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feat: add tinit #215

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279f7cc
feat: bring zfpkm_filter from rnaseq.py
JoshLoecker Dec 9, 2024
7e2fe3d
feat: added matrix builder
JoshLoecker Dec 9, 2024
9eaa2ac
feat: added tpm calculation
JoshLoecker Dec 9, 2024
3670016
feat: added fpkm calculation
JoshLoecker Dec 9, 2024
1cd4dbb
feat: added zfpkm transformation and calculation
JoshLoecker Dec 9, 2024
dd8698e
feat: added zfpkm plotting
JoshLoecker Dec 9, 2024
01db1ef
feat: aded calculate z score
JoshLoecker Dec 9, 2024
a47f752
feat: added cpm filtering
JoshLoecker Dec 9, 2024
b6460c2
feat: added tpm quantile filtering
JoshLoecker Dec 9, 2024
e0c98b4
feat: added root filtering logic
JoshLoecker Dec 9, 2024
a4d6f2f
feat: added logic for performing statistical tests
JoshLoecker Dec 9, 2024
e9665bf
feat: create metadata df
JoshLoecker Dec 9, 2024
dc7c1fe
refactor: allow passing specific filepaths
JoshLoecker Dec 9, 2024
f35e09a
refactor: rename variable names for easier reuse
JoshLoecker Dec 9, 2024
fc803bc
style: update log message, more pythonic code
JoshLoecker Dec 10, 2024
8bdddd9
style: variable rename
JoshLoecker Dec 10, 2024
e0d84be
feat: update to match new approach
JoshLoecker Dec 10, 2024
9674459
revert: use mrna instead of polya
JoshLoecker Dec 10, 2024
cde6606
refactor: check files returned
JoshLoecker Dec 10, 2024
b14d3f9
feat: allow specifying specific directories
JoshLoecker Dec 10, 2024
d52b0ee
style: use more descriptive variable names
JoshLoecker Dec 10, 2024
fe1d406
refactor: use early continue
JoshLoecker Dec 10, 2024
8f1d027
style: update warning messages
JoshLoecker Dec 10, 2024
0ef736e
style: rename variables
JoshLoecker Dec 10, 2024
3825aa2
refactor: move filtering technique to types
JoshLoecker Dec 10, 2024
b0fa60e
fix: do not use more cores than necessary
JoshLoecker Dec 10, 2024
911aaaa
Merge branch 'main' into develop
JoshLoecker Dec 11, 2024
2bfe760
Merge branch 'main' into develop
JoshLoecker Dec 11, 2024
9539711
chore: merge dependabot updates into hotfix
JoshLoecker Dec 11, 2024
06403a4
Merge branch 'main' into hotfix
JoshLoecker Dec 11, 2024
40344dc
Merge pull request #204 from HelikarLab/hotfix
JoshLoecker Dec 11, 2024
f8ebcbf
Merge branch 'develop' into remove-hardcoded-paths/rnaseq-gen
JoshLoecker Dec 11, 2024
6bd06e1
fix: use parenthesis to validate calculations
JoshLoecker Dec 11, 2024
f24347d
refactor: ignore missing variables for now
JoshLoecker Dec 11, 2024
1956721
chore: ignore complex function
JoshLoecker Dec 11, 2024
179c673
Merge pull request #199 from HelikarLab/remove-hardcoded-paths/rnaseq…
JoshLoecker Dec 11, 2024
65bd2a3
chore: remove unused imports
JoshLoecker Dec 11, 2024
3cc9bec
refactor: remove command line interface
JoshLoecker Dec 11, 2024
0f9bd3a
feat: process input data more pythonically
JoshLoecker Dec 11, 2024
1402016
refactor: do not use hardcoded filepaths
JoshLoecker Dec 11, 2024
450c9e9
chore: ruff formatting
JoshLoecker Dec 11, 2024
01b31df
style: use better variable name & reorganize
JoshLoecker Dec 11, 2024
06e0932
feat: process the provided file paths
JoshLoecker Dec 11, 2024
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
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1 change: 1 addition & 0 deletions .github/dependabot.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
target-branch: "hotfix"
schedule:
# Check for updates to GitHub Actions every weekday
interval: "daily"
10 changes: 2 additions & 8 deletions .github/workflows/continuous_integration.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,8 @@ jobs:
- name: Install uv
uses: astral-sh/setup-uv@v4

- name: Create Virtual Environment
run: uv venv

- name: Install Jupyter
run: uv pip install jupyter nbconvert

- name: Strip Notebook Output
run: uv run jupyter nbconvert --clear-output --inplace "main/COMO.ipynb"
run: uv tool run --from nbconvert jupyter-nbconvert --clear-output --inplace "main/COMO.ipynb"

- name: Format Python Imports
uses: astral-sh/ruff-action@v2
Expand Down Expand Up @@ -62,7 +56,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [ "3.10" ]
python-version: [ "3.10", "3.11", "3.12" ]
steps:
- name: Checkout
uses: actions/checkout@v4
Expand Down
10 changes: 4 additions & 6 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/opensource-nepal/commitlint
rev: v1.2.0
- repo: https://github.com/commitizen-tools/commitizen
rev: master
hooks:
- id: commitlint
name: Commit Lint
- id: commitizen
stages: [ commit-msg ]
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