pybiolib 1.2.1304__py3-none-any.whl → 1.2.1310__py3-none-any.whl

biolib/_internal/push_application.py

@@ -21,7 +21,7 @@ from biolib.biolib_api_client.biolib_app_api import BiolibAppApi
 from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger
-from biolib.typing_utils import Iterable, Optional, Set, TypedDict
+from biolib.typing_utils import Dict, Iterable, Optional, Set, TypedDict
 from biolib.utils.app_uri import parse_app_uri
 
 REGEX_MARKDOWN_INLINE_IMAGE = re.compile(r'!\[(?P<alt>.*)\]\((?P<src>.*)\)')
@@ -109,8 +109,10 @@ def _process_docker_status_updates_with_progress_bar(status_updates: Iterable[Do
 
 
 def _process_docker_status_updates_with_logging(status_updates: Iterable[DockerStatusUpdate], action: str) -> None:
-    layer_progress = {}
-    layer_status = {}
+    layer_progress: Dict[str, float] = {}
+    layer_status: Dict[str, str] = {}
+    layer_details: Dict[str, Dict[str, int]] = {}
+    layer_bytes_at_last_log: Dict[str, int] = {}
     last_log_time = time.time()
 
     logger.info(f'{action} Docker image...')
@@ -128,6 +130,7 @@ def _process_docker_status_updates_with_logging(status_updates: Iterable[DockerS
                 percentage = (current / total * 100) if total > 0 else 0
                 layer_progress[layer_id] = percentage
                 layer_status[layer_id] = f'{action.lower()}'
+                layer_details[layer_id] = {'current': current, 'total': total}
             elif update.get('status') == 'Layer already exists':
                 layer_progress[layer_id] = 100
                 layer_status[layer_id] = 'already exists'
@@ -146,16 +149,33 @@ def _process_docker_status_updates_with_logging(status_updates: Iterable[DockerS
                 logger.info(f'{action} Docker image - {status}')
 
         if current_time - last_log_time >= 10.0:
-            _log_progress_summary(action, layer_progress, layer_status)
+            _log_progress_summary(
+                action,
+                layer_progress,
+                layer_status,
+                layer_details,
+                layer_bytes_at_last_log,
+                current_time - last_log_time,
+            )
+            layer_bytes_at_last_log = {lid: details['current'] for lid, details in layer_details.items()}
             last_log_time = current_time
 
-    _log_progress_summary(action, layer_progress, layer_status)
+    _log_progress_summary(
+        action, layer_progress, layer_status, layer_details, layer_bytes_at_last_log, time.time() - last_log_time
+    )
     if action == 'Pushing':
         logger.info('Pushing final image manifest...')
     logger.info(f'{action} Docker image completed')
 
 
-def _log_progress_summary(action: str, layer_progress: dict, layer_status: dict) -> None:
+def _log_progress_summary(
+    action: str,
+    layer_progress: Dict[str, float],
+    layer_status: Dict[str, str],
+    layer_details: Dict[str, Dict[str, int]],
+    layer_bytes_at_last_log: Dict[str, int],
+    time_delta: float,
+) -> None:
     if not layer_progress and not layer_status:
         return
 
@@ -174,7 +194,36 @@ def _log_progress_summary(action: str, layer_progress: dict, layer_status: dict)
         if status in ['preparing', 'waiting', 'pushing', 'uploading'] and layer_progress.get(layer_id, 0) < 100
     ]
 
-    if active_layers:
+    if active_layers and layer_details:
+        total_bytes_transferred = 0
+        layer_info_parts = []
+
+        for layer_id in active_layers[:5]:
+            if layer_id in layer_details:
+                details = layer_details[layer_id]
+                current = details['current']
+                total = details['total']
+                percentage = layer_progress.get(layer_id, 0)
+
+                bytes_since_last = current - layer_bytes_at_last_log.get(layer_id, 0)
+                total_bytes_transferred += bytes_since_last
+
+                current_mb = current / (1024 * 1024)
+                total_mb = total / (1024 * 1024)
+                layer_info_parts.append(f'{layer_id}: {current_mb:.1f}/{total_mb:.1f} MB ({percentage:.1f}%)')
+
+        speed_info = ''
+        if time_delta > 0 and total_bytes_transferred > 0:
+            speed_mbps = (total_bytes_transferred / (1024 * 1024)) / time_delta
+            speed_info = f' @ {speed_mbps:.2f} MB/s'
+
+        more_layers_info = ''
+        if len(active_layers) > 5:
+            more_layers_info = f' (+ {len(active_layers) - 5} more)'
+
+        if layer_info_parts:
+            logger.info(f'Active layers: {", ".join(layer_info_parts)}{speed_info}{more_layers_info}')
+    elif active_layers:
         logger.info(f'Active layers: {", ".join(active_layers[:5])}{"..." if len(active_layers) > 5 else ""}')
 
 

biolib/jobs/job.py

@@ -498,11 +498,11 @@ class Result:
             stdout_and_stderr_package = base64.b64decode(stdout_and_stderr_package_b64)
             stdout_and_stderr = StdoutAndStderr(stdout_and_stderr_package).deserialize()
 
-            sys.stdout.write(stdout_and_stderr.decode())
+            sys.stdout.buffer.write(stdout_and_stderr)
             if not IS_RUNNING_IN_NOTEBOOK:  # for some reason flushing in jupyter notebooks breaks \r handling
-                sys.stdout.flush()
+                sys.stdout.buffer.flush()
         # flush after having processed all packages
-        sys.stdout.flush()
+        sys.stdout.buffer.flush()
 
     def show(self) -> None:
         self._refetch_job_dict()
@@ -522,11 +522,11 @@ class Result:
             logger.info(f'--- The result {self.id} has already completed (no streaming will take place) ---')
             logger.info('--- The stdout log is printed below: ---')
             sys.stdout.flush()
-            print(self.get_stdout().decode(), file=sys.stdout)
-            sys.stdout.flush()
+            sys.stdout.buffer.write(self.get_stdout())
+            sys.stdout.buffer.flush()
             logger.info('--- The stderr log is printed below: ---')
-            print(self.get_stderr().decode(), file=sys.stderr)
-            sys.stderr.flush()
+            sys.stderr.buffer.write(self.get_stderr())
+            sys.stderr.buffer.flush()
             logger.info(f'--- The job {self.id} has already completed. Its output was printed above. ---')
             return
 

{pybiolib-1.2.1304.dist-info → pybiolib-1.2.1310.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1304
+Version: 1.2.1310
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1304.dist-info → pybiolib-1.2.1310.dist-info}/RECORD

@@ -16,7 +16,7 @@ biolib/_internal/lfs/__init__.py,sha256=gSWo_xg61UniYgD7yNYxeT4I9uaXBCBSi3_nmZjn
 biolib/_internal/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
 biolib/_internal/libs/__init__.py,sha256=Jdf4tNPqe_oIIf6zYml6TiqhL_02Vyqwge6IELrAFhw,98
 biolib/_internal/libs/fusepy/__init__.py,sha256=AWDzNFS-XV_5yKb0Qx7kggIhPzq1nj_BZS5y2Nso08k,41944
-biolib/_internal/push_application.py,sha256=Ljv7cFeaWRlMdHwn93lhooD227_ZvG8oIRTWHdDdB2M,19177
+biolib/_internal/push_application.py,sha256=CzZTInul84L4fGh63P-wQwOMc3UsunECHRx-Mf1jun4,21153
 biolib/_internal/runtime.py,sha256=srQo9nbmbNI15eZtb2Dea5f2MWBiNMVW6tDUVr7wiPM,517
 biolib/_internal/string_utils.py,sha256=N7J7oGu6_yA_z0pOiKqxEh__lRdiDLh6kigeDkQEZ5g,265
 biolib/_internal/templates/__init__.py,sha256=NVbhLUMC8HITzkLvP88Qu7FHaL-SvQord-DX3gh1Ykk,24
@@ -142,7 +142,7 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=4g1xMYmfp5yzSOdwjf3pUUULF9QjqBJb4uQ25FHrFrk,13688
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=aC3MfyNOC3z1HEK60OASjaS23Bwq0z6Wkjty56JFj7o,29065
+biolib/jobs/job.py,sha256=-yF9JnHH0CEJIqp3qV9Dsv8AwBi_H1alqcKwhh3AORI,29075
 biolib/jobs/job_result.py,sha256=_xqQu9z9BqPQrU6tjqKPuKlQDt5W0Zw5xiQvzEBkDyE,5266
 biolib/jobs/types.py,sha256=rFs6bQWsNI-nb1Hu9QzOW2zFZ8bOVt7ax4UpGVASxVA,1034
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -158,8 +158,8 @@ 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=rImaghQGuIqTVWks6b9P2yKuN34uePUYPUFW_Wyoa4A,6737
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1304.dist-info/METADATA,sha256=9hWDP_mnzSSpALZigTvNoptUNQcEbYdCiasZlR8z4a8,1644
-pybiolib-1.2.1304.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1304.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1304.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1304.dist-info/RECORD,,
+pybiolib-1.2.1310.dist-info/METADATA,sha256=LNNxEg6rvoh17x8AIKHxVEHRW5CsI2k_Ybi3VrT_o6o,1644
+pybiolib-1.2.1310.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1310.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1310.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1310.dist-info/RECORD,,