Viashpy 0.6.0 (#20)

* CI: Use viash-actions/setup for installing viash

* Remove bin folder

* Fix bugs and update CI

* Python 3.12

* Propagate is True by default

* Undo logging statement change

* Add CHANGELOG entries and fix logging

* Add CHANGELOG entry

* Enabling different pytest versions in CI

* tox's --skip-env accepts regex matching

* Remove dots from python versions in matrix

* Does this substitution work?

* Remove quotes

* Fix regex

* Pytester was only added in pytest 6.2

* Dot not install pytest twice

* Try removing deprecationwarnings

* Fix formatting

* Fix tests for python 3.12

* Take extra warnings into account

* Simplify memory specification

* Fix formatting

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
  strategy:
  matrix:
  os: [ubuntu-latest, macos-latest]
- python-version: ["3.9", "3.10", "3.11"]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
 
  steps:
  - uses: actions/checkout@v4
@@ -36,16 +36,15 @@ jobs:
  - name: Install tox
  run: python -m pip install tox
  - name: Test
- run: tox -e py${{ matrix.python-version }}
+ run: |
+ PYTHON_ENV="${{ matrix.python-version }}"
+ PYTHON_ENV_NO_DOTS=${PYTHON_ENV//.}
+ tox run --skip-env '^(?!py'$PYTHON_ENV_NO_DOTS').+'
  integration_tests:
  runs-on: ubuntu-latest
  steps:
  - uses: actions/checkout@v4
- - name: Fetch viash
- run: |
- bin/init -n
- tree .
- bin/viash -h
+ - uses: viash-io/viash-actions/setup@v4
  - name: Viash ns test
  run: |
- ./bin/viash ns test -s tests/integration/ -p docker --memory 1GB
+ viash ns test -s tests/integration/ -p docker --memory 1GB

CHANGELOG.rst

@@ -2,6 +2,25 @@
 Changelog
 *********
 
+0.6.0 (TBD)
+===========
+
+Breaking Changes
+----------------
+* The minimum supported version of pytest is now `6.2` (PR #20).
+
+Minor Changes
+-------------
+* Added support for python 3.12 (PR #20).
+* (development) Removed the bin/ folder in favour of a viash project config (`_viash.yaml`) (PR #20).
+
+Bug fixes
+---------
+* Fix `run_component` setting `--memory` and `--cpu` at the incorrect location in the `viash run` command (PR #20).
+* Fix tests for pytest versions older than `7.0` (PR #20).
+* Match the logging level to the level in the config from pytest (see pytests' `--log-cli-level`) (PR #20)
+
+
 0.5.0 (6/10/2023)
 ================
 

_viash.yaml

@@ -0,0 +1 @@
+viash_version: 0.8.2

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = 'setuptools.build_meta'
 write_to = "viashpy/__version__.py"
 
 [tool.black]
-target-version = ['py39', 'py310', 'py311']
+target-version = ['py39', 'py310', 'py311', 'py312']
 exclude = '''
 (
  \.egg

setup.cfg

@@ -48,7 +48,7 @@ setup_requires =
  setuptools-scm
  setuptools_scm_git_archive
 install_requires =
- pytest >= 3.5
+ pytest >= 6.2
  PyYAML ~= 6.0
 
 [options.extras_require]

tests/conftest.py

@@ -1 +1,21 @@
+from _pytest.logging import get_log_level_for_setting
+import logging
+
 pytest_plugins = "pytester"
+
+
+def pytest_configure(config):
+ # Some of the pytest functions used here are not officially exposed through
+ # their API. We test for different pytest versions so should be OK.
+ level = get_log_level_for_setting(config, "log_cli_level")
+ if not level:
+ level = logging.WARNING
+ handler = logging.StreamHandler()
+ handler.setLevel(level)
+ # Set levels on the root logger. Logging events are passed up
+ # the chain to the root logger, which will emit the events.
+ # For this to happen, the non-root loggers need to have set 'propagate'
+ # to 'True', which is the default.
+ root_logger = logging.getLogger()
+ root_logger.setLevel(level)
+ root_logger.addHandler(handler)

tests/integration/test_run_component/dummy_config.vsh.yaml

@@ -23,7 +23,9 @@ functionality:
  test_resources:
  - type: python_script
  path: test_script.py
+ - path: /tests/integration/test_run_component/dummy_config.vsh.yaml
 platforms:
+ - type: native
  - type: docker
  image: python:3.10
  test_setup:
@@ -32,5 +34,11 @@ platforms:
  - type: python
  packages:
  - /viashpy
- - type: native
+ - ruamel.yaml
+ - type: apt
+ packages:
+ - default-jdk
+ - type: docker
+ run: |
+ curl -fsSL dl.viash.io | bash; mv viash /usr/local/bin/
  - type: nextflow

tests/integration/test_run_component/test_script.py

@@ -1,7 +1,10 @@
 import pytest
 import sys
+from pathlib import Path
 from io import StringIO
-from contextlib import redirect_stdout
+from ruamel.yaml import YAML
+from contextlib import redirect_stdout, redirect_stderr
+import uuid
 
 ### VIASH START # noqa: E266
 meta = {
@@ -10,29 +13,83 @@
 ### VIASH END # noqa: E266
 
 
-def test_run_component(run_component):
- captured_output = run_component(["--output", "bar.txt"])
- with open("bar.txt", "r") as open_output_file:
- contents = open_output_file.read()
- assert contents == "foo!"
- assert (
- captured_output is not None
- ), "Some output from stdout or stderr should have been captured"
- assert b"This is a logging statement" in captured_output
+@pytest.fixture()
+def random_config_path(tmp_path):
+ def wrapper():
+ unique_filename = f"{str(uuid.uuid4())}.vsh.yaml"
+ temp_file = tmp_path / unique_filename
+ return temp_file
 
+ return wrapper
 
-if __name__ == "__main__":
+
+class TestRunExecutable:
+ meta = meta
+
+ def test_run_component(self, run_component):
+ captured_output = run_component(["--output", "bar.txt"])
+ with open("bar.txt", "r") as open_output_file:
+ contents = open_output_file.read()
+ assert contents == "foo!"
+ assert (
+ captured_output is not None
+ ), "Some output from stdout or stderr should have been captured"
+ assert b"This is a logging statement" in captured_output
+
+
+class TestRunUsingConfig:
+ meta = meta
+
+ @pytest.fixture()
+ def viash_source_config_path(self, random_config_path):
+ yaml_interface = YAML(typ="safe", pure=True)
+ yaml_interface.default_flow_style = False
+ original_config = yaml_interface.load(
+ Path(f"{meta['resources_dir']}/dummy_config.vsh.yaml")
+ )
+ del original_config["functionality"]["test_resources"]
+ del original_config["functionality"]["resources"][1]
+ result_path = random_config_path()
+ yaml_interface.dump(original_config, result_path)
+ return result_path
+
+ def test_run_component_check_correct_memory_syntax(self, run_component):
+ captured_output = run_component(["--output", "bar.txt"])
+ with open("bar.txt", "r") as open_output_file:
+ contents = open_output_file.read()
+ assert contents == "foo!"
+ assert (
+ captured_output is not None
+ ), "Some output from stdout or stderr should have been captured"
+ assert (
+ b"--memory looks like a parameter but is not a defined parameter and will instead be treated as a positional argument"
+ not in captured_output
+ )
+
+
+def run_pytest_and_capture_output():
  temp_stdout = StringIO()
+ temp_stderr = StringIO()
  print(f"meta: {meta}")
+ with redirect_stdout(temp_stdout), redirect_stderr(temp_stderr):
+ exit_code = pytest.main(
+ [__file__, "--log-cli-level", "DEBUG"], plugins=["viashpy"]
+ )
+ stdout_str = temp_stdout.getvalue()
+ stderr_str = temp_stderr.getvalue()
+ print(f"stdout: {stdout_str}\nstderr: {stderr_str}\nexit_code: {exit_code}")
+ return stdout_str, stderr_str, exit_code
+
+
+if __name__ == "__main__":
  assert (
  meta["memory_gb"] is not None
  ), "This test should be executed with some --memory set."
- with redirect_stdout(temp_stdout):
- result = pytest.main([__file__], plugins=["viashpy"])
- stdout_str = temp_stdout.getvalue()
- print(stdout_str)
+
+ stdout_str, stderr_str, exit_code = run_pytest_and_capture_output()
  assert (
  "Different values were defined in the 'meta' dictionary that limit memory, choosing the one with the smallest unit"
  not in stdout_str
  )
- sys.exit(result)
+
+ sys.exit(exit_code)