diff --git a/docs/changelog.md b/docs/changelog.md index 42fabbdc4..9095091b3 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -2,10 +2,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. -## [1.7.0] -- 2024-xx-xx +## [1.7.0] -- 2024-01-26 ### Added -- `--portable` flag to looper report +- `--portable` flag to `looper report` to create a portable version of the html report - `--lump-j` allows grouping samples into a defined number of jobs ### Changed diff --git a/docs/looper-report.md b/docs/looper-report.md index c98f5aa8c..6cd4a79ea 100644 --- a/docs/looper-report.md +++ b/docs/looper-report.md @@ -6,6 +6,8 @@ Looper can create a browsable html report of all project results using the comma looper report --looper-config .your_looper_config.yaml ``` +Beginning in Looper 1.7.0, the ``--portable`` flag can be used to create a shareable, zipped version of the html report. + An example html report out put can be found here: [PEPATAC Gold Summary](https://pepatac.databio.org/en/latest/files/examples/gold/gold_summary.html) Note: pipestat must be configured by looper to perform this operation. Please see the pipestat section for more information: [Using pipestat](pipestat.md) \ No newline at end of file diff --git a/docs/usage.md b/docs/usage.md index 8cf62d869..fe102ddcd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,7 +6,7 @@ Each task is controlled by one of the following commands: `run`, `rerun`, `runp` - `looper run`: Runs pipelines for each sample, for each pipeline. This will use your `compute` settings to build and submit scripts to your specified compute environment, or run them sequentially on your local computer. -- `looper runp`: Runs [project-level pipelines](http://looper.databio.org/en/latest/pipeline-tiers/#project-pipelines). These are pipelines run once per project instead of once per sample. +- `looper runp`: Runs pipelines for each pipeline for project. - `looper rerun`: Exactly the same as `looper run`, but only runs jobs with a failed flag. @@ -26,7 +26,7 @@ Each task is controlled by one of the following commands: `run`, `rerun`, `runp` Here you can see the command-line usage instructions for the main looper command and for each subcommand: ## `looper --help` ```console -version: 1.6.0 +version: 1.7.0 usage: looper [-h] [--version] [--logfile LOGFILE] [--dbg] [--silent] [--verbosity V] [--logdev] [--commands] {run,rerun,runp,table,report,destroy,check,clean,inspect,init,init-piface,link} @@ -57,7 +57,7 @@ options: --silent Silence logging. Overrides verbosity. --verbosity V Set logging level (1-5 or logging module level name) --logdev Expand content of logging message format. - --commands show program's primary commands + --commands show program's version number and exit For subcommand-specific options, type: 'looper -h' https://github.com/pepkit/looper @@ -66,7 +66,7 @@ https://github.com/pepkit/looper ## `looper run --help` ```console usage: looper run [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] [-s S] - [-c K [K ...]] [-u X] [-n N] [--looper-config LOOPER_CONFIG] + [-c K [K ...]] [-u X] [-n N] [-j J] [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [--sel-flag [SELFLAG ...]] [--exc-flag [EXCFLAG ...]] [-a A [A ...]] @@ -86,8 +86,11 @@ options: -x S, --command-extra S String to append to every command -y S, --command-extra-override S Same as command-extra, but overrides values in PEP -f, --skip-file-checks Do not perform input file checks - -u X, --lump X Total input file size (GB) to batch into one job - -n N, --lumpn N Number of commands to batch into one job + -u X, --lump-s X Lump by size: total input file size (GB) to batch + into one job + -n N, --lump-n N Lump by number: number of samples to batch into one + job + -j J, --lump-j J Lump samples into number of jobs. --looper-config LOOPER_CONFIG Looper configuration file (YAML) -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file @@ -170,10 +173,11 @@ sample selection arguments: ## `looper rerun --help` ```console usage: looper rerun [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] - [-s S] [-c K [K ...]] [-u X] [-n N] [--looper-config LOOPER_CONFIG] - [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] - [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] - [--sel-flag [SELFLAG ...]] [--exc-flag [EXCFLAG ...]] [-a A [A ...]] + [-s S] [-c K [K ...]] [-u X] [-n N] [-j J] + [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] + [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] + [--sel-excl [E ...] | --sel-incl [I ...]] [--sel-flag [SELFLAG ...]] + [--exc-flag [EXCFLAG ...]] [-a A [A ...]] [config_file] Resubmit sample jobs with failed flags. @@ -190,8 +194,11 @@ options: -x S, --command-extra S String to append to every command -y S, --command-extra-override S Same as command-extra, but overrides values in PEP -f, --skip-file-checks Do not perform input file checks - -u X, --lump X Total input file size (GB) to batch into one job - -n N, --lumpn N Number of commands to batch into one job + -u X, --lump-s X Lump by size: total input file size (GB) to batch + into one job + -n N, --lump-n N Lump by number: number of samples to batch into one + job + -j J, --lump-j J Lump samples into number of jobs. --looper-config LOOPER_CONFIG Looper configuration file (YAML) -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file @@ -225,7 +232,7 @@ sample selection arguments: usage: looper report [-h] [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [--sel-flag [SELFLAG ...]] - [--exc-flag [EXCFLAG ...]] [-a A [A ...]] [--project] + [--exc-flag [EXCFLAG ...]] [-a A [A ...]] [--project] [--portable] [config_file] Create browsable HTML report of project results. @@ -243,6 +250,7 @@ options: Path to looper project config file -a A [A ...], --amend A [A ...] List of amendments to activate --project Process project-level pipelines + --portable Makes html report portable. sample selection arguments: Specify samples to include or exclude based on sample attribute values diff --git a/looper/_version.py b/looper/_version.py index ae836b722..14d9d2f58 100644 --- a/looper/_version.py +++ b/looper/_version.py @@ -1 +1 @@ -__version__ = "1.7.0a1" +__version__ = "1.7.0" diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt index 56f84746e..0f3963a5e 100644 --- a/requirements/requirements-all.txt +++ b/requirements/requirements-all.txt @@ -6,7 +6,7 @@ logmuse>=0.2.0 pandas>=2.0.2 pephubclient>=0.1.2 peppy>=0.40.0 -pipestat>=0.7.1a1 +pipestat>=0.8.0 pyyaml>=3.12 rich>=9.10.0 ubiquerg>=0.5.2