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Release 3.0.0 #23

Merged
merged 215 commits into from
Jan 2, 2025
Merged

Release 3.0.0 #23

merged 215 commits into from
Jan 2, 2025

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saramonzon
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luissian added 30 commits November 2, 2023 16:53
@luissian
first change to new format
6022168
@luissian
First changes to the new refactorization
5c7e3e3
@luissian
Implemented analyze_schema in multiple cpus
dc10a7a
@luissian
Liting analyze_schema
dacde99
@luissian
Added code to test alfaclust results
beb0413
@luissian
Implemented Analyze schema
a25365c
@luissian
Merge pull request #11 from luissian/develop
d212ab4 
Refactorization of Analyze schema
@luissian @saramonzon
Update analyze schema with Comments in previous PR. Added liting work…
0874569 
…flow
@luissian @saramonzon
fixiing some liting
a3b02f5
@luissian @saramonzon
fixiing more liting errors
1335166
@luissian @saramonzon
changed file extension for old python files
4a21e14
@luissian @saramonzon
fixing latest liting
7b09ba2
@luissian @saramonzon
fixing latest liting 2
fdae124
@luissian @saramonzon
fixing latest liting 3
ff975a0
@luissian @saramonzon
checking liting in functions which are defined the type of variable
c5792fe
@luissian @saramonzon
Checking testing file
a67d30f
@luissian @saramonzon
first draft to run test
d1412cf
@luissian @saramonzon
first draft to run test
ad0a2cf
@luissian @saramonzon
added deps to github action test
38ed823
@luissian @saramonzon
Updated test and environment for conda installation
50011e3
@luissian @saramonzon
Removed python packages from conda and move to pip
38c69c2
@luissian @saramonzon
remove Self from annotation
a04af8e
@luissian @saramonzon
liting
ee8f6d6
@luissian @saramonzon
Updated with comments in PR#13. Adding testing analyze schema with te…
9deea44 
…st data
@luissian @saramonzon
fixing liting and error testing
e6a81fb
@luissian @saramonzon
Again trying to fix liting and testing
ccbe7c6
@luissian @saramonzon
modified schema input parameter
844a2ea
@luissian @saramonzon
correcting wrong path of schema
7235f22
@luissian @saramonzon
including echo ls to know which is the working path
70f451e
@luissian @saramonzon
including ls to know which is the working path
dd2429c
saramonzon added 29 commits May 2, 2024 08:54
@saramonzon @luissian
rewritten filter_df function, now filtering both rows and columns, ma…
c4b9110 
…trix is printed as well as two distance matrices
@saramonzon @luissian
rename variable for clarity, add dtype to read_csv
8f46223
@saramonzon @luissian
clarified help messages, fixed default value for keeping a locus in d…
4d4607c 
…istance matrix fil
@saramonzon @luissian
removed missing pdb
dbfda28
@saramonzon @luissian
fixed big fingers typo
317a99a
@saramonzon @luissian
variable renaming and fixed bounds for condition
2e7ce82
@saramonzon @luissian
minor modifications in graph for mash blast corr script
f805814
@saramonzon @luissian
added filter with regex
769758f
@saramonzon @luissian
added notebook for benchmarking analysis
418c4f2
@saramonzon @luissian
added masking after filtering per row in df_filter
bd2f495
@saramonzon @luissian
black linting
7e381ca
@saramonzon
fix snp output printing
df4e0f6
@saramonzon
minor modifications adding seqsphere for notebook, added blast_id_lis…
7b6729a 
…t.py
@saramonzon
modifications in jup notebook
455e7dc
@saramonzon
change name from taranis to taranys
ae50002
@saramonzon
rename folder and delete unused files
c55e33e
@saramonzon
changed permissions to file
da77627
@saramonzon
deleted setup.py, added pip publish workflow to github actions
0d1099e
@saramonzon
modified pyproject.toml
332ddd8
@saramonzon
moved to correct path pypi_publish workflow
a3e29c3
@saramonzon
added contributing guidelines file
7b6bd65
@saramonzon
fix path in pypi workflow
cfb5db6
@saramonzon
updated and fixed dependencies
bdf21a9
@saramonzon
renamed param in analyze schema
c511058
@saramonzon
fixes in params help, added show default when appropiate
e0f7f25
@saramonzon
readme docs are updated
4901b30
@saramonzon
added changelog
cc713b8
@saramonzon
updated gitignore
fb2c7ab
@saramonzon
fix tests workflow gact
1de6d7a
@saramonzon saramonzon merged commit b52a1ce into main Jan 2, 2025
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2 participants
@saramonzon @luissian