RLS Version 1.1.0

Many changes to the language and the internal code warrant a new release: Full ChangeLog * Fix CIGAR interpretation (#109) occurring when I is present * Call bwa mem so that it behaves in a deterministic way (independently of the number of threads used) * Add `include_fragments` option to orf_find * Add early check for column headers in `count()` * Add ``sense`` argument to `count()` * Add line numbers to FastQ parsing errors * Fix __extra_args argument in map() * Add `discard_singles` function * Add `interleaved` option to fastq() * `load_mocat_sample` now fails if `pair.2` exists but `pair.1` doesn't * Reintroduce zstd compression (after fixes upstream)
ngless-toolkit · Feb 1, 2020 · 84e6c4a · 84e6c4a
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diff --git a/ChangeLog b/ChangeLog
@@ -1,4 +1,4 @@
-Version 1.0.1+
+Version 1.1.0 2019-01-25 by luispedro
 	* Reintroduce zstd compression (after fixes upstream)
 	* Fix CIGAR interpretation (#109) occurring when I is present
 	* Call bwa mem so that it behaves in a deterministic way (independently of

diff --git a/NGLess/Version.hs b/NGLess/Version.hs
@@ -1,4 +1,4 @@
-{- Copyright 2013-2019 NGLess Authors
+{- Copyright 2013-2020 NGLess Authors
  - License: MIT
  -}
 {-# LANGUAGE TemplateHaskell, CPP #-}
@@ -19,7 +19,7 @@ versionStr :: String
 versionStr = showVersion version
 
 dateStr :: String
-dateStr = "unreleased (post 1.0.1)"
+dateStr = "January 25 2020"
 
 gitHashStr :: String
 gitHashStr = $(gitHash)

diff --git a/docs/sources/conf.py b/docs/sources/conf.py
@@ -49,7 +49,7 @@
 
 # General information about the project.
 project = u'NGLess'
-copyright = u'2013-2019, NGLess Authors'
+copyright = u'2013-2020, NGLess Authors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

diff --git a/docs/sources/whatsnew.rst b/docs/sources/whatsnew.rst
@@ -2,25 +2,21 @@
 What's New (History)
 ====================
 
-Post Version 1.0.1
-------------------
+Version 1.1.0
+-------------
 
 User-visible improvements
 ~~~~~~~~~~~~~~~~~~~~~~~~~
-- ZSTD compression is available for output and intermediate files use it for
-  reduced temporary space usage (and possibly faster processing).
-- The `countfile <https://ngless.embl.de/Functions.html#countfile>`__ now
-  reorders its input if it is not ordered. This is necessary for correct usage.
+
+- Added `discard_singles() function <Functions.html#discard_singles>`__.
 - Added ``include_fragments`` option to `orf_find()
   <Functions.html#orf_find>`__.
+- The `countfile <https://ngless.embl.de/Functions.html#countfile>`__ now
+  reorders its input if it is not ordered. This is necessary for correct usage.
 - More flexible loading of ``functional_map`` arguments in `count
   <https://ngless.embl.de/Functions.html#count>`__ to accept multiple comment
   lines at the top of the file as produced by `eggnog-mapper
   <http://eggnog-mapper.embl.de/>`__.
-- Faster check for column headers in ``functional_map`` argument to `count()
-  <https://ngless.embl.de/Functions.html#count>`__ function: now it is
-  performed *as soon as possible* (including at the top of the script if the
-  arguments are literal strings), thus NGLess can fail faster.
 - Added ``sense`` argument to the `count
   <https://ngless.embl.de/Functions.html#count>`__ function, generalizing the
   previous ``strand`` argument (which is deprecated). Whereas before it was
@@ -38,6 +34,22 @@ User-visible improvements
   "as needed" basis.
 - `len <https://ngless.embl.de/Functions.html#len>`__ now works on lists
 
+Internal improvements
+~~~~~~~~~~~~~~~~~~~~~
+
+- ZSTD compression is available for output and intermediate files use it for
+  reduced temporary space usage (and possibly faster processing).
+- Faster check for column headers in ``functional_map`` argument to `count()
+  <https://ngless.embl.de/Functions.html#count>`__ function: now it is
+  performed *as soon as possible* (including at the top of the script if the
+  arguments are literal strings), thus NGLess can fail faster.
+- ZSTD compression is available for output and intermediate files use it for
+  reduced temporary space usage (and possibly faster processing).
+- Faster check for column headers in ``functional_map`` argument to `count()
+  <https://ngless.embl.de/Functions.html#count>`__ function: now it is
+  performed *as soon as possible* (including at the top of the script if the
+  arguments are literal strings), thus NGLess can fail faster.
+
 Version 1.0.1
 -------------
 

diff --git a/package.yaml b/package.yaml
@@ -1,5 +1,5 @@
 name:           NGLess
-version:        '1.0.1'
+version:        '1.1.0'
 category:       Domain Specific Language
 author:         Luis Pedro Coelho and others (see AUTHORS)
 maintainer:     [email protected]

diff --git a/stack.yaml b/stack.yaml
@@ -4,13 +4,12 @@
 
 # NOTE: When bumping stack's lts version, remember to rebuild and upload the
 # docker images (build-scripts/docker_bases/) used by GitLab
-resolver: lts-14.1
+resolver: lts-14.20
 compiler-check: newer-minor
 
 
 # Packages to be pulled from upstream that are not in the resolver (e.g., acme-missiles-0.3)
-extra-deps:
- - conduit-algorithms-0.0.11.0
+extra-deps: []
 
 allow-newer: true
 

diff --git a/tests/argv/expected.stdout.txt b/tests/argv/expected.stdout.txt
@@ -1,4 +1,4 @@
-NGLess v1.0.1 (C) NGLess authors
+NGLess v1.1.0 (C) NGLess authors
 https://ngless.embl.de/
 
 When publishing results from this script, please cite the following references:

diff --git a/tests/error-ofile-complex/expected.stdout.txt b/tests/error-ofile-complex/expected.stdout.txt
@@ -1,4 +1,4 @@
-NGLess v1.0.1 (C) NGLess authors
+NGLess v1.1.0 (C) NGLess authors
 https://ngless.embl.de/
 
 When publishing results from this script, please cite the following references:

diff --git a/tests/exampleModule/expected.stdout.txt b/tests/exampleModule/expected.stdout.txt
@@ -1,4 +1,4 @@
-NGLess v1.0.1 (C) NGLess authors
+NGLess v1.1.0 (C) NGLess authors
 https://ngless.embl.de/
 
 When publishing results from this script, please cite the following references:

diff --git a/tests/len_list/expected.stdout.txt b/tests/len_list/expected.stdout.txt
@@ -1,4 +1,4 @@
-NGLess v1.0.1 (C) NGLess authors
+NGLess v1.1.0 (C) NGLess authors
 https://ngless.embl.de/
 
 When publishing results from this script, please cite the following references:

diff --git a/tests/parse_odd_corners/expected.stdout.txt b/tests/parse_odd_corners/expected.stdout.txt
@@ -1,4 +1,4 @@
-NGLess v1.0.1 (C) NGLess authors
+NGLess v1.1.0 (C) NGLess authors
 https://ngless.embl.de/
 
 When publishing results from this script, please cite the following references:

diff --git a/tests/readlines/expected.stdout.txt b/tests/readlines/expected.stdout.txt
@@ -1,4 +1,4 @@
-NGLess v1.0.1 (C) NGLess authors
+NGLess v1.1.0 (C) NGLess authors
 https://ngless.embl.de/
 
 When publishing results from this script, please cite the following references: