temporary status - runs dopplerview scripts ~correctly. Whole architecture needs clarifying since somewhat unreadable

Author: AdrienGordon

.gitignore

@@ -1,3 +1,9 @@
+# Temporary workspace files
+system_design/
+AGENTS.md
+uv.lock
+test/
+
 # Byte-compiled / cache
 __pycache__/
 *.py[cod]
@@ -21,6 +27,7 @@ dist/
 wheelhouse/
 
 # Test / coverage
+.tmp/
 .pytest_cache/
 .tox/
 .nox/
@@ -63,4 +70,4 @@ Desktop.ini
 process_result.csv
 pipelines.txt
 requirements-optional.txt
-eyeflow_matlab/
+eyeflow_matlab/

pyproject.toml

@@ -4,15 +4,23 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "EyeFlow"
-version = "0.1.0"
+version = "0.2.0"
 description = "Cohort-analysis engine for retinal Doppler holography"
 readme = "README.md"
 requires-python = ">=3.10"
 license = { text = "GPL-3.0-only" }
 
 # =============== [ DEPENDENCIES ] ===============
 
-dependencies = ["numpy>=1.24", "h5py>=3.9", "sv-ttk>=2.6", "tkinterdnd2"]
+dependencies = [
+    "numpy>=1.24",
+    "h5py>=3.9",
+    "scipy>=1.10",
+    "scikit-image>=0.20",
+    "joblib>=1.3",
+    "sv-ttk>=2.6",
+    "tkinterdnd2",
+]
 
 [project.optional-dependencies]
 # For specific pipelines

src/app_settings.py

@@ -12,7 +12,7 @@
 APP_NAME = "EyeFlow"
 SETTINGS_FILENAME = "settings.json"
 DEFAULT_SETTINGS_FILENAME = "default_settings.json"
-LAST_BATCH_LOG_FILENAME = "last_batch_log.txt"
+LAST_BATCH_LOG_FILENAME = "last_EF_log.txt"
 VERSION_PATTERN = re.compile(r'^version\s*=\s*"([^"]+)"\s*$')
 INVALID_PATH_CHARS_PATTERN = re.compile(r'[<>:"/\\|?*]+')