From e61db24b3b77e97d2e65daacfd1b5ee92da374ad Mon Sep 17 00:00:00 2001 From: Chadwick Boulay Date: Mon, 23 Sep 2024 16:33:52 -0400 Subject: [PATCH 1/6] Fixup tests importing utils --- tests/conftest.py | 3 +++ tests/{ => helpers}/__init__.py | 0 tests/{ => helpers}/util.py | 0 3 files changed, 3 insertions(+) create mode 100644 tests/conftest.py rename tests/{ => helpers}/__init__.py (100%) rename tests/{ => helpers}/util.py (100%) diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..5e85fe6 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,3 @@ +import sys +import os +sys.path.append(os.path.join(os.path.dirname(__file__), 'helpers')) diff --git a/tests/__init__.py b/tests/helpers/__init__.py similarity index 100% rename from tests/__init__.py rename to tests/helpers/__init__.py diff --git a/tests/util.py b/tests/helpers/util.py similarity index 100% rename from tests/util.py rename to tests/helpers/util.py From 6efde90f49ac6706ba4152bf87f77755319ab669 Mon Sep 17 00:00:00 2001 From: Chadwick Boulay Date: Mon, 23 Sep 2024 16:39:21 -0400 Subject: [PATCH 2/6] Refactor from poetry to uv --- .../python-publish-ezmsg-sigproc.yml | 35 +- .github/workflows/python-tests.yml | 46 +- .gitignore | 2 + poetry.lock | 476 ------------------ pyproject.toml | 60 ++- src/ezmsg/sigproc/__init__.py | 5 +- uv.lock | 454 +++++++++++++++++ 7 files changed, 522 insertions(+), 556 deletions(-) delete mode 100644 poetry.lock create mode 100644 uv.lock diff --git a/.github/workflows/python-publish-ezmsg-sigproc.yml b/.github/workflows/python-publish-ezmsg-sigproc.yml index a7365a3..24ce149 100644 --- a/.github/workflows/python-publish-ezmsg-sigproc.yml +++ b/.github/workflows/python-publish-ezmsg-sigproc.yml @@ -1,10 +1,4 @@ # This workflow will upload a Python Package using Twine when a release is created -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries - -# This workflow uses actions that are not certified by GitHub. -# They are provided by a third-party and are governed by -# separate terms of service, privacy policy, and support -# documentation. name: Upload Python Package - ezmsg-sigproc @@ -22,20 +16,15 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.8" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install build - - - name: Build ezmsg-sigproc - run: python -m build . - - name: Publish ezmsg-sigproc - uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 - with: - password: ${{ secrets.PYPI_API_TOKEN_SIGPROC }} - packages_dir: dist + + - name: Install uv + uses: astral-sh/setup-uv@v2 + + - name: Build Package + run: uv build + + - name: Publish Package + env: + TWINE_USERNAME: __token__ + TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN_SIGPROC }} + run: uvx twine upload dist/* diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml index 958b1e6..5fa3d15 100644 --- a/.github/workflows/python-tests.yml +++ b/.github/workflows/python-tests.yml @@ -11,7 +11,7 @@ jobs: build: strategy: matrix: - python-version: [3.8, 3.9, "3.10"] + python-version: [3.9, "3.10", "3.11", "3.12"] os: - "ubuntu-latest" - "windows-latest" @@ -21,31 +21,21 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@v2 with: - python-version: ${{ matrix.python-version }} - - - name: Upgrade pip and install pipx - run: | - python -m pip install --upgrade pip pipx flake8 - - - name: Install Poetry via pipx - run: | - pipx install poetry - echo "$HOME/.local/bin/" >> $GITHUB_PATH - - - name: Install dependencies with Poetry - run: | - poetry install --with test - - - 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 ezmsg-sigproc - run: | - poetry run python -m pytest -v tests + enable-cache: true + cache-dependency-glob: "uv.lock" + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + + - name: Install the project + run: uv sync --all-extras --dev + + - name: Lint + run: + uv tool run ruff check --output-format=github src + + - name: Run tests + run: uv run pytest tests diff --git a/.gitignore b/.gitignore index e463b94..743bd3c 100644 --- a/.gitignore +++ b/.gitignore @@ -141,3 +141,5 @@ cython_debug/ # JetBrains .idea/ + +src/ezmsg/sigproc/__version__.py \ No newline at end of file diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 4317f63..0000000 --- a/poetry.lock +++ /dev/null @@ -1,476 +0,0 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by 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"https://files.pythonhosted.org/packages/26/9f/ad63fc0248c5379346306f8668cda6e2e2e9c95e01216d2b8ffd9ff037d0/typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d", size = 37438 }, +] From ea924aca832c4567ed71ffab018bf1e8834aa661 Mon Sep 17 00:00:00 2001 From: Chadwick Boulay Date: Mon, 23 Sep 2024 18:22:16 -0400 Subject: [PATCH 3/6] Comment out linter for now --- .github/workflows/python-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml index 5fa3d15..45f2699 100644 --- a/.github/workflows/python-tests.yml +++ b/.github/workflows/python-tests.yml @@ -33,9 +33,9 @@ jobs: - name: Install the project run: uv sync --all-extras --dev - - name: Lint - run: - uv tool run ruff check --output-format=github src +# - name: Lint +# run: +# uv tool run ruff check --output-format=github src - name: Run tests run: uv run pytest tests From 211e2484d57d9981026d54eaa0edcba68dc0af7f Mon Sep 17 00:00:00 2001 From: Chadwick Boulay Date: Mon, 23 Sep 2024 18:47:32 -0400 Subject: [PATCH 4/6] Pytest ignore warnings --- pyproject.toml | 4 ++++ tests/test_spectrum.py | 10 +++++----- tests/test_synth.py | 10 +++++----- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 090e005..4a9f35c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,3 +43,7 @@ packages = ["src/ezmsg"] dev-dependencies = [ "ruff>=0.6.7", ] + +[tool.pytest.ini_options] +norecursedirs = "tests/helpers" +addopts = "-p no:warnings" diff --git a/tests/test_spectrum.py b/tests/test_spectrum.py index 000cc1e..d48607b 100644 --- a/tests/test_spectrum.py +++ b/tests/test_spectrum.py @@ -175,7 +175,7 @@ def test_spectrum_vs_sps_fft(complex: bool): assert np.allclose(test_spec, sp_res) -class TestSpectrumSettings(ez.Settings): +class SpectrumSettingsTest(ez.Settings): synth_settings: EEGSynthSettings window_settings: WindowSettings spectrum_settings: SpectrumSettings @@ -183,8 +183,8 @@ class TestSpectrumSettings(ez.Settings): term_settings: TerminateOnTotalSettings = field(default_factory=TerminateOnTotalSettings) -class TestSpectrumIntegration(ez.Collection): - SETTINGS = TestSpectrumSettings +class SpectrumIntegrationTest(ez.Collection): + SETTINGS = SpectrumSettingsTest SOURCE = EEGSynth() WIN = Window() @@ -221,7 +221,7 @@ def test_spectrum_system( test_filename = get_test_fn(test_name) ez.logger.info(test_filename) - settings = TestSpectrumSettings( + settings = SpectrumSettingsTest( synth_settings=EEGSynthSettings( fs=fs, n_time=n_time, @@ -246,7 +246,7 @@ def test_spectrum_system( total=target_messages, ) ) - system = TestSpectrumIntegration(settings) + system = SpectrumIntegrationTest(settings) ez.run(SYSTEM=system) messages: typing.List[AxisArray] = [_ for _ in message_log(test_filename)] diff --git a/tests/test_synth.py b/tests/test_synth.py index 6828979..68ae49d 100644 --- a/tests/test_synth.py +++ b/tests/test_synth.py @@ -308,14 +308,14 @@ def f_test(t): return amp * np.sin(2 * np.pi * freq * t + phase) # TODO: test SinGenerator in a system. -class TestEEGSynthSettings(ez.Settings): +class EEGSynthSettingsTest(ez.Settings): synth_settings: EEGSynthSettings log_settings: MessageLoggerSettings term_settings: TerminateOnTotalSettings = field(default_factory=TerminateOnTotalSettings) -class TestEEGSynthIntegration(ez.Collection): - SETTINGS = TestEEGSynthSettings +class EEGSynthIntegrationTest(ez.Collection): + SETTINGS = EEGSynthSettingsTest SOURCE = EEGSynth() SINK = MessageLogger() @@ -345,7 +345,7 @@ def test_eegsynth_system( test_filename = get_test_fn(test_name) ez.logger.info(test_filename) - settings = TestEEGSynthSettings( + settings = EEGSynthSettingsTest( synth_settings=EEGSynthSettings( fs=fs, n_time=n_time, @@ -360,7 +360,7 @@ def test_eegsynth_system( ) ) - system = TestEEGSynthIntegration(settings) + system = EEGSynthIntegrationTest(settings) ez.run(SYSTEM=system) messages: typing.List[AxisArray] = [_ for _ in message_log(test_filename)] From 6eaf03e357851e4008ea37cec8ceba1af47fb9e3 Mon Sep 17 00:00:00 2001 From: Chadwick Boulay Date: Mon, 23 Sep 2024 21:22:54 -0400 Subject: [PATCH 5/6] affine test allclose instead of array_equal --- tests/test_affine_transform.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_affine_transform.py b/tests/test_affine_transform.py index 22d1b9f..019d155 100644 --- a/tests/test_affine_transform.py +++ b/tests/test_affine_transform.py @@ -33,22 +33,22 @@ def test_affine_generator(): gen = affine_transform(weights=csv_path, axis="ch", right_multiply=False) ax_arr_out = gen.send(axis_arr_in) - assert np.array_equal(ax_arr_out.data, expected_out) + assert np.allclose(ax_arr_out.data, expected_out) # Try again as str, not Path gen = affine_transform(weights=str(csv_path), axis="ch", right_multiply=False) ax_arr_out = gen.send(axis_arr_in) - assert np.array_equal(ax_arr_out.data, expected_out) + assert np.allclose(ax_arr_out.data, expected_out) # Try again as direct ndarray gen = affine_transform(weights=weights, axis="ch", right_multiply=False) ax_arr_out = gen.send(axis_arr_in) - assert np.array_equal(ax_arr_out.data, expected_out) + assert np.allclose(ax_arr_out.data, expected_out) # One more time, but we pre-transpose the weights and do not override right_multiply gen = affine_transform(weights=weights.T, axis="ch", right_multiply=True) ax_arr_out = gen.send(axis_arr_in) - assert np.array_equal(ax_arr_out.data, expected_out) + assert np.allclose(ax_arr_out.data, expected_out) def test_affine_passthrough(): From 9534975ddce3b1a44eb389b2c7ba1ed5104473ae Mon Sep 17 00:00:00 2001 From: Chadwick Boulay Date: Mon, 23 Sep 2024 21:33:07 -0400 Subject: [PATCH 6/6] test_aclock_agen give a little more buffer for clock wonkiness --- tests/test_synth.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_synth.py b/tests/test_synth.py index 68ae49d..ef7cad3 100644 --- a/tests/test_synth.py +++ b/tests/test_synth.py @@ -54,7 +54,7 @@ async def test_aclock_agen(dispatch_rate: typing.Optional[float]): t_elapsed = time.time() - t_start assert all([_ == ez.Flag() for _ in result]) if dispatch_rate: - assert (run_time - 1 / dispatch_rate) < t_elapsed < (run_time + 0.1) + assert (run_time - 1.1 / dispatch_rate) < t_elapsed < (run_time + 0.1) else: assert t_elapsed < (n_target * 1e-4) # 100 usec per iteration is pretty generous