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ggirelli
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* Added zenodo shield. * Bump rich from 9.12.0 to 9.12.3 (#11) * Bump rich from 9.12.3 to 9.12.4 (#12) * Bump pandas from 1.2.2 to 1.2.3 (#13) * Added parser functions for HUSH, oligo-melting, and OligoArrayAux * Added assert for dtype compatibility * Added dtypes and expected database columns * Changed entry points for db related actions * Implemented db make script * Added final message. * Cosmetic changes. * Added interface for database-related scripts. * Cleaned * Added basic info script * Added DataBase and Record classes * Simplified using DataBase class. * Prepared to store other information on chromosomes (e.g., record no) * Implemented script to dump tsv to std. * Updated chromosome-related asserts, logs, and properties * Added header printing and tqdm progression * Added chromosome prefix option. Switched from defaultdict to dict for pickling * Added dump description * Added record sorting step. * Added sorted check * Cosmetic * Added ChromosomeData and ChromosomeIndex classes * Added missing declaration and exposed chromosome index * Switched from rich to tqdm. Fixed index visibility in wrappers * Added options for region dumping. * Removed redundant function * Implemented database jumping and window walk * Updated version tag and promoted to beta. Added 3.9 to GHAction. * Added Typed classifier * Linked new database and old walker. * Removed old database module. * Added indexing progress bar * Fixed dump of a region. * Changed default database index bin size to 100 kb * Fixed issue of empty index bins. * Blacked. * Refactored ChromosomeData and added ChromosomeDict class. * Dropped sequence_length column. Fixed pickling of ChromosomeData. * Added reindex entry point. * Bump rich from 9.12.4 to 9.13.0 (#15) * Bump tqdm from 4.58.0 to 4.59.0 (#16) * Split chromosome classes from database. Added docstrings. * Implementing new walker. * Implemented walker with growing focus region. * Moved database walking to walker class * Added tests. * Added test_data to package. * Added pytest setup * Fixed pytest setup * Added pytest to and updated dependencies * Moved GenomicRegion to new region module * Moved pytest and black to dev dependencies * Implemented region builder and multi walk * Implementing new query script * Fixed decoding * Added docstrings * Hidden some prototype code tagged by vulture * Fixed links * Fixed link to repo * Fixed threads check. * Updated version management. * Dropped support for Python 3.7 * Removed default number of queried probes. * Bump rich from 9.13.0 to 10.0.0 (#19) * Bump numpy from 1.20.1 to 1.20.2 (#18) * Bump rich from 10.0.0 to 10.0.1 (#20) * Bump tqdm from 4.59.0 to 4.60.0 (#23) * Bump pytest from 6.2.2 to 6.2.3 (#22) * Bump rich from 10.0.1 to 10.1.0 (#21) * Bump pandas from 1.2.3 to 1.2.4 (#24) * Bump black from 20.8b1 to 21.4b0 (#25) * Bump black from 21.4b0 to 21.4b1 (#26) * Bump black from 21.4b1 to 21.4b2 (#27) * Bump black from 21.4b2 to 21.5b0 (#28) * Bump pytest from 6.2.3 to 6.2.4 (#29) * Bump rich from 10.1.0 to 10.2.0 (#32) * Bump black from 21.5b0 to 21.5b1 (#31) * Bump numpy from 1.20.2 to 1.20.3 (#30) * Bump rich from 10.2.0 to 10.2.2 (#34) * Bump black from 21.5b1 to 21.5b2 (#36) * Bump tqdm from 4.60.0 to 4.61.0 (#35) * Bump rich from 10.2.2 to 10.3.0 (#37) * Bump black from 21.5b2 to 21.6b0 (#38) * Bump tqdm from 4.61.0 to 4.61.1 (#39) * Bump rich from 10.3.0 to 10.4.0 (#40) * Bump pandas from 1.2.4 to 1.2.5 (#41) * Bump numpy from 1.20.3 to 1.21.0 (#42) * Bump pandas from 1.2.5 to 1.3.0 (#43) * Bump rich from 10.4.0 to 10.5.0 (#45) * Bump tqdm from 4.61.1 to 4.61.2 (#44) * Bump rich from 10.5.0 to 10.6.0 (#46) * Bump black from 21.6b0 to 21.7b0 (#47) * Bump numpy from 1.21.0 to 1.21.1 (#48) * Bump tqdm from 4.61.2 to 4.62.0 (#50) * Bump pandas from 1.3.0 to 1.3.1 (#49) * Bump rich from 10.6.0 to 10.7.0 (#51) * Bump tqdm from 4.62.0 to 4.62.1 (#52) * Bump pandas from 1.3.1 to 1.3.2 (#53) * Bump tqdm from 4.62.1 to 4.62.2 (#54) * Bump rich from 10.7.0 to 10.9.0 (#55) * Bump black from 21.7b0 to 21.8b0 (#56) * Bump pytest from 6.2.4 to 6.2.5 (#57) * 'Refactored by Sourcery' (#58) Co-authored-by: Sourcery AI <> * Blacked, flaked, and mypyed * Bump pandas from 1.3.2 to 1.3.3 (#59) * Bump black from 21.8b0 to 21.9b0 (#60) * Bump rich from 10.9.0 to 10.10.0 (#61) * Bump tqdm from 4.62.2 to 4.62.3 (#62) * Bump rich from 10.10.0 to 10.11.0 (#63) * Argparse to click (#65) * Updated dependencies * Preparing for click. * Swapped argparse for click and using dataclasses * 'Refactored by Sourcery' (#66) Co-authored-by: Sourcery AI <> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Blacked * 'Refactored by Sourcery' (#67) Co-authored-by: Sourcery AI <> * Blacked. * Now passing tests. * Added biopython dependency and extract_kmers script. (#68) * 'Refactored by Sourcery' (#70) Co-authored-by: Sourcery AI <> * Improved extract_kmers script * 'Refactored by Sourcery' (#71) Co-authored-by: Sourcery AI <> * Mypyed after sorcery refactoring * Bump rich from 10.11.0 to 10.12.0 (#72) * Added autocompletion. (#73) * Added autocompletion. * 'Refactored by Sourcery' (#74) Co-authored-by: Sourcery AI <> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> * Fixed __path__ * Added missing fasta header starting character * Bump click from 8.0.1 to 8.0.3 (#75) * Added compatibility with previous database pickled arguments. * Added pre-commits. * Fixed spelling * Added support for hush gzipped files * Create .deepsource.toml * Fix comparison constant position (#76) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Replace `dict` call with comprehension (#77) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove unnecessary use of comprehension (#78) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Change methods not using its bound instance to staticmethods (#79) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove assert statement from non-test files (#80) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Set `check` flag to `True` (#82) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove implicit `object` from the base class (#83) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove assert statement from non-test files (#84) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Refactor unnecessary `else` / `elif` when `if` block has a `continue` statement (#85) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement (#86) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Use literal syntax to create data structure (#87) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Merge collapsible `if` statements (#88) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * fix: added docstring explaining emptiness. * fix: added docstring explaining emptiness. * Refactor unnecessary `else` / `elif` when `if` block has a `raise` statement (#89) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove unnecessary `pass` (#90) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove methods with unnecessary super delegation. (#91) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * fix: probe selection & unreachable statements * Remove unused private attribute (#92) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * fix: Multi-line docstring closing quotes should be on a separate line * fix: swapped single for double quotes * fix: inconsistent return statements * fix: blacked. * fix: process from shell, escaping parameters * fix: inconsistent return statements * fix: removed unused private attribute * fix: escaping shell subprocess cmd * fix: open files with `with` statement * fix: quoted upon subprocess spawning * Merge collapsible `with` statements (#95) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * fix: blacked * 'Refactored by Sourcery' (#81) Co-authored-by: Sourcery AI <> * Dropped broken scripts test. * fix: added test placeholder * Bump pandas from 1.3.3 to 1.3.4 (#97) * Bump black from 21.9b0 to 21.10b0 (#98) * Bump rich from 10.12.0 to 10.13.0 (#99) * Bump black from 21.10b0 to 21.11b0 (#100) * Bump rich from 10.13.0 to 10.14.0 (#101) * Bump black from 21.11b0 to 21.11b1 (#102) * fix: wrong condition of path_exists function * fix: correct variable names * fix: assertions on input params * Bump rich from 10.14.0 to 10.15.0 (#103) * Bump rich from 10.15.0 to 10.15.1 (#104) * Bump rich from 10.15.1 to 10.15.2 (#105) * Bump black from 21.11b1 to 21.12b0 (#106) * fix: minor assert change * fix: trove classifier * doc: updated with version flag * docs: updated version flag * feat: updated lock file Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
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