pybiolib 1.2.264__py3-none-any.whl → 1.2.298__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -44,6 +44,8 @@ class DockerExecutor:
         self._send_system_exception = options['send_system_exception']
         self._send_stdout_and_stderr = options['send_stdout_and_stderr']
         self._random_docker_id = compute_node_utils.random_string(15)
+        self._reserved_system_ram = int(os.sysconf('SC_PAGE_SIZE') * os.sysconf('SC_PHYS_PAGES') * 0.06) + 500_000_000
+        logger_no_user_data.info(f"System RAM reserved: {self._reserved_system_ram}")
 
         if utils.IS_RUNNING_IN_CLOUD:
             self._compute_process_dir = os.getenv('BIOLIB_USER_DATA_PATH')
@@ -374,7 +376,9 @@ class DockerExecutor:
 
             if utils.IS_RUNNING_IN_CLOUD:
                 cloud_job = self._options['cloud_job']
-                create_container_args['mem_limit'] = f'{cloud_job["reserved_memory_in_bytes"] - 500_000_000}b'
+                create_container_args['mem_limit'] = (
+                    f'{cloud_job["reserved_memory_in_bytes"] - self._reserved_system_ram}b'
+                )
                 create_container_args['nano_cpus'] = cloud_job['reserved_cpu_in_nano_shares']
                 create_container_args['pids_limit'] = 10_000
 

biolib/jobs/job.py

@@ -178,9 +178,13 @@ class Job:
             time.sleep(2)
         logger.info(f'Job {self.id} has finished.')
 
-    def open_browser(self) -> None:
+    def get_shareable_link(self) -> str:
         api_client = BiolibApiClient.get()
-        results_url_to_open = f'{api_client.base_url}/results/{self.id}/?token={self._auth_token}'
+        shareable_link = f'{api_client.base_url}/results/{self.id}/?token={self._auth_token}'
+        return shareable_link
+
+    def open_browser(self) -> None:
+        results_url_to_open = self.get_shareable_link()
         if IS_RUNNING_IN_NOTEBOOK:
             print(f'Opening results page at: {results_url_to_open}')
             print('If your browser does not open automatically, click on the link above.')

{pybiolib-1.2.264.dist-info → pybiolib-1.2.298.dist-info}/METADATA

@@ -1,8 +1,7 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.264
+Version: 1.2.298
 Summary: BioLib Python Client
-Home-page: https://github.com/biolib
 License: MIT
 Keywords: biolib
 Author: biolib
@@ -28,6 +27,7 @@ Requires-Dist: importlib-metadata (>=1.6.1)
 Requires-Dist: pyyaml (>=5.3.1)
 Requires-Dist: rich (>=12.4.4)
 Requires-Dist: typing_extensions (>=3.10.0) ; python_version < "3.8"
+Project-URL: Homepage, https://github.com/biolib
 Description-Content-Type: text/markdown
 
 # PyBioLib

{pybiolib-1.2.264.dist-info → pybiolib-1.2.298.dist-info}/RECORD

@@ -1,5 +1,3 @@
-LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-PYPI_README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
 biolib/__init__.py,sha256=4Rfa0AJKztqkCG5D67kFgSwdOUiBTa5HkAzIOqHNREU,4431
 biolib/_data_record/data_record.py,sha256=zKvnh5T-dIVY46-kgVzMBoZ666ZhcTCFQnWvZT0D6RM,12026
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -78,7 +76,7 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=97S0FH5cmDVh9k5bMdKw_oTbhlvWNMTYHlCWsMcTVr0,29118
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=J-wv7FTb_HJnfRdIByiOdtj18Fw5nYvVm-n0D1mrqwA,29377
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/job_worker/executors/types.py,sha256=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
@@ -103,7 +101,7 @@ biolib/compute_node/webserver/worker_thread.py,sha256=GRRBUqXdMKvbjyLQhYlqGIbFKe
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=m7FB7hot8CMOVrNyWGPB6FTkWQJwI0ytpIvtPxfoPME,7684
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=W0r9_AbHha1lC99U_kUuzDmavFQe7WLxs83Wp3g_3ZU,20330
+biolib/jobs/job.py,sha256=qXDjaI5YbxEHLYtF-vflfdz6j4AEb83ioqSZli5aOgM,20453
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
@@ -120,8 +118,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.264.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.264.dist-info/METADATA,sha256=pJKjfgwqbhssh25YE8ksBIKSVzRqJ3wFQP7UUXec854,1558
-pybiolib-1.2.264.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-pybiolib-1.2.264.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.264.dist-info/RECORD,,
+pybiolib-1.2.298.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.298.dist-info/METADATA,sha256=1ICb34Tjx7C3IheyO4nd-bkMwwM1JmW64ozEFCSbFXk,1570
+pybiolib-1.2.298.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+pybiolib-1.2.298.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.298.dist-info/RECORD,,

{pybiolib-1.2.264.dist-info → pybiolib-1.2.298.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 2.0.1
 Root-Is-Purelib: true
 Tag: py3-none-any

PYPI_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 -U pybiolib
-import biolib
-samtools = biolib.load('samtools/samtools')
-print(samtools.cli(args='--help'))
-```
-
-### Command Line Example
-```bash
-pip3 install -U pybiolib
-biolib run samtools/samtools --help
-```

pybiolib-1.2.264.dist-info/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2020 BioLib Inc
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.