looper 1.6.0a2__py3-none-any.whl → 1.7.0__py3-none-any.whl

looper/_version.py

@@ -1 +1 @@
-__version__ = "1.6.0a2"
+__version__ = "1.7.0"

looper/cli_looper.py

@@ -219,19 +219,27 @@ def build_parser():
         for subparser in [run_subparser, rerun_subparser]:
             subparser.add_argument(
                 "-u",
-                "--lump",
+                "--lump-s",
                 default=None,
                 metavar="X",
                 type=html_range(min_val=0, max_val=100, step=0.1, value=0),
-                help="Total input file size (GB) to batch into one job",
+                help="Lump by size: total input file size (GB) to batch into one job",
             )
             subparser.add_argument(
                 "-n",
-                "--lumpn",
+                "--lump-n",
                 default=None,
                 metavar="N",
                 type=html_range(min_val=1, max_val="num_samples", value=1),
-                help="Number of commands to batch into one job",
+                help="Lump by number: number of samples to batch into one job",
+            )
+            subparser.add_argument(
+                "-j",
+                "--lump-j",
+                default=None,
+                metavar="J",
+                type=int,
+                help="Lump samples into number of jobs.",
             )
 
         check_subparser.add_argument(
@@ -495,6 +503,18 @@ def build_parser():
             help="Number of attributes to display",
             type=int,
         )
+        parser.add_argument(
+            "--commands",
+            action="version",
+            version="{}".format(" ".join(subparsers.choices.keys())),
+        )
+
+        report_subparser.add_argument(
+            "--portable",
+            help="Makes html report portable.",
+            action="store_true",
+        )
+
         result.append(parser)
     return result
 

looper/conductor.py

@@ -6,6 +6,7 @@ import os
 import subprocess
 import time
 import yaml
+from math import ceil
 from copy import copy, deepcopy
 from json import loads
 from subprocess import check_output
@@ -132,6 +133,7 @@ class SubmissionConductor(object):
         compute_variables=None,
         max_cmds=None,
         max_size=None,
+        max_jobs=None,
         automatic=True,
         collate=False,
     ):
@@ -166,6 +168,8 @@ class SubmissionConductor(object):
             include in a single job script.
         :param int | float | NoneType max_size: Upper bound on total file
             size of inputs used by the commands lumped into single job script.
+        :param int | float | NoneType max_jobs: Upper bound on total number of jobs to
+            group samples for submission.
         :param bool automatic: Whether the submission should be automatic once
             the pool reaches capacity.
         :param bool collate: Whether a collate job is to be submitted (runs on
@@ -200,6 +204,16 @@ class SubmissionConductor(object):
                 "{}".format(self.extra_pipe_args)
             )
 
+        if max_jobs:
+            if max_jobs == 0 or max_jobs < 0:
+                raise ValueError(
+                    "If specified, max job command count must be a positive integer, greater than zero."
+                )
+
+            num_samples = len(self.prj.samples)
+            samples_per_job = num_samples / max_jobs
+            max_cmds = ceil(samples_per_job)
+
         if not self.collate:
             self.automatic = automatic
             if max_cmds is None and max_size is None:

looper/looper.py

@@ -404,8 +404,9 @@ class Runner(Executor):
                 extra_args=args.command_extra,
                 extra_args_override=args.command_extra_override,
                 ignore_flags=args.ignore_flags,
-                max_cmds=args.lumpn,
-                max_size=args.lump,
+                max_cmds=args.lump_n,
+                max_size=args.lump_s,
+                max_jobs=args.lump_j,
             )
             submission_conductors[piface.pipe_iface_file] = conductor
 
@@ -547,12 +548,16 @@ class Reporter(Executor):
         p = self.prj
         project_level = args.project
 
+        portable = args.portable
+
         if project_level:
             psms = self.prj.get_pipestat_managers(project_level=True)
             print(psms)
             for name, psm in psms.items():
                 # Summarize will generate the static HTML Report Function
-                report_directory = psm.summarize(looper_samples=self.prj.samples)
+                report_directory = psm.summarize(
+                    looper_samples=self.prj.samples, portable=portable
+                )
                 print(f"Report directory: {report_directory}")
         else:
             for piface_source_samples in self.prj._samples_by_piface(
@@ -567,7 +572,9 @@ class Reporter(Executor):
                 print(psms)
                 for name, psm in psms.items():
                     # Summarize will generate the static HTML Report Function
-                    report_directory = psm.summarize(looper_samples=self.prj.samples)
+                    report_directory = psm.summarize(
+                        looper_samples=self.prj.samples, portable=portable
+                    )
                     print(f"Report directory: {report_directory}")
 
 

looper/project.py

@@ -111,9 +111,7 @@ class Project(peppyProject):
         compute settings.
     """
 
-    def __init__(
-        self, cfg=None, amendments=None, divcfg_path=None, runp=False, **kwargs
-    ):
+    def __init__(self, cfg=None, amendments=None, divcfg_path=None, **kwargs):
         super(Project, self).__init__(cfg=cfg, amendments=amendments)
         prj_dict = kwargs.get("project_dict")
         pep_config = kwargs.get("pep_config", None)
@@ -122,7 +120,7 @@ class Project(peppyProject):
 
         # init project from pephub pep_config:
         if prj_dict is not None and cfg is None:
-            self.from_dict(prj_dict)
+            self._from_dict(prj_dict)
             self["_config_file"] = os.getcwd()  # for finding pipeline interface
             self["pep_config"] = pep_config
 
@@ -916,7 +914,7 @@ def make_set(items):
     try:
         # Check if user input single integer value for inclusion/exclusion criteria
         if len(items) == 1:
-            items = list(map(int, items))  # list(int(items[0]))
+            items = list(map(str, items))  # list(int(items[0]))
     except:
         if isinstance(items, str):
             items = [items]

{looper-1.6.0a2.dist-info → looper-1.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: looper
-Version: 1.6.0a2
+Version: 1.7.0
 Summary: A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
 Home-page: https://github.com/pepkit/looper
 Author: Nathan Sheffield, Vince Reuter, Michal Stolarczyk, Johanna Klughammer, Andre Rendeiro
@@ -22,8 +22,8 @@ Requires-Dist: jinja2
 Requires-Dist: logmuse >=0.2.0
 Requires-Dist: pandas >=2.0.2
 Requires-Dist: pephubclient >=0.1.2
-Requires-Dist: peppy >=0.40.0.a4
-Requires-Dist: pipestat >=0.6.0a9
+Requires-Dist: peppy >=0.40.0
+Requires-Dist: pipestat >=0.8.0
 Requires-Dist: pyyaml >=3.12
 Requires-Dist: rich >=9.10.0
 Requires-Dist: ubiquerg >=0.5.2

{looper-1.6.0a2.dist-info → looper-1.7.0.dist-info}/RECORD

@@ -1,18 +1,18 @@
 looper/__init__.py,sha256=f_z9YY4ibOk7eyWoaViH_VaCXMlPQeiftbnibSFj-3E,1333
 looper/__main__.py,sha256=8CX2ae8mUQNI_Z8pdBT4i5UFqROFX1awyFnuYCKuYXg,238
-looper/_version.py,sha256=LyKCp03C0l6j9csFpO9LhsN-rNU_LmTHK3ql3ULRXUI,24
+looper/_version.py,sha256=lEEx5lwinUby-YNl7w-VFGUcjcibsJ9EuzgJ2W7ocrU,22
 looper/cli_divvy.py,sha256=J07x83sqC4jJeu3_yS6KOARPWmwKGAV7JvN33T5zDac,5907
-looper/cli_looper.py,sha256=0SYyPAPg8MEGOnp_vjn0Mxohe7Annr56hwDBX_DqM5U,25769
-looper/conductor.py,sha256=BmMATwtkHoPSsffYopCQ1WxK83O3UjOTFRrakgD6DzA,30231
+looper/cli_looper.py,sha256=se-EbQ4nucWxMiU0VLnmV0Kss-JMjSmWih6vHaOiLi0,26367
+looper/conductor.py,sha256=9k0r_vsHCP25MrDjz7GR16_EEdqP9JZELYZJVm6ny1g,30777
 looper/const.py,sha256=bPj4lTuj2l6gwHROWqj16iHfJFo9ghZAz8THNREWW4U,8558
 looper/divvy.py,sha256=qa1ebbQTfNupAyDfhfEJ6mbZ_V3zk-D_E-Tck7miJ38,15688
 looper/exceptions.py,sha256=r6SKKt-m8CXQnXGDnuiwoA6zBJhIZflygBKjX4RCloI,3419
-looper/looper.py,sha256=f__lSwDgzTcFpv5kUIrR-XdC49_YPvdVZTBfBdkm2J8,30251
+looper/looper.py,sha256=U3mNqXRDZRzmFXV26TcPQYKPdY1plPvMraNHTnps4mQ,30448
 looper/parser_types.py,sha256=d3FHt54f9jo9VZMr5SQkbghcAdABqiYZW2JBGO5EBnw,2327
 looper/pipeline_interface.py,sha256=y46tB1_73d1FX8N1w4-GGvRBJ7rqhenuUYVtUfIhK5s,14974
 looper/plugins.py,sha256=MaMdPmK9U_4FkNJE5kccohBbY1i2qj1NTEucubFOJek,5747
 looper/processed_project.py,sha256=jZxoMYafvr-OHFxylc5ivGty1VwXBZhl0kgoFkY-174,9837
-looper/project.py,sha256=Ldsa__wLNnDpKFfN0cOCWQnL-pTuVrPbbHJPHFt9fcU,36196
+looper/project.py,sha256=nkNP7ftVs82Tnk2Yn6FUp60_D6bjE9sSvySE0SHqsmg,36171
 looper/utils.py,sha256=i7srIXPEnQjtNaoP0ziRpdYfB7HNY5_3rW5LoKIM15I,27257
 looper/default_config/divvy_config.yaml,sha256=wK5kLDGBV2wwoyqg2rl3X8SXjds4x0mwBUjUzF1Ln7g,1705
 looper/default_config/divvy_templates/localhost_bulker_template.sub,sha256=yn5VB9Brt7Hck9LT17hD2o8Kn-76gYJQk_A-8C1Gr4k,164
@@ -55,9 +55,9 @@ looper/schemas/divvy_config_schema.yaml,sha256=7GJfKLc3VX4RGjHnOE1zxwsHXhj_ur9za
 looper/schemas/pipeline_interface_schema_generic.yaml,sha256=D16Rkpj03H9WnvA_N18iNU-hH_HwOuyESJ8Hk5hZSXc,1518
 looper/schemas/pipeline_interface_schema_project.yaml,sha256=-ZWyA0lKXWik3obuLNVk3IsAZYfbLVbCDvJnD-Fcluo,1567
 looper/schemas/pipeline_interface_schema_sample.yaml,sha256=x0OwVnijJpvm50DscvvJujdK4UAI7d71pqVemQS-D-0,1564
-looper-1.6.0a2.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-looper-1.6.0a2.dist-info/METADATA,sha256=VZ2Qj4IYbM8GRd7Bt6zfEDrPhwGy5dIoCunh83nzgWk,1740
-looper-1.6.0a2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-looper-1.6.0a2.dist-info/entry_points.txt,sha256=AEL1eb0gPLYvAEUewM35Ng4scXGZIWJK4Mxdj3Hm8Fw,83
-looper-1.6.0a2.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
-looper-1.6.0a2.dist-info/RECORD,,
+looper-1.7.0.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+looper-1.7.0.dist-info/METADATA,sha256=pGYwFxwYKiFtzUuYx4t0q-cMKmCF_fhsKwAFlbwBfP0,1733
+looper-1.7.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+looper-1.7.0.dist-info/entry_points.txt,sha256=AEL1eb0gPLYvAEUewM35Ng4scXGZIWJK4Mxdj3Hm8Fw,83
+looper-1.7.0.dist-info/top_level.txt,sha256=I0Yf7djsoQAMzwHBbDiQi9hGtq4Z41_Ma5CX8qXG8Y8,7
+looper-1.7.0.dist-info/RECORD,,