable loading bad pixels masks from file
- Add sphinx documentation
- Add file readers for APS Polar (4-ID), Ptycho-SAXS (12-ID-E), and ISN (19-ID) instruments
- Update file reader names to be more consistent
- Add support for transposing diffraction patterns
- Bundle xdrlib so MDA file readers work with python 3.13+

Author: stevehenke

README.rst

@@ -1,85 +1,51 @@
 Ptychodus
 =========
 
-`ptychodus`_ is a ptychography analysis application that supports multiple reconstruction libraries.
+`Ptychodus <https://github.com/AdvancedPhotonSource/ptychodus>`_
+is a ptychography data analysis application that reads instrument data,
+prepares the data for processing, and supports calling several reconstruction
+libraries for phase retrieval. Ptychodus can be used interactively or
+integrated into a data pipeline.
 
 
 Standard Installation
 ---------------------
 
-1. Install `miniforge <https://github.com/conda-forge/miniforge>`_.
+To install ptychodus from PyPI with the most common optional dependencies:
 
-2. Install ptychodus.
-
-   * To install `ptychodus` with the GUI and all optional packages:
-
-     .. code-block:: shell
-
-           $ conda create -c conda-forge -n ptychodus ptychodus-all
-
-   * To install `ptychodus` with the GUI and no optional packages:
-
-     .. code-block:: shell
-
-           $ conda create -c conda-forge -n ptychodus ptychodus
-
-   * To install `ptychodus` without the GUI or optional packages:
-
-     .. code-block:: shell
-
-           $ conda create -c conda-forge -n ptychodus ptychodus-core
-
-3. Activate the `ptychodus` conda environment to run ptychodus.
-
-   .. code-block:: shell
-
-       $ conda activate ptychodus
-       $ ptychodus -h
-
-       usage: ptychodus [-h] [-b {reconstruct,train}] [-f FILE_PREFIX] [-s SETTINGS_FILE] [-v] [-w OUTPUT_DIR]
-
-       ptychodus is a ptychography analysis application
+.. code-block:: shell
 
-       options:
-         -h, --help            show this help message and exit
-         -b {reconstruct,train}, --batch {reconstruct,train}
-                               run action non-interactively
-         -f FILE_PREFIX, --file-prefix FILE_PREFIX
-                               replace file path prefix in settings
-         -s SETTINGS_FILE, --settings SETTINGS_FILE
-                               use settings from file
-         -v, --version         show program's version number and exit
-         -w OUTPUT_DIR, --write OUTPUT_DIR
-                               stage reconstruction inputs to directory
+    $ python -m pip install ptychodus[globus,gui,ptychi]
 
-       $ ptychodus
+Instructions for installing in containers and from conda-forge are provided in
+the ``docs`` directory.
 
 
 Developer Installation
 ----------------------
 
-* For a developer installation:
+- For a developer installation:
 
 .. code-block:: shell
 
    $ git clone https://github.com/AdvancedPhotonSource/ptychodus.git
-   $ conda create -c conda-forge -n ptychodus --file ptychodus/requirements-dev.txt
+   $ conda create -n ptychodus --file ptychodus/requirements-dev.txt
    $ conda activate ptychodus
    $ pip install -e ./ptychodus
 
-* To install the `pty-chi`_ backend:
+- To install `pty-chi <https://github.com/AdvancedPhotonSource/pty-chi>`_
 
 .. code-block:: shell
 
    $ pip install ptychi
 
-* To install the `PtychoNN`_ backend:
+- To install `PtychoNN <https://github.com/mcherukara/PtychoNN>`_
 
 .. code-block:: shell
 
-   $ conda install -n ptychodus -c conda-forge ptychonn
+   $ conda install -n ptychodus ptychonn
 
-* Launch `ptychodus`:
+- Launch `ptychodus`:
 
 .. code-block:: shell
 
@@ -91,8 +57,3 @@ Reporting Bugs
 --------------
 
 Open a bug at https://github.com/AdvancedPhotonSource/ptychodus/issues.
-
-.. _`ptychodus`: https://github.com/AdvancedPhotonSource/ptychodus
-.. _`pty-chi`: https://github.com/AdvancedPhotonSource/pty-chi
-.. _`PtychoNN`: https://github.com/mcherukara/PtychoNN
-.. _`PvaPy`: https://github.com/epics-base/pvaPy

doc/api.rst

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/dist.rst

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd