v0.1.1 to main

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.11"] # Adjust to your primary version
+        python-version: ["3.14"]
 
     steps:
       - name: Check out repository
@@ -30,9 +30,6 @@ jobs:
       - name: Install the project
         run: uv sync
 
-      - name: Run Pipeline (Annotate, FASTA, miRNA)
-        # This acts as our end-to-end integration test.
-        # Since it runs on a fresh machine, it WILL attempt to connect to S3
-        # anonymously, download the assets, and process test/tester.txt
+      - name: Run Pipeline
         run: |
-          uv run main.py -c test_config.json -v 2 annotate fasta mirna
+          uv run main.py -c test_config.json -v 2 annotate -d 'arraystar,circbase' fasta -d 'arraystar,circbase' mirna -a 'miRanda,TargetScan' rbp

config.json

@@ -6,17 +6,17 @@
   },
   "samples": {
     "vromann": {
-      "input": "test/vromann.txt",
+      "file_path": "test/vromann.txt",
       "reference": "hg38",
       "zero_based": true
     },
     "glioblastoma_plus_dcc": {
-      "input": "test/rnase_plus/glioblastoma_RNase_plus_dcc.txt",
+      "file_path": "test/rnase_plus/glioblastoma_RNase_plus_dcc.txt",
       "reference": "hg38",
       "zero_based": true
     },
     "glioblastoma_plus_ciriquant": {
-      "input": "test/rnase_plus/glioblastoma_RNase_plus_ciriquant.txt",
+      "file_path": "test/rnase_plus/glioblastoma_RNase_plus_ciriquant.txt",
       "reference": "hg38",
       "zero_based": true
     }

config.py

@@ -27,7 +27,7 @@
 }
 
 class ToolConfig(TypedDict, total=False):
-    input: List[str]
+    file_path: List[str]
     reference: Union[str, List[str], None]
     zero_based: Union[bool, List[bool], None]
     max_tasks: int
@@ -74,14 +74,14 @@ def print_config_panel(config: ToolConfig, user_config_path: Optional[str] = Non
 
     sample_table = Table(show_header=True, header_style="bold blue", box=box.ROUNDED, expand=True)
     sample_table.add_column("Sample Name", style="bold green")
-    sample_table.add_column("Input File", style="yellow")
+    sample_table.add_column("File Path", style="yellow")
     sample_table.add_column("Ref", style="cyan", justify="center")
     sample_table.add_column("0-based", style="magenta", justify="center")
 
     for sample_name, sample_info in config.get("samples", {}).items():
         sample_table.add_row(
             sample_name,
-            str(sample_info.get("input", sample_info.get("file_path", ""))),
+            str(sample_info.get("file_path", "")),
             str(sample_info.get("reference", "")),
             str(sample_info.get("zero_based", ""))
         )

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pycircdb"
-version = "0.1.0"
+version = "0.1.1"
 description = "pycircdb: integrated circRNA database annotation for computational workflows."
 readme = "README.md"
 authors = [{ name = "Barry Digby", email = "b.digby237@gmail.com" }]