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Integration of Percolator node #13

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Merged
StSchulze merged 29 commits into from
Nov 6, 2026
Merged

Integration of Percolator node #13

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754df88
Added the instanovo parser, need to add test and fix ruff errors
cal3502 Jun 29, 2026
828e229
Added instanovo parser with tests
cal3502 Jun 30, 2026
b3eb349
Added relevant uftypes
cal3502 Jun 30, 2026
3db88da
Updated pyproject to include Instanovo
cal3502 Jun 30, 2026
84e538b
Fixed ruff errors
cal3502 Jun 30, 2026
59429dd
Updated pyproject to include flowkit to fix a dependency error
cal3502 Jun 30, 2026
76bd370
Removoed flowkit due to package discrepencies
cal3502 Jun 30, 2026
eeeb6dc
Removed Instanovo due to package discrepencies
cal3502 Jun 30, 2026
8648d28
Updated Uftypes
cal3502 Jun 30, 2026
56a532d
Added tests to test instanovo
cal3502 Jun 30, 2026
ac54bc6
Changed Instanovo pytest to better check that the unode is actually a…
cal3502 Jun 30, 2026
ee56838
Changes to test file to check the command line and unode to allow com…
cal3502 Jul 7, 2026
bf440ad
Added percolator unode and tests
cal3502 Jul 7, 2026
cc53c34
Changes to unode and tests
cal3502 Jul 8, 2026
262b19a
Added recources and modified unode to make sure test works, will most…
cal3502 Jul 8, 2026
5b9989c
Changes to delete rows that do not have an is_decoy value
cal3502 Jul 15, 2026
9f0f794
Changes to ruff formatting and inclusion of Percolator LICENSE.txt
cal3502 Jul 15, 2026
e6f8a46
Renamed Percolator unode and test file
cal3502 Jul 15, 2026
f7ce044
Deleted pycaches
cal3502 Jul 15, 2026
bd02cc9
Changed percolator unode in order to better fit with current urgap st…
cal3502 Oct 8, 2026
92a7065
Made a more robust percolator test
cal3502 Nov 6, 2026
e92dca1
Merge remote-tracking branch 'origin/main' into feature/percolator
cal3502 Nov 6, 2026
5a5dc38
Update main.yaml
StSchulze Nov 6, 2026
f25a314
Update main.yaml
StSchulze Nov 6, 2026
0f37734
Update test_percolator.py
StSchulze Nov 6, 2026
9593ec2
Update percolator_3_7_1.py
StSchulze Nov 6, 2026
c36f3f3
Update percolator_3_7_1.py
StSchulze Nov 6, 2026
73214e9
Update percolator_3_7_1.py
StSchulze Nov 6, 2026
0a4afb6
Removed unified csvs as they were not needed and moved percolator lis…
cal3502 Nov 6, 2026
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8 changes: 2 additions & 6 deletions .github/workflows/main.yaml
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Expand Up @@ -68,12 +68,8 @@ jobs:
run: java -version
- name: Install Mono
run: |
sudo apt update
sudo apt install -y dirmngr gnupg apt-transport-https ca-certificates
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF
echo "deb https://download.mono-project.com/repo/ubuntu stable-focal main" | sudo tee /etc/apt/sources.list.d/mono-official-stable.list
sudo apt update
sudo apt install -y mono-complete
sudo apt-get update
sudo apt-get install -y mono-complete
- name: Verify Mono installation
run: mono --version
- name: Run integration tests
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