From f90e728ac01b912076d833db875557b627615462 Mon Sep 17 00:00:00 2001
From: dennisbrookner <debrookner@gmail.com>
Date: Thu, 26 Oct 2023 11:22:36 -0400
Subject: [PATCH 1/3] add new CLI and instructions for dev install

---
 README.rst                    |  8 +++++++-
 docs/cli/find_spots.rst       | 24 ++++++++++++++++++++++++
 docs/cli/functions.md         |  4 +++-
 docs/cli/index.rst            | 24 ++++++++++++++++++++++++
 docs/cli/plot_wavelengths.rst | 24 ++++++++++++++++++++++++
 5 files changed, 82 insertions(+), 2 deletions(-)
 create mode 100644 docs/cli/find_spots.rst
 create mode 100644 docs/cli/index.rst
 create mode 100644 docs/cli/plot_wavelengths.rst

diff --git a/README.rst b/README.rst
index b610104..f7865e6 100644
--- a/README.rst
+++ b/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
diff --git a/docs/cli/find_spots.rst b/docs/cli/find_spots.rst
new file mode 100644
index 0000000..7478435
--- /dev/null
+++ b/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
diff --git a/docs/cli/functions.md b/docs/cli/functions.md
index 439cf8b..5e38954 100644
--- a/docs/cli/functions.md
+++ b/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
 
 ```
diff --git a/docs/cli/index.rst b/docs/cli/index.rst
new file mode 100644
index 0000000..fd71dad
--- /dev/null
+++ b/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
diff --git a/docs/cli/plot_wavelengths.rst b/docs/cli/plot_wavelengths.rst
new file mode 100644
index 0000000..467fc42
--- /dev/null
+++ b/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

From ee87b8e599738de7fb800b4bc7c88e9f7af7dcef Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Oct 2023 15:25:27 +0000
Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/laue_dials/__init__.py                        |  6 ++----
 src/laue_dials/algorithms/laue.py                 |  5 +++--
 src/laue_dials/command_line/find_spots.py         |  4 ++--
 src/laue_dials/command_line/index.py              | 14 ++++++--------
 src/laue_dials/command_line/integrate.py          |  3 +--
 src/laue_dials/command_line/optimize_indexing.py  |  3 +--
 src/laue_dials/command_line/plot_wavelengths.py   |  3 +--
 src/laue_dials/command_line/predict.py            |  3 +--
 src/laue_dials/command_line/refine.py             |  7 +++++--
 src/laue_dials/command_line/sequence_to_stills.py |  3 +--
 10 files changed, 23 insertions(+), 28 deletions(-)

diff --git a/src/laue_dials/__init__.py b/src/laue_dials/__init__.py
index 5e28345..e451f10 100644
--- a/src/laue_dials/__init__.py
+++ b/src/laue_dials/__init__.py
@@ -2,11 +2,9 @@
 
 if sys.version_info[:2] >= (3, 8):
     # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
-    from importlib.metadata import (PackageNotFoundError,  # pragma: no cover
-                                    version)
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
 else:
-    from importlib_metadata import (PackageNotFoundError,  # pragma: no cover
-                                    version)
+    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
 
 try:
     # Change here if project is renamed and does not equal the package name
diff --git a/src/laue_dials/algorithms/laue.py b/src/laue_dials/algorithms/laue.py
index 491eccf..7b989d1 100644
--- a/src/laue_dials/algorithms/laue.py
+++ b/src/laue_dials/algorithms/laue.py
@@ -100,8 +100,9 @@ def gen_beam_models(expts, refls):
     # Imports
     from copy import deepcopy
 
-    from dials.algorithms.refinement.prediction.managed_predictors import \
-        ExperimentsPredictorFactory
+    from dials.algorithms.refinement.prediction.managed_predictors import (
+        ExperimentsPredictorFactory,
+    )
 
     # Instantiate new ExperimentList/reflection_table
     new_expts = ExperimentList()
diff --git a/src/laue_dials/command_line/find_spots.py b/src/laue_dials/command_line/find_spots.py
index 5071c8b..5ff2c0c 100644
--- a/src/laue_dials/command_line/find_spots.py
+++ b/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:
 
diff --git a/src/laue_dials/command_line/index.py b/src/laue_dials/command_line/index.py
index 968e357..e36f80a 100644
--- a/src/laue_dials/command_line/index.py
+++ b/src/laue_dials/command_line/index.py
@@ -8,22 +8,20 @@
 
 import libtbx.phil
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 
-from laue_dials.algorithms.monochromatic import (initial_index,
-                                                 scan_varying_refine)
+from laue_dials.algorithms.monochromatic import initial_index, scan_varying_refine
 
 logger = logging.getLogger("laue-dials.command_line.index")
 
 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:
 
diff --git a/src/laue_dials/command_line/integrate.py b/src/laue_dials/command_line/integrate.py
index 0ef9e6c..3886dd3 100644
--- a/src/laue_dials/command_line/integrate.py
+++ b/src/laue_dials/command_line/integrate.py
@@ -17,8 +17,7 @@
 from cctbx import sgtbx
 from dials.array_family import flex
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 
 from laue_dials.algorithms.integration import SegmentedImage
 
diff --git a/src/laue_dials/command_line/optimize_indexing.py b/src/laue_dials/command_line/optimize_indexing.py
index 6e2fc96..bf7cdf9 100644
--- a/src/laue_dials/command_line/optimize_indexing.py
+++ b/src/laue_dials/command_line/optimize_indexing.py
@@ -13,8 +13,7 @@
 import numpy as np
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 from dxtbx.model import ExperimentList
 
 logger = logging.getLogger("laue-dials.command_line.optimize_indexing")
diff --git a/src/laue_dials/command_line/plot_wavelengths.py b/src/laue_dials/command_line/plot_wavelengths.py
index fa3be19..49fac8a 100644
--- a/src/laue_dials/command_line/plot_wavelengths.py
+++ b/src/laue_dials/command_line/plot_wavelengths.py
@@ -8,8 +8,7 @@
 
 import libtbx.phil
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 from matplotlib import pyplot as plt
 
 logger = logging.getLogger("laue-dials.command_line.plot_wavelengths")
diff --git a/src/laue_dials/command_line/predict.py b/src/laue_dials/command_line/predict.py
index a8e132f..e65c511 100644
--- a/src/laue_dials/command_line/predict.py
+++ b/src/laue_dials/command_line/predict.py
@@ -16,8 +16,7 @@
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 from dxtbx.model import ExperimentList
 
 from laue_dials.algorithms.outliers import gen_kde
diff --git a/src/laue_dials/command_line/refine.py b/src/laue_dials/command_line/refine.py
index d1a5f5f..cae01bf 100644
--- a/src/laue_dials/command_line/refine.py
+++ b/src/laue_dials/command_line/refine.py
@@ -19,8 +19,11 @@
 from dxtbx.model import ExperimentList
 from dxtbx.model.experiment_list import ExperimentListFactory
 
-from laue_dials.algorithms.laue import (gen_beam_models, remove_beam_models,
-                                        store_wavelengths)
+from laue_dials.algorithms.laue import (
+    gen_beam_models,
+    remove_beam_models,
+    store_wavelengths,
+)
 
 logger = logging.getLogger("laue-dials.command_line.refine")
 
diff --git a/src/laue_dials/command_line/sequence_to_stills.py b/src/laue_dials/command_line/sequence_to_stills.py
index cbce992..34c090a 100644
--- a/src/laue_dials/command_line/sequence_to_stills.py
+++ b/src/laue_dials/command_line/sequence_to_stills.py
@@ -14,8 +14,7 @@
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 from dxtbx.model import MosaicCrystalSauter2014
 from dxtbx.model.experiment_list import Experiment, ExperimentList
 from libtbx.phil import parse

From e48c022d7e5c586499e17fe516c428e89843bcda Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]" <pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Oct 2023 15:25:54 +0000
Subject: [PATCH 3/3] Commit formatting and linting fixes

---
 src/laue_dials/__init__.py                        | 6 ++++--
 src/laue_dials/algorithms/laue.py                 | 5 ++---
 src/laue_dials/command_line/index.py              | 6 ++++--
 src/laue_dials/command_line/integrate.py          | 3 ++-
 src/laue_dials/command_line/optimize_indexing.py  | 3 ++-
 src/laue_dials/command_line/plot_wavelengths.py   | 3 ++-
 src/laue_dials/command_line/predict.py            | 3 ++-
 src/laue_dials/command_line/refine.py             | 7 ++-----
 src/laue_dials/command_line/sequence_to_stills.py | 3 ++-
 9 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/src/laue_dials/__init__.py b/src/laue_dials/__init__.py
index e451f10..5e28345 100644
--- a/src/laue_dials/__init__.py
+++ b/src/laue_dials/__init__.py
@@ -2,9 +2,11 @@
 
 if sys.version_info[:2] >= (3, 8):
     # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
-    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+    from importlib.metadata import (PackageNotFoundError,  # pragma: no cover
+                                    version)
 else:
-    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
+    from importlib_metadata import (PackageNotFoundError,  # pragma: no cover
+                                    version)
 
 try:
     # Change here if project is renamed and does not equal the package name
diff --git a/src/laue_dials/algorithms/laue.py b/src/laue_dials/algorithms/laue.py
index 7b989d1..491eccf 100644
--- a/src/laue_dials/algorithms/laue.py
+++ b/src/laue_dials/algorithms/laue.py
@@ -100,9 +100,8 @@ def gen_beam_models(expts, refls):
     # Imports
     from copy import deepcopy
 
-    from dials.algorithms.refinement.prediction.managed_predictors import (
-        ExperimentsPredictorFactory,
-    )
+    from dials.algorithms.refinement.prediction.managed_predictors import \
+        ExperimentsPredictorFactory
 
     # Instantiate new ExperimentList/reflection_table
     new_expts = ExperimentList()
diff --git a/src/laue_dials/command_line/index.py b/src/laue_dials/command_line/index.py
index e36f80a..70741df 100644
--- a/src/laue_dials/command_line/index.py
+++ b/src/laue_dials/command_line/index.py
@@ -8,9 +8,11 @@
 
 import libtbx.phil
 from dials.util import show_mail_handle_errors
-from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
+from dials.util.options import (ArgumentParser,
+                                reflections_and_experiments_from_files)
 
-from laue_dials.algorithms.monochromatic import initial_index, scan_varying_refine
+from laue_dials.algorithms.monochromatic import (initial_index,
+                                                 scan_varying_refine)
 
 logger = logging.getLogger("laue-dials.command_line.index")
 
diff --git a/src/laue_dials/command_line/integrate.py b/src/laue_dials/command_line/integrate.py
index 3886dd3..0ef9e6c 100644
--- a/src/laue_dials/command_line/integrate.py
+++ b/src/laue_dials/command_line/integrate.py
@@ -17,7 +17,8 @@
 from cctbx import sgtbx
 from dials.array_family import flex
 from dials.util import show_mail_handle_errors
-from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
+from dials.util.options import (ArgumentParser,
+                                reflections_and_experiments_from_files)
 
 from laue_dials.algorithms.integration import SegmentedImage
 
diff --git a/src/laue_dials/command_line/optimize_indexing.py b/src/laue_dials/command_line/optimize_indexing.py
index bf7cdf9..6e2fc96 100644
--- a/src/laue_dials/command_line/optimize_indexing.py
+++ b/src/laue_dials/command_line/optimize_indexing.py
@@ -13,7 +13,8 @@
 import numpy as np
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
+from dials.util.options import (ArgumentParser,
+                                reflections_and_experiments_from_files)
 from dxtbx.model import ExperimentList
 
 logger = logging.getLogger("laue-dials.command_line.optimize_indexing")
diff --git a/src/laue_dials/command_line/plot_wavelengths.py b/src/laue_dials/command_line/plot_wavelengths.py
index 49fac8a..fa3be19 100644
--- a/src/laue_dials/command_line/plot_wavelengths.py
+++ b/src/laue_dials/command_line/plot_wavelengths.py
@@ -8,7 +8,8 @@
 
 import libtbx.phil
 from dials.util import show_mail_handle_errors
-from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
+from dials.util.options import (ArgumentParser,
+                                reflections_and_experiments_from_files)
 from matplotlib import pyplot as plt
 
 logger = logging.getLogger("laue-dials.command_line.plot_wavelengths")
diff --git a/src/laue_dials/command_line/predict.py b/src/laue_dials/command_line/predict.py
index e65c511..a8e132f 100644
--- a/src/laue_dials/command_line/predict.py
+++ b/src/laue_dials/command_line/predict.py
@@ -16,7 +16,8 @@
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
+from dials.util.options import (ArgumentParser,
+                                reflections_and_experiments_from_files)
 from dxtbx.model import ExperimentList
 
 from laue_dials.algorithms.outliers import gen_kde
diff --git a/src/laue_dials/command_line/refine.py b/src/laue_dials/command_line/refine.py
index cae01bf..d1a5f5f 100644
--- a/src/laue_dials/command_line/refine.py
+++ b/src/laue_dials/command_line/refine.py
@@ -19,11 +19,8 @@
 from dxtbx.model import ExperimentList
 from dxtbx.model.experiment_list import ExperimentListFactory
 
-from laue_dials.algorithms.laue import (
-    gen_beam_models,
-    remove_beam_models,
-    store_wavelengths,
-)
+from laue_dials.algorithms.laue import (gen_beam_models, remove_beam_models,
+                                        store_wavelengths)
 
 logger = logging.getLogger("laue-dials.command_line.refine")
 
diff --git a/src/laue_dials/command_line/sequence_to_stills.py b/src/laue_dials/command_line/sequence_to_stills.py
index 34c090a..cbce992 100644
--- a/src/laue_dials/command_line/sequence_to_stills.py
+++ b/src/laue_dials/command_line/sequence_to_stills.py
@@ -14,7 +14,8 @@
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
+from dials.util.options import (ArgumentParser,
+                                reflections_and_experiments_from_files)
 from dxtbx.model import MosaicCrystalSauter2014
 from dxtbx.model.experiment_list import Experiment, ExperimentList
 from libtbx.phil import parse