def initialize_repo(project_root):
"""This function is used for initializing a popper repository."""
if pu.is_popperized():
pu.fail('Repository has already been popperized')
return
config = {
'metadata': {
'access_right': "open",
'license': "CC-BY-4.0",
'upload_type': "publication",
'publication_type': "article"
},
'pipelines': {},
'popperized': ["github/popperized"]
}
pu.write_config(config)
with open(os.path.join(project_root, '.gitignore'), 'a') as f:
f.write('.cache\n')
f.write('popper_logs\n')
f.write('popper_status\n')
pu.info('Popperized repository ' + project_root, fg='blue', bold=True)
def initialize_repo(project_root):
if pu.is_popperized():
pu.fail('Repository has already been popperized')
with open(os.path.join(project_root, '.popper.yml'), 'w') as f:
f.write('{ metadata: { }, pipelines: { } }\n')
pu.info('Popperized repository ' + project_root, fg='blue', bold=True)
def cli(ctx, name, stages, envs, existing, infer_stages):
"""Initializes a repository or a pipeline. Without an argument, this
command initializes a popper repository. If an argument is given, a
pipeline or paper folder is initialized. If the given name is 'paper',
then a 'paper' folder is created. Otherwise, a pipeline named NAME is
created and initialized inside the 'pipelines' folder.
By default, the stages of a pipeline are: setup, run, post-run, validate
and teardown. To override these, the `--stages` flag can be provided, which
expects a comma-separated list of stage names.
The teardown stage is to be provided at the end if the --stages flag is
being used.
If the --existing flag is given, the NAME argument is treated as a path to
a folder, which is assumed to contain bash scripts. --stages must be given.
"""
# check if the the teardown stage is the last stage of the pipeline
if stages and 'teardown' in stages and stages.split(',')[-1] != 'teardown':
raise BadArgumentUsage(
'--stages = Teardown should be the last stage.' +
' Consider renaming it or putting it at the end.')
project_root = pu.get_project_root()
# init repo
if name is None:
initialize_repo(project_root)
return
if not pu.is_popperized():
pu.fail("Repository has not been popperized yet. See 'init --help'")
if isdir(os.path.join(project_root, name)) and existing:
# existing pipeline
abs_path = os.path.join(project_root, name)
relative_path = name
if infer_stages:
stages = ",".join(
map(lambda x: x[:-3], sorted(glob.glob1(abs_path, '*.sh'))))
else:
initialize_existing_pipeline(abs_path, stages, envs)
elif name == 'paper':
# create a paper pipeline
abs_path = os.path.join(project_root, 'paper')
relative_path = os.path.join('paper')
initialize_paper(abs_path, envs)
else:
# new pipeline
abs_path = os.path.join(project_root, 'pipelines', name)
relative_path = os.path.join('pipelines', name)
initialize_new_pipeline(abs_path, stages, envs)
pu.update_config(name, stages, envs, relative_path)
pu.info('Initialized pipeline ' + name, fg='blue', bold=True)
def initialize_repo(project_root):
"""This function is used for initializing a popper repository."""
if pu.is_popperized():
pu.fail('Repository has already been popperized')
with open(os.path.join(project_root, '.popper.yml'), 'w') as f:
f.write('{ metadata: { }, pipelines: { } }\n')
with open(os.path.join(project_root, '.gitignore'), 'a') as f:
f.write('popper_logs\n')
f.write('popper_status\n')
pu.info('Popperized repository ' + project_root, fg='blue', bold=True)
def cli(ctx):
"""Initializes a repository by creating the .popper.yml file.
"""
project_root = scm.get_root_folder()
if pu.is_popperized(project_root):
pu.fail('Repository has already been popperized')
return
pu.write_config(project_root, pu.init_config)
with open(os.path.join(project_root, '.gitignore'), 'a') as f:
f.write(pu.gitignore_content)
# write README
pu.info('Popperized repository {}\n'.format(project_root))
def initialize_repo(project_root):
"""This function is used for initializing a popper repository."""
content = pt.ReadMe()
if pu.is_popperized():
pu.fail('Repository has already been popperized')
return
pu.write_config(pu.init_config)
with open(os.path.join(project_root, '.gitignore'), 'a') as f:
f.write(pu.gitignore_content)
# write README
content.init_project()
pu.info('Popperized repository ' + project_root, fg='blue', bold=True)
def cli(ctx, name, stages, envs, existing):
"""Initializes a repository or a pipeline. Without an argument, this
command initializes a popper repository. If an argument is given, a
pipeline or paper folder is initialized. If the given name is 'paper',
then a 'paper' folder is created. Otherwise, a pipeline named NAME is
created and initialized inside the 'pipelines' folder.
By default, the stages of a pipeline are: setup, run, post-run, validate
and teardown. To override these, the `--stages` flag can be provided, which
expects a comma-separated list of stage names.
If the --existing flag is given, the NAME argument is treated as a path to
a folder, which is assumed to contain bash scripts. --stages must be given.
"""
project_root = pu.get_project_root()
# init repo
if name is None:
initialize_repo(project_root)
return
if not pu.is_popperized():
pu.fail("Repository has not been popperized yet. See 'init --help'")
if isdir(os.path.join(project_root, name)) and existing:
# existing pipeline
abs_path = os.path.join(project_root, name)
relative_path = name
initialize_existing_pipeline(abs_path, stages, envs)
elif name == 'paper':
# create a paper pipeline
abs_path = os.path.join(project_root, 'paper')
relative_path = os.path.join('paper')
initialize_paper(abs_path, envs)
else:
# new pipeline
abs_path = os.path.join(project_root, 'pipelines', name)
relative_path = os.path.join('pipelines', name)
initialize_new_pipeline(abs_path, stages, envs)
pu.update_config(name, stages, envs, relative_path)
pu.info('Initialized pipeline ' + name, fg='blue', bold=True)
def cli(ctx):
"""Scaffolds a workflow.
"""
project_root = scm.get_root_folder()
if not pu.is_popperized(project_root):
pu.fail('Repository has not been popperized')
return
curr_dir = os.getcwd()
actions_dir = os.path.join(curr_dir, 'actions')
for filename in os.listdir(project_root):
if filename.endswith('.workflow'):
pu.fail('.workflow file already present !')
if not os.path.exists(actions_dir):
os.mkdir(actions_dir)
os.mkdir(os.path.join(actions_dir, 'example'))
else:
if not os.path.exists(os.path.join(actions_dir, 'example')):
os.mkdir(os.path.join(actions_dir, 'example'))
# Generate actions files
with open(os.path.join(project_root, 'main.workflow'), 'w') as f:
f.write(pu.main_workflow_content % os.path.relpath(
os.path.join(actions_dir, 'example'), project_root)
)
with open(os.path.join(actions_dir, 'example/Dockerfile'), 'w') as df:
df.write(pu.dockerfile_content)
with open(os.path.join(actions_dir, 'example/entrypoint.sh'), 'w') as ef:
ef.write(pu.entrypoint_content)
with open(os.path.join(actions_dir, 'example/README.md'), 'w') as rf:
rf.write(pu.readme_content)
pu.info('', '', 'Successfully scaffolded. \n')
