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)