refactor `Spectrum` class #193

CunliangGeng · 2023-12-04T14:27:14Z

Refactor the whole Spectrum class. There are quite some commits, but the major idea of these changes are simple:

remove attributes, properties and methods that are not used anywhere
change attribute to property if necessary
update class arguments and their order
update the order of attributes and methods
add typings
add docstrings
add unit tests for all methods

You could find more details about the changes in each commit.

CunliangGeng · 2023-12-04T14:27:45Z

Current dependencies on/for this PR:

dev
- PR refactor filtering of user specified strains #178
  - PR Enable GCF loader to filter singleton GCFs #181
    - PR return list for get_bgcs methods of BGC loaders #182
      - PR rename strains.py to strain.py #183
        
        PR remove deprecated functions of loading genomics data #184
        
        PR update the process of loading genomics data #185
        
        PR rename genomics.py to utils.py #186
        
        PR remove deprecated functions of loading metabolomics data #187
        
        PR refactor class MolecularFamily #188
        PR refactor class GCF #189
        PR enable parallel testing using pytest-xdist #190
        PR Enable filtering of singleton molecular families #191
        PR Remove class SingletonFamily and MF attribute id #192
        PR refactor Spectrum class #193 👈
        PR remove unused mgf.py and its test file #194
        PR Update logics of loading metabolomics data #196
        PR Update loading of genomics data #197
        PR deprecate the method _load_class_info #198
        PR remove loading of optional data #199
        PR remove filtering of common strains during loading #200
        PR update logics of loading mibig data #201
        PR refactor initiation of paths to metabolomics files #202
        
        PR Update logics of loading metabolomics data #195

This stack of pull requests is managed by Graphite.

src/nplinker/metabolomics/spectrum.py

`parent_mz` refers to `precursor_mz` in the context, so removing `parent_mz` and keep `precursor_mz`.

Remove `id` and use `spectrum_id` as the unique identifier of spectrum.

- add optional arguments `metadata` and `annotations` - update and order the attributes - add docstring and typings

method `__cmp__` is not supported in python 3.

Property can be used as a way to provide computed attribute.

The specific method `keep_top_k` is only required by class `SpecLib`, so better to move it there.

- remove `None` from typing and keep only `float` - change default value to 0 - update spectrum loader

- remove argument `annotations` - remove property `gnps_annotations` - add attribute `gnps_annotations`

…thod

CunliangGeng mentioned this pull request Dec 4, 2023

remove unused mgf.py and its test file #194

Merged

CunliangGeng requested a review from gcroci2 December 4, 2023 14:39

CunliangGeng mentioned this pull request Dec 5, 2023

Update logics of loading metabolomics data #195

Closed

CunliangGeng force-pushed the 11-27-remove_SingletonFamily_and_id branch from 583384f to b4ab6e1 Compare December 5, 2023 15:54

CunliangGeng force-pushed the 11-27-refactor_Spectrum branch from e09bcb1 to 54a9f64 Compare December 5, 2023 15:54

CunliangGeng force-pushed the 11-27-remove_SingletonFamily_and_id branch from b4ab6e1 to 5ad51fe Compare December 11, 2023 13:04

CunliangGeng force-pushed the 11-27-refactor_Spectrum branch from 54a9f64 to 7b7fed8 Compare December 11, 2023 13:04

This was referenced Dec 11, 2023

Update logics of loading metabolomics data #196

Merged

Update loading of genomics data #197

Merged

deprecate the method _load_class_info #198

Merged

remove loading of optional data #199

Merged

remove filtering of common strains during loading #200

Merged

gcroci2 reviewed Dec 13, 2023

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src/nplinker/metabolomics/spectrum.py Show resolved Hide resolved

gcroci2 approved these changes Dec 13, 2023

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CunliangGeng force-pushed the 11-27-remove_SingletonFamily_and_id branch from 5ad51fe to a0d5ea7 Compare December 14, 2023 08:33

CunliangGeng force-pushed the 11-27-refactor_Spectrum branch from 7b7fed8 to 87caba4 Compare December 14, 2023 08:33

CunliangGeng added 25 commits December 19, 2023 13:28

remove unused method to_jcamp_str

263caa2

remove attribute n_peaks

d3694c9

remove attributes max_ms2_intensity and total_ms2_intensity

ad227ab

remove unused attribute edges

eaececa

remove parameter and attribute parent_mz

2716ecb

`parent_mz` refers to `precursor_mz` in the context, so removing `parent_mz` and keep `precursor_mz`.

remove parameter and attribute id

9f96b38

Remove `id` and use `spectrum_id` as the unique identifier of spectrum.

adjust the order of parameter spectrum_id to 1st place

baa1096

refactor method __init__

d337d69

- add optional arguments `metadata` and `annotations` - update and order the attributes - add docstring and typings

reorder methods and properties

f99a246

remove method __cmp__

b125d07

method `__cmp__` is not supported in python 3.

remove unused method __lt__

f3ee36a

update methods __str__ and __repr__

71ae23b

change attribute normalised_peaks to property

d58a0b2

Property can be used as a way to provide computed attribute.

split arguments peaks to two args mz and intensity

2a704dd

change the return type of property peaks to numpy 2D array

8f676be

move method keep_top_k to the class SpecLib

4ddc133

The specific method `keep_top_k` is only required by class `SpecLib`, so better to move it there.

remove property normalised_peaks

1c88f2f

change default value of argument rt

1935334

- remove `None` from typing and keep only `float` - change default value to 0 - update spectrum loader

remove arg annotations and add attribute gnps_annotations

67a371c

- remove argument `annotations` - remove property `gnps_annotations` - add attribute `gnps_annotations`

remove unused global variable GNPS_KEY

274f5a5

add typing for attribute gnps_id

f7e5bfb

add typings and docstring for strains attribute and has_strain me…

39371b0

…thod

update class docstrings

4514060

update Spectrum loader

15a4851

add unit tests for Spectrum class

ab84fab

CunliangGeng force-pushed the 11-27-refactor_Spectrum branch from f2f89ad to ab84fab Compare December 19, 2023 13:28

CunliangGeng merged commit 49d7e22 into dev Dec 19, 2023
1 check failed

CunliangGeng deleted the 11-27-refactor_Spectrum branch December 19, 2023 13:30

This was referenced Dec 20, 2023

update logics of loading mibig data #201

Merged

refactor initiation of paths to metabolomics files #202

Merged

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refactor `Spectrum` class #193

refactor `Spectrum` class #193

CunliangGeng commented Dec 4, 2023 •

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CunliangGeng commented Dec 4, 2023 •

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refactor Spectrum class #193

refactor Spectrum class #193

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CunliangGeng commented Dec 4, 2023 • edited Loading

CunliangGeng commented Dec 4, 2023 • edited Loading

refactor `Spectrum` class #193

refactor `Spectrum` class #193

CunliangGeng commented Dec 4, 2023 •

edited

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CunliangGeng commented Dec 4, 2023 •

edited

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