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Fix startup #228

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653e001
refactor: use new one-context approach
JoshLoecker Dec 17, 2024
b5d89aa
refactor: import required modules
JoshLoecker Dec 17, 2024
bb140ab
feat: create understandable dataclasses
JoshLoecker Dec 17, 2024
8102b0f
refactor: remove unused modules
JoshLoecker Dec 17, 2024
d7caa25
refactor: remove multi-context-specific code
JoshLoecker Dec 17, 2024
672ae38
feat: do not use hardcoded paths
JoshLoecker Dec 17, 2024
f825055
fix: do not overlap with built-in filenames
JoshLoecker Dec 17, 2024
8352572
feat: numpy typing; count rows/columns function
JoshLoecker Dec 17, 2024
75c9753
fix: allow not setting index
JoshLoecker Dec 17, 2024
8600054
fix: use new data_types file
JoshLoecker Dec 17, 2024
e8086f8
fix: function renaming; remove unused variables
JoshLoecker Dec 17, 2024
3ca7ea4
fix: do not require pydantic
JoshLoecker Dec 17, 2024
cb896b9
fix: use new file name
JoshLoecker Dec 17, 2024
d620960
fix: zfpkm should be performed on rows, not cols
JoshLoecker Dec 17, 2024
9541824
style: reorganize code
JoshLoecker Dec 17, 2024
4ba45e0
style: rename arguments
JoshLoecker Dec 17, 2024
0a0824e
fix: ignore mismatched types
JoshLoecker Dec 17, 2024
2dbebb6
fix: misspelling
JoshLoecker Dec 17, 2024
cf06da4
feat: move zscore graphing to its own module
JoshLoecker Dec 25, 2024
e14af0c
fix: explicit import graphing
JoshLoecker Dec 25, 2024
a509786
fix: hotfix - zscore ceiling is incorrect
JoshLoecker Dec 25, 2024
941e073
chore(deps): bump astral-sh/ruff-action from 2 to 3 (#213)
dependabot[bot] Jan 6, 2025
fdfd0ec
chore(deps): bump astral-sh/setup-uv from 4 to 5
dependabot[bot] Jan 6, 2025
6d74649
Merge pull request #212 from HelikarLab/dependabot/github_actions/ast…
JoshLoecker Jan 6, 2025
fb384ec
fix: pin numpy to less than version 2; update scanpy
JoshLoecker Jan 12, 2025
e659eb2
refactor!: moved `return_placeholder_data` to `como.utils`
JoshLoecker Jan 12, 2025
b5d0a91
fix: properly return row and column values
JoshLoecker Jan 12, 2025
4079deb
feat: added function to set up logging throughout COMO
JoshLoecker Jan 12, 2025
bf7f139
feat: added function to log and raise an error
JoshLoecker Jan 12, 2025
237d1fc
refactor!: moved Algorithms to data_types
JoshLoecker Jan 12, 2025
34ccd44
refactor!: moved Compartments to data_types
JoshLoecker Jan 12, 2025
038ab17
refactor: re-organized constants
JoshLoecker Jan 12, 2025
c337e4d
fix: removed items from __all__ that were moved
JoshLoecker Jan 12, 2025
99676ed
refactor: imported required packages and types
JoshLoecker Jan 12, 2025
8662f7c
fix: added Algorithm as top level import
JoshLoecker Jan 12, 2025
c454e8d
fix: added CobraCompartments as top-level import
JoshLoecker Jan 12, 2025
510c77c
fix: process ids as string type
JoshLoecker Jan 12, 2025
3e93488
refactor: combine async file reading
JoshLoecker Jan 12, 2025
e99d3bd
refactor: remove un-used function
JoshLoecker Jan 12, 2025
c1c6d00
refactor: fix async reading of data
JoshLoecker Jan 12, 2025
5c912b3
feat: allow passing strings for dataframes
JoshLoecker Jan 12, 2025
e942b85
fix: importing of required and unused modules
JoshLoecker Jan 12, 2025
0345a14
feat: use new log_and_raise_error
JoshLoecker Jan 12, 2025
4d66cd3
feat: set appropriate logging
JoshLoecker Jan 12, 2025
40cdfd4
feat: combine lines async file reading
JoshLoecker Jan 12, 2025
509ed96
feat: create Enum from rna types
JoshLoecker Jan 12, 2025
55c04d1
fix: use new RNA type enum
JoshLoecker Jan 12, 2025
d7ecd50
refactor: convert literals to Enums
JoshLoecker Jan 12, 2025
c69fd1a
fix: re-organize code
JoshLoecker Jan 12, 2025
189cfe5
fix: added dataclasses for simplification of data
JoshLoecker Jan 12, 2025
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
fc4ee6e
Fix ruff linting errors (#218)
JoshLoecker Oct 2, 2025
39e10f1
hotfix: log full name of directory if not found (#225)
JoshLoecker Oct 2, 2025
e94788c
Fix Single Cell Processing (#214)
JoshLoecker Oct 2, 2025
ae0c52b
Fix RNA-seq Processing and Boolean Activity Determination (#227)
JoshLoecker Oct 6, 2025
dfadcea
chore: move development dependencies to `dependency-groups.dev`
JoshLoecker Oct 6, 2025
3fe2dbf
Merge remote-tracking branch 'origin/develop' into fix-startup
JoshLoecker Oct 6, 2025
c8292ce
chore: merge imports
JoshLoecker Oct 6, 2025
894be61
chore: remove unused imports
JoshLoecker Oct 6, 2025
cd16b5f
chore: create explicit variable for `re.search()` call
JoshLoecker Oct 6, 2025
c07457e
chore: use `cast` for better type hints
JoshLoecker Oct 6, 2025
e6e7076
chore: expand docstring
JoshLoecker Oct 6, 2025
3ec6b1d
chore: expand docstring
JoshLoecker Oct 6, 2025
7294534
chore: ignore inheriting from `(str, enum.Enum)` instead of `enum.Str…
JoshLoecker Oct 6, 2025
f0ec80b
chore: expand docstring
JoshLoecker Oct 6, 2025
51bd8db
fix: initial fix for modifying sequence while iterating
JoshLoecker Oct 6, 2025
ce193d1
chore: use `|` for type union
JoshLoecker Oct 6, 2025
af5069d
chore: ruff formatting
JoshLoecker Oct 6, 2025
1283fdb
fix: use `[i]` to assign values instead of `.append()`
JoshLoecker Oct 6, 2025
833760b
fix: do not install on python 3.10
JoshLoecker Oct 6, 2025

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