Merge pull request EESSI#120 from smoors/format

code formatting

.github/workflows/linting.yml

@@ -0,0 +1,25 @@
+name: Static Analysis
+on: [push, pull_request, workflow_dispatch]
+permissions: read-all
+
+jobs:
+ python-linting:
+ runs-on: ubuntu-22.04
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+ with:
+ persist-credentials: false
+
+ - name: Set up Python
+ uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # v4.7.0
+ with:
+ python-version: '3.10'
+
+ - name: Install Python packages
+ run: |
+ pip install --upgrade pip
+ pip install --upgrade flake8
+
+ - name: Run flake8 to verify PEP8-compliance of Python code
+ run: flake8

config/aws_mc.py

@@ -43,8 +43,8 @@
  'name': 'x86_64-skylake-16c-30gb',
  'access': ['--partition=x86-64-intel-skylake-node', '--export=NONE'],
  'descr': 'Skylake, 16 cores, 30 GB',
- },
- {
+  },
+  {
  'name': 'x86_64-zen2-16c-30gb',
  'access': ['--partition=x86-64-amd-zen2-node', '--export=NONE'],
  'descr': 'Zen2, 16 cores, 30 GB',

config/github_actions.py

@@ -1,7 +1,7 @@
 # ReFrame configuration file that can be used in GitHub Actions with EESSI
 
 from eessi.testsuite.common_config import common_logging_config
-from eessi.testsuite.constants import * # noqa: F403
+from eessi.testsuite.constants import *
 
 
 site_configuration = {
@@ -26,18 +26,18 @@
  }
  ],
  'max_jobs': 1
-  }
-  ]
-  }
-  ],
+ }
+ ]
+ }
+ ],
  'environments': [
  {
  'name': 'default',
  'cc': 'cc',
  'cxx': '',
  'ftn': ''
-  }
-  ],
+ }
+ ],
  'general': [
  {
  'purge_environment': True,

config/it4i_karolina.py

@@ -47,50 +47,50 @@
  ],
  'launcher': 'mpirun',
  # Use --export=None to avoid that login environment is passed down to submitted jobs
- 'access':  ['-p qcpu', '-A DD-23-96', '--export=None'],
+ 'access': ['-p qcpu', '-A DD-23-96', '--export=None'],
  'environs': ['default'],
  'max_jobs': 120,
  'features': [
  FEATURES[CPU],
  ] + list(SCALES.keys()),
  'descr': 'CPU Universal Compute Nodes, see https://docs.it4i.cz/karolina/hardware-overview/'
  },
-# We don't have GPU budget on Karolina at this time
-# {
-# 'name': 'qgpu',
-# 'scheduler': 'slurm',
-# 'prepare_cmds': [
-# 'source %s' % common_eessi_init(),
-# # Pass job environment variables like $PATH, etc., into job steps
-# 'export SLURM_EXPORT_ENV=ALL',
-# # Needed when using srun launcher
-# # 'export SLURM_MPI_TYPE=pmix', # WARNING: this broke the GROMACS on Vega
-# # Avoid https://github.com/EESSI/software-layer/issues/136
-# # Can be taken out once we don't care about old OpenMPI versions anymore (pre-4.1.1)
-# 'export OMPI_MCA_pml=ucx',
-# ],
-# 'launcher': 'mpirun',
-# # Use --export=None to avoid that login environment is passed down to submitted jobs
-# 'access': ['-p gpu', '-A DD-23-96', '--export=None'],
-# 'environs': ['default'],
-# 'max_jobs': 60,
-# 'devices': [
-# {
-# 'type': DEVICE_TYPES[GPU],
-# 'num_devices': 8,
-# }
-# ],
-# 'resources': [
-# {
-# 'name': '_rfm_gpu',
-# 'options': ['--gpus-per-node={num_gpus_per_node}'],
-# }
-# ],
-# 'features': [
-# FEATURES[GPU],
-# ] + list(SCALES.keys()),
-# 'descr': 'GPU partition with accelerated nodes, see https://docs.it4i.cz/karolina/hardware-overview/'
-# },
+ # We don't have GPU budget on Karolina at this time
+ # {
+ # 'name': 'qgpu',
+ # 'scheduler': 'slurm',
+ # 'prepare_cmds': [
+ # 'source %s' % common_eessi_init(),
+ # # Pass job environment variables like $PATH, etc., into job steps
+ # 'export SLURM_EXPORT_ENV=ALL',
+ # # Needed when using srun launcher
+ # # 'export SLURM_MPI_TYPE=pmix', # WARNING: this broke the GROMACS on Vega
+ # # Avoid https://github.com/EESSI/software-layer/issues/136
+ # # Can be taken out once we don't care about old OpenMPI versions anymore (pre-4.1.1)
+ # 'export OMPI_MCA_pml=ucx',
+ # ],
+ # 'launcher': 'mpirun',
+ # # Use --export=None to avoid that login environment is passed down to submitted jobs
+ # 'access': ['-p gpu', '-A DD-23-96', '--export=None'],
+ # 'environs': ['default'],
+ # 'max_jobs': 60,
+ # 'devices': [
+ # {
+ # 'type': DEVICE_TYPES[GPU],
+ # 'num_devices': 8,
+ # }
+ # ],
+ # 'resources': [
+ # {
+ # 'name': '_rfm_gpu',
+ # 'options': ['--gpus-per-node={num_gpus_per_node}'],
+ # }
+ # ],
+ # 'features': [
+ # FEATURES[GPU],
+ # ] + list(SCALES.keys()),
+ # 'descr': 'GPU partition with accelerated nodes, https://docs.it4i.cz/karolina/hardware-overview/'
+ # },
  ]
  },
  ],

config/izum_vega.py

@@ -47,7 +47,7 @@
  ],
  'launcher': 'mpirun',
  # Use --export=None to avoid that login environment is passed down to submitted jobs
- 'access':  ['-p cpu', '--export=None'],
+ 'access': ['-p cpu', '--export=None'],
  'environs': ['default'],
  'max_jobs': 120,
  'resources': [
@@ -76,7 +76,7 @@
  ],
  'launcher': 'mpirun',
  # Use --export=None to avoid that login environment is passed down to submitted jobs
- 'access':  ['-p gpu', '--export=None'],
+ 'access': ['-p gpu', '--export=None'],
  'environs': ['default'],
  'max_jobs': 60,
  'devices': [

config/settings_example.py

@@ -20,7 +20,7 @@
 import os
 
 from eessi.testsuite.common_config import common_logging_config, format_perfvars, perflog_format
-from eessi.testsuite.constants import * # noqa: F403
+from eessi.testsuite.constants import *
 
 
 site_configuration = {
@@ -35,10 +35,10 @@
  'partitions': [
  {
  'name': 'cpu_partition',
- 'descr': 'CPU partition'
+ 'descr': 'CPU partition',
  'scheduler': 'slurm',
  'launcher': 'mpirun',
- 'access':  ['-p cpu', '--export=None'],
+ 'access': ['-p cpu', '--export=None'],
  'prepare_cmds': ['source /cvmfs/pilot.eessi-hpc.org/latest/init/bash'],
  'environs': ['default'],
  'max_jobs': 4,
@@ -62,20 +62,20 @@
  },
  {
  'name': 'gpu_partition',
- 'descr': 'GPU partition'
+ 'descr': 'GPU partition',
  'scheduler': 'slurm',
  'launcher': 'mpirun',
- 'access':  ['-p gpu', '--export=None'],
+ 'access': ['-p gpu', '--export=None'],
  'prepare_cmds': ['source /cvmfs/pilot.eessi-hpc.org/latest/init/bash'],
  'environs': ['default'],
  'max_jobs': 4,
  # We recommend to rely on ReFrame's CPU autodetection,
  # and only define the 'processor' field if autodetection fails
  # 'processor': {
- # 'num_cpus': 72,
- # 'num_sockets': 2,
- # 'num_cpus_per_socket': 36,
- # 'num_cpus_per_core': 1,
+ # 'num_cpus': 72,
+ # 'num_sockets': 2,
+ # 'num_cpus_per_socket': 36,
+ # 'num_cpus_per_core': 1,
  # },
  'resources': [
  {

config/surf_snellius.py

@@ -41,7 +41,7 @@
  'scheduler': 'slurm',
  'prepare_cmds': ['source %s' % common_eessi_init()],
  'launcher': 'mpirun',
- 'access':  ['-p rome', '--export=None'],
+ 'access': ['-p rome', '--export=None'],
  'environs': ['default'],
  'max_jobs': 120,
  'resources': [
@@ -60,7 +60,7 @@
  'scheduler': 'slurm',
  'prepare_cmds': ['source %s' % common_eessi_init()],
  'launcher': 'mpirun',
- 'access':  ['-p genoa', '--export=None'],
+ 'access': ['-p genoa', '--export=None'],
  'environs': ['default'],
  'max_jobs': 120,
  'resources': [
@@ -80,7 +80,7 @@
  'scheduler': 'slurm',
  'prepare_cmds': ['source %s' % common_eessi_init()],
  'launcher': 'mpirun',
- 'access':  ['-p gpu', '--export=None'],
+ 'access': ['-p gpu', '--export=None'],
  'environs': ['default'],
  'max_jobs': 60,
  'devices': [

config/vsc_hortense.py

@@ -143,7 +143,7 @@ def command(self, job):
  }
  ],
  'devices': [
- {
+  {
  'type': DEVICE_TYPES[GPU],
  'num_devices': 4,
  }

eessi/testsuite/common_config.py

@@ -69,33 +69,35 @@ def common_logging_config(prefix=None):
  ],
  }]
 
+
 def common_eessi_init(eessi_version=None):
  """
  Returns the full path that should be sourced to initialize the EESSI environment for a given version of EESSI.
- If no eessi_version is passed, the EESSI_VERSION environment variable is read. If that is also not defined, default behaviour is to use `latest`.
+ If no eessi_version is passed, the EESSI_VERSION environment variable is read.
+ If that is also not defined, default behaviour is to use `latest`.
  :param eessi_version: version of EESSI that should be sourced (e.g. '2023.06' or 'latest') [optional]
  """
  # Check which EESSI_CVMFS_REPO we are running under
  eessi_cvmfs_repo = os.getenv('EESSI_CVMFS_REPO', None)
  if eessi_cvmfs_repo is None:
- err_msg = "Environment variable 'EESSI_CVMFS_REPO' was not found. "
- err_msg += "Did you initialize the EESSI environment before running the test suite?"
+ err_msg = "Environment variable 'EESSI_CVMFS_REPO' was not found."
+ err_msg += " Did you initialize the EESSI environment before running the test suite?"
  raise ValueError(err_msg)
  if eessi_cvmfs_repo == '/cvmfs/pilot.eessi-hpc.org':
- if eessi_version == None:
+ if eessi_version is None:
  # Try also EESSI_VERSION for backwards compatibility with previous common_eessi_init implementation
  eessi_version = os.getenv('EESSI_PILOT_VERSION', os.getenv('EESSI_VERSION', 'latest'))
  else:
- # software.eessi.io, or another where we assume the same variable names to be used
- if eessi_version == None:
+  # software.eessi.io, or another where we assume the same variable names to be used
+ if eessi_version is None:
  eessi_version = os.getenv('EESSI_VERSION', None)
  # Without EESSI_VERSION, we don't know what to do. There is no default/latest version
  # So, report error
- if eessi_version == None:
- err_msg = "Environment variable 'EESSI_VERSION' was not found. "
- err_msg += "Did you initialize the EESSI environment before running the test suite?"
+ if eessi_version is None:
+ err_msg = "Environment variable 'EESSI_VERSION' was not found."
+ err_msg += " Did you initialize the EESSI environment before running the test suite?"
  raise ValueError(err_msg)
- 
+
  if eessi_cvmfs_repo == '/cvmfs/pilot.eessi-hpc.org' and eessi_version == 'latest':
  return '/cvmfs/pilot.eessi-hpc.org/latest/init/bash'
  else:

eessi/testsuite/hooks.py

@@ -90,8 +90,8 @@ def assign_tasks_per_compute_unit(test: rfm.RegressionTest, compute_unit: str, n
 
  # Check if either node_part, or default_num_cpus_per_node and default_num_gpus_per_node are set correctly
  if not (
- type(test.node_part) == int
- or (type(test.default_num_cpus_per_node) == int and type(test.default_num_gpus_per_node) == int)
+ isinstance(test.node_part, int)
+ or (isinstance(test.default_num_cpus_per_node, int) and isinstance(test.default_num_gpus_per_node, int))
  ):
  raise ValueError(
  f'Either node_part ({test.node_part}), or default_num_cpus_per_node ({test.default_num_cpus_per_node}) and'

eessi/testsuite/tests/apps/gromacs.py

@@ -30,6 +30,7 @@
 """
 
 import reframe as rfm
+from reframe.core.builtins import parameter, run_after # added only to make the linter happy
 
 from hpctestlib.sciapps.gromacs.benchmarks import gromacs_check