Add docs

.github/workflows/Docs4NIST.yml

@@ -0,0 +1,16 @@
+name: "Build Documentation"
+
+on: [push, pull_request, delete]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usnistgov/[email protected]
+        with:
+          docs-folder: docs/
+          formats: |-
+            epub
+            pdf
+          pre-build-command: 'pip install -e .'
+          pip-requirements: 'requirements-all.txt'

AFL/automation/instrument/CDSAXSLabview.py

@@ -113,7 +113,8 @@ def measureTransmission(self,exp=5,fn='trans',set_empty_transmission=False,retur
 
 
 
-        '''with (LabviewConnection() if lv is None else lv) as lv:
+        '''
+        with (LabviewConnection() if lv is None else lv) as lv:
             self.status_txt = 'Moving beamstop out for transmission...'
             self.moveAxis(self.config['nmc_beamstop_out'],block=True,lv=lv)
             self.moveAxis(self.config['nmc_sample_out'],block=True,lv=lv)

AFL/automation/instrument/PySpecClient.py

@@ -1,4 +1,4 @@
-import numpy as np
+import numpy as np
 from pyspec.client.SpecConnection import SpecConnection
 from pyspec.client.SpecCounter import SpecCounter
 from pyspec.client.SpecConnectionsManager import SpecConnectionsManager

docs/Makefile

@@ -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)

docs/make.bat

@@ -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

docs/source/api.rst

@@ -0,0 +1,6 @@
+API
+===
+
+.. autosummary::
+    :toctree: generated
+    :recursive:

docs/source/conf.py

@@ -0,0 +1,39 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))  # Source code dir relative to this file
+
+
+project = 'AFL-automation'
+copyright = 'Contribution of the US Government.  Not subject to copyright in the United States.'
+author = 'NIST AFL Team'
+
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+	'sphinx.ext.duration',
+	'sphinx.ext.doctest',
+	'sphinx.ext.autodoc',
+	'sphinx.ext.autosummary',
+	]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,31 @@
+.. AFL-automation documentation master file, created by
+   sphinx-quickstart on Tue May 28 13:58:39 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to AFL-automation's documentation!
+==========================================
+
+AFL-automation is a framework for instrument control.  It powers the NIST AFL, but is more useful than that.  It enables the easy conversion of Python classes - drivers - into robust HTTP microservices with authentication, task queueing, UI generation, data management, and more.
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   AFL.automation
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

requirements-all.txt

@@ -0,0 +1,42 @@
+alphashape==1.3.1
+bokeh==3.5.1
+fabio==2024.4.0
+Flask==2.2.5
+Flask_Cors==4.0.1
+Flask_JWT_Extended==4.6.0
+gpflow==2.9.2
+h5py==3.11.0
+ipython==8.26.0
+ipywidgets==8.1.3
+matplotlib==3.9.1.post1
+nice==1.1
+numpy<2
+opentrons==7.5.0
+pandas==2.2.2
+paramiko==3.4.0
+periodictable==1.7.1
+Pillow==10.4.0
+Pint==0.24.3
+plotly==5.23.0
+pyFAI==2024.5.0
+pyparsing==3.1.2
+pyserial==3.5
+certif-pyspec<1.4
+pytest
+Requests==2.32.3
+sans==1.2.3
+sasdata
+sasmodels
+scikit_learn==1.5.1
+scipy==1.14.0
+seabreeze==2.9.2
+setuptools==72.1.0
+Shapely==2.0.5
+six==1.16.0
+scikit-image
+tensorflow==2.17.0
+tiled==0.1.0b6
+tqdm==4.66.5
+Werkzeug==3.0.3
+xarray==2024.7.0
+zeroconf==0.132.2