Merge pull request #69 from tlambert03/cov

test: enable codecov
Janelia-Trackathon-2023 · Nov 1, 2023 · d3560d1 · d3560d1
2 parents ed2b7b1 + 681fb93
commit d3560d1
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Showing 4 changed files with 22 additions and 17 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -9,6 +9,10 @@ on:
   pull_request:
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   # check-manifest:
   #   runs-on: ubuntu-latest
@@ -22,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
@@ -35,17 +39,16 @@ jobs:
           cache-dependency-path: "pyproject.toml"
           cache: "pip"
 
-      # if running a cron job, we add the --pre flag to test against pre-releases
       - name: Install dependencies
         run: |
           python -m pip install -U pip
           python -m pip install -e .[test]
 
       - name: Test
-        run: pytest --color=yes #--cov --cov-report=xml --cov-report=term-missing
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
 
-      # - name: Coverage
-      #   uses: codecov/codecov-action@v3
+      - name: Coverage
+        uses: codecov/codecov-action@v3
 
   benchmark:
     name: Benchmark

diff --git a/README.md b/README.md
@@ -6,6 +6,7 @@
 [![CI](https://github.com/Janelia-Trackathon-2023/traccuracy/actions/workflows/ci.yml/badge.svg)](https://github.com/Janelia-Trackathon-2023/traccuracy/actions/workflows/ci.yml)
 [![Benchmarking](https://github.com/Janelia-Trackathon-2023/traccuracy/actions/workflows/benchmark-report.yml/badge.svg)](https://janelia-trackathon-2023.github.io/traccuracy/dev/bench/)
 [![Documentation Status](https://readthedocs.org/projects/traccuracy/badge/?version=latest)](https://traccuracy.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/Janelia-Trackathon-2023/traccuracy/branch/main/graph/badge.svg)](https://codecov.io/gh/Janelia-Trackathon-2023/traccuracy)
 
 
 `traccuracy` provides a suite of benchmarking functions that can be used to evaluate cell

diff --git a/pyproject.toml b/pyproject.toml
@@ -167,17 +167,18 @@ pretty = true
 
 
 # https://coverage.readthedocs.io/en/6.4/config.html
-# [tool.coverage.report]
-# exclude_lines = [
-#     "pragma: no cover",
-#     "if TYPE_CHECKING:",
-#     "@overload",
-#     "except ImportError",
-#     "\\.\\.\\.",
-#     "raise NotImplementedError()",
-# ]
-# [tool.coverage.run]
-# source = ["src"]
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "@overload",
+    "except ImportError",
+    "\\.\\.\\.",
+    "raise NotImplementedError()",
+    "pass",
+]
+[tool.coverage.run]
+source = ["traccuracy"]
 
 # https://github.com/mgedmin/check-manifest#configuration
 # [tool.check-manifest]

diff --git a/src/traccuracy/__init__.py b/src/traccuracy/__init__.py
@@ -3,7 +3,7 @@
 
 try:
     __version__ = version("traccuracy")
-except PackageNotFoundError:
+except PackageNotFoundError:  # pragma: no cover
     __version__ = "uninstalled"
 
 from ._run_metrics import run_metrics