Fix termination signal #84
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Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](pandas-dev/pandas@v1.5.3...v2.0.3) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <[email protected]>
djperrefort
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Oct 5, 2023
* Bump actions/checkout from 3 to 4 (#81) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Updates CI (#82) * Fix termination signal (#84) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
djperrefort
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Oct 17, 2023
* Adds CI for running tests (#15) * Adds CI for running tests * Fix CI typo * Adds setup step for python * Adds minimal pyproject.toml file * Update pyproject.toml * Adds missing --with directive * Adds missing description field * Adds missing docstring [skip ci] * Updates the way coverage is run * Expand .gitignore * Exceptions top (#16) * Moves exception pattern checking into dedicated method * Update top of file comments for clarity * Deletes test placeholder * Fix boolean typo * Add codacy badges to readme (#17) * Adds tests for piping shell commands (#20) * Drop accumulator pattern for node names (#21) * Use builtin support for logging (#22) * Switch to builtin logging * Explicitly set logging level * Moves logging to /var * Log directly to syslog * Add missing import * Replace accumulator (#23) * Replace accumulator patterns with single iteration * Fix typo in list unpacking * Eod cleanup (#24) * Drop support for regex ignore patterns * Increase number/detail of log messages * Drop Python2 support and impliment Python3 features * Delete test_check_ignore_node.py * Simplify set logic * Adds ability to whitelist UID and UID ranges (#25) * Adds basic whitelist * Replaces usernames with uid * Updates docs and comments * Ignore uid from 0 to 15000 * Formally package source code for pip installability (#28) * Move source into a package * Add GPL3 license * Update pyproject.toml * Removes 'if __name__' conditional * Drop /home/djperrefort/GitHub/pitt-crc/shinigami reference in testing CI * Update test suite structure to match package structure * Add CI workflow for publishing to PyPI (#30) * Updates Readme and Package Docs (#31) * Updates README * Updates package docstring * Adds ability to load settings from settings file (#32) * Introduces settings module * Configure settings to load from disk * Add dedicated method for loading settings from disk * Adds ability to skip FileNotFoundError error * Adds basic CLI parsing (#34) * Initial commit of cli module * Fixes outdated import signature * Mves main function into Application class * Mid-flight cleanup pass * Updates import signatures in test suite * Adds support for async execution across nodes in the same cluster (#35) * Execute SSH commands asynchronously * Run async functins using asyncio.gather * Fix typo in SSH connection * Run all remote commands through SSH object * Imposes limit on max SSH connections * PEP8 * Drops old tests * Adds dummy test coverage for ci * Drops Settings.load_from_disk method (#36) * Adds debug option to CLI (#37) * Build out test coverage (#38) * Adds tests for parser debug option * Adds tests for Settings class * Adds tests for id_in_whitelist function * Adds verbosity argument to CLI (#39) * Adds configurable logging * Adds verbosity argument * Adds tests for logging configuration * Adds tests for CLI --debug option (#40) * Delete lock file * Fix syntax typo in async generator * Eliminate global semaphre and glbal settings to address cncurrency locks * Logs errors collected by asyncio.gather * Move semaphore inside event loop * Adds nde name to SSH related logs * Pre-review cleanup * Minor capitalization typos * Drop yaml for json * Update setup instructions README.md There was a typo in the cron job example. * Run AI linter (#50) * Makes Application.settings private * Runs AI linter * Adds ssh timeout option (#49) * Drop whitelisting functionality for GIDs (#51) * Drops GID whitelist * Drops GID related tests * Move logic for loading settings into Settings class (#53) * Move logic for loading settings into Settings class * Revert changes to parser class * Raise error on file not found * Revert last commit * Terminate orphaned processes matching blacklisted user IDs (#55) * Terminate orphaned processes in userlist * Rename whitelist to blacklist * Kill processes using group ID * Fix bug in fetching of remote process data * updates tests * Lower pandas requirement * Adds test coverage for settings file parsing (#56) * Adds test coverage for settings file parsing * PEP8 * Update testing CI to use slurm * Adds rudementary test to try out slurm support * Replace settings file with CLI arguments (#80) * Outline CLI options to replace settings module * Print help text on error * Parse UID list as json string * Dynamically determine valid arguments from func signature * Add log message when there are no processes to terminate * Add nargs='+' to uid-whitelist arg * Updates docstring * Adds missing type hints * Introduce dedicat ssh argument group * Abstract away SSH options in function signatures * Adds tests for argument parsing * Drops application tests * Makes logging setup private * Shorten line lengths * Merge V0.3.3 updates into v0.4.x (#86) * Bump actions/checkout from 3 to 4 (#81) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Updates CI (#82) * Fix termination signal (#84) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix conflicts in workflow files * Add docker test env back into testing matrix * Drops applciation logging tests * Updates test node names * Adds newer python versions to CI * Updats expected node names * Run codacy report from bash shell --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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