From 84e6c4a7a7744a3fcfe162684aaa41804e558e83 Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Mon, 20 Jan 2020 13:59:12 +0800 Subject: [PATCH] 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) --- ChangeLog | 2 +- NGLess/Version.hs | 4 +-- docs/sources/conf.py | 2 +- docs/sources/whatsnew.rst | 32 +++++++++++++------ package.yaml | 2 +- stack.yaml | 5 ++- tests/argv/expected.stdout.txt | 2 +- tests/error-ofile-complex/expected.stdout.txt | 2 +- tests/exampleModule/expected.stdout.txt | 2 +- tests/len_list/expected.stdout.txt | 2 +- tests/parse_odd_corners/expected.stdout.txt | 2 +- tests/readlines/expected.stdout.txt | 2 +- 12 files changed, 35 insertions(+), 24 deletions(-) diff --git a/ChangeLog b/ChangeLog index 33a0ecf0..25d89658 100644 --- 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 index aa9dd691..f6bba089 100644 --- 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 index 83f2c857..b5905e84 100644 --- 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 index 95ff5bfa..2db5974f 100644 --- 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 `__ now - reorders its input if it is not ordered. This is necessary for correct usage. + +- Added `discard_singles() function `__. - Added ``include_fragments`` option to `orf_find() `__. +- The `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 `__ to accept multiple comment lines at the top of the file as produced by `eggnog-mapper `__. -- Faster check for column headers in ``functional_map`` argument to `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 `__ function, generalizing the previous ``strand`` argument (which is deprecated). Whereas before it was @@ -38,6 +34,22 @@ User-visible improvements "as needed" basis. - `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() + `__ 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() + `__ 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 index f66cf5a5..aa1d70e9 100644 --- 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: luis@luispedro.org diff --git a/stack.yaml b/stack.yaml index 263ad0b8..5a6a6d66 100644 --- 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 index dcfc2774..b8b76a63 100644 --- 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 index 913ca3eb..7d80f9ed 100644 --- 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 index b8197b7a..a2975151 100644 --- 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 index 207f3ade..13802145 100644 --- 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 index ec2ef8e3..4f62f560 100644 --- 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 index c86a21d4..dfea1508 100644 --- 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: