Merge branch 'reSub-v1' into reSub/nuc-threshold

Author: mfs4rd

.github/workflows/ci.yml

@@ -0,0 +1,20 @@
+name: CI
+
+on: [push, workflow_dispatch]
+
+jobs:
+  lock-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@94a823180e06fcde4ad29308721954a521c96ed0 # v4.4
+      - run: pdm lock --check
+  requirements-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@94a823180e06fcde4ad29308721954a521c96ed0 # v4.4
+      - run: pdm export -f requirements -o new_requirements.txt
+      - run: diff requirements.txt new_requirements.txt

EMT_data_analysis/figure_generation/colony_mask.py

@@ -245,12 +245,8 @@ def cgal_vertices_faces_triangle_mesh(Q: Polyhedron_3):
     )
 
     args = parser.parse_args()
-<<<<<<< HEAD
     if args.data_id is None:
         for data_id in const.EXAMPLE_ACM_IDS:
             main(data_id, args.output_directory)
     else:
         main(args.data_id, args.output_directory)
-=======
-    main(args.manifest_path, args.feature_path, args.movie_id, args.output_directory)
->>>>>>> 51c2829 (Remove typo)

README.md

@@ -17,9 +17,11 @@ sudo apt-get install libxml2-dev libxslt-dev python-dev
 ```bash
 python -m venv venv
 source venv/bin/activate
-pip install -e .
+pip install -r requirements.txt
 ```
 
+(Alternatively, if you have `pdm`, you can run `pdm sync`.)
+
 # How to run:
 
 ## 1 - Feature extraction