Upgrade packages and clean a bit

.github/workflows/build.yml

@@ -6,13 +6,13 @@ jobs:
   build:
     runs-on: self-hosted
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install dependencies
       run: poetry install --no-root
     - name: Build figures
       run: make all -j 6
     - name: Upload files
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: files
         path: output/*.svg

.github/workflows/pytest.yml

@@ -9,15 +9,15 @@ jobs:
   build:
     runs-on: self-hosted
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup submodule
       run: git submodule update --init --recursive
     - name: Install dependencies
       run: poetry install --no-root
     - name: Test with pytest
       run: poetry run pytest --cov=lineage --cov-report=xml --cov-config=.github/workflows/coveragerc
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests

lineage/import_lineage.py

@@ -87,9 +87,8 @@ def assign_observs_AU565(cell: CellVar, lineage, uniq_id: int) -> CellVar:
     cell.obs = np.array([1, 0, 0, 0], dtype=float)
     parent_id = lineage["parentTrackId"].unique()
     # cell fate: die = 0, divide = 1
-    if not (
-        uniq_id in parent_id
-    ):  # if the cell has not divided, means either died or reached experiment end time
+    # if the cell has not divided, means either died or reached experiment end time
+    if uniq_id not in parent_id:
         if (
             np.max(lineage.loc[lineage["trackId"] == uniq_id]["frame"]) == 49
         ):  # means reached end of experiment

lineage/states/stateCommon.py

@@ -115,5 +115,5 @@ def gamma_estimator(
             constraints=linc,
         )
 
-    assert res.success or ("maximum number of function evaluations" in res.message)
+    assert res.success
     return np.exp(res.x)