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Fix Startup Components #226

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4baf95a
feat: write to provided filepath
JoshLoecker Dec 11, 2024
9f97001
refactor: remove hardcoded filepaths
JoshLoecker Dec 11, 2024
bfe8d7e
refactor: pythonic approach to processing
JoshLoecker Dec 11, 2024
c401696
fix: arguments to write data
JoshLoecker Dec 11, 2024
870cdb9
Merge pull request #205 from HelikarLab/remove-hardcoded-paths/proteo…
JoshLoecker Dec 11, 2024
93ac383
Merge branch 'main' of github.com:HelikarLab/COMO into remove-hardcod…
JoshLoecker Dec 11, 2024
c7da971
feat: allow specifiying files to process
JoshLoecker Dec 11, 2024
4c381ca
fix: no longer require rna processing type
JoshLoecker Dec 11, 2024
e30b3cf
Merge pull request #206 from HelikarLab/remove-hardcoded-paths/proteo…
JoshLoecker Dec 11, 2024
bb880c0
Merge branch 'main' into develop
JoshLoecker Dec 11, 2024
5baf606
Merge branch 'main' into develop
JoshLoecker Dec 11, 2024
7543065
feat: add gurobi as an optional dependency
JoshLoecker Dec 12, 2024
875d0a4
fix: import the correct variable
JoshLoecker Dec 13, 2024
0c0d991
fix: divide by zero error; grouping too many items
JoshLoecker Dec 13, 2024
fdb66dc
style: rearrange code
JoshLoecker Dec 17, 2024
43afd4f
refactor: remove command line interface
JoshLoecker Dec 17, 2024
ad6e68d
feat: use MyGene instead of BioDBNet
JoshLoecker Dec 17, 2024
59e4cfe
refactor: import required modules
JoshLoecker Dec 17, 2024
7a028f9
style: use pythonic variable names
JoshLoecker Dec 17, 2024
35de93e
refactor: remove encompassing for loop
JoshLoecker Dec 17, 2024
3adf9c6
refactor: do not drop/set index
JoshLoecker Dec 17, 2024
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
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
c64d2d0
style: format code, Jupyter Notebook(s), and Python imports with `ruff`
JoshLoecker Jun 3, 2025
cb6fbe7
feat: added sanity checks from MATLAB CobraToolbox
SarahNakamura Jul 8, 2025
1557654
fix: issues with clean installation
SarahNakamura Jul 8, 2025
526615f
refactor: set reference model objective
SarahNakamura Jul 8, 2025
3852f86
fix: use correct method to merge z_matrices
SarahNakamura Jul 8, 2025
9732446
fix: use 'Reaction' instead of 'Boundary'
SarahNakamura Jul 8, 2025
5e1dce7
feat: create sanity check package
SarahNakamura Jul 8, 2025
f44db1f
refactor: make new function for ensuring metabolite exists; use Path …
SarahNakamura Jul 8, 2025
12282f8
chore: use github permalink for matlab source code
SarahNakamura Jul 8, 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
85b709e
Merge remote-tracking branch 'origin/develop' into startup-fixed
JoshLoecker Oct 2, 2025
857f2e9
style(ruff): ruff formatting
JoshLoecker Oct 2, 2025
a0e4d38
style(ruff): ignore unfixable lint errors
JoshLoecker Oct 2, 2025
a8fc5bb
fix(ruff): remove unused variable (RUF059)
JoshLoecker Oct 2, 2025
e8dc71f
style(ruff): set `strict=True` for `zip()` (B905)
JoshLoecker Oct 2, 2025
f90fe03
style: format code, Jupyter Notebook(s), and Python imports with `ruff`
JoshLoecker Oct 2, 2025
b975c5a
chore: retrigger checks
JoshLoecker Oct 2, 2025
48f5a3e
chore(pyproject): bump maximum python version
JoshLoecker Oct 2, 2025
4298e7f
refactor(cobra_sanity_check): improve code structure and readability
JoshLoecker Oct 2, 2025
fdfadea
refactor(fast-leak-test): rename file and improve function signatures…
JoshLoecker Oct 2, 2025
9ff64f3
refactor: use improved fast_leak_test function
JoshLoecker Oct 2, 2025
1211220
fix(ruff): linting errors
JoshLoecker Oct 2, 2025
58653d9
chore: update uv.lock
JoshLoecker Oct 2, 2025

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