aiida-hyperqueue 0.2.1__tar.gz → 0.4.0__tar.gz

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/PKG-INFO

@@ -1,9 +1,9 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: aiida-hyperqueue
-Version: 0.2.1
+Version: 0.4.0
 Summary: AiiDA plugin for the HyperQueue metascheduler
 Author: Marnik Bercx, Jusong Yu
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Classifier: Framework :: AiiDA
 Classifier: Development Status :: 3 - Alpha
@@ -13,7 +13,7 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python
 License-File: LICENSE
-Requires-Dist: aiida-core~=2.0,<2.7
+Requires-Dist: aiida-core~=2.7
 Requires-Dist: sphinx ; extra == "docs"
 Requires-Dist: myst-parser ; extra == "docs"
 Requires-Dist: sphinx-design ; extra == "docs"
@@ -29,6 +29,7 @@ Project-URL: Source, https://github.com/aiidateam/aiida-hyperqueue
 Provides-Extra: docs
 Provides-Extra: pre-commit
 Provides-Extra: tests
+Import-Name: aiida_hyperqueue
 
 [![Build Status](https://github.com/aiidateam/aiida-hyperqueue/workflows/ci/badge.svg)](https://github.com/aiidateam/aiida-hyperqueue/actions)
 [![Docs status](https://readthedocs.org/projects/aiida-hyperqueue/badge)](http://aiida-hyperqueue.readthedocs.io/)

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/__init__.py

@@ -1,8 +1,7 @@
-# -*- coding: utf-8 -*-
 """
 aiida_hyperqueue
 
 AiiDA plugin for the HyperQueue metascheduler
 """
 
-__version__ = "0.2.1"
+__version__ = "0.4.0"

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/__init__.py

@@ -1,5 +1,4 @@
-# -*- coding: utf-8 -*-
-from .root import cmd_root  # noqa: F401
+from .alloc import cmd_add, cmd_list, cmd_remove  # noqa: F401
 from .install import cmd_install  # noqa: F401
+from .root import cmd_root  # noqa: F401
 from .server import cmd_info, cmd_start, cmd_stop  # noqa: F401
-from .alloc import cmd_list, cmd_add, cmd_remove  # noqa: F401

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/alloc.py

@@ -1,7 +1,6 @@
-# -*- coding: utf-8 -*-
 import click
 
-from aiida.cmdline.params import options, arguments
+from aiida.cmdline.params import arguments, options
 from aiida.cmdline.utils import echo
 
 from .root import cmd_root

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/install.py

@@ -1,10 +1,10 @@
-# -*- coding: utf-8 -*-
-import click
-import tempfile
-import requests
 import tarfile
+import tempfile
 from pathlib import Path
 
+import click
+import requests
+
 from aiida import orm
 from aiida.cmdline.utils import echo
 
@@ -81,7 +81,7 @@ def cmd_install(
         with computer.get_transport() as transport:
             # Get the abs path of remote bin dir
             retval, stdout, stderr = transport.exec_command_wait(
-                f"echo {str(remote_bin_dir)}"
+                f"echo {remote_bin_dir!s}"
             )
             if retval != 0:
                 echo.echo_critical(
@@ -102,7 +102,7 @@ def cmd_install(
             )
 
             # XXX: should transport.put take care of this already??
-            transport.exec_command_wait(f"chmod +x {str(remote_bin_dir / 'hq')}")
+            transport.exec_command_wait(f"chmod +x {remote_bin_dir / 'hq'!s}")
 
             # write to bashrc
             if write_bashrc:

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/params/arguments.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 from aiida.cmdline.params import arguments as core_arguments
 
 COMPUTER = core_arguments.COMPUTER

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/params/options.py

@@ -1,9 +1,9 @@
-# -*- coding: utf-8 -*-
 """Reusable options for CLI commands."""
 
 import functools
 
 import click
+
 from aiida.cmdline.params import options as core_options
 from aiida.cmdline.params import types as core_types
 

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/root.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Command line interface `aiida-hq` for aiida-hyperqueue.
 The CLI implementation prototype from `aiida-pseudo`.
 """

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/cli/server.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
 import click
 
 from aiida.cmdline.utils import echo
 
-from .root import cmd_root
 from .params import arguments
+from .root import cmd_root
 
 
 @cmd_root.group("server")

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/aiida_hyperqueue/scheduler.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 ###########################################################################
 # Copyright (c), The AiiDA team. All rights reserved.                     #
 # This file is part of the AiiDA code.                                    #
@@ -14,8 +13,8 @@ import typing as t
 import warnings
 
 from aiida.common.extendeddicts import AttributeDict
-from aiida.schedulers import Scheduler, SchedulerError
-from aiida.schedulers.datastructures import JobInfo, JobState, JobResource, JobTemplate
+from aiida.schedulers import BashCliScheduler, Scheduler, SchedulerError
+from aiida.schedulers.datastructures import JobInfo, JobResource, JobState, JobTemplate
 
 # Mapping of HyperQueue states to AiiDA `JobState`s
 _MAP_STATUS_HYPERQUEUE = {
@@ -62,25 +61,26 @@ class HyperQueueJobResource(JobResource):
         try:
             resources.num_cpus = kwargs.pop("num_cpus")
         except KeyError:
+            # For backward compatibility where `num_machines` and `num_mpiprocs_per_machine`
+            # are set. `num_mpiprocs_per_machine` is normally injected by aiida-core's
+            # `Scheduler.preprocess_resources` from the computer's
+            # `default_mpiprocs_per_machine`, which is `None` when the computer defines no
+            # default — hence the `or`-fallback to 1 rather than a `pop` default.
+            num_mpiprocs_per_machine = kwargs.pop("num_mpiprocs_per_machine", None) or 1
             try:
-                # For backward compatibility where `num_machines` and `num_mpiprocs_per_machine` are setting
-                # TODO: I only setting the default value as 1 for `num_mpiprocs_per_machine` because aiida-quantumespresso override
-                # resources default with `num_machines` set to 1 and then get builder with such setting.
-                # The `num_mpiprocs_per_machine` sometime can be read from "Default #procs/machine" of computer setup but if it is not exist
-                # the builder can not be properly get without passing `option` to builder generator.
-                # It is anyway a workaround for backward compatibility so this default is implemented despite it is quite specific for the qe plugin.
-                resources.num_cpus = kwargs.pop("num_machines") * kwargs.pop(
-                    "num_mpiprocs_per_machine", 1
+                resources.num_cpus = (
+                    kwargs.pop("num_machines") * num_mpiprocs_per_machine
                 )
             except KeyError:
                 raise KeyError(
                     "Must specify `num_cpus`, or (`num_machines` and `num_mpiprocs_per_machine`)"
                 )
             else:
-                message = "The `num_machines` and `num_mpiprocs_per_machine` for setting hyperqueue resources are deprecated. "
-                "Please set `num_cpus` and `memory_mb`."
-
-                message = f"{message} (this will be removed in aiida-hyperqueue v1.0)"
+                message = (
+                    "The `num_machines` and `num_mpiprocs_per_machine` for setting hyperqueue "
+                    "resources are deprecated. Please set `num_cpus` and `memory_mb`. "
+                    "(this will be removed in aiida-hyperqueue v1.0)"
+                )
                 warnings.warn(message, AiiDAHypereQueueDeprecationWarning, stacklevel=3)
         else:
             if not isinstance(resources.num_cpus, int):
@@ -98,15 +98,20 @@ class HyperQueueJobResource(JobResource):
 
     @classmethod
     def accepts_default_mpiprocs_per_machine(cls):
-        """Return True if this subclass accepts a `default_mpiprocs_per_machine` key, False otherwise."""
-        return False
+        """Return True if this subclass accepts a `default_mpiprocs_per_machine` key, False otherwise.
+
+        Accepting it lets the backward-compatibility `num_machines` path pick up the
+        computer's ``default_mpiprocs_per_machine`` instead of silently running on a
+        single CPU.
+        """
+        return True
 
     def get_tot_num_mpiprocs(self):
         """Return the total number of cpus of this job resource."""
         return self.num_cpus
 
 
-class HyperQueueScheduler(Scheduler):
+class HyperQueueScheduler(BashCliScheduler):
     """Support for the HyperQueue scheduler (https://it4innovations.github.io/hyperqueue/stable/)."""
 
     _logger = Scheduler._logger.getChild("hyperqueue")

{aiida_hyperqueue-0.2.1 → aiida_hyperqueue-0.4.0}/pyproject.toml

@@ -21,10 +21,10 @@ classifiers = [
     "Natural Language :: English",
     "Programming Language :: Python",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 dependencies = [
-    "aiida-core~=2.0,<2.7",
+    "aiida-core~=2.7",
 ]
 
 [project.urls]

aiida_hyperqueue-0.2.1/.github/workflows/cd.yml

@@ -1,52 +0,0 @@
-name: cd
-
-on:
-    push:
-        tags:
-        - 'v[0-9]+.[0-9]+.[0-9]+*'
-
-jobs:
-
-    validate-release-tag:
-
-        if: github.repository == 'aiidateam/aiida-hyperqueue'
-        runs-on: ubuntu-latest
-
-        steps:
-        -   name: Checkout source
-            uses: actions/checkout@v3
-
-        -   name: Set up Python 3.10
-            uses: actions/setup-python@v4
-            with:
-                python-version: '3.10'
-
-        -   name: Validate the tag version against the package version
-            run: python .github/workflows/validate_release_tag.py $GITHUB_REF
-
-    publish:
-
-        name: Publish to PyPI
-        needs: [validate-release-tag]
-        runs-on: ubuntu-latest
-        environment: deployment
-        permissions:
-            id-token: write
-
-        steps:
-        -   name: Checkout source
-            uses: actions/checkout@v3
-
-        -   name: Set up Python 3.10
-            uses: actions/setup-python@v4
-            with:
-                python-version: '3.10'
-
-        -   name: Install flit
-            run: pip install flit~=3.8
-
-        -   name: Build with flit
-            run: flit build
-
-        -   name: Publish to PyPI using Trusted Publishing
-            uses: pypa/gh-action-pypi-publish@release/v1

aiida_hyperqueue-0.2.1/.github/workflows/ci.yml

@@ -1,30 +0,0 @@
-name: ci
-
-on: [push, pull_request]
-
-jobs:
-
-  tests:
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    strategy:
-      matrix:
-        python-version: ["3.10"]
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install .[tests]
-
-    - name: Run test suite
-      run: |
-        chmod og-rw ~
-        pytest --cov aiida_hyperqueue --cov-append .

aiida_hyperqueue-0.2.1/.github/workflows/update_changelog.py

@@ -1,96 +0,0 @@
-#!/bin/bash
-# -*- coding: utf-8 -*-
-"""Script for automatically updating the `CHANGELOG.md` based on the commits since the latest release tag."""
-
-from pathlib import Path
-import re
-import subprocess
-
-DEFAULT_CHANGELOG_SECTIONS = """
-### ‼️ Breaking changes
-
-
-### ✨ New features
-
-
-### 🗑️ Deprecations
-
-
-### 👌 Improvements
-
-
-### 🐛 Bug fixes
-
-
-### 📚 Documentation
-
-
-### 🔧 Maintenance
-
-
-### ⬆️ Update dependencies
-
-
-### 🧪 Tests
-
-
-### ♻️ Refactor
-
-"""
-
-
-def update_changelog():
-    """Update the `CHANGELOG.md` for a first draft of the release."""
-
-    print("🔍 Checking the current version number")
-    current_changelog = Path("CHANGELOG.md").read_text(encoding="utf-8")
-
-    from aiida_hyperqueue import __version__
-
-    if str(__version__) in current_changelog:
-        print("🛑 Current version already in `CHANGELOG.md`. Skipping...")
-        return
-
-    print("⬆️ Found updated version number, adapting `CHANGELOG.md`.")
-    tags = subprocess.run(
-        ["git", "tag", "--sort=v:refname"],
-        capture_output=True,
-        check=True,
-        encoding="utf-8",
-    ).stdout
-    latest_tag = re.findall(r"(v\d+\.\d+\.\d+)\n", tags)[-1]
-
-    print(f"🔄 Comparing with latest tag `{latest_tag}`.")
-    commits = subprocess.run(
-        ["git", "log", "--pretty=format:'%h|%H|%s'", f"{latest_tag}..origin/main"],
-        capture_output=True,
-        check=True,
-        encoding="utf-8",
-    ).stdout
-
-    pr_pattern = re.compile(r"\(\S(?P<pr_number>\d+)\)")
-
-    changelog_message = f"## v{__version__}\n" + DEFAULT_CHANGELOG_SECTIONS
-
-    for commit in commits.splitlines():
-        # Remove the PR number from the commit message
-        pr_match = pr_pattern.search(commit)
-
-        if pr_match is not None:
-            pr_number = pr_match.groupdict()["pr_number"]
-            commit = commit.replace(rf"(#{pr_number})", "")
-
-        # Add the commit hash (short) to link to the changelog
-        commit = commit.strip("'")
-        hash_short, hash_long, message = commit.split("|", maxsplit=2)
-        message += f" [[{hash_short}](https://github.com/aiidateam/aiida-hyperqueue/commit/{hash_long})]"
-        changelog_message += f"\n* {message}"
-
-    with Path("CHANGELOG.md").open("w", encoding="utf8") as handle:
-        handle.write(changelog_message + "\n\n" + current_changelog)
-
-    print("🚀 Success! Finalise the `CHANGELOG.md` and let's get this baby released.")
-
-
-if __name__ == "__main__":
-    update_changelog()

aiida_hyperqueue-0.2.1/.github/workflows/validate_release_tag.py

@@ -1,45 +0,0 @@
-# -*- coding: utf-8 -*-
-"""Validate that the version in the tag label matches the version of the package."""
-
-import argparse
-import ast
-from pathlib import Path
-
-
-def get_version_from_module(content: str) -> str:
-    """Get the ``__version__`` attribute from a module.
-
-    .. note:: This has been adapted from :mod:`setuptools.config`.
-    """
-    try:
-        module = ast.parse(content)
-    except SyntaxError as exception:
-        raise OSError("Unable to parse module.") from exception
-
-    try:
-        return next(
-            ast.literal_eval(statement.value)
-            for statement in module.body
-            if isinstance(statement, ast.Assign)
-            for target in statement.targets
-            if isinstance(target, ast.Name) and target.id == "__version__"
-        )
-    except StopIteration as exception:
-        raise OSError(
-            "Unable to find the `__version__` attribute in the module."
-        ) from exception
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument("GITHUB_REF", help="The GITHUB_REF environmental variable")
-    args = parser.parse_args()
-    assert args.GITHUB_REF.startswith(
-        "refs/tags/v"
-    ), f'GITHUB_REF should start with "refs/tags/v": {args.GITHUB_REF}'
-    tag_version = args.GITHUB_REF[11:]
-    package_version = get_version_from_module(
-        Path("aiida_hyperqueue/__init__.py").read_text(encoding="utf-8")
-    )
-    error_message = f"The tag version `{tag_version}` is different from the package version `{package_version}`"
-    assert tag_version == package_version, error_message

aiida_hyperqueue-0.2.1/.gitignore

@@ -1,14 +0,0 @@
-*.pyc
-*.swo
-*.swp
-~*
-*~
-.project
-*.egg*
-.DS_Store
-.coverage
-.pytest_cache
-.vscode
-build/
-dist/
-pip-wheel-metadata/

aiida_hyperqueue-0.2.1/.pre-commit-config.yaml

@@ -1,17 +0,0 @@
-# Install pre-commit hooks via:
-# pre-commit install
-repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
-      hooks:
-        - id: end-of-file-fixer
-        - id: fix-encoding-pragma
-        - id: mixed-line-ending
-        - id: trailing-whitespace
-        - id: check-json
-
-    - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.6.5
-      hooks:
-      - id: ruff-format
-      - id: ruff

aiida_hyperqueue-0.2.1/.readthedocs.yml

@@ -1,26 +0,0 @@
-version: 2
-
-# YAML adapted from aiida-core .readthedocs.yml
-
-# Disable all unneeded formats
-formats: []
-
-build:
-  os: ubuntu-22.04
-  tools:
-    python: '3.11'
-  jobs:
-    # Use uv to speed up the build
-    # https://docs.readthedocs.io/en/stable/build-customization.html#install-dependencies-with-uv
-    post_create_environment:
-    - asdf plugin add uv
-    - asdf install uv 0.2.9
-    - asdf global uv 0.2.9
-    post_install:
-    - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install .[docs]
-
-# Let the build fail if there are any warnings
-sphinx:
-  builder: html
-  configuration: docs/source/conf.py
-  fail_on_warning: true

aiida_hyperqueue-0.2.1/CHANGELOG.md

@@ -1,25 +0,0 @@
-## v0.2.1
-
-* Add `update_changelog.py` script [[9b03acb](https://github.com/aiidateam/aiida-hyperqueue/commit/9b03acbf9cb804ef7f3c35c6d5b7495b917dacc6)]
-* Add upper limit to `aiida-core` [[fd7a62f](https://github.com/aiidateam/aiida-hyperqueue/commit/fd7a62feae23f99899a025cfe411531576bf93fd)]
-
-## v0.2.0
-
-- [#18](https://github.com/aiidateam/aiida-hyperqueue/pull/18) A large refactoring with following changes:
-
-    - correctly support memory setup for resources.
-    - support turn on hyperthreading with latest version of hyperqueue.
-    - Support install hq to remote computer over CLI.
-    - adding unit tests with submit to real hq using the fixture from hyperqueue repo.
-    - Fix the submit bug for hq > 0.12 that resources are configured twice in job script and submit command.
-
-- [#26](https://github.com/aiidateam/aiida-hyperqueue/pull/26) Change alloc add worker name (name appear in slurm queue) `aiida` -> `ahq`
-- [#24](https://github.com/aiidateam/aiida-hyperqueue/pull/24) Use JSON format as output for hq job list and hq submit
-
-## v0.1.1
-
-Only a small fix to the `README.md` was added here, this release is mainly to test the automated deployment to PyPI.
-
-## v0.1.0
-
-First release on PyPI, tested with HyperQueue v0.15.0.

aiida_hyperqueue-0.2.1/docs/.gitignore

@@ -1 +0,0 @@
-build/

aiida_hyperqueue-0.2.1/docs/Makefile

@@ -1,41 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -n -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: all help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext customdefault
-
-## Runs nit-picky and converting warnings into errors to
-## make sure the documentation is properly written
-customdefault:
-	$(SPHINXBUILD) -b html -nW $(ALLSPHINXOPTS) $(BUILDDIR)/html
-
-all: html
-
-clean:
-	rm -r $(BUILDDIR)
-
-html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-
-view:
-	xdg-open $(BUILDDIR)/html/index.html