Add comprehensive test suite and coverage utilities

.coveragerc

@@ -0,0 +1,84 @@
+# Coverage.py configuration file
+# https://coverage.readthedocs.io/en/latest/config.html
+
+[run]
+# The source code directories to measure
+source = cellmap_flow
+
+# Files to omit from coverage
+omit = 
+    */tests/*,
+    */test_*,
+    */__pycache__/*,
+    */.*,
+    */venv/*,
+    */virtualenv/*,
+    */site-packages/*,
+    setup.py,
+    conftest.py,
+    */migrations/*,
+    */node_modules/*,
+
+# Enable branch coverage
+branch = True
+
+# Disable parallel mode to avoid file conflicts
+parallel = False
+
+# Specify data file location
+data_file = .coverage
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+    if TYPE_CHECKING:
+
+    # Don't complain about abstract methods
+    @(abc\.)?abstractmethod
+
+# Ignore warnings about missing files
+ignore_errors = True
+
+# Show line numbers of missing statements
+show_missing = True
+
+# Set precision for percentage display
+precision = 2
+
+# Sort by name for consistent output
+sort = Name
+
+[html]
+# Directory for HTML coverage report
+directory = htmlcov
+
+# Title for HTML report
+title = cellmap-flow Coverage Report
+
+# Show contexts for each covered line
+show_contexts = True
+
+[xml]
+# Output file for XML report (for CI/CD systems)
+output = coverage.xml
+
+[json]
+# Output file for JSON report
+output = coverage.json
+
+# Show contexts in JSON report
+show_contexts = True

.github/workflows/test-coverage.yml

@@ -0,0 +1,122 @@
+name: Tests and Coverage
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11, 3.12]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip packages
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[test]"
+
+    - name: Run tests with coverage
+      run: |
+        python -m pytest tests/ \
+          --cov=cellmap_flow \
+          --cov-report=xml \
+          --cov-report=term-missing \
+          --cov-branch \
+          -v
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false
+
+  coverage-report:
+    runs-on: ubuntu-latest
+    needs: test
+    if: github.event_name == 'pull_request'
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[test]"
+        pip install coverage-badge
+
+    - name: Run coverage
+      run: |
+        python -m pytest tests/ \
+          --cov=cellmap_flow \
+          --cov-report=json \
+          --cov-report=html \
+          --cov-branch
+
+    - name: Generate coverage badge
+      run: |
+        coverage-badge -o coverage.svg
+
+    - name: Upload coverage reports as artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-reports
+        path: |
+          htmlcov/
+          coverage.svg
+          coverage.json
+        retention-days: 30
+
+  coverage-comment:
+    runs-on: ubuntu-latest
+    needs: test
+    if: github.event_name == 'pull_request'
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[test]"
+
+    - name: Run coverage
+      run: |
+        python -m pytest tests/ \
+          --cov=cellmap_flow \
+          --cov-report=json
+
+    - name: Coverage comment
+      uses: py-cov-action/python-coverage-comment-action@v3
+      with:
+        GITHUB_TOKEN: ${{ github.token }}

.gitignore

@@ -162,4 +162,4 @@ cython_debug/
 #.idea/
 
 # Misc
-.vscode/
+.vscode/

Makefile

@@ -0,0 +1,19 @@
+# Simple Makefile for cellmap-flow project
+
+.PHONY: test test-cov clean install install-dev
+
+test:
+	python -m pytest tests/ -v
+
+test-cov:
+	python tests/coverage_utils.py
+
+clean:
+	python tests/coverage_utils.py --clean
+	rm -rf .pytest_cache __pycache__ htmlcov
+
+install:
+	pip install -e .
+
+install-dev:
+	pip install -e ".[dev]"

README.md

@@ -10,6 +10,8 @@ Please feel free to explore and contribute, but note that there may be frequent
 
 <p align="center">
   <a href="#"><img src="https://img.shields.io/badge/Status-Under_Construction-orange.svg" alt="Under Construction" /></a>
+  <a href="https://github.com/janelia-cellmap/cellmap-flow/actions/workflows/test-coverage.yml"><img src="https://github.com/janelia-cellmap/cellmap-flow/workflows/Tests%20and%20Coverage/badge.svg" alt="Tests" /></a>
+  <a href="https://codecov.io/gh/janelia-cellmap/cellmap-flow"><img src="https://codecov.io/gh/janelia-cellmap/cellmap-flow/branch/main/graph/badge.svg" alt="Coverage Status" /></a>
 </p>
 
 <p align="center">
@@ -125,3 +127,5 @@ To run TensorFlow models, we suggest installing TensorFlow via conda: `conda ins
 cellmap_flow_multiple --script -s /groups/cellmap/cellmap/zouinkhim/cellmap-flow/example/model_spec.py -n script_base --dacapo -r 20241204_finetune_mito_affs_task_datasplit_v3_u21_kidney_mito_default_cache_8_1 -i 700000 -n using_dacapo -d /nrs/cellmap/data/jrc_ut21-1413-003/jrc_ut21-1413-003.zarr/recon-1/em/fibsem-uint8/s0
 ```
 
+See [tests/README.md](tests/README.md) for detailed information about the test structure and coverage goals.
+

cellmap_flow/dashboard/app.py

@@ -27,19 +27,11 @@
 import time
 
 logger = logging.getLogger(__name__)
-# Explicitly set template and static folder paths for package installation
-template_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "templates")
-static_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "static")
-app = Flask(__name__, template_folder=template_dir, static_folder=static_dir)
+app = Flask(__name__)
 CORS(app)
 NEUROGLANCER_URL = None
 INFERENCE_SERVER = None
-CUSTOM_CODE_FOLDER = os.path.expanduser(
-    os.environ.get(
-        "CUSTOM_CODE_FOLDER",
-        "~/Desktop/cellmap/cellmap-flow/example/example_norm",
-    )
-)
+CustomCodeFolder = "/Users/zouinkhim/Desktop/cellmap/cellmap-flow/example/example_norm"
 
 
 @app.route("/")
@@ -155,7 +147,7 @@ def process():
             # Save custom code to a file with date and time
             timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
             filename = f"custom_code_{timestamp}.py"
-            filepath = os.path.join(CUSTOM_CODE_FOLDER, filename)
+            filepath = os.path.join(CustomCodeFolder, filename)
 
             with open(filepath, "w") as file:
                 file.write(custom_code)

cellmap_flow/utils/data.py

@@ -122,7 +122,7 @@ def _get_config(self):
         config.output_channels = len(
             config.channels
         )  # 0:all_mem,1:organelle,2:mito,3:er,4:nucleus,5:pm,6:vs,7:ld
-        config.block_shape = np.array(tuple(out_shape) + (len(channels),))
+        config.block_shape = np.array(tuple(out_shape) + (len(config.channels),))
 
         return config