Code

v0.14.1 release#219

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Merged

donaldcampbelljr merged 44 commits intomasterdatabio/pypiper:masterfrom devdatabio/pypiper:devCopy head branch name to clipboardApr 19, 2024

+104-114

Commits

Commits on Sep 6, 2023

• try getting just stage name, but fall back to str representation of stage; close #197

  vreuter

  committed
  0c9b16f

Commits on Oct 4, 2023

• version 0.13.3a1 for pipestat 0.6.0a1

  donaldcampbelljr

  committed
  0b430c7

Commits on Nov 7, 2023

• updated to pipestat 0.6.0

  khoroshevskyi

  committed
  d9c818d

• Merge branch 'dev' into new_pipestat

  khoroshevskyi

  authored
  e30fe6e

• updated requirements

  khoroshevskyi

  committed
  e00e8d8

• testing, drop python 3.7

  khoroshevskyi

  committed
  39b6e99

• Merge pull request #198 from vreuter/vr/stage-log-message-197

  Show description for 6914fd5
  khoroshevskyi

  authored
  6914fd5

Commits on Nov 8, 2023

• fix f-string quote issue for python 3.10

  donaldcampbelljr

  committed
  1c2c844

Commits on Nov 10, 2023

• minor refactor to use pipestat properties instead of cfg dict

  donaldcampbelljr

  committed
  5b46682

• update changelog and version number

  donaldcampbelljr

  committed
  d360ba1

• Merge pull request #199 from databio/new_pipestat

  Show description for 4db1637
  donaldcampbelljr

  authored
  4db1637

Commits on Nov 14, 2023

• update v0.13.3 and changelog

  donaldcampbelljr

  committed
  4ea21c2

• fix _refresh_stats bug and change version to 0.14.0

  donaldcampbelljr

  committed
  ed6b7fb

Commits on Nov 15, 2023

• potential fix for #201

  donaldcampbelljr

  committed
  b0c5f8d

• changelog

  donaldcampbelljr

  committed
  d7b9c8c

• v0.14.0a1 prerelease

  donaldcampbelljr

  committed
  f92d034

Commits on Nov 20, 2023

• report_object -> change message_raw to be a values dict to conform with pipestat output schemas

  donaldcampbelljr

  committed
  1a677da

• self.pipestat_results_file should take priority over self.pipeline_stats_file related to databio/pepatac#257

  donaldcampbelljr

  committed
  ed95993

Commits on Nov 27, 2023

• make pipestat_results_file = pipeline_stats_file if it is not provided

  donaldcampbelljr

  committed
  cc84070

• set pipeline_stats_file if pipestat_results_file IS provided, remove checking for the first record_identifier during get_stat

  donaldcampbelljr

  committed
  2de4e84

Commits on Dec 8, 2023

• add pipestat_pipeline_type, defaulting to sample

  donaldcampbelljr

  committed
  d544644

Commits on Dec 14, 2023

• pipestat req version bump, v0.14.0a2 bump for pre-release

  donaldcampbelljr

  committed
  649c985

Commits on Dec 22, 2023

• v0.14.0 release prep

  donaldcampbelljr

  committed
  9349aa8

Commits on Jan 17, 2024

• https updates

  nsheff

  committed
  b7d3f6b

Commits on Feb 15, 2024

• Merge branch 'master' into dev

  nsheff

  committed
  69fa47e

Commits on Feb 17, 2024

• log outfile directly, and clean up logging code. Fix #210

  nsheff

  committed
  87f1074

• use f-strings in example pipelines

  nsheff

  committed
  65ed31d

Commits on Feb 18, 2024

• simplify syntax

  vreuter

  committed
  bddeddc

• separate what can and can't cause exception

  vreuter

  committed
  005869e

• copy the kwargs to avoid modification

  vreuter

  committed
  d8504f6

• homogenize messaging about logger establishment

  vreuter

  committed
  28a608a

• organize logger construction for pipeline manager, and homogenize treatment of arguments across branches

  vreuter

  committed
  9b2ccbc

• tweak syntax

  vreuter

  committed
  76ffdc6

• use default strict=False behavior for logger via CLI

  vreuter

  committed
  7baa056

• move up logfile setting to set up solution for #212

  vreuter

  committed
  a83025b

• check that logfile for logger doesn't match manager's own logfile; #212

  vreuter

  committed
  ba423a4

• test solution for #212

  vreuter

  committed
  97821e9

• apply new black formatting

  vreuter

  committed
  fcb02fa

Commits on Feb 19, 2024

• Fix #213, remove pipestat_project_name, refactor pipestat_sample_name to pipestat_record_identifier, update doc strings

  donaldcampbelljr

  committed
  94806df

Commits on Feb 20, 2024

• Merge pull request #215 from databio/vr/logfile-212

  Show description for 59e1afb
  vreuter

  authored
  59e1afb

Commits on Apr 4, 2024

• #209 Switch force_overwrite to default to True

  donaldcampbelljr

  committed
  04abc1f

• version bump on requirements #216

  donaldcampbelljr

  committed
  5413eec

Commits on Apr 19, 2024

• update version and changelog for 0.14.1 release

  donaldcampbelljr

  committed
  3e10213

• lint

  donaldcampbelljr

  committed
  703580d