anthropics / life-sciences Duplication

anthropics / life-sciences

Duplication

Places in code with 6 or more lines that are exactly the same.

Intro

For duplication, we look at places in code where there are 6 or more lines of code that are exactly the same.
Before duplication is calculated, the code is cleaned to remove empty lines, comments, and frequently duplicated constructs such as imports.
You should aim at having as little as possible (<5%) of duplicated code as high-level of duplication can lead to maintenance difficulties, poor factoring, and logical contradictions.

Learn more...

To learn more about duplications and techniques for eliminating duplication, Sokrates recommends the following resources:

Avoid Repetition, MartinFlower.com (IEEE Software article)
Refactoring duplicated code, sourcemaking.com
Beck Design Rules, MartinFowler.com
DRY (Don't Repeat Yourself) Principle, Wikipedia
The Cut-and-Paste Programming Software Development Anti-Pattern, sourcemaking.com
Code Smells / Duplicated Code, Jeff Atwood, codinghorror.com:

"Duplicated code is the bane of software development. Stamp out duplication whenever possible. You should always be on the lookout for more subtle cases of near-duplication, too. Don't Repeat Yourself!"

Reducing Coupling, MartinFlower.com (IEEE Software article):

"There are several ways to describe coupling, but it boils down to this: If changing one module in a program requires changing another module, then coupling exists. ... Duplication always implies coupling, because changing one piece of duplicate code implies changing the other."

Duplication Overall

7% duplication:

6,798 cleaned lines of cleaned code (without empty lines, comments, and frequently duplicated constructs such as imports)
486 duplicated lines

82 duplicates

dependency graphs: 2D graph | 2D graph (with duplicates)... | 3D graph | 3D graph (with duplicates)...

Duplication per Extension

Duplication per Component (primary)

Longest Duplicates

The list of 50 longest duplicates.

See data for all 82 duplicates...

Size	#	Folders	Files	Lines	Code
23	x 2	clinical-trial-protocol-skill/scripts clinical-trial-protocol-skill/scripts	sample_size_calculator.py sample_size_calculator.py	127:149 (7%) 287:309 (7%)	view
13	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	208:226 (2%) 578:597 (2%)	view
13	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	231:248 (2%) 603:620 (2%)	view
11	x 2	clinical-trial-protocol-skill/scripts clinical-trial-protocol-skill/scripts	sample_size_calculator.py sample_size_calculator.py	19:47 (3%) 167:195 (3%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	101:110 (1%) 584:595 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	101:110 (1%) 158:167 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	158:167 (1%) 233:243 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	214:225 (1%) 605:615 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	214:225 (1%) 233:243 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	158:167 (1%) 584:595 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	233:243 (1%) 584:595 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	158:167 (1%) 214:225 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	97:107 (1%) 512:522 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	158:167 (1%) 605:615 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	101:110 (1%) 233:243 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	584:595 (1%) 605:615 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	101:110 (1%) 605:615 (1%)	view
9	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	101:110 (1%) 214:225 (1%)	view
8	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	118:126 (1%) 174:182 (1%)	view
8	x 2	scvi-tools/scripts scvi-tools/scripts	model_utils.py prepare_data.py	90:97 (2%) 83:90 (9%)	view
8	x 2	clinical-trial-protocol-skill/scripts clinical-trial-protocol-skill/scripts	sample_size_calculator.py sample_size_calculator.py	154:161 (2%) 314:321 (2%)	view
8	x 2	instrument-data-to-allotrope/scripts instrument-data-to-allotrope/scripts	export_parser.py export_parser.py	396:403 (3%) 420:427 (3%)	view
8	x 2	scvi-tools/scripts scvi-tools/scripts	integrate_datasets.py train_model.py	99:109 (6%) 60:72 (3%)	view
8	x 2	nextflow-development/scripts/config/pipelines nextflow-development/scripts/config/pipelines	atacseq.yaml rnaseq.yaml	31:39 (4%) 30:38 (6%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	44:50 (1%) 142:148 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	69:75 (1%) 155:161 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	32:38 (1%) 57:63 (1%)	view
7	x 2	nextflow-development/scripts/config/pipelines nextflow-development/scripts/config/pipelines	sarek.yaml sarek.yaml	161:167 (3%) 171:177 (3%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	57:63 (1%) 82:88 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	69:75 (1%) 142:148 (1%)	view
7	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	174:180 (1%) 547:553 (1%)	view
7	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	118:124 (1%) 547:553 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	57:63 (1%) 69:75 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	44:50 (1%) 119:125 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	32:38 (1%) 82:88 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	32:38 (1%) 69:75 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	106:112 (1%) 142:148 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	32:38 (1%) 106:112 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	69:75 (1%) 106:112 (1%)	view
7	x 2	scvi-tools/scripts scvi-tools/scripts	model_utils.py train_model.py	184:190 (2%) 28:35 (3%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	69:75 (1%) 119:125 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	119:125 (1%) 155:161 (1%)	view
7	x 2	scvi-tools/scripts scvi-tools/scripts	integrate_datasets.py model_utils.py	102:109 (5%) 173:181 (2%)	view
7	x 2	nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py	233:239 (1%) 516:522 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	69:75 (1%) 82:88 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	119:125 (1%) 142:148 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	106:112 (1%) 155:161 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	32:38 (1%) 119:125 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	57:63 (1%) 155:161 (1%)	view
7	x 2	nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py	82:88 (1%) 142:148 (1%)	view

Most Frequent Duplicates

The list of 10 most frequently found duplicates.

Size	#	Folders	Files	Lines	Code
6	x 9	nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py	33:38 (1%) 45:50 (1%) 58:63 (1%) 70:75 (1%) 83:88 (1%) 107:112 (1%) 120:125 (1%) 143:148 (1%) 156:161 (1%)	view
6	x 9	nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts nextflow-development/scripts	manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py manage_genomes.py	32:37 (1%) 44:49 (1%) 57:62 (1%) 69:74 (1%) 82:87 (1%) 106:111 (1%) 119:124 (1%) 142:147 (1%) 155:160 (1%)	view
6	x 7	nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py	101:106 (1%) 158:163 (1%) 214:219 (1%) 233:238 (1%) 516:521 (1%) 584:589 (1%) 605:610 (1%)	view
6	x 7	nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py	102:107 (1%) 159:164 (1%) 215:220 (1%) 234:239 (1%) 517:522 (1%) 585:590 (1%) 606:611 (1%)	view
6	x 6	nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py	103:109 (1%) 160:166 (1%) 216:222 (1%) 235:241 (1%) 586:592 (1%) 607:613 (1%)	view
6	x 6	nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py ncbi_utils.py	104:110 (1%) 161:167 (1%) 217:225 (1%) 236:243 (1%) 587:595 (1%) 608:615 (1%)	view
6	x 3	scvi-tools/scripts scvi-tools/scripts scvi-tools/scripts	integrate_datasets.py train_model.py model_utils.py	103:109 (4%) 64:72 (2%) 174:181 (1%)	view
6	x 3	scvi-tools/scripts scvi-tools/scripts scvi-tools/scripts	integrate_datasets.py train_model.py model_utils.py	102:107 (4%) 63:70 (2%) 173:178 (1%)	view
6	x 3	nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py ncbi_utils.py	119:124 (1%) 175:180 (1%) 548:553 (1%)	view
6	x 3	nextflow-development/scripts/utils nextflow-development/scripts/utils nextflow-development/scripts/utils	ncbi_utils.py ncbi_utils.py ncbi_utils.py	118:123 (1%) 174:179 (1%) 547:552 (1%)	view