Prepare for v0.0.9 release #14

wardsimon · 2020-05-13T07:34:50Z

Update to easyInterface including polarization and dictionary fixes

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Your code builds clean without any errors or warnings
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* Undo/redo is broken for manual editing * Sample editing is still not fully implemented

auto-comment · 2020-05-13T07:34:55Z

Thank you for your contribution to easyInterface.
Please ensure:

You include a description of the pull request
Your code builds clean without any errors or warnings
You are using approved terminology
You have added unit tests

codecov · 2020-05-13T08:00:09Z

Codecov Report

Merging #14 into pre-release will not change coverage.
The diff coverage is n/a.

@@             Coverage Diff              @@
##           pre-release      #14   +/-   ##
============================================
  Coverage        85.42%   85.42%           
============================================
  Files               18       18           
  Lines             2944     2944           
============================================
  Hits              2515     2515           
  Misses             429      429

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AndrewSazonov

I just have a few minor comment, as added above, to be considered for future code refactoring.

AndrewSazonov · 2020-05-14T12:16:10Z

easyInterface/Diffraction/DataClasses/DataObj/Experiment.py

@@ -48,6 +54,20 @@
    }
 }

+POLAR_DETAILS = {


I would propose to use a full name here, POLARIZATION_DETAILS, because POLAR sounds more like polar coordinates.

AndrewSazonov · 2020-05-14T12:19:10Z

easyInterface/Diffraction/DataClasses/DataObj/Experiment.py

@@ -254,16 +282,20 @@ def default(cls, polarised: bool = False):
        x = []
        y_obs = []
        sy_obs = []
+        y_obs_diff = None
+        sy_obs_diff = None
        y_obs_up = None
        sy_obs_up = None
        y_obs_down = None
        sy_obs_down = None
        if polarised:


We should consider to make a enum with type of experiment, instead of using this boolean polarised.

AndrewSazonov · 2020-05-14T12:22:37Z

easyInterface/Diffraction/DataClasses/DataObj/Experiment.py

@@ -324,11 +358,66 @@ def __repr__(self) -> str:
        return '{} Experimental phases'.format(len(self))


+class chi2(LoggedPathDict):


We should consider to rename this class into something like RefinementType, as chi2 is associated with calculation of the goodness-of-fit.

AndrewSazonov · 2020-05-14T12:25:07Z

easyInterface/Diffraction/DataClasses/DataObj/Experiment.py

@@ -353,6 +446,10 @@ def __init__(self, name: str, wavelength: Base, offset: Base, phase: ExperimentP
        self.setItemByPath(['offset', 'tooltip'], EXPERIMENT_DETAILS['offset']['tooltip'])
        self.setItemByPath(['offset', 'url'], EXPERIMENT_DETAILS['offset']['url'])

+        self.setItemByPath(['field', 'header'], EXPERIMENT_DETAILS['field']['header'])


field should probably be renamed into magnetic_field, because electric field could also be a part of metadata.

AndrewSazonov · 2020-05-14T12:30:54Z

easyInterface/Diffraction/Interface.py

@@ -352,7 +368,7 @@ def updatePhases(self) -> NoReturn:
            self.project_dict.setItemByPath(['info', 'phase_ids'], list(phases.keys()))
            self.project_dict.endBulkUpdate()
        else:
-            k, v = self.project_dict['phases'].dictComparison(phases)
+            k, v, t = self.project_dict['phases'].dictComparison(phases)


Should we use a less cryptic names, such as keys, values? And what is t? It seems that t is not used.

AndrewSazonov · 2020-05-14T12:32:14Z

easyInterface/Diffraction/Interface.py

@@ -473,7 +507,7 @@ def setPhase(self, phase: Phase) -> NoReturn:
        if isinstance(phase, Phase):
            new_phase_name = phase['phasename']
            if new_phase_name in self.project_dict['phases'].keys():
-                k, v = self.project_dict.getItemByPath(['phases', new_phase_name]).dictComparison(phase)
+                k, v, t = self.project_dict.getItemByPath(['phases', new_phase_name]).dictComparison(phase)


Should we use a less cryptic names, such as keys, values? And what is t? It seems that t is not used.

AndrewSazonov · 2020-05-14T12:32:31Z

easyInterface/Diffraction/Interface.py

@@ -492,7 +526,7 @@ def setPhases(self, phases: Union[Phase, Phases]) -> NoReturn:
        """
        if isinstance(phases, Phase):
            new_phase_name = phases['phasename']
-            k, v = self.project_dict.getItemByPath(['phases', new_phase_name]).dictComparison(phases)
+            k, v, t = self.project_dict.getItemByPath(['phases', new_phase_name]).dictComparison(phases)


Should we use a less cryptic names, such as keys, values? And what is t? It seems that t is not used.

AndrewSazonov · 2020-05-14T12:32:47Z

easyInterface/Diffraction/Interface.py

@@ -547,7 +581,7 @@ def setExperiment(self, experiment: Experiment) -> NoReturn:
        if isinstance(experiment, Experiment):
            new_phase_name = experiment['name']
            if new_phase_name in self.project_dict['experiments'].keys():
-                k, v = self.project_dict.getItemByPath(['experiments', new_phase_name]).dictComparison(experiment)
+                k, v, t = self.project_dict.getItemByPath(['experiments', new_phase_name]).dictComparison(experiment)


Should we use a less cryptic names, such as keys, values? And what is t? It seems that t is not used.

AndrewSazonov · 2020-05-14T12:34:42Z

easyInterface/Utils/DictTools.py

        except TypeError as ex:
            raise KeyError(str(ex))

    def _realSetItemByPath(self, keys: list, value: Any) -> NoReturn:
        """Actually sets the value in a nested object by the key sequence."""
        self.getItemByPath(keys[:-1])[keys[-1]] = value

+    def _realAddItemByPath(self, keys: list, value: Any) -> NoReturn:
+        """Actually sets the value in a nested object by the key sequence."""


This comment seems to be not updated.

AndrewSazonov · 2020-05-14T12:35:26Z

easyInterface/Utils/DictTools.py

@@ -313,7 +321,7 @@ def asDict(self) -> dict:
                base_dict[key] = item.asDict()
        return base_dict

-    def dictComparison(self, another_dict: Union['PathDict', dict], ignore=None) -> Tuple[list, list]:
+    def dictComparison(self, another_dict: Union['PathDict', dict], ignore=None) -> Tuple[list, list, list]:
        """
        Compare self to a dictionary or PathDict and return the update path and value


This comment seems to be not updated.

AndrewSazonov

This part looks okay.

* Prepare for v0.0.9 release (#14) * Add polarised experiment * Add chi2 options * Calculate profile up/down * RE-implement chi2 * Add Polarization efficiency/level * Fix fitable values * Fix hidden refinement * Remove auto-refine * Temporary fix of min/max for polarization and efficiency * Fix calculated pattern values * Add calculated background * Fix background for polarised neutrons * Fixup creation of phaess and exps * Typo fixes [ci skip] * Fix polarisation (until cryspy is fixed) * Fix refine polarisation * Fix error on scale * Don't print to the console * Create empty cryspy obj if rcif path is None * Fix experiments as cif * 1st implementation of editable CIF at the back end * Undo/redo is broken for manual editing * Sample editing is still not fully implemented * Fix issue with complex numbers for the scattering length * Change space group name source * Add exp from cif compatibility * Add phase from cif compatibility * Allow to run bulk update without macro * Add datablock label to calculations cif * Part of back-end implementation of Main.cif Edit * Remove global_ from CIFs on saving * Simplify writing CIF files * Save calculations.cif to project * Switch to master branch for cryspy * Add calculations.cif * Intermediate fixes * Re-write of DictComparison * Fix unit tests and dictTools * fix fit tests on windows/linux * More windows test fixes * Fix undo/redo for list types * More undo/redo work * Sort Backgrounds * Ugly hack to save name/keyword changes * Change keyword list to string * Sort background list of string keys numerically * Move filenames to master obj * Internal main_rcif to project_rcif * Move from phases to samples * Variable name changes * Rename phases to sample Co-authored-by: Andrew Sazonov <[email protected]> * Update Release.json Co-authored-by: Andrew Sazonov <[email protected]>

wardsimon and others added 30 commits April 6, 2020 16:18

Add polarised experiment [ci skip]

ebc920c

Add chi2 options

1d1ce31

Calculate profile up/down

991fa5f

RE-implement chi2

b8e76f2

Add Polarization efficiency/level [ci skip]

67df908

Fix fitable values

130e2f3

Fix hidden refinement [ci skip]

613e503

Remove auto-refine [ci skip]

16e8d6b

Temporary fix of min/max for polarization and efficiency

d08c43c

Fix calculated pattern values

2f1974d

Add calculated background

1859313

Fix background for polarised neutrons

88c16d1

Fixup creation of phaess and exps [ci skip]

23a5f27

Typo fixes [ci skip]

102f0c8

Fix polarisation (until cryspy is fixed)

be3679f

Fix refine polarisation

e2c08a6

Fix error on scale

56e64e1

Don't print to the console

2787feb

Create empty cryspy obj if rcif path is None

fe053a0

Fix experiments as cif

d26a9d9

1st implementation of editable CIF at the back end

4fae732

* Undo/redo is broken for manual editing * Sample editing is still not fully implemented

Fix issue with complex numbers for the scattering length

0be59bf

Change space group name source

b98b7f4

Add exp from cif compatibility

394c28c

Add phase from cif compatibility

372c2f8

Allow to run bulk update without macro

ea9b9f9

Add datablock label to calculations cif

361c32c

Part of back-end implementation of Main.cif Edit

efc6785

Remove global_ from CIFs on saving

b353469

Simplify writing CIF files

5ca0905

AndrewSazonov and others added 8 commits May 8, 2020 13:27

Save calculations.cif to project

d68abb1

Switch to master branch for cryspy

def44b3

Add calculations.cif

f71f4fa

Intermediate fixes [ci skip]

ffb5d3c

Re-write of DictComparison [ci skip]

db37255

Fix unit tests and dictTools

60a87ea

fix fit tests on windows/linux

9c4b31a

More windows test fixes

923e7eb

wardsimon self-assigned this May 13, 2020

wardsimon requested a review from AndrewSazonov May 13, 2020 07:34

wardsimon added the enhancement New feature or request label May 13, 2020

wardsimon and others added 6 commits May 13, 2020 11:01

Fix undo/redo for list types

35a022b

More undo/redo work

cc78bdd

Sort Backgrounds [ci skip]

448d08a

Ugly hack to save name/keyword changes

f9e2c3c

Change keyword list to string

fcffde2

Sort background list of string keys numerically

6827f35

AndrewSazonov approved these changes May 14, 2020

View reviewed changes

wardsimon and others added 5 commits May 14, 2020 16:16

Move filenames to master obj

6942174

Internal main_rcif to project_rcif

33a7099

Move from phases to samples

814d836

Variable name changes

f234aa7

Rename phases to sample [ci skip]

b392f94

wardsimon merged commit bec98bf into pre-release May 14, 2020

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Prepare for v0.0.9 release #14

Prepare for v0.0.9 release #14

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		@@ -324,11 +358,66 @@ def __repr__(self) -> str:
		return '{} Experimental phases'.format(len(self))


		class chi2(LoggedPathDict):

Prepare for v0.0.9 release #14

Prepare for v0.0.9 release #14

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codecov bot commented May 13, 2020 •

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