RLS Version 1.6.0-beta2

Changes with respect to 1.5.0
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* NGLess is now based on a new implementation written in Rust (previous
versions were written in Haskell). It is intended as a compatible replacement:
the same scripts produce the same results.
* NGLess now supports a single language version, "1.6". Scripts must declare
`ngless "1.6"`; declaring an older version (including "1.5") is now a hard
error. Update the version statement at the top of your scripts to `ngless
"1.6"`.
* Built-in modules (`parallel`, `samtools`, `mocat`, ...) now track the ngless
version: import them at version "1.6" going forward. Older module versions are
still accepted (with the latest behaviour) but print a deprecation warning.
* Removed the deprecated `strand` argument to `count()`; use `sense`
(`{both}`/`{sense}`/`{antisense}`) instead. `strand=True` is equivalent to
`sense={sense}`.
* Removed the deprecated `--search-dir` command-line flag (use
`--search-path`) and the unimplemented `--check-deprecation` flag.
* The output content hash reported by `auto_comments=[{hash}]` (and used to
name parallel lock/stats directories) is now computed with a simpler internal
serialization. It is still deterministic and content-addressed, but the hash
*values* differ from previous releases (they are an internal identifier, not a
stable cross-version value).
* ngless now writes an HTML run report again (the `<script>.output_ngless/`
directory, or the location given by `-o`/`--html-report-directory`; disable
with `--no-create-report`). The report is a single self-contained
`index.html` that embeds its data and makes no network requests, so it works
offline on compute clusters (the old report loaded AngularJS, jQuery,
Bootstrap and d3/nvd3 from CDNs). It shows the script (with links to the
quality-control and mapping statistics), the run log, per-file FASTQ QC with
per-position quality charts, and mapping statistics. The script listing is
syntax-highlighted. The directory also contains `script.ngl`, `fq.tsv` and
`mappings.tsv`. Inline scripts (passed with `-e`/`--script`) do *not* write a
report by default (they are typically quick one-liners); pass
`--create-report` or `-o`/`--html-report-directory` to force one.
* Importing the legacy `motus` or `soap` modules now aborts with a clear
guidance error (both are obsolete and unsupported)
* `count()` now errors early when more than one annotation source is given
(seqname mode, `gff_file`, `functional_map`, or `reference`) instead of
silently ignoring all but one
* A constant out-of-bounds list index (e.g. `x[5]` on a 3-element list) now
fails early, right after the list is assigned, with the same "Index access
on line N is invalid" message as earlier ngless versions
* Added the `{always_3_fq_files}` format flag to `write()`
* Better suggestions for mistyped arguments/flags (matching by prefix, e.g.
`ref=` for `reference=`)

Changes with respect to 1.6.0-beta1
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* The build now supports a single language version, "1.6": a script declaring
"1.5" (which beta1 still accepted with a warning) is now a hard error.
* Removed the deprecated `count()` `strand` argument (use `sense`), the
`--search-dir` command-line flag (use `--search-path`), and the unimplemented
`--check-deprecation` flag.
* The internal output content hash (`auto_comments=[{hash}]` and parallel
lock/stats directory names) is computed differently, so its values differ from
beta1. It remains deterministic and content-addressed.
* Otherwise beta2 restores a large set of features that beta1 had not yet
ported from earlier ngless versions -- transparent `.xz` support, the HTML run
report, parallel-module progress reporting, `format={sam|bam}` on `write()`,
`preprocess(keep_singles=False)`, `auto_comments=[{date}]`, reference-based
`count()`, enhanced FASTQ QC statistics, broader external module support,
and several performance and UX improvements.

Author: luispedro

pixi.toml

@@ -9,7 +9,10 @@ preview = ["pixi-build"]
 [tasks]
 
 [package]
-version = "1.6.beta1"
+# For "normal" versions, this can come from Cargo.toml, but for pre-releases,
+# we need to specify it here because of difference conventions between Cargo
+# and conda (-beta vs .beta).
+version = "1.6.beta2"
 
 [package.build]
 backend = { name = "pixi-build-rust", version = "*" }