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Utils update #234

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4008dc2
feat: use _log_and_raise_error function
JoshLoecker Jan 12, 2025
111465d
fix: drop na values
JoshLoecker Jan 12, 2025
14fb0fa
feat: async read matrix files
JoshLoecker Jan 12, 2025
f632679
refactor: calculate size more pythonically
JoshLoecker Jan 12, 2025
5690616
fix: use better variable for ensembl gene
JoshLoecker Jan 12, 2025
746099b
refactor: drop na values
JoshLoecker Jan 12, 2025
132660f
chore: fix logging message
JoshLoecker Jan 12, 2025
1f7d252
feat: use new LogLevel Enum
JoshLoecker Jan 12, 2025
7451732
fix: resolve context directory only if provided
JoshLoecker Jan 12, 2025
58b66e9
refactor: import/remove modules
JoshLoecker Jan 12, 2025
5c7e3b2
refactor: remove extra read_counts function
JoshLoecker Jan 12, 2025
369b5a1
fix: drop na values when building compiling matrix
JoshLoecker Jan 12, 2025
e708644
fix: fpkm calculations
JoshLoecker Jan 12, 2025
002c705
style: ruff formatting
JoshLoecker Jan 12, 2025
f8bf998
style: fix docstring
JoshLoecker Jan 12, 2025
e7f65e0
fix: zfpkm calculations
JoshLoecker Jan 12, 2025
93e9844
feat: use concurrent.futures for easier processing
JoshLoecker Jan 12, 2025
d6cb677
feat: allow setting bandwidth and peak parameters
JoshLoecker Jan 12, 2025
b2e5fe6
style: ruff whitespace fixes
JoshLoecker Jan 12, 2025
720543f
refactor: more efficient zfpkm plotting
JoshLoecker Jan 12, 2025
1daa66e
feat: use new RNAType Enum
JoshLoecker Jan 12, 2025
0b005b7
fix: drop na values
JoshLoecker Jan 12, 2025
cb6e995
refactor: provide bandwidth and peak parameters
JoshLoecker Jan 12, 2025
8c16d94
feat: allow force-plotting zfpkm
JoshLoecker Jan 12, 2025
97c7d1d
refactor: rename FilteringTechnique constants
JoshLoecker Jan 12, 2025
b67cd84
style: ruff whitespace and log message formatting
JoshLoecker Jan 12, 2025
638de62
refactor: use _process, not _save_rnaseq_tests
JoshLoecker Jan 12, 2025
ba85237
refactor: provide path to rnaseq matrix
JoshLoecker Jan 12, 2025
681e871
refactor: process provided rnaseq matrix
JoshLoecker Jan 12, 2025
f4d6be9
fix: proper check if dataframe is empty/None
JoshLoecker Jan 12, 2025
54cd8ac
fix: only write normalized matrix if data exists
JoshLoecker Jan 12, 2025
ea9654d
fix: proper calculation of high confidence genes
JoshLoecker Jan 12, 2025
e663406
refactor: remove internal _create_metadata_df func
JoshLoecker Jan 12, 2025
fda629e
refactor: proper usage of _set_up_logging function
JoshLoecker Jan 12, 2025
59f7f95
fix: proper usage of _log_and_raise_error function
JoshLoecker Jan 12, 2025
3b63b7d
refactor: proper processing of metadata
JoshLoecker Jan 12, 2025
0ff2eb7
refactor: move logic to out of main function
JoshLoecker Jan 12, 2025
7770643
fix: add proper function parameters
JoshLoecker Jan 12, 2025
bdc0f05
refactor: import required modules
JoshLoecker Jan 12, 2025
475b27a
fix: proper calling of _log_and_raise_error
JoshLoecker Jan 12, 2025
2c65b08
feat: allow providing log level and location
JoshLoecker Jan 12, 2025
e9d9193
refactor: import required modules
JoshLoecker Jan 12, 2025
632bfa8
refactor: remove data-specific Enums
JoshLoecker Jan 12, 2025
f9669a6
refactor: async data loading
JoshLoecker Jan 12, 2025
938f6cb
refactor: use new RNAType; _log_and_raise_error
JoshLoecker Jan 12, 2025
ed2044e
refactor: drop na values
JoshLoecker Jan 12, 2025
6074d6b
feat: add logging
JoshLoecker Jan 12, 2025
9b52049
refactor: type hinting; drop na values
JoshLoecker Jan 12, 2025
38a9f1e
feat: added function to update missing genome data
JoshLoecker Jan 12, 2025
11cd6b4
refactor: build and use new parameter data types
JoshLoecker Jan 12, 2025
0d484a2
refactor: pass new parameter data types
JoshLoecker Jan 12, 2025
07fc452
refactor: calculate variables near their usage
JoshLoecker Jan 12, 2025
c371c12
style: more verbose variable name
JoshLoecker Jan 12, 2025
026f1cc
feat: add functions for building batch data
JoshLoecker Jan 12, 2025
ebf3edd
feat: add function for validating data soruces
JoshLoecker Jan 12, 2025
0f1d584
refactor!: provide None as default argument
JoshLoecker Jan 12, 2025
f0a2aab
refactor: better building of source data variables
JoshLoecker Jan 12, 2025
b9bade6
feat: allow providing log levela and location
JoshLoecker Jan 12, 2025
325b559
refactor: move variable creation closer to usage
JoshLoecker Jan 12, 2025
463d545
refactor: use _log_and_raise_error
JoshLoecker Jan 12, 2025
f1c242d
refactor: import required modules
JoshLoecker Jan 12, 2025
437082a
refactor!: move Solver to data_types
JoshLoecker Jan 12, 2025
4694a5a
refactor: remove _Arguments cli parsing
JoshLoecker Jan 12, 2025
91a538f
fix: bracket and logical gene rule creation
JoshLoecker Jan 12, 2025
675a26b
refactor: reduce extraneous function usage
JoshLoecker Jan 12, 2025
618edc7
style: ruff whitespace formatting
JoshLoecker Jan 12, 2025
70371fe
refactor: remove extraneous variable
JoshLoecker Jan 12, 2025
cd36b5e
refactor: pythonic if-statement calculation
JoshLoecker Jan 12, 2025
d5f1fdf
refactor: remove extraneous comment + variables
JoshLoecker Jan 12, 2025
b586e25
style: more verbose parameter names
JoshLoecker Jan 12, 2025
498e84a
refactor: async usage where possible
JoshLoecker Jan 12, 2025
1668b35
refactor: type hinting
JoshLoecker Jan 12, 2025
f162b94
refactor: pythonic collection of gene activity
JoshLoecker Jan 12, 2025
52f335f
fix: update mapping process to be more readable
JoshLoecker Jan 12, 2025
eab0713
refactor: import required modules
JoshLoecker Jan 12, 2025
23a01f0
refactor: move dataclasses to data_types.py
JoshLoecker Jan 12, 2025
a207fcc
refactor: make async functions
JoshLoecker Jan 12, 2025
5d918c5
refactor: simplify processing, use async
JoshLoecker Jan 12, 2025
97cc2a9
refactor: use relevant data types
JoshLoecker Jan 12, 2025
aabcb8f
refactor: pythonic approach to z score calculation
JoshLoecker Jan 12, 2025
0a795e1
refactor: async create directories
JoshLoecker Jan 12, 2025
fdf415f
refactor: move when early return happens
JoshLoecker Jan 12, 2025
8c1ef04
fix: remove unused z score calculation
JoshLoecker Jan 12, 2025
60eb969
fix: store gene ids as string
JoshLoecker Jan 12, 2025
9cf76c2
refactor: more efficient pandas melting
JoshLoecker Jan 12, 2025
c7d1477
fix: graph title name
JoshLoecker Jan 12, 2025
3e38a0f
refactor: add appropriate column names
JoshLoecker Jan 12, 2025
e323a9a
refactor: rename parameter names
JoshLoecker Jan 12, 2025
b575d40
refactor: log for early return
JoshLoecker Jan 12, 2025
b2d7b24
feat: async create directories
JoshLoecker Jan 12, 2025
d847da2
style: add logging
JoshLoecker Jan 12, 2025
3a47f20
refactor: remove old z score calculation code
JoshLoecker Jan 12, 2025
229ea7c
refactor: better function name
JoshLoecker Jan 12, 2025
77c9ff1
refactor: pythonic z score calculation
JoshLoecker Jan 12, 2025
3df7503
style: log for early return
JoshLoecker Jan 12, 2025
7a41401
refactor: remove old z score calculation code
JoshLoecker Jan 12, 2025
fc7b95b
refactor: more efficient pandas melting
JoshLoecker Jan 12, 2025
78a1ab6
refactor: temporarily remove z score graphing
JoshLoecker Jan 12, 2025
f34b1db
refactor: use new function names
JoshLoecker Jan 12, 2025
71ee8cc
refactor: use matplotlib for plot creation
JoshLoecker Jan 12, 2025
b6cf039
refactor: exchange plotly for seaborn
JoshLoecker Jan 12, 2025
4c424b5
feat: validate that source types process in order
JoshLoecker Jan 12, 2025
22b82ef
refactor: add logging, use _log_and_raise_error
JoshLoecker Jan 12, 2025
82ce6b3
refactor: remove plotly graphing
JoshLoecker Jan 12, 2025
b846efd
feat: do not throw error if missing png path
JoshLoecker Jan 12, 2025
a43485f
refactor: move NamedTuple to data_types
JoshLoecker Jan 12, 2025
0264c3c
fix: comment unused variables
JoshLoecker Jan 12, 2025
be4e89e
fix: comment unused variables
JoshLoecker Jan 12, 2025
ab96976
fix: line too long
JoshLoecker Jan 12, 2025
8a0f4c6
style: ruff formatting and linting fixes
JoshLoecker Jan 12, 2025
7e53dac
fix: allow undocumented public package
JoshLoecker Jan 12, 2025
bd65dbe
fix: do not create virtual environment to format notebooks
JoshLoecker Jan 12, 2025
e419816
fix: use python 3.10 to evade errors
JoshLoecker Jan 12, 2025
7fa8d00
fix: use uv tool to run nbconvert
JoshLoecker Jan 12, 2025
c6f02bc
style: format code, Jupyter Notebook(s), and Python imports with `ruff`
JoshLoecker Jan 12, 2025
0646150
feat: expand test suite to include python 3.11 and 3.12
JoshLoecker Jan 12, 2025
3412c31
Merge remote-tracking branch 'origin/fix/single-cell-processing' into…
JoshLoecker Jan 12, 2025
9a72ae5
fix: check if provided data is a path before checking if it exists
JoshLoecker Jan 12, 2025
8259105
fix: read StringIO data instead of attempting to make dataframe from it
JoshLoecker Jan 12, 2025
330ed84
fix: statsmodels version dependent on python version
JoshLoecker Jan 12, 2025
b6b6633
fix: use tpm instead of quantile
JoshLoecker Jan 13, 2025
21f780b
fix: typo
JoshLoecker Jan 13, 2025
b119787
chore: update uv lock
JoshLoecker Jan 13, 2025
a441231
chore: code re-arrangement
JoshLoecker Jan 13, 2025
09e1852
chore: remove aiofiles as a dependency
JoshLoecker Jan 13, 2025
80f32d4
fix: renamed RNAType.(trna,mrna) to RNAType.(TRNA,MRNA)
JoshLoecker Jan 14, 2025
2c1687b
fix: re-attempt processing if JSON decode error occurs
JoshLoecker Jan 14, 2025
0f317f3
refactor: remove dependency on aiofiles
JoshLoecker Jan 14, 2025
2229c51
fix: do not call listify twice
JoshLoecker Jan 14, 2025
9a6a42d
refactor: remove dependency on aiofiles
JoshLoecker Jan 14, 2025
f288015
refactor: allow providing a list of model filepaths to write to
JoshLoecker Jan 14, 2025
c0d3816
fix: check that license information is present if using gurobi
JoshLoecker Jan 14, 2025
df86903
feat: add NONE for no logging
JoshLoecker Jan 14, 2025
f925078
refactor: remove dependency on aiofiles
JoshLoecker Jan 14, 2025
13aa4ae
style: ruff formatting
JoshLoecker Jan 31, 2025
1ac47f0
fix: make parent directories before saving files
JoshLoecker Jan 31, 2025
72c3630
refactor: use critical log instead of warning
JoshLoecker Jan 31, 2025
8be741d
refactor: reset exection output and count
JoshLoecker Jan 31, 2025
35a0bf2
fix: rename column names
JoshLoecker Jan 31, 2025
13f3253
chore: increase line length
JoshLoecker Jun 3, 2025
12aa4ad
refactor: updated to be more python-like
JoshLoecker Jun 3, 2025
a3c4b28
style: ruff formatting; error handling
JoshLoecker Jun 3, 2025
c0f5f00
refactor: remove unwrapping aio file reading for better consistency/r…
JoshLoecker Jun 3, 2025
f1a4137
feat: add dataclasses to handle types more easily
JoshLoecker Jun 3, 2025
8c71b57
refactor: add logging
JoshLoecker Jun 3, 2025
b632a72
refactor: added slots to dataclass for reduced memory usage; ruff for…
JoshLoecker Jun 3, 2025
f651a85
refactor: better managing/converting of ensembl and entrez gene IDs
JoshLoecker Jun 3, 2025
5a30ced
refactor: more efficient tpm calculation
JoshLoecker Jun 3, 2025
645eeef
refactor: use pandas dataframes instead of numpy arrays for developer…
JoshLoecker Jun 3, 2025
146a806
refactor: fix plot generation
JoshLoecker Jun 3, 2025
a9d7800
refactor: ruff formatting
JoshLoecker Jun 3, 2025
992469a
refactor: ruff formatting
JoshLoecker Jun 3, 2025
8c00a1f
refactor: ruff formatting
JoshLoecker Jun 3, 2025
d651700
style: better variable naming
JoshLoecker Jun 3, 2025
66bc302
refactor: fix creating evaluable gene reaction rules
JoshLoecker Jun 3, 2025
a2cb161
style: ruff formatting
JoshLoecker Jun 3, 2025
5e331ee
refactor: only publish package when tag starts with 'v'
JoshLoecker Jun 3, 2025
f572104
refactor: use better method of converting to numeric dtype
JoshLoecker Aug 7, 2025
3a547ea
chore: bump package requirements
JoshLoecker Sep 5, 2025
ca99e0a
fix: swap minimum and maximum bounds for exchange reactions
JoshLoecker Sep 5, 2025
efbeed1
feat: provide `identifier_column` for dynamic splitting of gene expre…
JoshLoecker Sep 5, 2025
aac7bbd
feat: use async file reading
JoshLoecker Sep 5, 2025
d1dae99
refactor!: rename `graph` to `plot`
JoshLoecker Sep 5, 2025
b7983c3
chore: remove trailing underscore; do not write index
JoshLoecker Sep 5, 2025
009fbb2
feat: add identifier column check for gene expression data processing
JoshLoecker Sep 5, 2025
0a7c0a6
fix: replace '-' with pd.NA in drug target genes DataFrame
JoshLoecker Sep 5, 2025
3468625
style: ruff formatting
JoshLoecker Sep 5, 2025
6561c24
refactor: use pd.NA instead of checking "-"
JoshLoecker Sep 5, 2025
bf56069
fix: only drop NA values from ensembl_gene_id, not entire dataframe
JoshLoecker Sep 5, 2025
dc324d5
feat: added function to build heatmap of conditions vs pathways
JoshLoecker Sep 5, 2025
74d883d
feat: added function to plot z score distribution
JoshLoecker Sep 5, 2025
b55215d
feat: added `pipelines` module to make using utilities easier
JoshLoecker Sep 5, 2025
40efbe1
fix: merge conflict
JoshLoecker Sep 5, 2025
d65a219
chore: fix typo
JoshLoecker Sep 5, 2025
3e671d9
style: format code, Jupyter Notebook(s), and Python imports with `ruff`
JoshLoecker Sep 5, 2025
1e0a5bb
fix: break up complex conditional
JoshLoecker Sep 5, 2025
6adaa7b
fix: _validate_source_arguments requires arg expansion
JoshLoecker Sep 5, 2025
c26f437
fix: typo
JoshLoecker Sep 5, 2025
da2beaf
fix: typo
JoshLoecker Sep 5, 2025
5eb0254
Merge remote-tracking branch 'origin/fix-startup' into fix-startup
JoshLoecker Sep 5, 2025
462ef3f
refactor: simplify function signatures and improve docstrings
JoshLoecker Sep 5, 2025
df84aea
fix: invalid collection of gene counts
JoshLoecker Sep 5, 2025
bcb6689
fix(rnaseq_preprocess): ensure correct order of async file reads and …
JoshLoecker Sep 5, 2025
feb7d11
chore: add type hint
JoshLoecker Sep 10, 2025
dbf12f4
refactor: use python optional-groups instead of uv dependency-groups
JoshLoecker Sep 10, 2025
700489b
feat: added Kolmogorov-Smirnoff tests
JoshLoecker Sep 18, 2025
eafaa9f
feat: added Mann-Whitney U-tests
JoshLoecker Sep 18, 2025
315d5c6
feat: added Fisher Exact tests
JoshLoecker Sep 18, 2025
16d5c83
feat: added unit tests for KS statistics
JoshLoecker Sep 18, 2025
ae1ca04
feat: added unit tests for Mann Whitney statistics
JoshLoecker Sep 18, 2025
d26bc77
feat: added unit tests for Fisher's Exact statistics
JoshLoecker Sep 18, 2025
371a0ad
refactor: rename variables for better understanding
JoshLoecker Oct 1, 2025
5419d95
refactor: only return a `cobra.Model` reconstruction
JoshLoecker Oct 1, 2025
b5cea99
refactor: add comments stating purpose of code blocks
JoshLoecker Oct 2, 2025
3ea0070
feat: optionally force include exchange reactions
JoshLoecker Oct 2, 2025
b9104ae
chore: more specific type hints
JoshLoecker Oct 2, 2025
85aee68
feat(dev): make private classes public
JoshLoecker Oct 2, 2025
b0479e2
fix: allow .xml or .sbml model types
JoshLoecker Oct 2, 2025
35882d7
style: reword log messages
JoshLoecker Oct 2, 2025
437e013
fix: use better variable name
JoshLoecker Oct 2, 2025
57ced4f
feat(dev): optional lowercasing of dataframe column names
JoshLoecker Oct 2, 2025
bff3654
feat(dev): fix ty warning
JoshLoecker Oct 2, 2025
18dce42
style(ruff): automatic formatting
JoshLoecker Oct 2, 2025
bf22bbf
fix(backport): remove match case for python 3.9
JoshLoecker Oct 2, 2025
ba1fb49
feat(dev): add type hints
JoshLoecker Oct 2, 2025
159ea2c
chore: remove unused package
JoshLoecker Oct 2, 2025
75957f8
feat(dev): make private functions public
JoshLoecker Oct 2, 2025
85ead76
chore: raise error if provided unexpected type
JoshLoecker Oct 2, 2025
112e363
refactor: use public function names
JoshLoecker Oct 2, 2025
2f85a28
fix: remove unused variable
JoshLoecker Oct 2, 2025
12e1623
fix: write index
JoshLoecker Oct 2, 2025
da52de6
refactor: use more explicit variable creation
JoshLoecker Oct 2, 2025
34f82eb
refactor: comment unused code
JoshLoecker Oct 2, 2025
00c97ae
refactor: index is now gene identifier, set columns accordingly
JoshLoecker Oct 2, 2025
981d867
fix(type): use proper type hint
JoshLoecker Oct 2, 2025
36a7600
fix(type): make private functions public
JoshLoecker Oct 2, 2025
b2d4739
refactor: use public utility functions
JoshLoecker Oct 2, 2025
03c94d2
refactor: use public utility functions
JoshLoecker Oct 2, 2025
0d5f986
refactor: use public utility functions; remove unused imports
JoshLoecker Oct 2, 2025
1baddaf
fix(backport): use if-else instead of match for python 3.9
JoshLoecker Oct 2, 2025
6bcaaef
perf: remove nested function for k_over_a calculation
JoshLoecker Oct 2, 2025
bcc1751
fix(dev): rename function for better understanding
JoshLoecker Oct 2, 2025
c4bf288
fix(dev): remove unused comment
JoshLoecker Oct 2, 2025
380742c
refactor: raise error if gene count information not found
JoshLoecker Oct 2, 2025
8695113
style(ruff): automatic formatting
JoshLoecker Oct 2, 2025
2c98335
style(dev): add code branch for reading data
JoshLoecker Oct 2, 2025
8b3cbae
refactor: use public functions
JoshLoecker Oct 2, 2025
0ac2662
refactor: import required packages
JoshLoecker Oct 2, 2025
3be752a
refactor: add type hints
JoshLoecker Oct 2, 2025
72a5538
fix: do not use double underscore for private names
JoshLoecker Oct 2, 2025
2fe2dcf
refactor: `_log_and_raise_error` types that it returns None, no need …
JoshLoecker Oct 2, 2025
7d80ba1
refactor: explicit variable declaration
JoshLoecker Oct 2, 2025
405edbc
refactor: explicit type hint
JoshLoecker Oct 2, 2025
9ebe942
refactor: use yield for more efficient computing
JoshLoecker Oct 2, 2025
245ea78
refactor: explicit type hint
JoshLoecker Oct 2, 2025
0c1c18b
refactor: use async to open files
JoshLoecker Oct 2, 2025
afd78ff
refactor: explicit variable declaration
JoshLoecker Oct 2, 2025
8ee34c2
fix: fill with numpy type, not string
JoshLoecker Oct 2, 2025
10e4e6a
refactor(type): explicit None on no-op
JoshLoecker Oct 2, 2025
9ae5b76
refactor: remove unused variable
JoshLoecker Oct 2, 2025
3bce753
fix: only take columns if they are a part of the data given
JoshLoecker Oct 2, 2025
387798f
refactor: provide full path to file on error
JoshLoecker Oct 2, 2025
e88392f
refactor: use public functions
JoshLoecker Oct 2, 2025
040cf98
refactor: explicit if-else usage
JoshLoecker Oct 2, 2025
101a94c
refactor: explicit `Path` object creation
JoshLoecker Oct 2, 2025
ded4a5d
refactor: explicit type hint
JoshLoecker Oct 2, 2025
acb5a46
Bump python (#230)
JoshLoecker Oct 6, 2025
c2293ad
Update lock file (#229)
JoshLoecker Oct 6, 2025
bb2573c
Fix integration (#231)
JoshLoecker Oct 6, 2025
cd12ad9
Move ref models (#232)
JoshLoecker Oct 6, 2025

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