pybiolib 0.2.951__py3-none-any.whl → 1.2.1890__py3-none-any.whl

pybiolib-1.2.1890.dist-info/RECORD

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+pybiolib-1.2.1890.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1890.dist-info/RECORD,,

{pybiolib-0.2.951.dist-info → pybiolib-1.2.1890.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry 1.0.7
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pybiolib-1.2.1890.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+biolib = biolib:call_cli

README.md

@@ -1,17 +0,0 @@
-# PyBioLib
-
-PyBioLib is a Python package for running BioLib applications from Python scripts, and the command line.
-
-### Python Example
-```python
-# pip3 install pybiolib
-import biolib
-samtools = biolib.load('samtools/samtools')
-print(samtools.cli(args='--help'))
-```
-
-### Command Line Example
-```bash
-pip3 install pybiolib
-biolib run samtools/samtools --help
-```

biolib/app/app_result.py

@@ -1,68 +0,0 @@
-import re
-import time
-from pathlib import Path
-from typing import Dict
-
-import nest_asyncio  # type: ignore # necessary import fix required for async to work in notebooks
-
-from biolib import cli_utils
-from biolib.biolib_logging import logger
-
-nest_asyncio.apply()
-
-
-class AppResult:
-    def __init__(self, stdout: bytes, stderr: bytes, exitcode: int, files: Dict[str, bytes]):
-        self._stdout = stdout
-        self._stderr = stderr
-        self._exitcode = exitcode
-        self._files = files
-
-    def __str__(self):
-        return cli_utils.get_pretty_print_module_output_string(self._stdout, self._stderr, self._exitcode)
-
-    def ipython_markdown(self):
-        import IPython.display  # type:ignore # pylint: disable=import-error, import-outside-toplevel
-        markdown_str = self._stdout.decode('utf-8')
-        # prepend ./biolib_results/ to all paths
-        # ie [SeqLogo](./SeqLogo2.png) test ![SeqLogo](./SeqLogo.png)
-        # ![SeqLogo](SeqLogo.png)  ![SeqLogo](/SeqLogo.png)
-        # is transformed to ![SeqLogo](./biolib_results/SeqLogo2.png) test ![SeqLogo](./biolib_results/SeqLogo.png)
-        # ![SeqLogo](./biolib_results/SeqLogo.png)  ![SeqLogo](./biolib_results/SeqLogo.png)
-        markdown_str_modified = re.sub(
-            r'\!\[([^\]]*)\]\((\.\/|\/|)([^\)]*)\)',
-            r'![\1](./biolib_results/\3)',
-            markdown_str,
-        )
-        IPython.display.display(IPython.display.Markdown(markdown_str_modified))
-
-    def save_files(self, output_dir: str):
-        logger.debug("Output Files:")
-
-        for file_path, file_data in self._files.items():
-            # Remove leading slash of file_path
-            new_file_path = Path(output_dir) / Path(file_path.lstrip('/'))
-            if new_file_path.exists():
-                new_file_path.rename(f'{new_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}')
-
-            dir_path = new_file_path.parent
-            if dir_path:
-                dir_path.mkdir(parents=True, exist_ok=True)
-
-            with open(new_file_path, 'wb') as output_file:
-                output_file.write(file_data)
-            logger.debug(f"  - {new_file_path}")
-
-        logger.debug('\n')
-
-    @property
-    def stdout(self) -> bytes:
-        return self._stdout
-
-    @property
-    def stderr(self) -> bytes:
-        return self._stderr
-
-    @property
-    def exitcode(self) -> int:
-        return self._exitcode

biolib/app/utils.py

@@ -1,62 +0,0 @@
-import logging
-import os
-import sys
-import random
-import subprocess
-import time
-import pathlib
-
-import requests.exceptions
-
-from biolib.biolib_api_client import BiolibApiClient
-from biolib.biolib_api_client.biolib_job_api import BiolibJobApi
-from biolib.biolib_binary_format import ModuleOutput
-from biolib.biolib_errors import BioLibError
-from biolib.biolib_logging import logger
-
-
-# TODO: type return value as ModuleOutput class
-def run_job(job, module_input_serialized: bytes):
-    host = '127.0.0.1'
-    port = str(random.choice(range(5000, 65000)))
-    node_url = f'http://{host}:{port}'
-    job_id = job['public_id']
-    logger.debug(f'Starting local compute node at {node_url}')
-    start_cli_path = pathlib.Path(__file__).parent.parent.resolve() / 'start_cli.py'
-    python_executable_path = sys.executable
-    compute_node_process = subprocess.Popen(
-        args=[python_executable_path, start_cli_path, 'start', '--host', host, '--port', port],
-        env=dict(os.environ, BIOLIB_LOG=logging.getLevelName(logger.level)),
-    )
-    try:
-        for retry in range(20):
-            time.sleep(1)
-            try:
-                BiolibJobApi.save_compute_node_job(
-                    job=job,
-                    module_name='main',
-                    access_token=BiolibApiClient.get().access_token,
-                    node_url=node_url
-                )
-                break
-
-            except requests.exceptions.ConnectionError:
-                if retry == 19:
-                    raise BioLibError('Could not connect to local compute node') from None
-                logger.debug('Could not connect to local compute node retrying...')
-
-        BiolibJobApi.start_cloud_job(job_id, module_input_serialized, node_url)
-        BiolibJobApi.await_compute_node_status(
-            retry_interval_seconds=1.5,
-            retry_limit_minutes=30,
-            status_to_await='Result Ready',
-            compute_type='Compute Node',
-            job_id=job_id,
-            node_url=node_url,
-        )
-
-        result = BiolibJobApi.get_cloud_result(job_id, node_url)
-        return ModuleOutput(result).deserialize()
-
-    finally:
-        compute_node_process.terminate()