pybiolib 1.1.801__tar.gz → 1.1.809__tar.gz

{pybiolib-1.1.801 → pybiolib-1.1.809}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.801
+Version: 1.1.809
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.801 → pybiolib-1.1.809}/biolib/cli/__init__.py

@@ -4,7 +4,7 @@ import click
 
 from biolib import utils
 from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.cli import init, lfs, push, run, run_dev, start, runtime
+from biolib.cli import init, lfs, push, run, start, runtime
 
 
 @click.version_option(version=utils.BIOLIB_PACKAGE_VERSION, prog_name='pybiolib')
@@ -23,8 +23,6 @@ cli.add_command(lfs.lfs)
 cli.add_command(push.push)
 cli.add_command(run.run)
 cli.add_command(runtime.runtime)
-# TODO: Remove this function
-cli.add_command(run_dev.run_dev)  # type: ignore
 cli.add_command(start.start)
 
 # allow this script to be called without poetry in dev e.g. by an IDE debugger

{pybiolib-1.1.801 → pybiolib-1.1.809}/biolib/compute_node/remote_host_proxy.py

@@ -248,6 +248,7 @@ http {{
             # Note: Using $1 here as URI part from regex must be used for proxy_pass
             proxy_pass               {base_url}/api/jobs/$1;
             proxy_set_header         authorization $bearer_token_on_post;
+            proxy_set_header         caller-job-uuid "{self._job_uuid}";
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;
         }}

{pybiolib-1.1.801 → pybiolib-1.1.809}/biolib/experiments/experiment.py

@@ -76,6 +76,12 @@ class Experiment:
 
         print(f'All jobs of experiment {self.name} have finished')
 
+    def add_job(self, job_id: str) -> None:
+        api.client.patch(
+            path=f'/jobs/{job_id}/',
+            data={'experiment_uuid': self.uuid}
+        )
+
     def export_job_list(self, export_format='dicts'):
         valid_formats = ('dicts', 'dataframe')
         if export_format not in valid_formats:

{pybiolib-1.1.801 → pybiolib-1.1.809}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.801"
+version = "1.1.809"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"

pybiolib-1.1.801/biolib/cli/run_dev.py

@@ -1,95 +0,0 @@
-# type: ignore
-# TODO: Remove this file and function
-import sys
-import click
-from docker.errors import ImageNotFound  # type: ignore
-
-from biolib import utils, cli_utils
-from biolib.app.utils import run_job
-from biolib.biolib_binary_format import ModuleInput
-from biolib.biolib_docker_client import BiolibDockerClient
-from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.biolib_api_client import CreatedJobDict
-from biolib.cli_utils import BiolibValidationError
-from biolib.typing_utils import Tuple
-from biolib.validators.validate_zip_file import validate_zip_file  # type: ignore
-
-
-@click.command(
-    context_settings=dict(ignore_unknown_options=True, allow_interspersed_args=False),
-    help='Run an application from a local directory',
-    hidden=True,
-)
-@click.argument('path', required=True)
-@click.argument('args', nargs=-1, type=click.UNPROCESSED)
-def run_dev(path: str, args: Tuple[str]) -> None:
-    app_path = cli_utils.validate_and_get_app_path(path)
-    logger.info(f'Running BioLib application in local directory {app_path}...')
-    tmp_directory, source_files_zip_path = cli_utils.create_temporary_directory_with_source_files_zip(app_path)
-
-    try:
-        validate_zip_file(source_files_zip_path, app_path)
-        yaml_data = cli_utils.get_yaml_data(app_path)
-        cli_utils.validate_yaml_config(yaml_data, source_files_zip_path)
-        app_version_mocked = cli_utils.get_mocked_app_version_from_yaml(yaml_data, source_files_zip_path)
-
-        for module in app_version_mocked['modules']:
-            try:
-                BiolibDockerClient.get_docker_client().images.get(module['image_uri'])
-            except ImageNotFound:
-                raise Exception(
-                    f"Could not find local docker image {module['image_uri']} specified in .biolib/config.yml"
-                ) from None
-
-        args = cli_utils.validate_and_get_args(list(args))
-        files_dict, args = cli_utils.get_files_dict_and_file_args(files=None, args=args)
-
-        def _get_stdin():
-            stdin = None
-            if not sys.stdin.isatty() and not utils.IS_DEV:
-                stdin = sys.stdin.read()
-            return stdin
-
-        module_input_serialized = ModuleInput().serialize(
-            stdin=_get_stdin() or b'',
-            files=files_dict,
-            arguments=args,
-        )
-
-        module_output = run_job(
-            module_input_serialized=module_input_serialized,
-            job=CreatedJobDict(
-                app_version=app_version_mocked,
-                arguments_override_command=False,
-                auth_token='',
-                caller_job=None,
-                created_at='',
-                federated_job_uuid=None,
-                public_id=utils.RUN_DEV_JOB_ID,
-                remote_hosts_with_warning=[],
-                state='in_progress',
-                user_id=None,
-            ),
-            force_local=True,
-        )
-
-        cli_utils.write_output_files(module_output['files'])  # type: ignore
-
-        print(cli_utils.get_pretty_print_module_output_string(
-            exitcode=module_output['exit_code'],  # type: ignore
-            stderr=module_output['stderr'],  # type: ignore
-            stdout=module_output['stdout'],  # type: ignore
-        ))
-
-    except Exception as exception:
-        # Exit on BiolibValidationError as we have already printed the validation errors
-        if isinstance(exception, BiolibValidationError):
-            logger_no_user_data.error('Validation check failed for config file at .biolib/config.yml')
-            exit(1)
-        raise exception
-
-    finally:
-        try:
-            tmp_directory.cleanup()
-        except IOError:
-            logger_no_user_data.error('Failed to clean up temporary source files zip directory')

pybiolib-1.1.801/setup.py

@@ -1,72 +0,0 @@
-# -*- coding: utf-8 -*-
-from setuptools import setup
-
-packages = \
-['biolib',
- 'biolib.api',
- 'biolib.app',
- 'biolib.biolib_api_client',
- 'biolib.biolib_binary_format',
- 'biolib.biolib_docker_client',
- 'biolib.cli',
- 'biolib.compute_node',
- 'biolib.compute_node.cloud_utils',
- 'biolib.compute_node.job_worker',
- 'biolib.compute_node.job_worker.executors',
- 'biolib.compute_node.job_worker.executors.remote',
- 'biolib.compute_node.job_worker.executors.tars',
- 'biolib.compute_node.webserver',
- 'biolib.experiments',
- 'biolib.jobs',
- 'biolib.lfs',
- 'biolib.runtime',
- 'biolib.templates',
- 'biolib.user',
- 'biolib.utils',
- 'biolib.utils.zip',
- 'biolib.validators']
-
-package_data = \
-{'': ['*']}
-
-install_requires = \
-['appdirs>=1.4.3',
- 'click>=8.0.0,<8.1.0',
- 'docker>=5.0.3',
- 'flask-cors>=3.0.10',
- 'flask>=2.0.1',
- 'gunicorn>=20.1.0',
- 'importlib-metadata>=1.6.1',
- 'pycryptodome>=3.9.9',
- 'pyjwt>=2.3.0',
- 'pyyaml>=5.3.1',
- 'requests>=2.25.1',
- 'rich>=12.4.4,<13.0.0']
-
-extras_require = \
-{':python_version < "3.8"': ['typing_extensions>=3.10.0',
-                             'typing_inspect>=0.5.0,<0.6.0']}
-
-entry_points = \
-{'console_scripts': ['biolib = biolib:call_cli']}
-
-setup_kwargs = {
-    'name': 'pybiolib',
-    'version': '1.1.801',
-    'description': 'BioLib Python Client',
-    'long_description': "# PyBioLib\n\nPyBioLib is a Python package for running BioLib applications from Python scripts and the command line.\n\n### Python Example\n```python\n# pip3 install -U pybiolib\nimport biolib\nsamtools = biolib.load('samtools/samtools')\nprint(samtools.cli(args='--help'))\n```\n\n### Command Line Example\n```bash\npip3 install -U pybiolib\nbiolib run samtools/samtools --help\n```\n",
-    'author': 'biolib',
-    'author_email': 'hello@biolib.com',
-    'maintainer': 'None',
-    'maintainer_email': 'None',
-    'url': 'https://github.com/biolib',
-    'packages': packages,
-    'package_data': package_data,
-    'install_requires': install_requires,
-    'extras_require': extras_require,
-    'entry_points': entry_points,
-    'python_requires': '>=3.6.3,<4.0.0',
-}
-
-
-setup(**setup_kwargs)