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1b57280
style: formatting changes
iblacksand Sep 13, 2024
e53c78f
add documentation for extra-feature file
iblacksand Sep 18, 2024
fa90597
Add support for adding extra_feature_file
iblacksand Sep 18, 2024
bad4f6d
remove extra_file check
iblacksand Sep 18, 2024
a9927df
skip feature file check
iblacksand Sep 18, 2024
67ca6c5
upgrade version number to 0.1.21
iblacksand Sep 18, 2024
05b316d
diagnostic printing
iblacksand Sep 19, 2024
4cad093
Add extra_feature_file genes to all_valid_ids
iblacksand Sep 19, 2024
ed5bf9f
fix indent issue
iblacksand Sep 19, 2024
b22c47e
fix extra_file path
iblacksand Sep 19, 2024
262d580
fix function names problem
iblacksand Sep 19, 2024
dbc1479
Use df for merging extra features
iblacksand Sep 19, 2024
1fc6f15
don't drop missing column
iblacksand Sep 19, 2024
cfdf84d
diagnostic logging
iblacksand Sep 19, 2024
62ba8b9
Remove duplicate gene pairs in extra_features
iblacksand Sep 19, 2024
5691803
use merge instead of concat
iblacksand Sep 19, 2024
28b76b3
drop duplicates more explicitly
iblacksand Sep 19, 2024
e075c75
remove extra logs
iblacksand Sep 19, 2024
49441ac
Add LLR calculation and plotting for extra features
iblacksand Sep 19, 2024
74448da
Remove excess logging and fix llr parameters
iblacksand Sep 19, 2024
b885a86
fix return value
iblacksand Sep 19, 2024
077e066
skip edge count check for extra features
iblacksand Sep 20, 2024
157f64c
check if dataset is extra feature before checking type
iblacksand Sep 20, 2024
76f5223
Merge remote-tracking branch 'origin/main' into feat-extra-features
iblacksand Sep 20, 2024
998a418
Add back LLR calculation for extra features
iblacksand Sep 20, 2024
f6bb066
Process extra feature file once instead of multiple times
iblacksand Sep 25, 2024
2b1f630
Migrate project structure to use maturin for rust file import
iblacksand Sep 27, 2024
1a0db66
Allow funmap to be run as cli
iblacksand Sep 27, 2024
9e53478
formatting changes
iblacksand Sep 27, 2024
bc18d72
Add only_extra_features key to config
iblacksand Sep 27, 2024
000ae50
update to use latest packages
iblacksand Sep 30, 2024
29e8c14
fix processing of extra_feature_df
iblacksand Sep 30, 2024
46c5fa8
Add documentation and fix messages
iblacksand Oct 1, 2024
d34fc2c
add unique gene identification
iblacksand Oct 1, 2024
47dcd5e
add format error checking
iblacksand Oct 1, 2024
ca2d1f6
save uniq_gene to pkl file in output_folder
iblacksand Oct 2, 2024
4e850bc
start align_file function
iblacksand Oct 4, 2024
799f39b
fix rust compilation error
iblacksand Oct 4, 2024
c67e533
add code for calculating new_index for each feature file
iblacksand Oct 7, 2024
1af42a1
File creation
iblacksand Oct 8, 2024
6de0073
create index file
iblacksand Oct 8, 2024
289185d
Remove unnecessary file read
iblacksand Oct 8, 2024
a49d5ec
Use new feature_df creation
iblacksand Oct 10, 2024
3cab234
temporarily hard code paths
iblacksand Oct 10, 2024
457a0b1
better error messaging
iblacksand Oct 10, 2024
a4f0bc2
add extra_feature_folder to config creation
iblacksand Oct 10, 2024
0a478d3
rename variables
iblacksand Oct 10, 2024
7fa7c0b
fix naming
iblacksand Oct 10, 2024
ac7eb2f
add missing imports
iblacksand Oct 10, 2024
36ca663
fix function call
iblacksand Oct 10, 2024
61a80a0
fix reordering dataframe
iblacksand Oct 10, 2024
8279aec
logging
iblacksand Oct 10, 2024
a177b40
fix column names
iblacksand Oct 10, 2024
e90285d
fix return type
iblacksand Oct 10, 2024
4be7af8
build sqlite db for extra_features
iblacksand Oct 11, 2024
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181 changes: 181 additions & 0 deletions .github/workflows/CI.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,181 @@
# This file is autogenerated by maturin v1.7.4
# To update, run
#
# maturin generate-ci github
#
name: CI

on:
push:
branches:
- main
- master
tags:
- '*'
pull_request:
workflow_dispatch:

permissions:
contents: read

jobs:
linux:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: ubuntu-latest
target: x86_64
- runner: ubuntu-latest
target: x86
- runner: ubuntu-latest
target: aarch64
- runner: ubuntu-latest
target: armv7
- runner: ubuntu-latest
target: s390x
- runner: ubuntu-latest
target: ppc64le
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: 3.x
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist --find-interpreter
sccache: 'true'
manylinux: auto
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-linux-${{ matrix.platform.target }}
path: dist

musllinux:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: ubuntu-latest
target: x86_64
- runner: ubuntu-latest
target: x86
- runner: ubuntu-latest
target: aarch64
- runner: ubuntu-latest
target: armv7
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: 3.x
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist --find-interpreter
sccache: 'true'
manylinux: musllinux_1_2
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-musllinux-${{ matrix.platform.target }}
path: dist

windows:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: windows-latest
target: x64
- runner: windows-latest
target: x86
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: 3.x
architecture: ${{ matrix.platform.target }}
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist --find-interpreter
sccache: 'true'
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-windows-${{ matrix.platform.target }}
path: dist

macos:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: macos-12
target: x86_64
- runner: macos-14
target: aarch64
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: 3.x
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist --find-interpreter
sccache: 'true'
- name: Upload wheels
uses: actions/upload-artifact@v4
with:
name: wheels-macos-${{ matrix.platform.target }}
path: dist

sdist:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Build sdist
uses: PyO3/maturin-action@v1
with:
command: sdist
args: --out dist
- name: Upload sdist
uses: actions/upload-artifact@v4
with:
name: wheels-sdist
path: dist

release:
name: Release
runs-on: ubuntu-latest
if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
needs: [linux, musllinux, windows, macos, sdist]
permissions:
# Use to sign the release artifacts
id-token: write
# Used to upload release artifacts
contents: write
# Used to generate artifact attestation
attestations: write
steps:
- uses: actions/download-artifact@v4
- name: Generate artifact attestation
uses: actions/attest-build-provenance@v1
with:
subject-path: 'wheels-*/*'
- name: Publish to PyPI
if: "startsWith(github.ref, 'refs/tags/')"
uses: PyO3/maturin-action@v1
env:
MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
with:
command: upload
args: --non-interactive --skip-existing wheels-*/*
12 changes: 12 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -109,3 +109,15 @@ ENV/
.DS_Store
results
*old

# python generated files
__pycache__/
*.py[oc]
build/
dist/
wheels/
*.egg-info

# venv
.venv
test_data
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