Merge branch 'qa'

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: check-docstring-first
@@ -25,12 +25,12 @@ repos:
       - id: end-of-file-fixer
       - id: sort-simple-yaml
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.2.0
     hooks:
       - id: black
         args: ['--line-length=119']
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.31.0
+    rev: v1.35.1
     hooks:
     - id: yamllint
     name: yamllint
@@ -39,6 +39,6 @@ repos:
     language: python
     types: [file, yaml]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
     - id: nbstripout

conda.recipe/meta.yaml

@@ -40,8 +40,8 @@ requirements:
     - dxchange
     - olefile
     - pooch
-    - panel
-    - param
+    - panel<1.3
+    - param<2
     - pyvista
     - holoviews
     - bokeh

src/imars3d/__init__.py

@@ -1,4 +1,5 @@
 """iMars3D: a Python package for neutron imaging and tomography reconstruction."""
+
 import logging
 from .backend import corrections, diagnostics, dataio, morph, preparation, reconstruction  # noqa: F401
 

src/imars3d/backend/__init__.py

@@ -1,4 +1,5 @@
 """iMars3D's backend packages: the core of the application."""
+
 from .autoredux import auto_reduction_ready  # noqa: F401
 from .autoredux import load_template_config  # noqa: F401
 from .autoredux import extract_info_from_path  # noqa: F401

src/imars3d/backend/__main__.py

@@ -9,6 +9,7 @@
 
 The built-in help will give the options when supplied a ``--help`` flag.
 """
+
 from imars3d.backend.workflow.engine import WorkflowEngineAuto
 import logging
 from pathlib import Path

src/imars3d/backend/dataio/__init__.py

@@ -1,2 +1,3 @@
 """data handling module for iMars3D."""
+
 from . import data  # noqa: F401

tests/unit/backend/corrections/test_beam_hardening.py

@@ -1,4 +1,5 @@
 """Unit test for beam hardening correction"""
+
 #!/usr/bin/env python
 import numpy as np
 import pytest

tests/unit/backend/workflow/test_engine.py

@@ -14,6 +14,7 @@
 
 class load_data(ParameterizedFunction):
     r"""mock loading a set of radiographs into a numpy array"""
+
     ct_files = Parameter(default=None)
     ct_dir = StringParam(default=None)
 
@@ -25,6 +26,7 @@ def __call__(self, **params):
 
 class save_data(ParameterizedFunction):
     r"""mock saving a set or radiographs to some directory"""
+
     ct = Parameter(default=None)
     workingdir = Parameter()
 
@@ -41,6 +43,7 @@ def __call__(self, **params):
 
 class reconstruction(ParameterizedFunction):
     r"""mock the reconstruction of the radiographs"""
+
     ct = Parameter(default=None)
     rot_center = Parameter(default=None)
 
@@ -52,6 +55,7 @@ def __call__(self, **params):
 
 class reconstruction_with_default(ParameterizedFunction):
     r"""mock the reconstruction of the radiographs"""
+
     ct = Parameter(default=None)
     rot_center = Parameter(default=0.0)