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pull main in spectrum-feature-generator #177

Merged
merged 12 commits into from
Aug 16, 2024
Merged
42 changes: 41 additions & 1 deletion .github/workflows/publish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ jobs:
- name: Install package and dependencies
run: |
python -m pip install --upgrade pip
pip install --only-binary :all: . pyinstaller
pip install --only-binary :all: .[ionmob] pyinstaller

- name: Install Inno Setup
uses: crazy-max/ghaction-chocolatey@v3
Expand Down Expand Up @@ -83,3 +83,43 @@ jobs:
tag: ${{ github.ref }}
file_glob: true
file: dist/*.exe

docker-image:
runs-on: ubuntu-latest
permissions:
packages: write
contents: read
attestations: write
id-token: write
steps:
- name: Check out the repo
uses: actions/checkout@v4

- name: Log in to the Container registry
uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}

- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
with:
images: ghcr.io/${{ github.repository }}

- name: Build and push Docker images
id: push
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
with:
context: .
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}

- name: Generate artifact attestation
uses: actions/attest-build-provenance@v1
with:
subject-name: ghcr.io/${{ github.repository }}
subject-digest: ${{ steps.push.outputs.digest }}
push-to-registry: true
2 changes: 1 addition & 1 deletion .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ jobs:
- name: Install package and dependencies
run: |
python -m pip install --upgrade pip
pip install --only-binary :all: . pyinstaller
pip install --only-binary :all: .[ionmob] pyinstaller

- name: Install Inno Setup
uses: crazy-max/ghaction-chocolatey@v1
Expand Down
3 changes: 3 additions & 0 deletions ms2rescore.spec
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ project = "ms2rescore"
bundle_name = "ms2rescore"
bundle_identifier = f"{bundle_name}.{__version__}"

extra_requirements = {"ionmob"}

# Requirements config
skip_requirements_regex = r"^(?:.*\..*)"

Expand All @@ -28,6 +30,7 @@ requirements = {
if "; extra ==" not in req # Exclude optional dependencies
}
requirements.update([project, "xgboost"])
requirements.update(extra_requirements)

hidden_imports = set()
datas = []
Expand Down
2 changes: 1 addition & 1 deletion ms2rescore/__init__.py
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs."""

__version__ = "3.1.0"
__version__ = "3.1.1"

from warnings import filterwarnings

Expand Down
3 changes: 3 additions & 0 deletions ms2rescore/gui/app.py
Original file line number Diff line number Diff line change
Expand Up @@ -383,6 +383,9 @@ def get(self) -> Dict:
config["deeplc"] = deeplc_config
if ionmob_enabled:
config["ionmob"] = ionmob_config
if im2deep_enabled:
config["im2deep"] = im2deep_config

return config


Expand Down
2 changes: 1 addition & 1 deletion ms2rescore/rescoring_engines/percolator.py
Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ def rescore(
"decoy-results-proteins": output_file_root + ".percolator.decoy.proteins.pout",
"weights": output_file_root + ".percolator.weights.tsv",
"verbose": LOG_LEVEL_MAP[log_level],
"num-threads": processes,
"num-threads": min(processes, 128), # Higher values not supported by Percolator
"post-processing-tdc": True,
}
if percolator_kwargs:
Expand Down
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