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test: enable codecov #69

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merged 2 commits into from
Nov 1, 2023
Merged

test: enable codecov #69

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test: enable testing
tlambert03 Oct 30, 2023
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tlambert03 Oct 30, 2023
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13 changes: 8 additions & 5 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ on:
pull_request:
workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
Comment on lines +12 to +14
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Just to make sure I understand, if we push a new commit on the same branch, this will cancel in progress workflows on the previous commit and then run the workflows on the new commit?

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@tlambert03 tlambert03 Oct 31, 2023 •
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yes sorry, should have commented on that. that's exactly right. it just saves CI time.
more here: https://docs.github.com/en/actions/using-jobs/using-concurrency#overview


jobs:
# check-manifest:
# runs-on: ubuntu-latest
Expand All @@ -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:
Expand All @@ -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
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -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
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23 changes: 12 additions & 11 deletions pyproject.toml
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Expand Up @@ -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]
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2 changes: 1 addition & 1 deletion src/traccuracy/__init__.py
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Expand Up @@ -3,7 +3,7 @@

try:
__version__ = version("traccuracy")
except PackageNotFoundError:
except PackageNotFoundError: # pragma: no cover
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__version__ = "uninstalled"

from ._run_metrics import run_metrics
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