Refactoring the easydiffraction library #156

AndrewSazonov · 2024-11-19T12:01:37Z

AndrewSazonov
Nov 19, 2024
Maintainer

In order to simplify code maintenance and following the ideas for working with calculators in EasyReflectometry, the following changes to the project structure are suggested.

Step 1

easydiffraction - Move to src/easydiffraction
- calculators - As before
  - __init__.py - As before
  - CFML.py - Move to src/easydiffraction/calculators/pycrysfml/calculator.py
    - class CFML - Rename to Pycrysfml
  - cryspy.py - Move to src/easydiffraction/calculators/cryspy/calculator.py
    - class Cryspy - As before
  - GSASII.py - Remove
  - pdffit2.py - Move to src/easydiffraction/calculators/pdffit2/calculator.py
    - class Pdffit2 - As before
- components - Temporary as before (to be addressed in Step 2)
  - __init__.py
  - phase.py
  - polarization.py
  - site.py
- elements - Temporary as before (to be addressed in Step 2)
  - Backgrounds
    - __init__.py
    - Background.py
    - Factorial.py
    - Point.py
  - Experiments
    - __init__.py
    - Experiment.py
    - Pattern.py
  - __init__.py
- Interfaces - Remove
  - __init__.py - Add to src/easydiffraction/calculators/__init__.py
  - CFML.py - Move to src/easydiffraction/calculators/pycrysfml/wrapper.py
    - class CFML - Rename to PycrysfmlWrapper
  - cryspy.py - Remove
  - cryspyV2.py - Move to src/easydiffraction/calculators/cryspy/wrapper.py
    - class CryspyV2 - Rename to CryspyWrapper
  - GSASII.py - Remove
  - interfaceTemplate.py - Move to src/easydiffraction/calculators/wrapper_base.py
    - class InterfaceTemplate - Rename to WrapperBase
  - pdffit2.py - Move to src/easydiffraction/calculators/pdffit2/wrapper.py
    - class Pdffit2 - Rename to Pdffit2Wrapper
  - types.py - Move to src/easydiffraction/calculators/wrapper_types.py (???)
- io - Remove
  - __init__.py - Remove
  - cif.py - Remove
    - cifV2ToV1 - Move to src/easydiffraction/calculators/cryspy/parser.py
    - cifV2ToV1_tof - Move to src/easydiffraction/calculators/cryspy/parser.py
  - cif_reader.py - From EDB. Move to EasyCrystallography
  - cryspy_parser.py - Move to src/easydiffraction/calculators/cryspy/parser.py
  - download.py - Remove
    - def download_from_repository -> Move to src/easydiffraction/utils.py
  - helpers.py - Remove
- Profiles - Temporary as before (to be addressed in Step 2)
  - __init__.py
  - Analysis.py
  - common.py
  - Container.py
  - Experiment.py
  - JobType.py
  - P1D.py
  - Sample.py
- __init__.py - As before
- interfaces.py - Move to src/easydiffraction/calculators/wrapper_factory.py
  - class InterfaceFactory - Rename to WrapperFactory
- Job.py - Rename to job.py
- Jobs.py - Remove
- main.py - As before
- Runner.py - Remove
- sample.py - Temporary as before (to be addressed in Step 2)
The next steps will follow when the first one is implemented.

rozyczko · 2024-11-21T04:38:16Z

rozyczko
Nov 21, 2024
Maintainer

cif.py - Remove

Also, dataBlockToCif is referenced in the application, so it should not be removed

The remaining classes CifIO etc. should probably be retained for potential future use as the content seems very useful.

1 reply

AndrewSazonov Nov 21, 2024
Maintainer Author

At this point, I've added cif.py back. Let's take a closer look at their functionality when the main refactoring is complete.

rozyczko · 2024-11-21T04:44:27Z

rozyczko
Nov 21, 2024
Maintainer

cryspy_parser.py

Only class Parameter and method def calcObjAndDictToEdExperiments need to be retained. The method can be removed from the class and referenced as a static, standalone method.

2 replies

AndrewSazonov Nov 21, 2024
Maintainer Author

As I see cifV2ToV1_tof and cifV2ToV1 are also needed...

rozyczko Nov 22, 2024
Maintainer

I mean, yes, apart of these two , which we discussed earlier :)

rozyczko · 2024-11-21T05:12:16Z

rozyczko
Nov 21, 2024
Maintainer

cif_reader.py probably should not be moved to Crystallography.
It takes CIF blocks and converts them into diffraction-specific dicts. Let's just keep it here.

0 replies

AndrewSazonov · 2024-11-21T18:56:05Z

AndrewSazonov
Nov 21, 2024
Maintainer Author

After Step 1, the structure is as follows:

src
- easydiffraction
  - calculators
    - cryspy
      - calculator.py
        
        class Cryspy
      - parser.py
      - wrapper.py
        
        class CryspyWrapper
    - pdffit2
      - calculator.py
        
        class Pdffit2
      - wrapper.py
        
        class Pdffit2Wrapper
    - pycrysfml
      - calculator.py
        
        class Pycrysfml
      - wrapper.py
        
        class PycrysfmlWrapper
    - __init__.py
    - wrapper_base.py
      - class WrapperBase
    - wrapper_factory.py
      - class WrapperFactory
    - wrapper_types.py
  - components
    - __init__.py
    - phase.py
    - polarization.py
    - site.py
  - elements
    - Backgrounds
      - __init__.py
      - Background.py
      - Factorial.py
      - Point.py
    - Experiments
      - __init__.py
      - Experiment.py
      - Pattern.py
    - __init__.py
  - io
    - __init__.py
    - cif.py
    - cif_reader.py
  - Profiles
    - __init__.py
    - Analysis.py
    - common.py
    - Container.py
    - Experiment.py
    - JobType.py
    - P1D.py
    - Sample.py
  - __init__.py
  - job.py
  - main.py
  - sample.py
  - utils.py

0 replies

rozyczko · 2024-11-24T10:08:38Z

rozyczko
Nov 24, 2024
Maintainer

For Step 2, starting with which files should be retained/deleted

Step 2

Components
- __init__.py
- phase.py - stays
- polarization.py - currently unused but will, when adding polarized
- site.py - unused, but might contain useful classes
elements
- Backgrounds
  - __init__.py
  - Background.py - stays
  - Factorial.py - unused, but might be useful later, do not delete
  - Point.py - stays
- Experiments
  - __init__.py
  - Experiment.py - unused, delete
  - Pattern.py - unused, delete
- __init__.py
Profiles
- Analysis.py - stays
- common.py - stays
  - class PowderBase - remove
- Container.py - stays
- Experiment.py - stays
- JobType.py - stays
- P1D.py - stays
- Sample.py - stays

0 replies

AndrewSazonov · 2024-11-25T16:25:27Z

AndrewSazonov
Nov 25, 2024
Maintainer Author

Suggested changes in step 2

src
- easydiffraction
  - ...
  - components - Remove
    - __init__.py - Remove
    - phase.py - Move to src/easydiffraction/job/model/phase.py (Check if we can use the EC phase directly)
    - polarization.py - Move to src/easydiffraction/job/experiment/polarization.py
    - site.py - Move to src/easydiffraction/job/model/site.py (Check if we can use the EC phase directly)
      - class PeriodicSite - Remove
      - class PeriodicAtoms - Remove
  - elements - Remove
    - Backgrounds - Move to src/easydiffraction/job/experiment/backgrounds
      - __init__.py - Move to src/easydiffraction/job/experiment/backgrounds/__init__.py
      - Background.py - Move to src/easydiffraction/job/experiment/backgrounds/background.py
      - Factorial.py - Move to src/easydiffraction/job/experiment/backgrounds/factorial.py
      - Point.py - Move to src/easydiffraction/job/experiment/backgrounds/point.py
    - Experiments - Remove
      - __init__.py - Remove
      - Experiment.py - Remove
      - Pattern.py - Remove
    - __init__.py - Remove
  - ...
  - Profiles
    - __init__.py - Remove
    - Analysis.py - Move to src/easydiffraction/job/analysis/analysis.py
    - common.py - Move to src/easydiffraction/job/experiment/common.py
      - class _PowderBase - Remove
    - Container.py - Move to src/easydiffraction/job/experiment/data_container.py
    - Experiment.py - Move to src/easydiffraction/job/experiment/experiment.py
    - JobType.py - Move to src/easydiffraction/job/experiment/experiment_type.py
      - class JobType - Rename to ExperimentType
    - P1D.py - Move to src/easydiffraction/job/experiment/pd_1d.py
    - Sample.py - Check if we can get rid of this file. If any of these methods are used, can we move them to another location?
  - __init__.py
  - job.py - Move to src/easydiffraction/job/job.py
  - main.py
  - sample.py - It behaves as a layer between Job and the main components of Job (model, experiment, ...). Check if we can get rid of this file and move its functionality to other classes. If this cannot be done quickly, move this file temporarily, e.g. to old_sample.py
  - utils.py

Expected structure after step 2

src
- easydiffraction
  - calculators
    - cryspy
      - calculator.py
        
        class Cryspy
      - parser.py
      - wrapper.py
        
        class CryspyWrapper
    - pdffit2
      - calculator.py
        
        class Pdffit2
      - wrapper.py
        
        class Pdffit2Wrapper
    - pycrysfml
      - calculator.py
        
        class Pycrysfml
      - wrapper.py
        
        class PycrysfmlWrapper
    - __init__.py
    - wrapper_base.py
      - class WrapperBase
    - wrapper_factory.py
      - class WrapperFactory
    - wrapper_types.py
  - job
    - analysis
      - __init__.py
      - analysis.py
    - experiment
      - backgrounds
        
        __init__.py
        
        background.py
        
        factorial.py
        
        point.py
      - __init__.py
      - common.py
      - data_container.py
      - experiment.py
      - experiment_type.py
        
        class ExperimentType
      - old_sample.py?
      - pd_1d.py
      - polarization.py
    - model
      - __init__.py
      - phase.py
      - site.py
    - project
      - __init__.py
    - summary
      - __init__.py
    - __init__.py
    - job.py
  - __init__.py
  - main.py
  - utils.py

0 replies

rozyczko · 2024-11-26T05:38:38Z

rozyczko
Nov 26, 2024
Maintainer

looks good but I would put old_sample in the model subdirectory, not experiment.
It's a container for (among other things) Phase and Phases, so probably belongs there better.

1 reply

AndrewSazonov Nov 26, 2024
Maintainer Author

src/easydiffraction/sample.py moved to src/easydiffraction/job/old_sample/old_sample.py
src/easydiffraction/Profiles/Sample.py moved to src/easydiffraction/job/experiment/simulation.py

Refactoring the easydiffraction library #156

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AndrewSazonov Nov 19, 2024 Maintainer

Step 1

Replies: 7 comments · 4 replies

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rozyczko Nov 21, 2024 Maintainer

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AndrewSazonov Nov 21, 2024 Maintainer Author

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rozyczko Nov 21, 2024 Maintainer

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AndrewSazonov Nov 21, 2024 Maintainer Author

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rozyczko Nov 22, 2024 Maintainer

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rozyczko Nov 21, 2024 Maintainer

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AndrewSazonov Nov 21, 2024 Maintainer Author

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rozyczko Nov 24, 2024 Maintainer

Step 2

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AndrewSazonov Nov 25, 2024 Maintainer Author

Suggested changes in step 2

Expected structure after step 2

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rozyczko Nov 26, 2024 Maintainer

Uh oh!

AndrewSazonov Nov 26, 2024 Maintainer Author

AndrewSazonov
Nov 19, 2024
Maintainer

Replies: 7 comments 4 replies

rozyczko
Nov 21, 2024
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AndrewSazonov Nov 21, 2024
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rozyczko
Nov 21, 2024
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rozyczko Nov 22, 2024
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rozyczko
Nov 21, 2024
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rozyczko
Nov 24, 2024
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rozyczko
Nov 26, 2024
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