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v1.0.1a1 #14

Merged
merged 189 commits into from
Dec 7, 2021
Merged

v1.0.1a1 #14

merged 189 commits into from
Dec 7, 2021

Commits on Feb 26, 2021

  1. Added zenodo shield.

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Commits on Mar 1, 2021

  1. Bump rich from 9.12.0 to 9.12.3 (#11)

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Commits on Mar 2, 2021

  1. Bump rich from 9.12.3 to 9.12.4 (#12)

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Commits on Mar 3, 2021

  1. Bump pandas from 1.2.2 to 1.2.3 (#13)

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Commits on Mar 4, 2021

  1. Added parser functions for HUSH, oligo-melting, and OligoArrayAux

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  2. Added assert for dtype compatibility

    @ggirelli
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  3. Added dtypes and expected database columns

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  4. Changed entry points for db related actions

    @ggirelli
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  5. Implemented db make script

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  6. Added final message.

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  7. Cosmetic changes.

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  8. Added interface for database-related scripts.

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  9. Cleaned

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  10. Added basic info script

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  11. Added DataBase and Record classes

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  12. Simplified using DataBase class.

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  13. Prepared to store other information on chromosomes (e.g., record no)

    @ggirelli
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  14. Implemented script to dump tsv to std.

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  15. Updated chromosome-related asserts, logs, and properties

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  16. Added header printing and tqdm progression

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  17. Added chromosome prefix option. Switched from defaultdict to dict for… 

    … pickling
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  18. Added dump description

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Commits on Mar 5, 2021

  1. Added record sorting step.

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  2. Added sorted check

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  3. Cosmetic

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  4. Added ChromosomeData and ChromosomeIndex classes

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  5. Added missing declaration and exposed chromosome index

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  6. Switched from rich to tqdm. Fixed index visibility in wrappers

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  7. Added options for region dumping.

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  8. Removed redundant function

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  9. Implemented database jumping and window walk

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  10. Updated version tag and promoted to beta. Added 3.9 to GHAction.

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  11. Added Typed classifier

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  12. Linked new database and old walker.

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  13. Removed old database module.

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  14. Added indexing progress bar

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  15. Fixed dump of a region.

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  16. Changed default database index bin size to 100 kb

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  17. Fixed issue of empty index bins.

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  18. Blacked.

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Commits on Mar 7, 2021

  1. Refactored ChromosomeData and added ChromosomeDict class.

    @ggirelli
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  2. Dropped sequence_length column. Fixed pickling of ChromosomeData.

    @ggirelli
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  3. Added reindex entry point.

    @ggirelli
    ggirelli committed Mar 7, 2021
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Commits on Mar 8, 2021

  1. Bump rich from 9.12.4 to 9.13.0 (#15)

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  2. Bump tqdm from 4.58.0 to 4.59.0 (#16)

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Commits on Mar 16, 2021

  1. Split chromosome classes from database. Added docstrings.

    @ggirelli
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  2. Implementing new walker.

    @ggirelli
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  3. Implemented walker with growing focus region.

    @ggirelli
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  4. Moved database walking to walker class

    @ggirelli
    ggirelli committed Mar 16, 2021
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  5. Added tests.

    @ggirelli
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  6. Added test_data to package.

    @ggirelli
    ggirelli committed Mar 16, 2021
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  7. Added pytest setup

    @ggirelli
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  8. Fixed pytest setup

    @ggirelli
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  9. Added pytest to and updated dependencies

    @ggirelli
    ggirelli committed Mar 16, 2021
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  10. Moved GenomicRegion to new region module

    @ggirelli
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  11. Moved pytest and black to dev dependencies

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  12. Implemented region builder and multi walk

    @ggirelli
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  13. Implementing new query script

    @ggirelli
    ggirelli committed Mar 16, 2021
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  14. Fixed decoding

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  15. Added docstrings

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  16. Hidden some prototype code tagged by vulture

    @ggirelli
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Commits on Mar 23, 2021

  1. Fixed links

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    ggirelli committed Mar 23, 2021
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  2. Fixed link to repo

    @ggirelli
    ggirelli committed Mar 23, 2021
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  3. Fixed threads check.

    @ggirelli
    ggirelli committed Mar 23, 2021
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  4. Updated version management.

    @ggirelli
    ggirelli committed Mar 23, 2021
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  5. Dropped support for Python 3.7

    @ggirelli
    ggirelli committed Mar 23, 2021
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  6. Removed default number of queried probes.

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Commits on Mar 29, 2021

  1. Bump rich from 9.13.0 to 10.0.0 (#19)

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  2. Bump numpy from 1.20.1 to 1.20.2 (#18)

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Commits on Mar 31, 2021

  1. Bump rich from 10.0.0 to 10.0.1 (#20)

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Commits on Apr 6, 2021

  1. Bump tqdm from 4.59.0 to 4.60.0 (#23)

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  2. Bump pytest from 6.2.2 to 6.2.3 (#22)

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  3. Bump rich from 10.0.1 to 10.1.0 (#21)

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Commits on Apr 14, 2021

  1. Bump pandas from 1.2.3 to 1.2.4 (#24)

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Commits on Apr 26, 2021

  1. Bump black from 20.8b1 to 21.4b0 (#25)

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Commits on Apr 28, 2021

  1. Bump black from 21.4b0 to 21.4b1 (#26)

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Commits on Apr 29, 2021

  1. Bump black from 21.4b1 to 21.4b2 (#27)

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Commits on May 5, 2021

  1. Bump black from 21.4b2 to 21.5b0 (#28)

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  2. Bump pytest from 6.2.3 to 6.2.4 (#29)

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Commits on May 15, 2021

  1. Bump rich from 10.1.0 to 10.2.0 (#32)

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  2. Bump black from 21.5b0 to 21.5b1 (#31)

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  3. Bump numpy from 1.20.2 to 1.20.3 (#30)

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Commits on May 21, 2021

  1. Bump rich from 10.2.0 to 10.2.2 (#34)

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Commits on Jun 1, 2021

  1. Bump black from 21.5b1 to 21.5b2 (#36)

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  2. Bump tqdm from 4.60.0 to 4.61.0 (#35)

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Commits on Jun 14, 2021

  1. Bump rich from 10.2.2 to 10.3.0 (#37)

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  2. Bump black from 21.5b2 to 21.6b0 (#38)

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  3. Bump tqdm from 4.61.0 to 4.61.1 (#39)

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Commits on Jun 21, 2021

  1. Bump rich from 10.3.0 to 10.4.0 (#40)

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Commits on Jun 22, 2021

  1. Bump pandas from 1.2.4 to 1.2.5 (#41)

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Commits on Jun 23, 2021

  1. Bump numpy from 1.20.3 to 1.21.0 (#42)

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Commits on Jul 3, 2021

  1. Bump pandas from 1.2.5 to 1.3.0 (#43)

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Commits on Jul 6, 2021

  1. Bump rich from 10.4.0 to 10.5.0 (#45)

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  2. Bump tqdm from 4.61.1 to 4.61.2 (#44)

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Commits on Jul 14, 2021

  1. Bump rich from 10.5.0 to 10.6.0 (#46)

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Commits on Jul 20, 2021

  1. Bump black from 21.6b0 to 21.7b0 (#47)

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  2. Bump numpy from 1.21.0 to 1.21.1 (#48)

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Commits on Aug 4, 2021

  1. Bump tqdm from 4.61.2 to 4.62.0 (#50)

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  2. Bump pandas from 1.3.0 to 1.3.1 (#49)

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Commits on Aug 11, 2021

  1. Bump rich from 10.6.0 to 10.7.0 (#51)

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Commits on Aug 16, 2021

  1. Bump tqdm from 4.62.0 to 4.62.1 (#52)

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  2. Bump pandas from 1.3.1 to 1.3.2 (#53)

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Commits on Aug 24, 2021

  1. Bump tqdm from 4.62.1 to 4.62.2 (#54)

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Commits on Aug 30, 2021

  1. Bump rich from 10.7.0 to 10.9.0 (#55)

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  2. Bump black from 21.7b0 to 21.8b0 (#56)

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Commits on Aug 31, 2021

  1. Bump pytest from 6.2.4 to 6.2.5 (#57)

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Commits on Sep 8, 2021

  1. 'Refactored by Sourcery' (#58) 

    Co-authored-by: Sourcery AI <>
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  2. Blacked, flaked, and mypyed

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Commits on Sep 13, 2021

  1. Bump pandas from 1.3.2 to 1.3.3 (#59)

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Commits on Sep 16, 2021

  1. Bump black from 21.8b0 to 21.9b0 (#60)

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Commits on Sep 21, 2021

  1. Bump rich from 10.9.0 to 10.10.0 (#61)

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  2. Bump tqdm from 4.62.2 to 4.62.3 (#62)

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Commits on Sep 25, 2021

  1. Bump rich from 10.10.0 to 10.11.0 (#63)

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Commits on Oct 6, 2021

  1. Argparse to click (#65) 

    * Updated dependencies

* Preparing for click.

* Swapped argparse for click and using dataclasses

* 'Refactored by Sourcery' (#66)

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  2. Blacked

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  3. 'Refactored by Sourcery' (#67) 

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  4. Blacked.

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  5. Now passing tests.

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  6. Added biopython dependency and extract_kmers script. (#68)

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  7. 'Refactored by Sourcery' (#70) 

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  8. Improved extract_kmers script

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  9. 'Refactored by Sourcery' (#71) 

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  10. Mypyed after sorcery refactoring

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  11. Bump rich from 10.11.0 to 10.12.0 (#72)

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  12. Added autocompletion. (#73) 

    * Added autocompletion.

* 'Refactored by Sourcery' (#74)

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  13. Fixed __path__

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Commits on Oct 7, 2021

  1. Added missing fasta header starting character

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Commits on Oct 12, 2021

  1. Bump click from 8.0.1 to 8.0.3 (#75)

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Commits on Oct 15, 2021

  1. Added compatibility with previous database pickled arguments.

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  2. Merge branch 'dev' of github.com:ggirelli/ifpd2 into dev

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Commits on Oct 18, 2021

  1. Added pre-commits.

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  2. Fixed spelling

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  3. Added support for hush gzipped files

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Commits on Oct 19, 2021

  1. Create .deepsource.toml

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  2. Fix comparison constant position (#76) 

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  3. Replace dict call with comprehension (#77) 

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  4. Remove unnecessary use of comprehension (#78) 

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  5. Change methods not using its bound instance to staticmethods (#79) 

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  6. Remove assert statement from non-test files (#80) 

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  7. Set check flag to True (#82) 

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  8. Remove implicit object from the base class (#83) 

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  9. Remove assert statement from non-test files (#84) 

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  10. Refactor unnecessary else / elif when if block has a continue… 

    … statement (#85)

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  11. Refactor unnecessary else / elif when if block has a return s… 

    …tatement (#86)

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  12. Use literal syntax to create data structure (#87) 

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  13. Merge collapsible if statements (#88) 

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  14. fix: added docstring explaining emptiness.

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  15. fix: added docstring explaining emptiness.

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  16. Refactor unnecessary else / elif when if block has a raise st… 

    …atement (#89)

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  17. Remove unnecessary pass (#90) 

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  18. Remove methods with unnecessary super delegation. (#91) 

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  19. fix: probe selection & unreachable statements

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  20. Remove unused private attribute (#92) 

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  21. fix: Multi-line docstring closing quotes should be on a separate line

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  22. Merge branch 'dev' of github.com:ggirelli/ifpd2 into dev

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  23. fix: swapped single for double quotes

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  24. fix: inconsistent return statements

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  25. fix: blacked.

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  26. fix: process from shell, escaping parameters

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  27. fix: inconsistent return statements

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  28. fix: removed unused private attribute

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  29. fix: escaping shell subprocess cmd

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  30. fix: open files with with statement

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  31. fix: quoted upon subprocess spawning

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  32. Merge collapsible with statements (#95) 

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  33. fix: blacked

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  34. 'Refactored by Sourcery' (#81) 

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  35. Dropped broken scripts test.

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  36. Merge branch 'dev' of github.com:ggirelli/ifpd2 into dev

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  37. fix: added test placeholder

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Commits on Oct 29, 2021

  1. Bump pandas from 1.3.3 to 1.3.4 (#97)

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Commits on Nov 1, 2021

  1. Bump black from 21.9b0 to 21.10b0 (#98)

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Commits on Nov 8, 2021

  1. Bump rich from 10.12.0 to 10.13.0 (#99)

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Commits on Nov 18, 2021

  1. Bump black from 21.10b0 to 21.11b0 (#100)

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  2. Bump rich from 10.13.0 to 10.14.0 (#101)

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Commits on Nov 19, 2021

  1. Bump black from 21.11b0 to 21.11b1 (#102)

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Commits on Nov 26, 2021

  1. fix: wrong condition of path_exists function

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  2. fix: correct variable names

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  3. fix: assertions on input params

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Commits on Nov 29, 2021

  1. Bump rich from 10.14.0 to 10.15.0 (#103)

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Commits on Nov 30, 2021

  1. Bump rich from 10.15.0 to 10.15.1 (#104)

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Commits on Dec 3, 2021

  1. Bump rich from 10.15.1 to 10.15.2 (#105)

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Commits on Dec 7, 2021

  1. Bump black from 21.11b1 to 21.12b0 (#106)

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  2. Merge branch 'dev' of github.com:ggirelli/ifpd2 into dev

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  3. fix: minor assert change

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  4. fix: trove classifier

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  5. doc: updated with version flag

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  6. docs: updated version flag

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  7. feat: updated lock file

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