From ae355c806571240cdebfa3bba1b2500eb173b3e5 Mon Sep 17 00:00:00 2001 From: Marija Dmitrijeva Date: Wed, 21 Feb 2024 13:43:13 +0100 Subject: [PATCH 1/5] Create python-package.yml --- .github/workflows/python-package.yml | 40 ++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/workflows/python-package.yml diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..3e4fb99 --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,40 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: CI for Python + +on: + push: + branches: [ "main" ] + pull_request: + branches: [ "main" ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest + run: | + pytest From b619a5607168ab32aebad61f14ec149568730c92 Mon Sep 17 00:00:00 2001 From: Marija Dmitrijeva Date: Wed, 21 Feb 2024 13:50:51 +0100 Subject: [PATCH 2/5] updated CI workflow --- .github/workflows/python-package.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3e4fb99..b8c139c 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -12,7 +12,9 @@ on: jobs: build: - runs-on: ubuntu-latest + runs-on: ${{matrix.os}} + matrix: + os: [ubuntu-latest, windows-latest, macOS-latest] strategy: fail-fast: false matrix: From 12150dc75b951618bc736018b53d3186a993e3c5 Mon Sep 17 00:00:00 2001 From: Marija Dmitrijeva Date: Wed, 21 Feb 2024 13:51:03 +0100 Subject: [PATCH 3/5] created extra test --- test_rarefy.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/test_rarefy.py b/test_rarefy.py index b97610f..3a50af3 100644 --- a/test_rarefy.py +++ b/test_rarefy.py @@ -35,3 +35,9 @@ def test_seed_reproducibility(): rarefied_1 = rarefy(x, depth=50, iterations=1, seed=42) rarefied_2 = rarefy(x, depth=50, iterations=1, seed=42) np.testing.assert_allclose(rarefied_1, rarefied_2, rtol=1e-6) + +def test_seed_reproducibility_fail(): + x = np.array([10, 20, 30, 40, 50]) + rarefied_1 = rarefy(x, depth=50, iterations=1, seed=27) + rarefied_2 = rarefy(x, depth=50, iterations=1, seed=35) + np.testing.assert_allclose(rarefied_1, rarefied_2, rtol=1e-6) From 312d46230feb4398b980871712500091e5b1a42f Mon Sep 17 00:00:00 2001 From: Marija Dmitrijeva Date: Wed, 21 Feb 2024 14:03:33 +0100 Subject: [PATCH 4/5] updated workflow --- .github/workflows/python-package.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index b8c139c..0042cc8 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -13,12 +13,11 @@ jobs: build: runs-on: ${{matrix.os}} - matrix: - os: [ubuntu-latest, windows-latest, macOS-latest] strategy: fail-fast: false matrix: python-version: ["3.9", "3.10", "3.11"] + os: [ubuntu-latest, macOS-latest] steps: - uses: actions/checkout@v3 From cbcbb7ed37ef680327f3decdfbd2da2940e059e9 Mon Sep 17 00:00:00 2001 From: Marija Dmitrijeva Date: Wed, 21 Feb 2024 14:21:12 +0100 Subject: [PATCH 5/5] corrected test --- test_rarefy.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test_rarefy.py b/test_rarefy.py index 3a50af3..275f893 100644 --- a/test_rarefy.py +++ b/test_rarefy.py @@ -39,5 +39,5 @@ def test_seed_reproducibility(): def test_seed_reproducibility_fail(): x = np.array([10, 20, 30, 40, 50]) rarefied_1 = rarefy(x, depth=50, iterations=1, seed=27) - rarefied_2 = rarefy(x, depth=50, iterations=1, seed=35) + rarefied_2 = rarefy(x, depth=50, iterations=1, seed=27) np.testing.assert_allclose(rarefied_1, rarefied_2, rtol=1e-6)