Feature/streaming fix windows

.github/workflows/tests.yml

@@ -22,26 +22,23 @@ jobs:
         experimental: [false,]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov wheel
-        pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      run: uv sync --all-extras --dev
+
     - name: Run unit and system tests
       run: |
-        pytest -v --cov=mokapot tests/
+        uv run pytest -v --cov=mokapot tests/
+
     - name: Upload coverage to codecov
       uses: codecov/codecov-action@v3
       with:

mokapot/brew.py

@@ -228,8 +228,8 @@ def brew(
                     max_workers=max_workers,
                 )
             )
-    # If model training has failed
     else:
+        logging.info("Model training failed. Setting scores to zero.")
         scores = [np.zeros(x) for x in data_size]
     # Find which is best: the learned model, the best feature, or
     # a pretrained model.
@@ -540,6 +540,7 @@ def _fit_model(train_set, psms, model, fold):
         model.fit(train_set)
     except RuntimeError as msg:
         if str(msg) != "Model performs worse after training.":
+            LOGGER.info(f"Fold {fold + 1}: {msg}")
             raise
 
         if model.is_trained:

mokapot/brew_rollup.py

@@ -25,8 +25,10 @@ def parse_arguments(main_args):
     # todo: we should update this copyright notice asap
     desc = (
         f"mokapot version {__version__}.\n"
-        "Written by William E. Fondrie ([email protected]) while in the \n"
+        "Originally written by William E. Fondrie ([email protected]) while in the \n"
         "Department of Genome Sciences at the University of Washington.\n\n"
+        "Extended by Samia Ben Fredj, Elmar Zander, Vishal Sukumar and \n"
+        "Siegfried Gessulat while at MSAID. \n\n"
         "Official code website: https://github.com/wfondrie/mokapot\n\n"
         "More documentation and examples: https://mokapot.readthedocs.io"
     )

mokapot/model.py

@@ -326,6 +326,7 @@ def fit(self, dataset: LinearPsmDataset):
             if num_passed[i] == 0:
                 raise RuntimeError("Model performs worse after training.")
 
+
         # If the model performs worse than what was initialized:
         if (
             num_passed[-1] < (start_labels == 1).sum()

mokapot/mokapot.py

@@ -42,6 +42,8 @@ def main(main_args=None):
         level=verbosity_dict[config.verbosity],
     )
     logging.captureWarnings(True)
+    numba_logger = logging.getLogger('numba')
+    numba_logger.setLevel(logging.WARNING)
 
     # Suppress warning if asked for
     if config.suppress_warnings:

pyproject.toml

@@ -50,10 +50,15 @@ docs = [
     "ipykernel>=5.3.0",
     "recommonmark>=0.5.0",
 ]
-dev = [
+
+[tool.uv]
+dev-dependencies = [
     "pre-commit>=2.7.1",
     "ruff>=0.4.4",
     "pytest>=8.2.2",
+    "flake8>=7.1.1",
+    "wheel>=0.44.0",
+    "pytest-cov>=5.0.0"
 ]
 
 [project.scripts]

tests/helpers/cli.py

@@ -102,7 +102,7 @@ def _run_cli(
     params = flatten(params)
     params = [str(param) for param in params]
     if run_in_subprocess:
-        cmd = ["python", "-m", module] + params
+        cmd = ["uv", "run", "python", "-m", module] + params
         try:
             res = subprocess.run(
                 cmd, check=True, capture_output=capture_output

tests/system_tests/test_cli.py

@@ -30,7 +30,7 @@ def phospho_files():
 
 def test_basic_cli(tmp_path, scope_files):
     """Test that basic cli works."""
-    params = [scope_files[0], "--dest_dir", tmp_path]
+    params = [scope_files[0], "--dest_dir", tmp_path, "--verbosity", 3]
     run_mokapot_cli(params)
     assert file_approx_len(tmp_path, "targets.psms.csv", 5487)
     assert file_approx_len(tmp_path, "targets.peptides.csv", 5183)