RLS Version 1.6.0

First stable release of the 1.6 series (previous 1.6 builds were betas).

- Cargo.toml / src/lib.rs (VERSION_STR_LONG, DATE_STR, and the matching unit
  test) / docs conf.py / pixi.toml / CLAUDE.md: version -> 1.6.0, release date
  4 August 2026. `--version` now reports "ngless v1.6.0 (release date: 4 August
  2026)".
- ChangeLog: rename the Unreleased block to Version 1.6.0, with a lead-in
  pointing at the beta1/beta2 blocks for the full delta against 1.5.0.
- docs/sources/whatsnew.rst: retitle from a beta note to "Released on August 4
  2026". Promote the two post-beta2 changes that are new relative to 1.5.0 (the
  early output-directory check and the module-import error listing searched
  locations) into the user-facing list; fold the rest, which restore 1.5
  behaviour the betas had not ported, into a section covering both pre-releases.

Install docs: 1.6.0 goes to bioconda, so drop the pre-release workaround of
pinning the .conda package by URL. pixi_install_ngless.toml now depends on
`ngless = ">=1.6.0,<2"` only -- the external tools (bwa, samtools, minimap2,
megahit, prodigal) come in as dependencies of the bioconda package, so they no
longer need to be listed. README.md and docs/sources/install.md are reworded
from "Beta releases (via pixi)" to "Using pixi" to match. This also fixes the
README manifest snippet, which had been missing its closing brace since the
1.6.0-beta2 release commit and was therefore invalid TOML.

Also remove the Docker and statically-linked-binary sections from both README.md
and docs/sources/install.md: they pointed at 1.4.2/1.5.0 artifacts and claimed
the download "bundles bwa, samtools and megahit", which is not true of the Rust
build (no external tools are embedded). Retarget the README release-docs link
from 1.5.0 to 1.6.0, and correct the functional test count in CLAUDE.md from 99
to 108.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0166PqYxwN7gA91X5RH6zzdq

Author: luispedro

CLAUDE.md

@@ -16,8 +16,9 @@ root (`Cargo.toml`, `src/`) is the sole, supported implementation. Many doc comm
 are **stale** — they still describe features as "deferred to a later milestone" or "a scaffold"
 even where the Rust code fully implements them. Do not trust those; treat the Rust code as the
 full implementation. `rust-migration.md` is the most
-accurate status doc (all 99 functional tests pass against the Rust binary). Current crate
-version is `1.6.0-beta2` (see `Cargo.toml`).
+accurate status doc (all 108 functional tests pass against the Rust binary). Current crate
+version is `1.6.0` (see `Cargo.toml`), released 4 August 2026 — the first stable release of
+the 1.6 series.
 
 ## Build & test
 
@@ -31,7 +32,7 @@ cargo fmt --all -- --check     # formatting is enforced in CI
 Functional test suite (the primary correctness bar):
 
 ```sh
-NGLESS_BIN=target/release/ngless ./run-tests.sh          # all 99 tests
+NGLESS_BIN=target/release/ngless ./run-tests.sh          # all 108 tests
 NGLESS_BIN=target/release/ngless ./run-tests.sh regression   # only tests/regression*
 ```
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ngless"
-version = "1.6.0-beta2"
+version = "1.6.0"
 edition = "2021"
 description = "NGLess: NGS processing with Less work — a domain-specific language for next-generation sequencing data"
 license = "MIT"

ChangeLog

@@ -1,4 +1,9 @@
-Unreleased
+Version 1.6.0 2026-08-04 by luispedro
+
+	This is the first stable release of the 1.6 series. See the 1.6.0-beta2 and
+	1.6.0-beta1 entries below for the full set of changes with respect to 1.5.0;
+	the most important one is that NGLess is now based on a new implementation
+	written in Rust and supports a single language version, "1.6".
 
 	Changes with respect to 1.6.0-beta2:
 	* Fixed the `encoding` argument to `fastq()` and `paired()` (and forwarded

README.md

@@ -57,57 +57,29 @@ The recommended way to install NGLess is through
 
     conda install -c bioconda ngless 
 
-### Beta releases (via pixi)
+### Using pixi
 
-Pre-release/beta builds are published as `.conda` packages on the [GitHub
-releases page](https://github.com/ngless-toolkit/ngless/releases) before they
-reach bioconda. The easiest way to install one (together with the external tools
-NGLess drives) is with [pixi](https://pixi.sh) and a manifest that pins the beta
-package by URL. The [`pixi_install_ngless.toml`](pixi_install_ngless.toml) file
-in this repository is a ready-to-use example:
+[pixi](https://pixi.sh) is an alternative to conda that installs NGLess into a
+self-contained, per-project environment. The external tools NGLess drives (bwa,
+minimap2, samtools, prodigal, megahit) are dependencies of the bioconda package,
+so they are pulled in automatically. The
+[`pixi_install_ngless.toml`](pixi_install_ngless.toml) file in this repository is
+a ready-to-use example:
 
     [dependencies]
-    prodigal = ">=2.6.3,<3"
-    megahit = ">=1.2.9,<2"
-    samtools = ">=1.23.1,<2"
-    minimap2 = ">=2.31,<3"
-    bwa = ">=0.7.19,<0.8"
-    ngless = { url = "https://github.com/ngless-toolkit/ngless/releases/download/v1.6.0-beta2/ngless-1.6.beta2-ha35fb5c_0.conda" 
+    ngless = ">=1.6.0,<2"
 
 pixi only reads a manifest named exactly `pixi.toml`, so copy the example into a
 fresh directory under that name:
 
-    mkdir ngless-beta && cp pixi_install_ngless.toml ngless-beta/pixi.toml
-    cd ngless-beta
+    mkdir ngless-env && cp pixi_install_ngless.toml ngless-env/pixi.toml
+    cd ngless-env
 
 Then install and run it with:
 
     pixi install
     pixi run ngless --version
 
-### Docker
-
-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:1.5.0 ngless --version
-
-Adapt the mount flags (``-v``) as needed.
-
-### Linux
-
-You can download a [statically linked version of NGless
-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/v1.5.0/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).
-
 ### From Source
 
 Installing/compiling from source is also possible. Clone
@@ -182,7 +154,7 @@ Haskell. Point the harness at the build via `NGLESS_BIN` (it needs the external
 - [Frequently Asked Questions (FAQ)](https://ngless.readthedocs.io/en/latest/faq.html)
 - [ngless mailing list](https://groups.google.com/forum/#!forum/ngless)
 - [What's new log](https://ngless.readthedocs.io/en/latest/whatsnew.html)
-- [NGless 1.5.0 Release Documentation](https://ngless.readthedocs.io/en/latest/whatsnew.html#version-1-5-0)
+- [NGless 1.6.0 Release Documentation](https://ngless.readthedocs.io/en/latest/whatsnew.html#version-1-6-0)
 
 ## Authors
 

docs/sources/conf.py

@@ -54,7 +54,7 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-release = '1.6.0-beta2'
+release = '1.6.0'
 version = '1.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/sources/install.md

@@ -9,13 +9,12 @@ The recommended way to install NGLess is through
 
 This will install the most recent released version
 
-## Beta releases (via pixi)
+## Using pixi
 
-Pre-release/beta builds are published as `.conda` packages on the [GitHub
-releases page](https://github.com/ngless-toolkit/ngless/releases) before they
-reach bioconda. The easiest way to install one, together with the external tools
-that NGLess drives (`bwa`, `samtools`, `minimap2`, `megahit`, `prodigal`), is
-with [pixi](https://pixi.sh) and a manifest that pins the beta package by URL.
+[pixi](https://pixi.sh) is an alternative to conda that installs NGLess into a
+self-contained, per-project environment. The external tools that NGLess drives
+(`bwa`, `samtools`, `minimap2`, `megahit`, `prodigal`) are dependencies of the
+bioconda package, so they are pulled in automatically.
 
 pixi only reads a manifest named exactly `pixi.toml`, so create a directory for
 the install and put the manifest there as `pixi.toml` (a ready-to-use copy ships
@@ -29,45 +28,13 @@ repository](https://github.com/ngless-toolkit/ngless/blob/master/pixi_install_ng
     version = "0.1.0"
 
     [dependencies]
-    prodigal = ">=2.6.3,<3"
-    megahit = ">=1.2.9,<2"
-    samtools = ">=1.23.1,<2"
-    minimap2 = ">=2.31,<3"
-    bwa = ">=0.7.19,<0.8"
-    ngless = { url = "https://github.com/ngless-toolkit/ngless/releases/download/v1.6.0-beta2/ngless-1.6.beta2-ha35fb5c_0.conda" }
+    ngless = ">=1.6.0,<2"
 
 Then, from that directory, install and run it with:
 
     pixi install
     pixi run ngless --version
 
-Update the `url` to point at the beta release you want to install.
-
-### Docker
-
-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
-
-Adapt the mount flags (``-v``) as needed. You can use the `latest` tag to get a
-more up to date version as well.
-
-
-## Linux (binary)
-
-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).
-
-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
-
-This downloaded file bundles bwa, samtools and megahit (also statically linked).
-
 ## From source
 
 Since version 1.6, NGLess is written in [Rust](https://www.rust-lang.org/) and

docs/sources/whatsnew.rst

@@ -5,7 +5,7 @@ What's New (History)
 Version 1.6.0
 -------------
 
-*Beta release (1.6.0-beta2, released on July 4 2026).*
+*Released on August 4 2026*
 
 Starting with version 1.6, **NGLess is based on a new implementation written in
 Rust** (previous versions were written in Haskell). See `Rust implementation
@@ -53,25 +53,49 @@ deprecation warning.
   half-written file), recompresses paired output concurrently under ``--jobs``,
   and sorts directly to BAM when a ``samtools_sort`` result feeds a BAM
   ``write()``.
+* Functions that take an output file now check the output directory *before* the
+  script runs, even when the file name is only computed at run time (e.g.
+  ``ofile=OUTPUT_DIRECTORY </> sample.name() + '.fna.gz'``). Previously, a
+  missing output directory was only reported once the write was reached, i.e.
+  after mapping or assembly had already run.
+* When an ``import`` of a local module cannot be found, the error lists every
+  location that was searched (and, if other versions of the module are
+  available, lists those too). Under ``--trace``, each candidate is printed as
+  it is checked.
 
 For the complete list, see the ``ChangeLog``.
 
-Changes with respect to 1.6.0-beta1
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If you were testing the earlier ``1.6.0-beta1`` pre-release:
-
-* The build now supports only ``ngless "1.6"``; declaring ``"1.5"`` (which
-  beta1 accepted with a warning) is now an error.
-* Removed the deprecated ``count()`` ``strand`` argument, the ``--search-dir``
-  flag, and the unimplemented ``--check-deprecation`` flag.
-* The internal output hash (``auto_comments=[{hash}]`` and the parallel
-  lock/stats directory names) changed its values; it remains deterministic and
-  content-addressed.
-* beta2 also restores many features 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)``, reference-based ``count()``, and more.
+Changes with respect to the 1.6.0 pre-releases
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you were testing the ``1.6.0-beta1`` or ``1.6.0-beta2`` pre-releases, note
+that the final release fixes several features that the pre-releases had not
+fully ported from 1.5:
+
+* The ``encoding`` argument to ``fastq()``/``paired()`` (and, through them,
+  ``load_fastq_directory()``/``load_mocat_sample()``) is honoured again; the
+  betas accepted it but always auto-detected the quality encoding.
+* External modules can declare ``references:`` again, so catalog modules such as
+  ``igc``, ``om-rgc``, and the gut-catalog modules resolve their bundled
+  references in ``map()`` and ``count()``.
+* The distinction between global and local module imports is restored: a plain
+  ``import`` is again only accepted for known modules (which are auto-downloaded
+  if not present locally), while a local-only module requires ``local import``.
+* External module commands see ``NGLESS_NR_CORES`` set to the configured worker
+  thread count instead of a hard-coded 1.
+* Fixed a deadlock where ``map()`` could hang forever on samples where ``bwa
+  mem`` writes a large amount of output to stderr.
+
+Relative to beta1 specifically, beta2 had already made ``ngless "1.6"`` the only
+accepted language version (beta1 accepted ``"1.5"`` with a warning), removed the
+deprecated ``count()`` ``strand`` argument, the ``--search-dir`` flag and the
+unimplemented ``--check-deprecation`` flag, and restored transparent ``.xz``
+support, the HTML run report, parallel-module progress reporting,
+``format={sam|bam}`` on ``write()``, ``preprocess(keep_singles=False)`` and
+reference-based ``count()``. The internal output hash
+(``auto_comments=[{hash}]`` and the parallel lock/stats directory names) also
+changed its values between beta1 and beta2; it remains deterministic and
+content-addressed.
 
 
 Version 1.5.0

pixi.toml

@@ -9,10 +9,10 @@ preview = ["pixi-build"]
 [tasks]
 
 [package]
-# 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
+# For "normal" versions such as this one, the version matches Cargo.toml. It only
+# needs to differ for pre-releases, because of different conventions between Cargo
 # and conda (-beta vs .beta).
-version = "1.6.beta2"
+version = "1.6.0"
 
 [package.build]
 backend = { name = "pixi-build-rust", version = "*" }

pixi_install_ngless.toml

@@ -9,9 +9,4 @@ version = "0.1.0"
 
 
 [dependencies]
-prodigal = ">=2.6.3,<3"
-megahit = ">=1.2.9,<2"
-samtools = ">=1.23.1,<2"
-minimap2 = ">=2.31,<3"
-bwa = ">=0.7.19,<0.8"
-ngless = { url = "https://github.com/ngless-toolkit/ngless/releases/download/v1.6.0-beta2/ngless-1.6.beta2-ha35fb5c_0.conda" }
+ngless = ">=1.6.0,<2"

src/lib.rs

@@ -52,8 +52,8 @@ pub mod values;
 /// and `Execs/Main.hs`).
 pub mod version {
     pub const VERSION_STR: &str = "1.6.0";
-    pub const VERSION_STR_LONG: &str = "1.6.0-beta2";
-    pub const DATE_STR: &str = "4 July 2026";
+    pub const VERSION_STR_LONG: &str = "1.6.0";
+    pub const DATE_STR: &str = "4 August 2026";
     // The Rust build does not yet embed external tool binaries (samtools/bwa/...).
     pub const EMBEDDED_STR: &str = "No";
 
@@ -290,7 +290,7 @@ mod tests {
     fn version_line_matches_haskell_format() {
         assert_eq!(
             version::version_line(),
-            "ngless v1.6.0-beta2 (release date: 4 July 2026)"
+            "ngless v1.6.0 (release date: 4 August 2026)"
         );
     }