RLS Version 1.5.0

The two big changes are:

1. the ability to use Yaml files to specify samples,
2. the introduction of `run_for_all` (and `run_for_all_samples`) functions to simplify the usage of the `parallel` module.

Several of the other changes were then to support these two features.
Additionally, some minor fixes and improvements were made.

Full ChangeLog:

- Add `load_sample_list` function to load samples in YAML format.
- Add `compress_level` argument to `write` function to specify the compression level.
- Added `name()` method to `ReadSet` objects, so you can do:

    input = load_fastq_directory("my-sample")
    print(input.name())

which will print `my-sample`.
- Added `println` function which works like `print` but prints a newline after the output.
- Make `print()` accept ints and doubles as well as strings.
- Added `run_for_all` function to `parallel` module, simplifying its API.
- When using the `parallel` module and a job fails, writes the log to the corresponding `.failed` file.
- External modules can now use the `sequenceset` type to represent a FASTA file.
- The `load_fastq_directory` function now supports `.xz` compressed files.
- The `parallel` module now checks for stale locks **before** re-trying failed tasks. The former model could lead to a situation where a particular sample failed deterministically and then blocked progress even when some locks were stale.

Bugfixes

- The `parallel` module should generate a `.failed` file for each failed job, but this was not happening in every case.
- Fixed parsing of GFF files to support negative values (reported by Josh Sekela on the mailing-list).

Author: luispedro

ChangeLog

@@ -1,4 +1,4 @@
-Version 1.5.0
+Version 1.5.0 2022-09-14 by luispedro
 	* Add `compress_level` option to `write()` function
 	* Add ability to specify samples using YAML format
 	* Make 'assemble' return NGLSequenceSet type and add sequenceset to

NGLess/Version.hs

@@ -20,7 +20,7 @@ versionStrLong :: String
 versionStrLong = "1.5.0"
 
 dateStr :: String
-dateStr = "Unreleased"
+dateStr = "14 September 2022"
 
 embeddedStr :: String
 #ifdef NO_EMBED_SAMTOOLS_BWA

README.md

@@ -24,7 +24,7 @@ If you are using NGLess, please cite:
 
 ## Example
 
-    ngless "1.4"
+    ngless "1.5"
     input = fastq(['ctrl1.fq','ctrl2.fq','stim1.fq','stim2.fq'])
     input = preprocess(input) using |read|:
         read = read[5:]
@@ -55,21 +55,21 @@ The recommended way to install NGLess is through
 Alternatively, a docker container with NGLess is available at
 [docker hub](https://hub.docker.com/r/nglesstoolkit/ngless):
 
-    docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.4.2 ngless --version
+    docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.5.0 ngless --version
 
 Adapt the mount flags (``-v``) as needed.
 
 ### Linux
 
 You can download a [statically linked version of NGless
-1.4.2](https://github.com/ngless-toolkit/ngless/releases/download/v1.4.2/NGLess-v1.4.2-Linux-static-full)
+1.5.0](https://github.com/ngless-toolkit/ngless/releases/download/v1.5.0/NGLess-v1.5.0-Linux-static-full)
 
 This should work across a wide range of Linux versions (please
 [report](https://github.com/ngless-toolkit/ngless/issues) any issues you encounter):
 
-    curl -L -O https://github.com/ngless-toolkit/ngless/releases/download/v1.4.2/NGLess-v1.4.2-Linux-static-full
-    chmod +x NGLess-v1.4.2-Linux-static-full
-    ./NGLess-v1.4.2-Linux-static-full
+    curl -L -O https://github.com/ngless-toolkit/ngless/releases/download/v1.5.0/NGLess-v1.5.0-Linux-static-full
+    chmod +x NGLess-v1.5.0-Linux-static-full
+    ./NGLess-v1.5.0-Linux-static-full
 
 This downloaded file bundles bwa, samtools and megahit (also statically linked).
 
@@ -130,7 +130,7 @@ For developers who have done this much more datasets for testing purposes can be
 - [Frequently Asked Questions (FAQ)](https://ngless.embl.de/faq.html)
 - [ngless mailing list](https://groups.google.com/forum/#!forum/ngless)
 - [What's new log](https://ngless.embl.de/whatsnew.html)
-- [NGless 1.4.0 Release Documentation](https://ngless.embl.de/whatsnew.html#version-1-4-0)
+- [NGless 1.5.0 Release Documentation](https://ngless.embl.de/whatsnew.html#version-1-5-0)
 
 ## Authors
 

docs/sources/whatsnew.rst

@@ -2,13 +2,15 @@
 What's New (History)
 ====================
 
-Unreleased (Github version)
----------------------------
+Version 1.5.0
+-------------
+
+*Released on September 14 2022*
 
 The two big changes are:
 
 1. the ability to use `Yaml <yaml-list.html`__ files to specify samples,
-2. the introduction of ``run_for_all`` (and ``run_for_all_samples``) functions to simplify the usage of the ``parallel`` module (see `standard library docs <stdlib.html>`__.
+2. the introduction of ``run_for_all`` (and ``run_for_all_samples``) functions to simplify the usage of the ``parallel`` module (see `standard library docs <stdlib.html>`__).
 
 Several of the other changes were then to support these two features.
 Additionally, some minor fixes and improvements were made.