ci,fix: fixed confidence out and ci migration

.github/workflows/docker.yml

@@ -16,26 +16,24 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
 
-      - name: Install build dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel build
+      - name: Set up Python
+        run: uv python install
 
-      - name: Build and publish
-        run: |
-          python -m build --wheel .
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
+      - name: Test-build the Docker image
+        run: make build-docker
+
       - name: Login to the GitHub Container Registry
         uses: docker/login-action@v3
         with:

.github/workflows/publish.yml

@@ -10,18 +10,22 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: '3.12'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine build
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
       - name: Build and publish
         env:
           TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
-          python -m build --sdist --wheel .
+          make build-sdist
+          make build-wheel
           twine upload dist/*

.github/workflows/tests.yml

@@ -26,6 +26,8 @@ jobs:
 
       - name: Install uv
         uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -40,3 +42,6 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
+
+      - name: Check Build
+        run: make build

Makefile

@@ -12,15 +12,19 @@ unit-test:
 check: ruff-lint format pre-commit
 	@echo "All checks passed"
 
-build: build-wheel build-docker
+build: build-wheel build-sdist build-docker
 	@echo "Build completed"
 
 build-wheel:
 	uv run --with build python -m build --wheel .
 
+build-sdist:
+	uv run --with build python -m build --sdist .
+
 build-docker:
 	uv run --with build python -m build --wheel --outdir dist .
 	docker build -t $(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG) .
+	docker run --rm -it $(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG) mokapot --help
 
 pre-commit:
 	pre-commit run --all-files

mokapot/confidence.py

@@ -244,7 +244,7 @@ def assign_confidence(
     qvalue_algorithm="tdc",
     sqlite_path=None,
     stream_confidence=False,
-):
+) -> list[Confidence]:
     """Assign confidence to PSMs peptides, and optionally, proteins.
 
     Parameters
@@ -283,8 +283,11 @@ def assign_confidence(
 
     Returns
     -------
-    None
+    list[Confidence]
     """
+
+    # Note: I am really not a big fan of how large this function is ...
+    # JSPP 2024-12-05
     is_sqlite = sqlite_path is not None
 
     if dest_dir is None:
@@ -368,6 +371,8 @@ def create_output_writer(path: Path, level: str, initialize: bool):
     if prefixes is None:
         prefixes = [None] * len(datasets)
 
+    out = []
+
     for dataset, score, prefix in zip(datasets, scores_list, prefixes):
         # todo: nice to have: move this column renaming stuff into the
         #   column defs module, and further, have standardized columns
@@ -507,7 +512,7 @@ def hash_data_row(data_row):
                 else:
                     LOGGER.info(f"\t- Found {count} unique {level}.")
 
-        out = Confidence(
+        con = Confidence(
             dataset=dataset,
             levels=levels_or_proteins,
             level_paths=level_data_path,
@@ -523,10 +528,11 @@ def hash_data_row(data_row):
             stream_confidence=stream_confidence,
             score_stats=score_stats,
         )
+        out.append(con)
         if not prefix:
             append_to_output_file = True
 
-        return out
+    return out
 
 
 @contextmanager