Merge pull request #102 from carnisj/release

prepare release 0.1.4

Author: carnisj

HISTORY.rst

@@ -1,6 +1,15 @@
+Version 0.1.4
+-------------
+
+* Feature: implement a new validation function valid_ndarray, implement tests and remove
+  the redundant code in modules.
+
+* Refactor: split the Detector class using inheritance, refactor scripts accordingly and
+  implement tests.
 
 * Feature: create a Beamline class with one child class for each beamline, move
-  all beamline-dependent methods from Setup to the respective class
+  all beamline-dependent methods from Setup to the respective class and implement some
+  tests.
 
 Version 0.1.3
 -------------

README.rst

@@ -165,13 +165,22 @@ The following detectors are implemented:
  * Merlin
  * Eiger2M
  * Eiger4M
+ * Dummy (user-defined pixel size and pixel number)
 
 The following classes are implemented:
 
- * Detector
- * Diffractometer and corresponding child classes (one per beamline)
+ * Beamline and corresponding child classes (one per supported beamline)
+ * Detector and corresponding child classes (one per supported detector)
+ * Diffractometer and corresponding child classes (one per supported beamline)
+ * RotationMatrix: used in methods from Diffractometer to generate rotation matrices
  * Setup
 
+In scripts, the initial step is to declare a detector instance and a setup instance with
+the related parameters (see the class documentation). The beamline and the
+diffractometer are not meant to be instantiated directly, this is done internally in
+Setup.
+
+
 .. bcdi.experiment end
 
 BCDI.facet_recognition: automatic facet detection in BCDI 3D reconstructions
@@ -186,7 +195,9 @@ This module provides tools for plotting the stereographic projection of a diffra
 peak or an object. There is also a script for facet detection on a reconstructed
 object, and for calculating statistics on facet strain. After meshing the object,
 facets are found using a density estimation of mesh triangles normals, followed by
-watershed segmentation.
+,watershed segmentation.
+See Carnis et al. Small 17, 2007702 (2021)
+https://doi.org/10.1002/smll.202007702
 
 .. bcdi.facet_recognition end
 
@@ -212,7 +223,7 @@ Description
 -----------
 
 This module provides methods used for pre-processing phased data. For example (but
-not limited to): hotpixels removal, filtering, masking...
+not limited to): centering, hotpixels removal, filtering, masking...
 
 .. bcdi.preprocessing end
 
@@ -256,6 +267,8 @@ kinematical sum. It can include a displacement field, noise, detector gaps etc..
 In forward CDI geometry, calculation of the Bragg peak positions in 3D for a
 mesocrystal, knowing the unit cell and unit cell parameter. It can be used to fit
 experimental data.
+See Carnis et al. Scientific Reports 9, 17357 (2019)
+https://doi.org/10.1038/s41598-019-53774-2
 
 .. bcdi.simulation end
 

bcdi/__init__.py

@@ -7,4 +7,4 @@
 #       authors:
 #         Jerome Carnis, carnis_jerome@yahoo.fr
 """The main bcdi package, which contains the whole framework."""
-__version__ = "0.1.3"
+__version__ = "0.1.4"

bcdi/experiment/__init__.py

@@ -13,9 +13,9 @@
 Classes
 -------
 
-- ``Detector``         -- detector declaration
+- ``Detector``         -- one child class for each supported detector
 - ``Beamline``         -- one child class for each supported beamline
-- ``Diffractometer``   -- diffractometer, one child class for each supported beamline
+- ``Diffractometer``   -- one child class for each supported beamline
 - ``Setup``            -- class gathering various parameters about the setup
 - ``RotationMatrix``   -- rotation matrix given the rotation axis and the angle
 

dodo.py

@@ -51,6 +51,7 @@ def task_clean_doc():
     """Remove the compiled documentation."""
 
     def delete_dir(dirname):
+        """Delete the directory if it exists."""
         path = os.path.join(get_path(), dirname).replace("\\", "/")
         if os.path.isdir(path):
             shutil.rmtree(path)
@@ -102,6 +103,7 @@ def task_clean_coverage():
     """Delete the coverage report."""
 
     def delete_coverage(filename):
+        """Delete the file if it exists."""
         path = os.path.join(get_path(), filename).replace("\\", "/")
         if os.path.isfile(path):
             os.unlink(path)
@@ -129,7 +131,7 @@ def task_tests():
     return {
         "actions": ["coverage run --source=bcdi -m unittest discover"],
         "targets": [".coverage"],
-        "verbosity": 2,
+        "verbosity": 1,
     }
 
 
@@ -153,7 +155,25 @@ def task_build_distribution():
     }
 
 
-def task_check_description():
+def task_clean_build():
+    """Remove the build directory"""
+
+    def delete_dir(dirname):
+        """Delete the directory if it exists."""
+        path = os.path.join(get_path(), dirname).replace("\\", "/")
+        if os.path.isdir(path):
+            shutil.rmtree(path)
+            print(f"\n\tDeleted {path}\n")
+        else:
+            print("\n\tNo build directory to delete.\n")
+
+    return {
+        "actions": [(delete_dir, ["build/"])],
+        "verbosity": 2,
+    }
+
+
+def task_check_long_description_pypi():
     """Check whether the long description will render correctly on PyPI."""
     return {
         "actions": ["twine check dist/*"],