version and docs updates for v1.7.0 release

pepkit · Jan 25, 2024 · 1d739fc · 1d739fc
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diff --git 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
@@ -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)
diff --git 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 <subcommand> -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
@@ -1 +1 @@
-__version__ = "1.7.0a1"
+__version__ = "1.7.0"
diff --git 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