Pytest, Existing GitLfs garnet-data repo connection and Code Coverage…

… Initialization (#4)

Updates in tests, pytest, codecoverage and garnet-data existing repository configurations

.github/workflows/garnetreduction.yml

@@ -0,0 +1,34 @@
+name: CI
+
+on:
+    workflow_dispatch:
+    pull_request:
+    push:
+        branches: [next, qa, main]
+        tags: ['v*']
+
+jobs:
+    tests:
+        runs-on: ubuntu-latest
+        defaults:
+            run:
+                shell: bash -l {0}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: mamba-org/setup-micromamba@v1
+              with:
+                environment-file: environment.yml
+                cache-environment-key: ${{ runner.os }}-env-${{ hashFiles('**/environment.yml') }}
+                cache-downloads-key: ${{ runner.os }}-downloads-${{ hashFiles('**/environment.yml') }}
+            - name: install garnet_reduction
+              run: |
+                    python -m pip install -e .
+            - name: run unit tests
+              run: |
+                    echo "running unit tests"
+                    xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov=src --cov-report=xml --cov-report=term-missing
+            - name: Upload coverage reports to Codecov
+              uses: codecov/codecov-action@v4.0.1
+              with:
+                    token: ${{ secrets.CODECOV_TOKEN }}
+                    slug: neutrons/garnet_reduction

.gitignore

@@ -25,6 +25,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+src/garnet/_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "tests/data/garnet-data"]
+	path = tests/data/garnet-data
+	url = https://code.ornl.gov/sns-hfir-scse/infrastructure/test-data/garnet-data.git
+	branch = main
+[submodule "garnet-data"]
+	update = merge

README.md

@@ -1 +1,23 @@
 # ![](garnet.svg)
+
+
+### Getting started
+
+Create conda environment
+```bash
+conda env create -f environment.yml
+```
+
+Activate garnet environment
+```bash
+conda activate garnet_reduction
+```
+
+Install in editable mode for developlment
+```bash
+python -m pip install -e .
+```
+
+
+[![CI](https://github.com/neutrons/garnet_reduction/actions/workflows/garnetreduction.yml/badge.svg?branch=next)](https://github.com/neutrons/garnet_reduction/actions/workflows/garnetreduction.yml/)
+[![codecov](https://codecov.io/gh/neutrons/garnet_reduction/graph/badge.svg?token=SV1HMY1XPW)](https://codecov.io/gh/neutrons/garnet_reduction)

codecov.yaml

@@ -0,0 +1,10 @@
+# Configuration file for codecov reporting code coverage
+
+# Percentage drop allowed
+coverage:
+  status:
+    project:
+      default:
+        # base on last build, but allow drop of upto this percent
+        target: 80.0
+        threshold: 2.0

environment.yml

@@ -10,7 +10,9 @@ dependencies:
   - matplotlib
   - pycifrw
   - pre-commit
+  - pytest
+  - pytest-qt
+  - pytest-cov
   - h5py
   - lmfit
   - mantidworkbench
-  - pytest

pyproject.toml

@@ -48,3 +48,11 @@ ignore = ["D203", # conflict with D211
           "ANN201", "D400", "D401", "D415", # Unnecessary
           "ARG002", "N802", "N803","N806", "D100","D101","D102","D103", "D104","D107","D417" # put it back in the future
           ]
+
+[tool.pytest.ini_options]
+markers = [
+    "resources_intensive: mark test as using a lot of computing resources: CPU, memory, etc.",
+    "mount_sns: mark a test as using /SNS/ data mount",
+    "mount_hfir: mark a test as using /HFIR/ data mount",
+    "datarepo: Tests that require the garnet_data submodule"
+    ]

src/garnet/reduction/normalization.py

@@ -59,7 +59,7 @@ def normalize(self):
         data.update_raw_path(self.plan)
 
         runs = self.plan["Runs"]
-
+        grouping_file = ""
         if data.laue:
             grouping_file = diag_file.replace(".nxs", ".xml")
 
@@ -152,7 +152,8 @@ def normalize(self):
 
         mtd.clear()
 
-        os.remove(grouping_file)
+        if grouping_file and os.path.exists(grouping_file):
+            os.remove(grouping_file)
 
         return output_file
 

tests/conftest.py

@@ -0,0 +1,47 @@
+"""pytest config"""
+
+import os
+
+import pytest
+
+
+def pytest_addoption(parser):
+    parser.addoption("--all", action="store_true", default=False, help="run slow tests")
+
+
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--all"):
+        # --all: do not skip slow tests
+        return
+    skip_slow = pytest.mark.skip(reason="need --all option to run")
+    for item in items:
+        if "resources_intensive" in item.keywords:
+            item.add_marker(skip_slow)
+
+
+@pytest.fixture(scope="session")
+def has_sns_mount():
+    """Fixture that returns True if the SNS data mount (e.g CORELLI shared) is available"""
+    sns_dir = "/SNS/CORELLI/shared/"
+    return os.path.exists(sns_dir)
+
+
+@pytest.fixture(scope="session")
+def has_hfir_mount():
+    """Fixture that returns True if the HFIR data mount (e.g HB3A shared) is available"""
+    hfir_dir = "/HFIR/HB3A/shared/"
+    return os.path.exists(hfir_dir)
+
+
+@pytest.fixture(scope="session")
+def has_datarepo():
+    """Fixture that returns True if the datarepo_dir is available"""
+    readme_data = os.path.join(os.path.dirname(os.path.abspath(__file__)), "data", "garnet-data", "README.md")
+    return os.path.exists(readme_data)
+
+
+@pytest.fixture(scope="session")
+def datarepo_dir():
+    """Return the directory **absolute** paths for test data."""
+    root_data = os.path.join(os.path.dirname(os.path.abspath(__file__)), "data", "garnet-data")
+    return root_data

tests/test_integration.py

@@ -1,96 +1,71 @@
 import os
-import shutil
 import subprocess
-import tempfile
 
 import numpy as np
 import pytest
-from garnet.config.instruments import beamlines
 from garnet.reduction.integration import PeakEllipsoid, PeakSphere
 from garnet.reduction.plan import ReductionPlan
 
 benchmark = "shared/benchmark/int"
 
 
-@pytest.mark.skipif(not os.path.exists("/SNS/CORELLI/"), reason="file mount")
-def test_corelli():
+@pytest.mark.resources_intensive
+@pytest.mark.mount_sns
+def test_corelli(tmpdir, has_sns_mount):
+    if not has_sns_mount:
+        pytest.skip("Test is skipped. SNS mount is not available.")
+
     config_file = "corelli_reduction_plan.yaml"
     reduction_plan = os.path.abspath(os.path.join("./tests/data", config_file))
     script = os.path.abspath("./src/garnet/workflow.py")
     command = ["python", script, config_file, "int", "16"]
 
-    with tempfile.TemporaryDirectory() as tmpdir:
-        os.chdir(tmpdir)
-
-        rp = ReductionPlan()
-        rp.load_plan(reduction_plan)
-        rp.save_plan(os.path.join(tmpdir, config_file))
-
-        instrument_config = beamlines[rp.plan["Instrument"]]
-        facility = instrument_config["Facility"]
-        name = instrument_config["Name"]
-        baseline_path = os.path.join("/", facility, name, benchmark)
+    rp = ReductionPlan()
+    rp.load_plan(reduction_plan)
+    saved_plan = os.path.join(tmpdir, config_file)
+    rp.set_output(saved_plan)
+    rp.save_plan(saved_plan)
 
-        subprocess.run(command, check=False)
+    command = ["python", script, saved_plan, "int", "16"]
+    subprocess.run(command, check=False)
 
-        if os.path.exists(baseline_path):
-            shutil.rmtree(baseline_path)
 
-        shutil.copytree(tmpdir, baseline_path)
+@pytest.mark.mount_hfir
+def test_wand2(tmpdir, has_hfir_mount):
+    if not has_hfir_mount:
+        pytest.skip("Test is skipped. HFIR mount is not available.")
 
-
-@pytest.mark.skipif(not os.path.exists("/HFIR/HB2C/"), reason="file mount")
-def test_wand2():
     config_file = "wand2_reduction_plan.yaml"
     reduction_plan = os.path.abspath(os.path.join("./tests/data", config_file))
     script = os.path.abspath("./src/garnet/workflow.py")
-    command = ["python", script, config_file, "int", "4"]
-
-    with tempfile.TemporaryDirectory() as tmpdir:
-        os.chdir(tmpdir)
-
-        rp = ReductionPlan()
-        rp.load_plan(reduction_plan)
-        rp.save_plan(os.path.join(tmpdir, config_file))
 
-        instrument_config = beamlines[rp.plan["Instrument"]]
-        facility = instrument_config["Facility"]
-        name = instrument_config["Name"]
-        baseline_path = os.path.join("/", facility, name, benchmark)
+    rp = ReductionPlan()
+    rp.load_plan(reduction_plan)
+    saved_plan = os.path.join(tmpdir, config_file)
+    rp.set_output(saved_plan)
+    rp.save_plan(saved_plan)
 
-        subprocess.run(command, check=False)
+    command = ["python", script, saved_plan, "int", "4"]
+    subprocess.run(command, check=False)
 
-        if os.path.exists(baseline_path):
-            shutil.rmtree(baseline_path)
 
-        shutil.copytree(tmpdir, baseline_path)
+@pytest.mark.mount_hfir
+def test_demand(tmpdir, has_hfir_mount):
+    if not has_hfir_mount:
+        pytest.skip("Test is skipped. HFIR mount is not available.")
 
-
-@pytest.mark.skipif(not os.path.exists("/HFIR/HB3A/"), reason="file mount")
-def test_demand():
     config_file = "demand_reduction_plan.yaml"
     reduction_plan = os.path.abspath(os.path.join("./tests/data", config_file))
     script = os.path.abspath("./src/garnet/workflow.py")
-    command = ["python", script, config_file, "int", "4"]
-
-    with tempfile.TemporaryDirectory() as tmpdir:
-        os.chdir(tmpdir)
-
-        rp = ReductionPlan()
-        rp.load_plan(reduction_plan)
-        rp.save_plan(os.path.join(tmpdir, config_file))
-
-        instrument_config = beamlines[rp.plan["Instrument"]]
-        facility = instrument_config["Facility"]
-        name = instrument_config["Name"]
-        baseline_path = os.path.join("/", facility, name, benchmark)
-
-        subprocess.run(command, check=False)
 
-        if os.path.exists(baseline_path):
-            shutil.rmtree(baseline_path)
+    rp = ReductionPlan()
+    rp.load_plan(reduction_plan)
+    saved_plan = os.path.join(tmpdir, config_file)
+    rp.set_output(saved_plan)
+    rp.save_plan(saved_plan)
 
-        shutil.copytree(tmpdir, baseline_path)
+    command = ["python", script, saved_plan, "int", "4"]
+    subprocess.run(command, check=False)
 
 
 def test_sphere():
@@ -176,7 +151,7 @@ def test_ellipsoid():
     radii = params[3:6]
     vectors = params[6:9]
 
-    S = ellipsoid.S_matrix(*ellipsoid.scale(*radii, s=0.25), *ellipsoid.angles(*vectors))
+    S = ellipsoid.S_matrix(*ellipsoid.scale(*radii), *ellipsoid.angles(*vectors))
 
     s = np.sqrt(np.linalg.det(S))
     sigma = np.sqrt(np.linalg.det(cov))