Fix/hosted sam2 unavailable

.dockerignore

@@ -0,0 +1,44 @@
+# VCS
+.git
+.gitignore
+.github/
+
+# Python cache/bytecode
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Build/packaging artifacts
+build/
+dist/
+*.egg-info/
+.eggs/
+
+# Test and coverage artifacts
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Local editor/tooling
+.vscode/
+.idea/
+.DS_Store
+
+# Local data and outputs
+tmp/
+out/
+results/
+results_cache/
+*.zip
+
+# Optional: keep large or generated content out of image context
+Data/
+fibermorph/test_data/

.gitattributes

@@ -0,0 +1,6 @@
+# Normalize line endings: text files always LF in the repo
+* text=auto eol=lf
+*.png binary
+*.tif binary
+*.tiff binary
+*.jpg binary

.github/workflows/conventional-prs.yaml

@@ -1,4 +1,5 @@
 name: PR
+
 on:
   pull_request_target:
     types:

.github/workflows/test.yaml

@@ -2,7 +2,7 @@ name: Test
 
 on:
   push:
-    branches: [ main, master ]
+    branches: [ main, master, fibermorph-dev, "feature/**" ]
   pull_request:
     branches: [ main, master ]
   workflow_dispatch:
@@ -23,28 +23,31 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: latest
-        virtualenvs-create: true
-        virtualenvs-in-project: true
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y --no-install-recommends \
+          libgl1 \
+          libglib2.0-0 \
+          libsm6 \
+          libxext6
 
-    - name: Cache Poetry dependencies
+    - name: Cache pip
       uses: actions/cache@v4
       with:
-        path: |
-          ~/.cache/pypoetry
-          .venv
-        key: ${{ runner.os }}-poetry-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
         restore-keys: |
-          ${{ runner.os }}-poetry-${{ matrix.python-version }}-
+          ${{ runner.os }}-pip-${{ matrix.python-version }}-
 
-    - name: Install dependencies
-      run: poetry install
+    - name: Install package and test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[gui]"
+        pip install pytest pytest-cov
 
     - name: Run tests with coverage
-      run: poetry run pytest --cov=fibermorph --cov-report=xml --cov-report=term
+      run: pytest --cov=fibermorph --cov-report=xml --cov-report=term
 
     - name: Upload coverage reports
       uses: codecov/codecov-action@v4
@@ -53,4 +56,4 @@ jobs:
         file: ./coverage.xml
         fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}
-      continue-on-error: true
+      continue-on-error: true

.gitignore

@@ -132,9 +132,7 @@ __pycache__
 coverage.xml
 .htmlcov/
 *.coverfibermorph/fibermorph_old.py
-
-# Claude Code local config (launch.json, settings, etc.)
-.claude/
+/.claude
 
 # Large test images live in tinalasisi/fibermorph_DemoData and are fetched on demand
 *.tif

.streamlit/config.toml

@@ -1,8 +1,10 @@
+# Lasisi Lab design system (fibermorph GUI)
 [theme]
-primaryColor = "#FF4B4B"
-backgroundColor = "#FFFFFF"
-secondaryBackgroundColor = "#F0F2F6"
-textColor = "#262730"
+base = "light"
+primaryColor = "#05686D"             # teal-700 — functional / click colour
+backgroundColor = "#FBFCFD"          # paper-2
+secondaryBackgroundColor = "#F2F2F2" # paper-3
+textColor = "#3F4251"                # ink-700 body; Open Sans loaded via CSS
 font = "sans serif"
 
 [server]

CONTRIBUTING.md

@@ -27,15 +27,15 @@ git checkout -b my-feature upstream/fibermorph-dev
 python3.12 -m venv .venv && source .venv/bin/activate   # Python 3.10–3.12
 pip install -e '.[gui]'      # editable install with the GUI extra
 pytest                       # run the test suite
-fibermorph-gui               # launch the GUI locally
+fibermorph-gui --local       # launch the GUI locally (without --local: hosted mode)
 ```
 
 ## Pull requests
 
 - **Target `fibermorph-dev`.**
 - Use a **Conventional Commits** PR title — the `title-format` CI check requires
   one. Start with a type: `feat:`, `fix:`, `docs:`, `refactor:`, `test:`,
-  `chore:`, `ci:`, etc. Example: `feat: validate wave-count on synthetic fibers`.
+  `chore:`, `ci:`, etc. Example: `fix: handle an empty curvature directory`.
 - Make sure `pytest` passes before requesting review.
 
 ## Test data

Dockerfile

@@ -0,0 +1,87 @@
+# ── Stage 1: CPU-only (default) ─────────────────────────────────────────────
+FROM python:3.11-slim-bookworm AS cpu
+
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    PIP_DISABLE_PIP_VERSION_CHECK=1 \
+    STREAMLIT_SERVER_HEADLESS=true \
+    STREAMLIT_SERVER_PORT=7860 \
+    STREAMLIT_SERVER_ADDRESS=0.0.0.0 \
+    STREAMLIT_BROWSER_GATHER_USAGE_STATS=false
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libgl1 \
+    libglib2.0-0 \
+    libsm6 \
+    libxext6 \
+    tini \
+    curl \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN useradd -m -u 1000 user
+USER user
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH
+WORKDIR $HOME/app
+
+COPY --chown=user . $HOME/app
+
+RUN python -m pip install --upgrade pip && \
+    python -m pip install ".[gui]"
+
+EXPOSE 7860
+
+HEALTHCHECK --interval=30s --timeout=10s --start-period=30s --retries=3 \
+  CMD curl -fsS http://127.0.0.1:7860/_stcore/health || exit 1
+
+ENTRYPOINT ["/usr/bin/tini", "--"]
+CMD ["fibermorph-gui"]
+
+
+# ── Stage 2: GPU (adds CUDA + SAM2) ─────────────────────────────────────────
+FROM nvidia/cuda:12.1.1-cudnn8-runtime-ubuntu22.04 AS gpu
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    PIP_DISABLE_PIP_VERSION_CHECK=1 \
+    STREAMLIT_SERVER_HEADLESS=true \
+    STREAMLIT_SERVER_PORT=7860 \
+    STREAMLIT_SERVER_ADDRESS=0.0.0.0 \
+    STREAMLIT_BROWSER_GATHER_USAGE_STATS=false
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    python3.11 \
+    python3.11-venv \
+    python3-pip \
+    libgl1 \
+    libglib2.0-0 \
+    libsm6 \
+    libxext6 \
+    tini \
+    curl \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN useradd -m -u 1000 user
+USER user
+ENV HOME=/home/user \
+    PATH=/home/user/.local/bin:$PATH
+WORKDIR $HOME/app
+
+COPY --chown=user . $HOME/app
+
+RUN python3.11 -m pip install --upgrade pip && \
+    python3.11 -m pip install ".[gui]" && \
+    python3.11 -m pip install torch --index-url https://download.pytorch.org/whl/cu121 && \
+    python3.11 -m pip install git+https://github.com/facebookresearch/segment-anything-2
+
+EXPOSE 7860
+
+HEALTHCHECK --interval=30s --timeout=10s --start-period=60s --retries=3 \
+  CMD curl -fsS http://127.0.0.1:7860/_stcore/health || exit 1
+
+ENTRYPOINT ["/usr/bin/tini", "--"]
+CMD ["fibermorph-gui"]