From 388703423db071f44fa16a1322b616ce014d2def Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 16 Mar 2025 16:42:28 +0100 Subject: [PATCH 1/8] convert to pixi & update GHA --- .gitattributes | 2 + .github/workflows/release-please.yml | 31 +- .github/workflows/test.yml | 104 +- .gitignore | 5 +- pixi.lock | 1580 ++++++++++++++++++++++++++ pyproject.toml | 87 +- 6 files changed, 1699 insertions(+), 110 deletions(-) create mode 100644 .gitattributes create mode 100644 pixi.lock diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..887a2c1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index 4766b98..f2758d0 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -17,34 +17,27 @@ jobs: release-type: python package-name: snakemake-interface-executor-plugins - publish: + publish-pypi: runs-on: ubuntu-latest needs: release-please if: ${{ needs.release-please.outputs.release_created }} - steps: - - uses: actions/checkout@v3 - - - uses: actions/setup-python@v2 - with: - python-version: "3.11" - - name: Install poetry - run: pip install poetry - - - name: Determine dependencies - run: poetry lock + steps: + - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 + - name: Install Pixi + uses: prefix-dev/setup-pixi@v0.8.3 with: - python-version: "3.11" - cache: poetry + environments: publish + pixi-version: v0.42.1 - - name: Install Dependencies using Poetry + - name: Build source and wheel distribution + check build + # this will build the source and wheel into the dist/ directory run: | - poetry install + pixi run --environment publish check-build - - name: Publish to PyPi + - name: Publish distribution to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 env: PYPI_USERNAME: __token__ PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }} - run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 2057e74..82b51c2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -7,88 +7,54 @@ on: pull_request: branches-ignore: [] +permissions: + contents: read + checks: write + issues: write + pull-requests: write + jobs: - formatting: + quality-control: runs-on: ubuntu-latest steps: - name: Check out the code - uses: actions/checkout@v3 - - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - - name: Install poetry - run: pip install poetry - - - name: Determine dependencies - run: poetry lock - - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - cache: poetry + uses: actions/checkout@v4 - - name: Install Dependencies using Poetry - run: poetry install - - - name: Check formatting - run: poetry run black --check . - - linting: - runs-on: ubuntu-latest - steps: - - name: Check out the code - uses: actions/checkout@v3 - - - uses: actions/setup-python@v4 + - name: Install Pixi + uses: prefix-dev/setup-pixi@v0.8.3 with: - python-version: "3.11" - - - name: Install poetry - run: pip install poetry + environments: dev + pixi-version: v0.42.1 + cache: true - - name: Determine dependencies - run: poetry lock - - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - cache: poetry + - name: Ruff Format + if: always() + run: | + pixi run --environment dev format --check - - name: Install Dependencies using Poetry - run: poetry install + - name: Ruff lint + if: always() + run: | + pixi run --environment dev lint --diff + # - name: Mypy + # if: always() + # run: | + # pixi run --environment dev type-check - - name: Check code - run: poetry run flake8 + - name: Collect QC + run: echo "All quality control checks passed" testing: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 + - name: Install Pixi + uses: prefix-dev/setup-pixi@v0.8.3 with: - python-version: "3.11" - - - name: Install poetry - run: pip install poetry - - - name: Determine dependencies - run: poetry lock - - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - cache: poetry - - - name: Install dependencies - run: | - pip install connection-pool # because it is incompatible with poetry - poetry install - - - name: Run pytest - run: poetry run coverage run -m pytest tests/tests.py + environments: dev + pixi-version: v0.42.1 + cache: true - - name: Run Coverage - run: poetry run coverage report -m + - name: Run tests + run: pixi run --environment dev test --show-capture=all -s -vv diff --git a/.gitignore b/.gitignore index bcc3d59..56de653 100644 --- a/.gitignore +++ b/.gitignore @@ -159,4 +159,7 @@ cython_debug/ # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ -poetry.lock \ No newline at end of file +poetry.lock +# pixi environments +.pixi +*.egg-info diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..89c5e9f --- /dev/null +++ b/pixi.lock @@ -0,0 +1,1580 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + osx-arm64: + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda + - 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-[tool.poetry.dependencies] -argparse-dataclass = "^2.0.0" -python = "^3.11" -throttler = "^1.2.2" -snakemake-interface-common = "^1.17.4" - -[tool.poetry.dev-dependencies] -black = "^24.0.0" -coverage = {extras = ["toml"], version = "^6.3.1"} -flake8 = "^4.0.1" -flake8-bugbear = "^22.1.11" -pytest = "^7.0" -snakemake = {git="https://github.com/snakemake/snakemake.git"} -snakemake-executor-plugin-cluster-generic = {git = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic.git"} +description = "This package provides a stable interface for interactions between Snakemake and its executor plugins." +authors = [{ name = "Johannes Köster", email = "johannes.koester@uni-due.de" }] +license = { text = "MIT" } +readme = "README.md" +requires-python = ">=3.11" +dependencies = [ + "snakemake-interface-common>=1.17.4", + "throttler>=1.2.2", + "argparse-dataclass>=2.0.0", +] [tool.coverage.run] omit = [".*", "*/site-packages/*"] @@ -31,3 +21,58 @@ fail_under = 63 [build-system] build-backend = "poetry.core.masonry.api" requires = ["poetry-core"] + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["osx-arm64"] + +[tool.pixi.pypi-dependencies] + +[tool.pixi.tasks] + +[tool.pixi.environments] +dev = { features = ["dev"] } +publish = { features = ["publish"] } + +[tool.pixi.feature.dev.pypi-dependencies] +snakemake-interface-executor-plugins = { path = ".", editable = true } +snakemake = { git = "https://github.com/snakemake/snakemake.git" } +snakemake-interface-common = { git = "https://github.com/snakemake/snakemake-interface-common.git" } +snakemake-executor-plugin-cluster-generic = { git = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic.git" } + +[tool.pixi.feature.dev.tasks.test] +cmd = [ + "pytest", + "--cov=snakemake_interface_executor_plugins", + "--cov-report=xml:coverage-report/coverage.xml", + "--cov-report=term-missing", + "tests/tests.py" +] +description = "Run tests and generate coverage report" + + +[tool.pixi.feature.dev.dependencies] +pytest = ">=8.3.5,<9" +ruff = ">=0.10.0,<0.11" +mypy = ">=1.15.0,<2" +pytest-cov = ">=6.0.0,<7" + +[tool.pixi.feature.dev.tasks] +format = "ruff format snakemake_interface_executor_plugins" +lint = "ruff check" +type-check = "mypy snakemake_interface_executor_plugins/" +qc = { depends-on = ["format", "lint", "type-check"] } + +[tool.mypy] +ignore_missing_imports = true + +# Publish +[tool.pixi.feature.publish.dependencies] +twine = ">=6.1.0,<7" +python-build = ">=1.2.2,<2" + +[tool.pixi.feature.publish.tasks] +build = { cmd = "python -m build", description = "Build the package into the dist/ directory" } +check-build = { cmd = "python -m twine check dist/*", depends-on = [ + "build", +], description = "Check that the package can be uploaded" } From dc7d34bb5a788f1633d216852406998708a2195d Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 16 Mar 2025 16:42:34 +0100 Subject: [PATCH 2/8] format --- snakemake_interface_executor_plugins/executors/base.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/snakemake_interface_executor_plugins/executors/base.py b/snakemake_interface_executor_plugins/executors/base.py index 1be689f..1f16f36 100644 --- a/snakemake_interface_executor_plugins/executors/base.py +++ b/snakemake_interface_executor_plugins/executors/base.py @@ -46,7 +46,8 @@ def isdigit(i): for resource, value in job.resources.items() if isinstance(value, int) # need to check bool seperately because bool is a subclass of int - and isdigit(value) and resource not in excluded_resources + and isdigit(value) + and resource not in excluded_resources } def get_resource_declarations(self, job: JobExecutorInterface): From 8ba09a684717e1f434cb7a5046e36bab6775340e Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 16 Mar 2025 17:23:32 +0100 Subject: [PATCH 3/8] fix all mypy errors --- .../executors/base.py | 5 ++++- .../executors/real.py | 12 ++++++++--- .../executors/remote.py | 21 +++++++++++++++---- snakemake_interface_executor_plugins/jobs.py | 5 +++-- .../scheduler.py | 6 ++++++ .../workflow.py | 9 ++++++++ 6 files changed, 48 insertions(+), 10 deletions(-) diff --git a/snakemake_interface_executor_plugins/executors/base.py b/snakemake_interface_executor_plugins/executors/base.py index 1f16f36..a6321cf 100644 --- a/snakemake_interface_executor_plugins/executors/base.py +++ b/snakemake_interface_executor_plugins/executors/base.py @@ -21,13 +21,16 @@ class SubmittedJobInfo: class AbstractExecutor(ABC): + workflow: WorkflowExecutorInterface + logger: LoggerExecutorInterface + def __init__( self, workflow: WorkflowExecutorInterface, logger: LoggerExecutorInterface, ): self.workflow = workflow - self.dag = workflow.dag + self.dag = workflow.dag # we cant type annotate this because dag type is in snakemake self.logger = logger def get_resource_declarations_dict(self, job: JobExecutorInterface): diff --git a/snakemake_interface_executor_plugins/executors/real.py b/snakemake_interface_executor_plugins/executors/real.py index dabb9b7..2d2207c 100644 --- a/snakemake_interface_executor_plugins/executors/real.py +++ b/snakemake_interface_executor_plugins/executors/real.py @@ -4,13 +4,13 @@ __license__ = "MIT" from abc import abstractmethod -from typing import Dict +from typing import Mapping from snakemake_interface_executor_plugins.executors.base import ( AbstractExecutor, SubmittedJobInfo, ) from snakemake_interface_executor_plugins.logging import LoggerExecutorInterface -from snakemake_interface_executor_plugins.settings import ExecMode +from snakemake_interface_executor_plugins.settings import ExecMode, ExecutorSettingsBase from snakemake_interface_executor_plugins.utils import ( encode_target_jobs_cli_args, format_cli_arg, @@ -21,6 +21,12 @@ class RealExecutor(AbstractExecutor): + # Class attributes with type annotations + workflow: WorkflowExecutorInterface + logger: LoggerExecutorInterface + executor_settings: ExecutorSettingsBase + snakefile: str + def __init__( self, workflow: WorkflowExecutorInterface, @@ -176,5 +182,5 @@ def format_job_exec(self, job: JobExecutorInterface) -> str: ) return args - def envvars(self) -> Dict[str, str]: + def envvars(self) -> Mapping[str, str]: return self.workflow.spawned_job_args_factory.envvars() diff --git a/snakemake_interface_executor_plugins/executors/remote.py b/snakemake_interface_executor_plugins/executors/remote.py index 74ef734..dabd69d 100644 --- a/snakemake_interface_executor_plugins/executors/remote.py +++ b/snakemake_interface_executor_plugins/executors/remote.py @@ -12,7 +12,7 @@ import sys import tempfile import threading -from typing import Generator, List +from typing import Generator, List, Optional from snakemake_interface_common.exceptions import WorkflowError from snakemake_interface_executor_plugins.executors.base import SubmittedJobInfo from snakemake_interface_executor_plugins.executors.real import RealExecutor @@ -36,7 +36,20 @@ class RemoteExecutor(RealExecutor, ABC): also for the cloud. """ - default_jobscript = "jobscript.sh" + # Class attributes with type annotations + default_jobscript: str = "jobscript.sh" + _next_seconds_between_status_checks: Optional[int] + max_status_checks_per_second: float + jobname: str + snakefile: str + is_default_jobscript: bool + jobscript: str + _tmpdir: Optional[str] + active_jobs: List[SubmittedJobInfo] + lock: threading.Lock + wait: bool + wait_thread: threading.Thread + status_rate_limiter: Throttler def __init__( self, @@ -118,7 +131,7 @@ def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]): ... def get_exec_mode(self) -> ExecMode: - return ExecMode.REMOTE + return ExecMode.REMOTE # type: ignore def get_python_executable(self): return ( @@ -128,7 +141,7 @@ def get_python_executable(self): else "python" ) - def get_job_args(self, job: JobExecutorInterface): + def get_job_args(self, job: JobExecutorInterface, **kwargs): waitfiles_parameter = "" if SharedFSUsage.INPUT_OUTPUT in self.workflow.storage_settings.shared_fs_usage: wait_for_files = [] diff --git a/snakemake_interface_executor_plugins/jobs.py b/snakemake_interface_executor_plugins/jobs.py index 8af4b2c..61b4338 100644 --- a/snakemake_interface_executor_plugins/jobs.py +++ b/snakemake_interface_executor_plugins/jobs.py @@ -5,9 +5,10 @@ from abc import ABC, abstractmethod import sys -from typing import Any, Iterable, Mapping, Optional, Sequence, Union +from typing import Any, Iterable, Mapping, Optional, Sequence, Union, List from snakemake_interface_common.rules import RuleInterface +from snakemake_interface_executor_plugins.utils import TargetSpec class JobExecutorInterface(ABC): @@ -58,7 +59,7 @@ def output(self) -> Iterable[str]: ... def register(self, external_jobid: Optional[str] = None) -> None: ... @abstractmethod - def get_target_spec(self) -> str: ... + def get_target_spec(self) -> List[TargetSpec]: ... @abstractmethod def rules(self) -> Iterable[RuleInterface]: ... diff --git a/snakemake_interface_executor_plugins/scheduler.py b/snakemake_interface_executor_plugins/scheduler.py index b7a3843..a5ac324 100644 --- a/snakemake_interface_executor_plugins/scheduler.py +++ b/snakemake_interface_executor_plugins/scheduler.py @@ -4,8 +4,14 @@ __license__ = "MIT" from abc import ABC, abstractmethod +from typing import Callable +from snakemake_interface_executor_plugins.jobs import JobExecutorInterface class JobSchedulerExecutorInterface(ABC): + submit_callback: Callable[[JobExecutorInterface], None] + finish_callback: Callable[[JobExecutorInterface], None] + error_callback: Callable[[JobExecutorInterface], None] + @abstractmethod def executor_error_callback(self, exception: Exception) -> None: ... diff --git a/snakemake_interface_executor_plugins/workflow.py b/snakemake_interface_executor_plugins/workflow.py index 868d75d..9e7e65d 100644 --- a/snakemake_interface_executor_plugins/workflow.py +++ b/snakemake_interface_executor_plugins/workflow.py @@ -21,6 +21,7 @@ GroupSettingsExecutorInterface, RemoteExecutionSettingsExecutorInterface, StorageSettingsExecutorInterface, + ExecutorSettingsBase, ) @@ -53,6 +54,10 @@ def group_settings(self) -> GroupSettingsExecutorInterface: ... @abstractmethod def executor_plugin(self) -> Optional[Plugin]: ... + @property + @abstractmethod + def executor_settings(self) -> ExecutorSettingsBase: ... + @property @abstractmethod def resource_scopes(self): ... @@ -72,3 +77,7 @@ def workdir_init(self): ... @property @abstractmethod def scheduler(self) -> JobSchedulerExecutorInterface: ... + + @property + @abstractmethod + def dag(self): ... From 17075b1b9b16770d76186deb333c14ba8c4f3bbf Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 16 Mar 2025 17:23:53 +0100 Subject: [PATCH 4/8] re-activate mypy type checks in CI --- .github/workflows/test.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 82b51c2..4c6a71d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -36,10 +36,11 @@ jobs: if: always() run: | pixi run --environment dev lint --diff - # - name: Mypy - # if: always() - # run: | - # pixi run --environment dev type-check + + - name: Mypy + if: always() + run: | + pixi run --environment dev type-check - name: Collect QC run: echo "All quality control checks passed" From 3e88db1a4cda1738a0b65e7c969ee115e9dff592 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 16 Mar 2025 17:27:20 +0100 Subject: [PATCH 5/8] fix: add linux to pixi config --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fdc71a0..f6b7f0b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ requires = ["poetry-core"] [tool.pixi.project] channels = ["conda-forge"] -platforms = ["osx-arm64"] +platforms = ["osx-arm64", "linux-64"] [tool.pixi.pypi-dependencies] From 6e43a00c6a000b072074c0794ee8cca8946dbcb2 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 16 Mar 2025 17:28:25 +0100 Subject: [PATCH 6/8] chore: lock --- pixi.lock | 814 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 813 insertions(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index 89c5e9f..f775857 100644 --- a/pixi.lock +++ b/pixi.lock @@ -6,6 +6,33 @@ environments: indexes: - 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