Merge pull request #37 from EliHei2/run-precommit

run-precommit

.github/ISSUE_TEMPLATE/➕-performance-improvement.md

@@ -1,10 +1,9 @@
 ---
 name: "➕ Performance Improvement"
 about: Suggest an improvement in the performance
-title: ''
-labels: ''
+title: ""
+labels: ""
 assignees: andrewmoorman, EliHei2
-
 ---
 
 **Describe the issue with the current implementation**

.github/ISSUE_TEMPLATE/🐛-bug-report.md

@@ -2,12 +2,12 @@
 name: "\U0001F41B Bug Report"
 about: Create a report to help us improve
 title: "[BUG]"
-labels: ''
+labels: ""
 assignees: andrewmoorman, EliHei2
-
 ---
 
 ---
+
 name: Bug Report
 about: Report a bug or unexpected behavior
 title: "[BUG] "
@@ -21,6 +21,7 @@ A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
@@ -33,6 +34,7 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots or logs to help explain your problem.
 
 **Environment (please complete the following information):**
+
 - OS: [e.g. macOS, Windows, Linux]
 - Python version: [e.g. 3.9]
 - Package version: [e.g. 1.2.3]

.github/ISSUE_TEMPLATE/🚀-feature-request.md

@@ -1,10 +1,9 @@
 ---
 name: "\U0001F680 Feature Request"
 about: Suggest an idea for this project
-title: ''
-labels: ''
-assignees: ''
-
+title: ""
+labels: ""
+assignees: ""
 ---
 
 **Is your feature request related to a problem? Please describe.**

.github/workflows/python-publish.yml

@@ -17,23 +17,22 @@ permissions:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/static.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Install package and documentation dependencies
         run: |

.pre-commit-config.yaml

@@ -1,22 +1,22 @@
 fail_fast: false
 default_language_version:
-    python: python3
+  python: python3
 default_stages:
-    - commit
-    - push
+  - commit
+  - push
 minimum_pre_commit_version: 2.16.0
 ci:
-    skip: []
+  skip: []
 repos:
-    - repo: https://github.com/psf/black
-      rev: 24.8.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
-      hooks:
-          - id: prettier
-    - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
-      hooks:
-          - id: blacken-docs
+  - repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.18.0
+    hooks:
+      - id: blacken-docs

.scripts/create_dataset.py

@@ -30,9 +30,7 @@ def main(args):
     download_file(transcripts_url, transcripts_path)
     download_file(nuclei_url, nuclei_path)
 
-    xs = XeniumSample().load_transcripts(
-        path=transcripts_path, min_qv=args.min_qv
-    )
+    xs = XeniumSample().load_transcripts(path=transcripts_path, min_qv=args.min_qv)
     xs.load_nuclei(path=nuclei_path)
 
     if args.parallel:
@@ -83,9 +81,7 @@ def main(args):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Create dataset from Xenium Human Pancreatic data."
-    )
+    parser = argparse.ArgumentParser(description="Create dataset from Xenium Human Pancreatic data.")
     parser.add_argument(
         "--raw_data_dir",
         type=str,
@@ -104,9 +100,7 @@ def main(args):
         required=True,
         help="URL for transcripts data.",
     )
-    parser.add_argument(
-        "--nuclei_url", type=str, required=True, help="URL for nuclei data."
-    )
+    parser.add_argument("--nuclei_url", type=str, required=True, help="URL for nuclei data.")
     parser.add_argument(
         "--min_qv",
         type=int,
@@ -125,21 +119,11 @@ def main(args):
         default=180,
         help="Step size in y direction for tiles.",
     )
-    parser.add_argument(
-        "--x_size", type=int, default=200, help="Width of each tile."
-    )
-    parser.add_argument(
-        "--y_size", type=int, default=200, help="Height of each tile."
-    )
-    parser.add_argument(
-        "--margin_x", type=int, default=None, help="Margin in x direction."
-    )
-    parser.add_argument(
-        "--margin_y", type=int, default=None, help="Margin in y direction."
-    )
-    parser.add_argument(
-        "--r_tx", type=int, default=3, help="Radius for building the graph."
-    )
+    parser.add_argument("--x_size", type=int, default=200, help="Width of each tile.")
+    parser.add_argument("--y_size", type=int, default=200, help="Height of each tile.")
+    parser.add_argument("--margin_x", type=int, default=None, help="Margin in x direction.")
+    parser.add_argument("--margin_y", type=int, default=None, help="Margin in y direction.")
+    parser.add_argument("--r_tx", type=int, default=3, help="Radius for building the graph.")
     parser.add_argument(
         "--val_prob",
         type=float,
@@ -158,9 +142,7 @@ def main(args):
         default=3,
         help="Number of nearest neighbors for nuclei.",
     )
-    parser.add_argument(
-        "--dist_nc", type=int, default=10, help="Distance threshold for nuclei."
-    )
+    parser.add_argument("--dist_nc", type=int, default=10, help="Distance threshold for nuclei.")
     parser.add_argument(
         "--k_tx",
         type=int,
@@ -179,12 +161,8 @@ def main(args):
         default=True,
         help="Whether to compute edge labels.",
     )
-    parser.add_argument(
-        "--sampling_rate", type=float, default=1, help="Rate of sampling tiles."
-    )
-    parser.add_argument(
-        "--parallel", action="store_true", help="Use parallel processing."
-    )
+    parser.add_argument("--sampling_rate", type=float, default=1, help="Rate of sampling tiles.")
+    parser.add_argument("--parallel", action="store_true", help="Use parallel processing.")
     parser.add_argument(
         "--num_workers",
         type=int,

.scripts/predict.py

@@ -30,9 +30,7 @@ def main(args: argparse.Namespace) -> None:
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Predict using the Segger model"
-    )
+    parser = argparse.ArgumentParser(description="Predict using the Segger model")
     parser.add_argument(
         "--dataset_path",
         type=str,
@@ -51,24 +49,16 @@ def main(args: argparse.Namespace) -> None:
         required=True,
         help="Path to the model checkpoint",
     )
-    parser.add_argument(
-        "--init_emb", type=int, default=8, help="Initial embedding size"
-    )
+    parser.add_argument("--init_emb", type=int, default=8, help="Initial embedding size")
     parser.add_argument(
         "--hidden_channels",
         type=int,
         default=64,
         help="Number of hidden channels",
     )
-    parser.add_argument(
-        "--out_channels", type=int, default=16, help="Number of output channels"
-    )
-    parser.add_argument(
-        "--heads", type=int, default=4, help="Number of attention heads"
-    )
-    parser.add_argument(
-        "--aggr", type=str, default="sum", help="Aggregation method"
-    )
+    parser.add_argument("--out_channels", type=int, default=16, help="Number of output channels")
+    parser.add_argument("--heads", type=int, default=4, help="Number of attention heads")
+    parser.add_argument("--aggr", type=str, default="sum", help="Aggregation method")
     parser.add_argument(
         "--score_cut",
         type=float,
@@ -81,9 +71,7 @@ def main(args: argparse.Namespace) -> None:
         default=4,
         help="Number of nearest neighbors for nuclei",
     )
-    parser.add_argument(
-        "--dist_nc", type=int, default=20, help="Distance threshold for nuclei"
-    )
+    parser.add_argument("--dist_nc", type=int, default=20, help="Distance threshold for nuclei")
     parser.add_argument(
         "--k_tx",
         type=int,

.scripts/train_model.py

@@ -95,39 +95,21 @@ def main(args):
         default=4,
         help="Batch size for validation",
     )
-    parser.add_argument(
-        "--init_emb", type=int, default=8, help="Initial embedding size"
-    )
+    parser.add_argument("--init_emb", type=int, default=8, help="Initial embedding size")
     parser.add_argument(
         "--hidden_channels",
         type=int,
         default=64,
         help="Number of hidden channels",
     )
-    parser.add_argument(
-        "--out_channels", type=int, default=16, help="Number of output channels"
-    )
-    parser.add_argument(
-        "--heads", type=int, default=4, help="Number of attention heads"
-    )
-    parser.add_argument(
-        "--aggr", type=str, default="sum", help="Aggregation method"
-    )
-    parser.add_argument(
-        "--accelerator", type=str, default="cuda", help="Type of accelerator"
-    )
-    parser.add_argument(
-        "--strategy", type=str, default="auto", help="Training strategy"
-    )
-    parser.add_argument(
-        "--precision", type=str, default="16-mixed", help="Precision mode"
-    )
-    parser.add_argument(
-        "--devices", type=int, default=4, help="Number of devices"
-    )
-    parser.add_argument(
-        "--epochs", type=int, default=100, help="Number of epochs"
-    )
+    parser.add_argument("--out_channels", type=int, default=16, help="Number of output channels")
+    parser.add_argument("--heads", type=int, default=4, help="Number of attention heads")
+    parser.add_argument("--aggr", type=str, default="sum", help="Aggregation method")
+    parser.add_argument("--accelerator", type=str, default="cuda", help="Type of accelerator")
+    parser.add_argument("--strategy", type=str, default="auto", help="Training strategy")
+    parser.add_argument("--precision", type=str, default="16-mixed", help="Precision mode")
+    parser.add_argument("--devices", type=int, default=4, help="Number of devices")
+    parser.add_argument("--epochs", type=int, default=100, help="Number of epochs")
     parser.add_argument(
         "--default_root_dir",
         type=str,