oh-my-batch 0.4.7__py3-none-any.whl → 0.4.9__py3-none-any.whl

oh_my_batch/batch.py

@@ -79,15 +79,22 @@ class BatchMaker:
         self._command.extend(cmd)
         return self
 
-    def make(self, path: str, concurrency=1, encoding='utf-8', mode='755'):
+    def make(self, path: str, concurrency=0, encoding='utf-8', mode='755'):
         """
         Make batch script files from the previous setup
 
         :param path: Path to save batch script files, use {i} to represent index
-        :param concurrency: Number of scripts to to make
+        :param concurrency: Number of scripts to to make, default is 0, which means make one script for each working directory
+        :param encoding: File encoding
+        :param mode: File mode, default is 755
         """
+
         header = '\n'.join(self._script_header)
         bottom = '\n'.join(self._script_bottom)
+
+        if concurrency < 1:
+            concurrency = len(self._work_dirs)
+
         for i, work_dirs in enumerate(split_list(self._work_dirs, concurrency)):
             body = []
             work_dirs_arr = "\n".join(shlex.quote(w) for w in work_dirs)

oh_my_batch/job.py

@@ -94,6 +94,25 @@ class BaseJobManager:
                 error = True
         if error:
             raise RuntimeError('Some jobs failed')
+    
+    def wait(self, *job_ids, timeout=None, interval=10):
+        """
+        Wait for jobs to finish
+
+        :param job_ids: Job ids to wait for
+        :param timeout: Timeout in seconds
+        :param interval: Interval in seconds for checking job status
+        """
+        current = time.time()
+        while True:
+            jobs = [{'id': j, 'state': JobState.NULL} for j in job_ids]
+            jobs = self._update_state(jobs)
+            if all(JobState.is_terminal(j['state']) for j in jobs):
+                break
+            if timeout and time.time() - current > timeout:
+                logger.error('Timeout, current state: %s', jobs)
+                break
+            time.sleep(interval)
 
     def _update_jobs(self, jobs: List[dict], max_tries: int, submit_opts: str):
         jobs = self._update_state(jobs)
@@ -135,7 +154,7 @@ class Slurm(BaseJobManager):
                 logger.error('Failed to query job status: %s', log_cp(cp))
                 return jobs
             out = cp.stdout.decode('utf-8')
-            logger.info('Job status:\n%s', out)
+            logger.debug('Job status:\n%s', out)
             new_state = parse_csv(out)
         else:
             new_state = []

{oh_my_batch-0.4.7.dist-info → oh_my_batch-0.4.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oh-my-batch
-Version: 0.4.7
+Version: 0.4.9
 Summary: 
 License: GPL
 Author: weihong.xu
@@ -13,7 +13,6 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: fire (>=0.5.0,<0.6.0)
 Description-Content-Type: text/markdown
 
@@ -28,7 +27,7 @@ A toolkit to manipulate batch tasks with command line. Designed for scientific c
 ## Features
 * `omb combo`: generate folders/files from different combinations of parameters
 * `omb batch`: generate batch scripts from multiple working directories
-* `omb job`: track the state of job in job schedular
+* `omb job`: track the state of job in job scheduler
 * `omb misc`: miscellaneous commands
 
 ## Install
@@ -36,24 +35,10 @@ A toolkit to manipulate batch tasks with command line. Designed for scientific c
 pip install oh-my-batch
 ```
 
-## Shell tips
-`oh-my-batch` is intended to help you implement computational workflows with shell scripts.
-To make the best use of `oh-my-batch`, you need to know some shell tips.
-
-* [Retry commands until success in shell script](https://stackoverflow.com/a/79191004/3099733)
-* [Run multiple line shell script with ssh](https://stackoverflow.com/a/32082912/3099733)
+## Examples
+* [TESLA workflow](./examples/tesla/): A customizable active learning workflow for training machine learning potentials.
 
 ## Use cases
-### Load functions in shell script
-You can load useful functions from `oh-my-batch` this way:
-
-```bash
-eval "$(omb misc export-shell-func)"
-# or
-omb misc export-shell-func > omb-func.sh && source omb-func.sh
-```
-
-This will load extra functions to your shell script, for example, `checkpoint`.
 
 ### Generate files from different combinations of parameters
 
@@ -145,3 +130,10 @@ The `--recovery` option will save the job information to `lammps-jobs.json` file
 If `omb job` is interrupted, you can rerun the exact same command to recover the job status,
 so that you don't need to resubmit the jobs that are still running or completed.
 
+
+## Shell tips
+`oh-my-batch` is intended to help you implement computational workflows with shell scripts.
+To make the best use of `oh-my-batch`, you need to know some shell tips.
+
+* [Retry commands until success in shell script](https://stackoverflow.com/a/79191004/3099733)
+* [Run multiple line shell script with ssh](https://stackoverflow.com/a/32082912/3099733)

{oh_my_batch-0.4.7.dist-info → oh_my_batch-0.4.9.dist-info}/RECORD

@@ -2,14 +2,14 @@ oh_my_batch/__init__.py,sha256=BsRNxZbqDWfaIZJGxzIDqCubRWztMGFDceW08TECuFs,98
 oh_my_batch/__main__.py,sha256=sWyFZMwWNvhkanwZSJRGfBBDoIevhC028dTSB67i6yI,61
 oh_my_batch/assets/__init__.py,sha256=Exub46UbQaz2V2eXpQeiVfnThQpXaNeuyjlGY6gBSZc,130
 oh_my_batch/assets/functions.sh,sha256=LaiavZBu84D7C1r-dWhf91vPTuHXCMV1DQZUIPVQnjE,1001
-oh_my_batch/batch.py,sha256=o4G7AlaBOUNtwCWfO5bGnPA-iWhhq_iJxpALy1oIYb8,3593
+oh_my_batch/batch.py,sha256=BBrRlkTw9sLS4s3xmRGW-Ok3-qZi68_iaNpfDO7iYv4,3827
 oh_my_batch/cli.py,sha256=Jyz8q2pUYke3mfJS6F_G9S9hApddgXxQw1BsN6Kfkjc,553
 oh_my_batch/combo.py,sha256=A5flYsjugcelj105P6Nq4M3kNGtdqh3c7QaSIL3hUcg,9954
-oh_my_batch/job.py,sha256=Foq-xyTj01KaCxZXmfXqTZ8orFL9ZVLix2dqT5w-B3Q,6515
+oh_my_batch/job.py,sha256=8qFYscHGzIQhX-HrAGxCCv7h2T8Ls1Fj0gmNEBdP5Go,7227
 oh_my_batch/misc.py,sha256=G_iOovRCrShBJJCc82QLN0CvMqW4adOefEoY1GedEiw,452
 oh_my_batch/util.py,sha256=5ve2QcviuF0UHFLrsXmjMTj0ogXJ4g05q1y-yWCFuOk,2409
-oh_my_batch-0.4.7.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-oh_my_batch-0.4.7.dist-info/METADATA,sha256=IbPGeI3srsM97vpX15osZ-dgb3s3pNLqIxsK9IdikT0,5384
-oh_my_batch-0.4.7.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-oh_my_batch-0.4.7.dist-info/entry_points.txt,sha256=ZY2GutSoNjjSyJ4qO2pTeseKUFgoTYdvmgkuZZkwi68,77
-oh_my_batch-0.4.7.dist-info/RECORD,,
+oh_my_batch-0.4.9.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+oh_my_batch-0.4.9.dist-info/METADATA,sha256=nnVCB-BUnDfpNBHX5LUNeLMl7aWTlMZ3bOtbd1WdyVE,5174
+oh_my_batch-0.4.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+oh_my_batch-0.4.9.dist-info/entry_points.txt,sha256=ZY2GutSoNjjSyJ4qO2pTeseKUFgoTYdvmgkuZZkwi68,77
+oh_my_batch-0.4.9.dist-info/RECORD,,

{oh_my_batch-0.4.7.dist-info → oh_my_batch-0.4.9.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any