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b24c202
merge
PascalIversen Nov 26, 2024
6009eed
new crit difference plot
PascalIversen Nov 26, 2024
9a264ac
scikit posthocs dependency
PascalIversen Nov 26, 2024
033b92f
pyproject dependency posthoc updated
PascalIversen Nov 26, 2024
7db3fb5
peotry lock
PascalIversen Nov 26, 2024
29fa969
Merge branch 'fixing_vis' of github.com:daisybio/drevalpy into fixing…
JudithBernett Dec 12, 2024
43aaf8a
updating vis branch
JudithBernett Dec 12, 2024
4edfaa1
Merge branch 'development' into fixing_vis
JudithBernett Feb 27, 2025
a79b28a
replace group-wise normalization with effect normalization
JudithBernett Mar 4, 2025
e38536d
Merge branch 'DIPK_fix_genes_for_cs' into fixing_vis
JudithBernett Mar 5, 2025
f3194ef
Merge branch 'development' into fixing_vis
JudithBernett Mar 11, 2025
ae11c0b
updating poetry lock
JudithBernett Mar 11, 2025
b319d11
removed partial correlation from tests
JudithBernett Mar 12, 2025
0b44db7
adjustments for visualization. Attention: not bug free
JudithBernett Mar 18, 2025
4df9ce5
fixed labels and added SSMD
PascalIversen Mar 18, 2025
2217320
size and label change
PascalIversen Mar 19, 2025
29712c4
standard errors part of the plots
PascalIversen Mar 19, 2025
2593049
add MSE SSMD and sort according to max SSMD
PascalIversen Mar 19, 2025
71ba908
cross study evaluation - unfinished
PascalIversen Mar 20, 2025
5e316a4
cs_tables work now.
PascalIversen Mar 21, 2025
d8ecb4b
minor visual fixes and saving cross study evaluation data
PascalIversen Mar 21, 2025
0a98262
refractoring and normalized metrics
PascalIversen Mar 21, 2025
2853953
Merge branch 'fixing_vis' of github.com:daisybio/drevalpy into fixing…
JudithBernett Mar 21, 2025
206227b
decluttering
PascalIversen Mar 21, 2025
71f9300
Merge branch 'fixing_vis' of github.com:daisybio/drevalpy into fixing…
JudithBernett Mar 21, 2025
21e88d9
new normalized regression sliders
JudithBernett Mar 21, 2025
8531e8c
fixed slider
JudithBernett Mar 21, 2025
d8476c4
fixed slider pt 2
JudithBernett Mar 21, 2025
9743287
computing normalized metrics
JudithBernett Mar 28, 2025
77e2a0a
adding result path
JudithBernett Mar 28, 2025
0c06b3e
updated feature documentation
JudithBernett Apr 14, 2025
7362be8
various fixes to visualization
JudithBernett Apr 16, 2025
2d723b3
Merge remote-tracking branch 'origin/development' into fixing_vis
JudithBernett Apr 16, 2025
17aecbb
fixing mypy and typeguard
JudithBernett Apr 16, 2025
0f4f341
moved functions to visualization.utils
JudithBernett Apr 16, 2025
a6a252f
changed return type from list to numpy array
JudithBernett Apr 16, 2025
68bf20d
adapted tests for more coverage
JudithBernett Apr 17, 2025
68e8b09
fixed mypy error
JudithBernett Apr 17, 2025
c5ebf5a
new versions, new safety check
JudithBernett Apr 17, 2025
dd23eab
Merge remote-tracking branch 'origin/development' into fixing_vis
JudithBernett Apr 17, 2025
ac28ab9
removed ray for safety
JudithBernett Apr 17, 2025
0e7b1a8
new design
JudithBernett Apr 17, 2025
b8b363b
added drug name and cellosaurus id to the result files and to the plots
JudithBernett Apr 17, 2025
cd773ff
forgot to push this change to create_report
JudithBernett Apr 17, 2025
d4aa8d7
swapping lco, ldo
JudithBernett Apr 17, 2025
a109833
fixed mypy and test_run_suite
JudithBernett Apr 23, 2025
a3ef5ca
new versions
JudithBernett Apr 23, 2025
666a80c
typo
PascalIversen Apr 23, 2025
44d5973
addressing @PascalIversen 's comments
JudithBernett Apr 23, 2025
522b3fd
Merge branch 'fixing_vis' of github.com:daisybio/drevalpy into fixing…
JudithBernett Apr 23, 2025
43cec75
changed argument back
JudithBernett Apr 23, 2025
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15 changes: 7 additions & 8 deletions .github/workflows/run_tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,13 @@ jobs:
fail-fast: false
matrix:
include:
- { python-version: "3.11", os: ubuntu-latest, session: "pre-commit" }
- { python-version: "3.11", os: ubuntu-latest, session: "safety" }
- { python-version: "3.11", os: ubuntu-latest, session: "mypy" }
- { python-version: "3.11", os: ubuntu-latest, session: "tests" }
- { python-version: "3.11", os: windows-latest, session: "tests" }
- { python-version: "3.11", os: ubuntu-latest, session: "typeguard" }
- { python-version: "3.11", os: ubuntu-latest, session: "xdoctest" }
- { python-version: "3.11", os: ubuntu-latest, session: "docs-build" }
- { python-version: "3.12", os: ubuntu-latest, session: "pre-commit" }
- { python-version: "3.12", os: ubuntu-latest, session: "mypy" }
- { python-version: "3.12", os: ubuntu-latest, session: "tests" }
- { python-version: "3.12", os: windows-latest, session: "tests" }
- { python-version: "3.12", os: ubuntu-latest, session: "typeguard" }
- { python-version: "3.12", os: ubuntu-latest, session: "xdoctest" }
- { python-version: "3.12", os: ubuntu-latest, session: "docs-build" }

env:
NOXSESSION: ${{ matrix.session }}
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15 changes: 15 additions & 0 deletions .github/workflows/safety_scan.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
name: Safety Action

on:
push: # Run on every push to any branch
pull_request: # Run on new pull requests

jobs:
security:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@main
- name: Run Safety CLI to check for vulnerabilities
uses: pyupio/safety-action@v1
with:
api-key: ${{ secrets.SAFETY_API_KEY }}
11 changes: 11 additions & 0 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,17 @@ DrEvalPy: Python Cancer Cell Line Drug Response Prediction Suite
:target: https://github.com/psf/black
:alt: Black

Origin story
*Long ago, the people of science lived in harmony. Researchers collaborated, data flowed freely, and models were tested with integrity.
But then, the H-Index Nation attacked.
Suddenly, impact factors ruled all, flashy results overshadowed rigorous testing, and biased benchmarks spread like wildfire. Science, once a beacon of knowledge, became clouded by competition and questionable practices.
Only a fair and unbiased framework could restore balance.
And when the field needed it most—drevalpy was born.
A framework designed to test drug response prediction models with fairness and transparency, cutting through bias and restoring the integrity of scientific evaluation.
Though the fight against bad practices is long, with drevalpy, balance may yet be restored.*



Focus on Innovating Your Models — DrEval Handles the Rest!
- DrEval is a toolkit that ensures drug response prediction evaluations are statistically sound, biologically meaningful, and reproducible.
- Focus on model innovation while using our automated standardized evaluation protocols and preprocessing workflows.
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