BiocPy/BiocFrame issues and pull requests

#113 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 5 months ago

#112 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#111 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#110 - Enhance docs

Pull Request - State: closed - Opened by jkanche 6 months ago

#109 - run code snippets in markdown

Pull Request - State: closed - Opened by jkanche 6 months ago

#108 - Interface with polars

Pull Request - State: closed - Opened by jkanche 6 months ago

#107 - Switch from `pandas` to `polars` for more efficient downstream tasks, e.g. faster queries

Issue - State: closed - Opened by abearab 6 months ago - 2 comments

#106 - Fix an issue when the frame is empty but `number_of_rows>0`

Pull Request - State: closed - Opened by jkanche 6 months ago

#105 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#104 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#103 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#102 - input version for manual builds

Pull Request - State: closed - Opened by jkanche 9 months ago

#101 - separate documentation as a callable workflow, update actions

Pull Request - State: closed - Opened by jkanche 9 months ago

#100 - add jupyter notebooks

Pull Request - State: closed - Opened by jkanche 9 months ago

#99 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#98 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#97 - Clean up `get_column` accessor

Pull Request - State: closed - Opened by jkanche 10 months ago

#96 - Use integers to specify number of rows.

Pull Request - State: closed - Opened by jkanche 10 months ago

#95 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#94 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#93 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#92 - Fix condition check for arguments when slicing

Pull Request - State: closed - Opened by jkanche 11 months ago - 1 comment

#91 - Split `BiocFrame` by a column

Pull Request - State: closed - Opened by jkanche 11 months ago - 1 comment

#90 - Register biocutils relaxed generics on `BiocFrame`

Pull Request - State: closed - Opened by jkanche 11 months ago

#89 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#88 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#87 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago

#86 - support empty biocframe with column names

Pull Request - State: closed - Opened by jkanche about 1 year ago

#85 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#84 - Use `Names` instead of `StringList`; bump biocutils to 0.1.2

Pull Request - State: closed - Opened by jkanche about 1 year ago

#83 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#82 - Moved the pandas converter into a classmethod.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#81 - Attach row names to the output of get_column_data() by default.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#80 - Cleaned up all docstrings by removing manual type hints.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#79 - Renamed mcols to column_data.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#78 - No special treatment of scalar arguments in get_slice().

Pull Request - State: closed - Opened by LTLA about 1 year ago - 3 comments

#77 - Refactored the getitem and slicing methods for more clarity.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#76 - Moved relaxed_combine_rows back into the main file.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#75 - Added a merge function to combine BiocFrames based on a key column.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#74 - Refactored the combine method into (flexible_)combine_rows functions.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#73 - Forgot to add a BiocFrame method for assign_rows.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#72 - Added a functional-style method to set a slice of the DF contents.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#71 - Set or remove columns by positional index or name.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#70 - Enable setting and removal of multiple columns at once.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#69 - Avoid pass-by-reference effects when setting or removing columns.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#68 - Either have `len()` be the number of columns, or rename `mcols()`

Issue - State: closed - Opened by LTLA about 1 year ago - 2 comments

#67 - Suggested fixes that I noticed

Issue - State: closed - Opened by LTLA about 1 year ago

#66 - Migrated methods and classes to the latest BiocUtils package.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#65 - Add a `replace_columns()` function

Issue - State: closed - Opened by LTLA about 1 year ago

#64 - `set_column` is always in-place

Issue - State: closed - Opened by LTLA about 1 year ago - 1 comment

#63 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#62 - Switch biocgenerics.format_table with biocutils.print_wrapped_table.

Pull Request - State: closed - Opened by LTLA about 1 year ago - 1 comment

#61 - add method `get_column`. Set deprecation warning for column().

Pull Request - State: closed - Opened by jkanche about 1 year ago

#60 - I see a `column` but no `get_column`

Issue - State: closed - Opened by LTLA about 1 year ago

#59 - Improved the repr and str methods for BiocFrames.

Pull Request - State: closed - Opened by LTLA about 1 year ago - 2 comments

#58 - Support partial replacement via row indices in BiocFrame.setitem.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#57 - `BiocFrame.setitem` doesn't work with row indices

Issue - State: closed - Opened by LTLA about 1 year ago

#56 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#55 - change to functional style for getters and setters

Pull Request - State: closed - Opened by jkanche about 1 year ago - 2 comments

#54 - Factors

Pull Request - State: closed - Opened by jkanche about 1 year ago

#53 - add minimum python version; update github action

Pull Request - State: closed - Opened by jkanche about 1 year ago

#52 - Implement our own Factor class to mimic R's behavior.

Pull Request - State: closed - Opened by LTLA about 1 year ago - 4 comments

#51 - Convert to a functional style

Issue - State: closed - Opened by LTLA about 1 year ago - 1 comment

#50 - Don't attach row names during subsetting

Issue - State: closed - Opened by LTLA about 1 year ago

#49 - Add mcols support for completeness.

Pull Request - State: closed - Opened by LTLA about 1 year ago

#48 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#47 - Implement `copy` and `deepcopy`

Pull Request - State: closed - Opened by jkanche about 1 year ago

#46 - implement generics for `rownames` and `colnames`

Pull Request - State: closed - Opened by jkanche about 1 year ago

#45 - quality of life improvments

Pull Request - State: closed - Opened by jkanche about 1 year ago

#44 - Update BiocFrame.py - doc errors

Pull Request - State: closed - Opened by vjcitn about 1 year ago - 1 comment

#43 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#42 - Add combine functionality

Pull Request - State: closed - Opened by jkanche about 1 year ago

#41 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#40 - remove pandas imports

Pull Request - State: closed - Opened by jkanche about 1 year ago

#39 - pandas is not quite optional as `to_pandas()` has `DataFrame` as a type hint

Issue - State: closed - Opened by LTLA about 1 year ago - 1 comment

#38 - really need a `concat` method

Issue - State: closed - Opened by jkanche about 1 year ago

#37 - do not add unnecessary column names

Pull Request - State: closed - Opened by jkanche about 1 year ago

#36 - nested BiocFrame construction adds unnecessary row names

Issue - State: closed - Opened by LTLA about 1 year ago

#35 - Dev/better hinting

Pull Request - State: closed - Opened by DiDeoxy about 1 year ago

#34 - minor updates to package

Pull Request - State: closed - Opened by jkanche about 1 year ago

#33 - BiocFrame init is missing a docstring

Issue - State: closed - Opened by DiDeoxy about 1 year ago

#32 - The "DataFrame" type hint does not work as is

Issue - State: closed - Opened by DiDeoxy about 1 year ago - 1 comment

#31 - Make `from_pandas` a classmethod

Issue - State: closed - Opened by DiDeoxy about 1 year ago - 1 comment

#30 - Value of `data` is `Any`.

Pull Request - State: closed - Opened by jkanche about 1 year ago

#29 - Fix `repr` displaying duplicate rows

Pull Request - State: closed - Opened by jkanche about 1 year ago

#28 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#27 - `repr` method shows duplicated rows

Issue - State: closed - Opened by LTLA about 1 year ago

#26 - Generalize row/column index subsetting to any `Sequence[int]`

Issue - State: closed - Opened by LTLA about 1 year ago

#25 - preserve types when slicing

Pull Request - State: closed - Opened by jkanche about 1 year ago

#24 - Type of column is incorrectly coerced to list by `column`

Issue - State: closed - Opened by LTLA about 1 year ago - 1 comment

#23 - refactor slicing, update docstrings

Pull Request - State: closed - Opened by jkanche about 1 year ago

#22 - Minor fixes

Pull Request - State: closed - Opened by jkanche about 1 year ago

#21 - Things to do

Issue - State: closed - Opened by LTLA about 1 year ago

#20 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#19 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#18 - fixed issues with printing and slicing single index.

Pull Request - State: closed - Opened by jkanche about 1 year ago

#17 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#16 - pre-commit-again

Pull Request - State: closed - Opened by jkanche over 1 year ago

#15 - update config

Pull Request - State: closed - Opened by jkanche over 1 year ago

#14 - PEPify all code

Pull Request - State: closed - Opened by jkanche over 1 year ago

GitHub / BiocPy/BiocFrame issues and pull requests