0.20.1: Prepare for it.

Author: wwood

CHANGELOG.md

@@ -1,4 +1,4 @@
-## v0.20.0
+## v0.20.0 / 0.20.1
 
 Major new function - Long-read input support (Nanopore >= R10.4.1 or PacBio HiFi recommended), thanks to @thepatientwait.
 

admin/build_dep_defs_from_pixi.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import yaml
-import toml
+import tomllib
 import subprocess
 import json
 import os
@@ -13,8 +13,8 @@
     lock_data = yaml.safe_load(f)
 
 # Load explicitly listed dependencies from pixi.toml
-with open(os.path.join(base_dir, "pixi.toml"), "r") as f:
-    pixi_data = toml.load(f)
+with open(os.path.join(base_dir, "pixi.toml"), "rb") as f:
+    pixi_data = tomllib.load(f)
 
 # Gather conda packages and versions from "pixi list --json"
 result = subprocess.run(
@@ -39,8 +39,15 @@
 
 # Explicitly declared packages in pixi.toml
 declared_conda = set()
-for section in ["dependencies", "host-dependencies"]:
-    for pkg, val in pixi_data.get(section, {}).items():
+for section in ["dependencies", "host-dependencies", ["feature","main","dependencies"], ["feature","main","host-dependencies"]]:
+    if isinstance(section, list):
+        d = pixi_data
+        for subsec in section:
+            d = d.get(subsec, {})
+    else:
+        d = pixi_data.get(section, {})
+    print(f"Found {len(d)} declared packages in section {section}.")
+    for pkg, val in d.items():
         pkg_lower = pkg.lower()
         declared_conda.add(pkg_lower)
 

admin/environment.yml

@@ -33,7 +33,7 @@ dependencies:
 - seqmagick=0.8.6
 - smafa=0.8.0
 - sqlalchemy=2.0.44
-- sqlite=3.50.4
+- sqlite=3.51.0
 - sqlparse=0.5.3
 - squarify=0.4.3
 - sra-tools=3.2.1

admin/release.py

@@ -23,6 +23,9 @@
 
     print("version is {}".format(version))
 
+    print("Building dependency definition files based on pixi.toml and pixi.lock") # TODO: Do we need to update pixi.lock first?
+    extern.run('pixi run admin/build_dep_defs_from_pixi.py')
+
     print("building docs")
     extern.run("pixi run python3 admin/build_docs.py --version {}".format(version))
 

admin/set_env_vars.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 SINGLEM_METAPACKAGE_PATH_RELATIVE="db/S5.4.0.GTDB_r226.metapackage_20250331.smpkg.zb"
-LYREBIRD_METAPACKAGE_PATH_RELATIVE="db/lyrebird_v0.3.0_phrog_v4.1_metapackage_2025_06_23.smpkg.zb"
+LYREBIRD_METAPACKAGE_PATH_RELATIVE="db/lyrebird_v0.3.1_phrog_v4.1_metapackage_20250720.smpkg.zb"
 GTDBTK_DATA_PATH_RELATIVE="db/release226"
 
 # For each of the above variables, check if the file exists in the relative path

docker/Dockerfile.in

@@ -27,7 +27,7 @@ RUN git clone https://github.com/wwood/singlem . && git checkout vSINGLEM_VERSIO
 
 # We install through pip, because installing via pip install -e . causes issues for apptainer
 # https://github.com/prefix-dev/pixi/issues/1387
-RUN pixi run --no-lockfile-update pip install singlem==SINGLEM_VERSION
+RUN pixi run --frozen bash -c 'pip install singlem==SINGLEM_VERSION'
 
 # Download default metapackage
 # Make the directory and its contents readable by others https://github.com/wwood/singlem/issues/155

docs/Installation.md

@@ -6,7 +6,7 @@ SingleM can be installed through
 [Bioconda](https://anaconda.org/bioconda/singlem). Lyrebird is installed by installing SingleM, and then using the `lyrebird` command instead of `singlem` e.g. use `lyrebird pipe ...` instead of `singlem pipe ...`.
 
 ```
-conda create -c conda-forge -c bioconda --override-channels --name singlem singlem'>='0.20.0
+conda create -c conda-forge -c bioconda --override-channels --name singlem singlem'>='0.20.1
 ```
 
 Test if it works by running
@@ -21,55 +21,55 @@ After this, you'll also need to procure the reference data (the "metapackage").
 ## Installation via DockerHub
 A docker image generated from the conda package is [available](https://hub.docker.com/r/wwood/singlem) on DockerHub. After installing Docker, run the following:
 ```
-docker pull wwood/singlem:0.20.0
+docker pull wwood/singlem:0.20.1
 ```
 
 Test if it works by running
 ```
-docker run wwood/singlem:0.20.0 -h
+docker run wwood/singlem:0.20.1 -h
 ```
 
 If the sequence data to be analyzed is in the current working directory, SingleM `pipe` can be used like so:
 ```
-docker run -v `pwd`:`pwd` wwood/singlem:0.20.0 pipe --sequences \
+docker run -v `pwd`:`pwd` wwood/singlem:0.20.1 pipe --sequences \
     `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
 ```
 Two things to note:
 
 1. The default SingleM reference data is included in the docker image, so running [singlem data](/tools/data) is not necessary for this installation method - you can jump straight to using `pipe`.
-2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `docker run wwood/singlem:0.20.0 pipe -h`.
+2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `docker run wwood/singlem:0.20.1 pipe -h`.
 
 A similar procedure is true for Lyrebird, except that the docker image is [different](https://hub.docker.com/r/wwood/lyrebird), so you need to run:
 ```
-docker pull wwood/lyrebird:0.20.0
-docker run wwood/lyrebird:0.20.0 -h
+docker pull wwood/lyrebird:0.20.1
+docker run wwood/lyrebird:0.20.1 -h
 ```
 
 ## Installation via Singularity / Apptainer
 SingleM can be installed via [Singularity](https://sylabs.io/singularity/) or [Apptainer](https://apptainer.org). After installing Singularity or Apptainer, run the following:
 ```
-singularity pull docker://wwood/singlem:0.20.0
+singularity pull docker://wwood/singlem:0.20.1
 ```
 
 Test if it works by running
 ```
-singularity run singlem_0.20.0.sif -h
+singularity run singlem_0.20.1.sif -h
 ```
 
 If the sequence data to be analyzed is in the current working directory, SingleM `pipe` can be used like so:
 ```
-singularity run -B `pwd`:`pwd` singlem_0.20.0.sif pipe --sequences \
+singularity run -B `pwd`:`pwd` singlem_0.20.1.sif pipe --sequences \
     `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
 ```
 Two things to note:
 
 1. The default SingleM reference data is included in the docker image, so running [singlem data](/tools/data) is not necessary for this installation method - you can jump straight to using `pipe`.
-2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `singularity run singlem_0.20.0.sif pipe -h`.
+2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `singularity run singlem_0.20.1.sif pipe -h`.
 
 A similar procedure is true for Lyrebird, except that the docker image is [different](https://hub.docker.com/r/wwood/lyrebird), so you need to run:
 ```
-singularity pull docker://wwood/lyrebird:0.20.0
-singularity run -B `pwd`:`pwd` lyrebird_0.20.0.sif -h
+singularity pull docker://wwood/lyrebird:0.20.1
+singularity run -B `pwd`:`pwd` lyrebird_0.20.1.sif -h
 ```
 
 ## Installation via PyPI