Merge pull request #29 from rs-station/docupdate

add new CLI and instructions for dev install

README.rst

@@ -37,12 +37,18 @@ To install ``laue-dials``, the DIALS code must first be installed using
 
    conda install -c conda-forge dials
 
-Then, using the DIALS python environment, run the following:
+Then, using the same python environment, run the following to install ``laue-dials`` from ``pip``:
 
 .. code:: python
 
    pip install laue-dials
 
+or alternatively, install the development version of ``laue-dials`` from GitHub:
+
+.. code:: python
+
+   pip install git+https://github.com/rs-station/laue-dials.git
+
 ``laue-dials`` consists of several command-line scripts for the processing of Laue diffraction data, which are
 
 .. code:: python

docs/cli/find_spots.rst

@@ -0,0 +1,24 @@
+.. _find_spots:
+
+laue_dials.find_spots
+=====================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.find_spots.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.find_spots.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.find_spots.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/functions.md

@@ -6,11 +6,13 @@
 .. toctree::
    :maxdepth: 1
 
-   initial_solution
+   find_spots
+   index
    sequence_to_stills
    optimize_indexing
    refine
    predict
    integrate
+   plot_wavelengths
 
 ```

docs/cli/index.rst

@@ -0,0 +1,24 @@
+.. _index:
+
+laue_dials.index
+================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.index.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.index.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.index.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/plot_wavelengths.rst

@@ -0,0 +1,24 @@
+.. _plot_wavelengths:
+
+laue_dials.plot_wavelengths
+===========================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.plot_wavelengths.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.plot_wavelengths.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.plot_wavelengths.working_phil
+   :expert-level: 2
+   :attributes-level: 2

src/laue_dials/command_line/find_spots.py

@@ -18,8 +18,8 @@
 
 This program takes a DIALS imported experiment list (generated with
 dials.import) and generates a reflection table of strong spots
-for the remainder of the pipeline. The output is a strong.refl file 
-that contains all the found strong spots for the experiment. 
+for the remainder of the pipeline. The output is a strong.refl file
+that contains all the found strong spots for the experiment.
 
 Examples:
 

src/laue_dials/command_line/index.py

@@ -19,11 +19,11 @@
 help_message = """
 
 This program takes a DIALS imported experiment list (generated with
-dials.import) and a strong reflection table and generates an initial 
-monochromatic indexing solution to feed into the remainder of the pipeline. 
-The outputs are a pair of files (monochromatic.expt, monochromatic.refl) 
+dials.import) and a strong reflection table and generates an initial
+monochromatic indexing solution to feed into the remainder of the pipeline.
+The outputs are a pair of files (monochromatic.expt, monochromatic.refl)
 that constitute a monochromatic estimate of a geometric solution for the
-experiment. 
+experiment.
 
 Examples: