diff --git a/.github/workflows/linting-common.yml b/.github/workflows/linting-common.yml index 089b79a6..4789752c 100644 --- a/.github/workflows/linting-common.yml +++ b/.github/workflows/linting-common.yml @@ -4,16 +4,13 @@ on: pull_request: paths: - 'icij-common/**.py' - push: - paths: - - 'icij-common/**.py' + - '.github/workflows/tests-common.yml' -# TODO: leverage some caching here jobs: linting-test-icij-common: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: ./.github/actions/pylint with: - path: icij-common \ No newline at end of file + path: icij-common diff --git a/.github/workflows/linting-worker.yml b/.github/workflows/linting-worker.yml index 40aa3169..ae6ce62e 100644 --- a/.github/workflows/linting-worker.yml +++ b/.github/workflows/linting-worker.yml @@ -13,7 +13,7 @@ jobs: linting-test-icij-worker: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: ./.github/actions/pylint with: - path: icij-worker \ No newline at end of file + path: icij-worker diff --git a/.github/workflows/publish-common.yml b/.github/workflows/publish-common.yml new file mode 100644 index 00000000..b8fdd5a3 --- /dev/null +++ b/.github/workflows/publish-common.yml @@ -0,0 +1,30 @@ +name: Publish icij-common + +on: + push: + tags: + - icij-common-* + +jobs: + publish-icij-common: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Install poetry + run: pipx install poetry + - name: Setup Python project + uses: actions/setup-python@v5 + with: + python-version: 3.9 + cache: poetry + - name: Install Python project + run: cd icij-common && poetry install --with dev --sync + # We assume tests have run in a previous workflow and just build and publish + - name: Build and publish + env: + PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }} + run: | + cd icij-common + poetry build + poetry config pypi-token.pypi {{ env.PYPI_API_TOKEN }} + poetry publish diff --git a/.github/workflows/publish-worker.yml b/.github/workflows/publish-worker.yml new file mode 100644 index 00000000..b644807a --- /dev/null +++ b/.github/workflows/publish-worker.yml @@ -0,0 +1,30 @@ +name: Publish icij-worker + +on: + push: + tags: + - icij-worker-* + +jobs: + publish-icij-worker: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Install poetry + run: pipx install poetry + - name: Setup Python project + uses: actions/setup-python@v5 + with: + python-version: 3.9 + cache: poetry + - name: Install Python project + run: cd icij-worker && poetry install --with dev --sync + # We assume tests have run in a previous workflow and just build and publish + - name: Build and publish + env: + PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }} + run: | + cd icij-worker + poetry build + poetry config pypi-token.pypi {{ env.PYPI_API_TOKEN }} + poetry publish diff --git a/.github/workflows/tests-common.yml b/.github/workflows/tests-common.yml new file mode 100644 index 00000000..4a13ef0a --- /dev/null +++ b/.github/workflows/tests-common.yml @@ -0,0 +1,42 @@ +name: Test for icij-common + +on: + pull_request: + paths: + - 'icij-common/**.py' + - '.github/workflows/tests-common.yml' + +jobs: + test-icij-common: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Install poetry + run: pipx install poetry + - name: Setup Python project + uses: actions/setup-python@v5 + with: + # TODO: use a version matrix here + python-version: 3.9 + cache: poetry + - name: Install Python project + run: cd icij-common && poetry install -v --with dev --sync + - name: Run tests + run: | + cd icij-common + poetry run python -m pytest -vvv --cache-clear --show-capture=all -r A . + services: + neo4j: + image: neo4j:4.4.17 + env: + NEO4J_AUTH: neo4j/theneo4jpassword + NEO4JLABS_PLUGINS: '["apoc"]' + options: >- + --health-cmd "cypher-shell -u neo4j -p theneo4jpassword -d neo4j 'CALL db.ping()'" + --health-interval 2s + --health-timeout 2s + --health-retries 10 + --health-start-period 20s + ports: + - 7475:7474 + - 7688:7687 diff --git a/.github/workflows/tests-worker.yml b/.github/workflows/tests-worker.yml new file mode 100644 index 00000000..06153641 --- /dev/null +++ b/.github/workflows/tests-worker.yml @@ -0,0 +1,41 @@ +name: Test for icij-worker + +on: + pull_request: + paths: + - 'icij-worker/**.py' + - '.github/workflows/tests-worker.yml' + +jobs: + test-icij-worker: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Install poetry + run: pipx install poetry + - name: Setup Python project + uses: actions/setup-python@v5 + with: + # TODO: use a version matrix here + python-version: 3.9 + cache: poetry + - run: cd icij-worker && poetry install -v --with dev --sync + - name: Run tests + run: | + cd icij-worker + poetry run python -m pytest -vvv --cache-clear --show-capture=all -r A . + services: + neo4j: + image: neo4j:4.4.17 + env: + NEO4J_AUTH: neo4j/theneo4jpassword + NEO4JLABS_PLUGINS: '["apoc"]' + options: >- + --health-cmd "cypher-shell -u neo4j -p theneo4jpassword -d neo4j 'CALL db.ping()'" + --health-interval 2s + --health-timeout 2s + --health-retries 10 + --health-start-period 20s + ports: + - 7475:7474 + - 7688:7687 diff --git a/README.md b/README.md index 6d078580..a1bcdb9e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -# Monorepository for ICIJ's Python libraries +# Monorepo for ICIJ Python libs -## Libraries -- [icij-common](icij-common) -- [icij-worker](icij-worker) \ No newline at end of file +## [icij-common](icij-common) [![Test for icij-common](https://github.com/ICIJ/icij-python/actions/workflows/tests-common.yml/badge.svg)](https://github.com/ICIJ/icij-python/actions/workflows/tests-common.yml) + +## [icij-worker](icij-worker) [![Test for icij-worker](https://github.com/ICIJ/icij-python/actions/workflows/tests-worker.yml/badge.svg)](https://github.com/ICIJ/icij-python/actions/workflows/tests-worker.yml) diff --git a/icij-common/.gitignore 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7b2511e4..00000000 --- a/icij-worker/.gitignore +++ /dev/null @@ -1 +0,0 @@ -pyproject.toml \ No newline at end of file diff --git a/icij-worker/icij_worker/tests/cli/conftest.py b/icij-worker/icij_worker/tests/cli/conftest.py index d4e42ba1..1c7029e1 100644 --- a/icij-worker/icij_worker/tests/cli/conftest.py +++ b/icij-worker/icij_worker/tests/cli/conftest.py @@ -1,7 +1,13 @@ import pytest +import typer from typer.testing import CliRunner @pytest.fixture(scope="session") def cli_runner() -> CliRunner: + # disable rich to avoid colors to show up in test string: + # https://github.com/tiangolo/typer/pull/647#issuecomment-1868190451 + # rich and pytest capture don't play well together: + # https://github.com/Textualize/rich/issues/317 + typer.core.rich = None return CliRunner(mix_stderr=False) diff --git a/icij-worker/icij_worker/tests/cli/test_cli.py b/icij-worker/icij_worker/tests/cli/test_cli.py index 9c1c2430..39c87cc9 100644 --- a/icij-worker/icij_worker/tests/cli/test_cli.py +++ b/icij-worker/icij_worker/tests/cli/test_cli.py @@ -9,15 +9,15 @@ @pytest.mark.parametrize("help_command", ["-h", "--help"]) def test_help(cli_runner: CliRunner, help_command: str): - result = cli_runner.invoke(cli_app, [help_command]) + result = cli_runner.invoke(cli_app, [help_command], color=False) assert result.exit_code == 0 output = result.stdout - assert "Usage: icij-worker [OPTIONS] COMMAND [ARGS]... " in output + assert "icij-worker [OPTIONS] COMMAND [ARGS]..." in output assert "--version" in output def test_version(cli_runner: CliRunner): - result = cli_runner.invoke(cli_app, ["--version"]) + result = cli_runner.invoke(cli_app, ["--version"], color=False) assert result.exit_code == 0 version = result.stdout with fail_if_exception(f"CLI app returned an invalid version: {version }"): diff --git a/icij-worker/icij_worker/tests/cli/test_workers.py b/icij-worker/icij_worker/tests/cli/test_workers.py index d30cd1d7..d59200aa 100644 --- a/icij-worker/icij_worker/tests/cli/test_workers.py +++ b/icij-worker/icij_worker/tests/cli/test_workers.py @@ -11,12 +11,12 @@ def test_workers_help(cli_runner: CliRunner, help_command: str): # When result = cli_runner.invoke( - cli_app, ["workers", help_command], catch_exceptions=False + cli_app, ["workers", help_command], catch_exceptions=False, color=False ) # Then assert result.exit_code == 0 output = result.stdout - assert "Usage: icij-worker workers [OPTIONS] COMMAND [ARGS]..." in output + assert "icij-worker workers [OPTIONS] COMMAND [ARGS]..." in output assert "start Start a pool of workers running the provided app" in output @@ -34,7 +34,7 @@ def test_workers_start( # Given test_app = "icij_worker.tests.conftest.APP" # When - result = cli_runner.invoke(cli_app, ["workers", "start", test_app]) + result = cli_runner.invoke(cli_app, ["workers", "start", test_app], color=False) # Then # Here the program will fail because the DB for the worker is not initialized, # since the CLI is running forever, launching a failing worker enables returning @@ -46,11 +46,11 @@ def test_workers_start( @pytest.mark.parametrize("help_command", ["-h", "--help"]) def test_workers_start_help(cli_runner: CliRunner, help_command: str): # When - result = cli_runner.invoke(cli_app, ["workers", "start", help_command]) + result = cli_runner.invoke(cli_app, ["workers", "start", help_command], color=False) # Then assert result.exit_code == 0 output = result.stdout - assert " Usage: icij-worker workers start [OPTIONS] APP" in output + assert "icij-worker workers start [OPTIONS] APP" in output assert "-n" in output assert "-n-workers" in output assert "-c" in output diff --git a/icij-worker/poetry.lock b/icij-worker/poetry.lock new file mode 100644 index 00000000..57c4be8e --- /dev/null +++ b/icij-worker/poetry.lock @@ -0,0 +1,454 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "astroid" +version = "3.1.0" +description = "An abstract syntax tree for Python with inference support." +optional = false +python-versions = ">=3.8.0" +files = [ + {file = "astroid-3.1.0-py3-none-any.whl", hash = "sha256:951798f922990137ac090c53af473db7ab4e70c770e6d7fae0cec59f74411819"}, + {file = "astroid-3.1.0.tar.gz", hash = "sha256:ac248253bfa4bd924a0de213707e7ebeeb3138abeb48d798784ead1e56d419d4"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} + +[[package]] +name = "click" +version = "8.1.7" +description = "Composable command line interface toolkit" +optional = false +python-versions = ">=3.7" +files = [ + {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, + {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + +[[package]] +name = "colorama" +version = "0.4.6" +description = "Cross-platform colored terminal text." +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +files = [ + {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, + {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, +] + +[[package]] +name = "dill" +version = "0.3.8" +description = "serialize all of Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "dill-0.3.8-py3-none-any.whl", hash = "sha256:c36ca9ffb54365bdd2f8eb3eff7d2a21237f8452b57ace88b1ac615b7e815bd7"}, + {file = "dill-0.3.8.tar.gz", hash = "sha256:3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca"}, +] + +[package.extras] +graph = ["objgraph (>=1.7.2)"] +profile = ["gprof2dot (>=2022.7.29)"] + +[[package]] +name = "exceptiongroup" +version = "1.2.0" +description = "Backport of PEP 654 (exception groups)" +optional = false +python-versions = ">=3.7" +files = [ + {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"}, + {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"}, +] + +[package.extras] +test = ["pytest (>=6)"] + +[[package]] +name = "icij-common" +version = "0.1.0" +description = "Common utils for ICIJ libs" +optional = false +python-versions = "^3.9" +files = [] +develop = true + +[package.dependencies] +pydantic = "^1.10" + +[package.source] +type = "directory" +url = "../icij-common" + +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +optional = false +python-versions = ">=3.7" +files = [ + {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, + {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, +] + +[[package]] +name = "isort" +version = "5.13.2" +description = "A Python utility / library to sort Python imports." +optional = false +python-versions = ">=3.8.0" +files = [ + {file = "isort-5.13.2-py3-none-any.whl", hash = "sha256:8ca5e72a8d85860d5a3fa69b8745237f2939afe12dbf656afbcb47fe72d947a6"}, + {file = "isort-5.13.2.tar.gz", hash = "sha256:48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109"}, +] + +[package.extras] +colors = ["colorama (>=0.4.6)"] + +[[package]] +name = "markdown-it-py" +version = "3.0.0" +description = "Python port of markdown-it. 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