Merge branch 'dev' into no-coassemble

rhysnewell · Nov 12, 2024 · a850c20 · a850c20
2 parents e2ccfeb + 37f8bd1
commit a850c20
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Showing 7 changed files with 12 additions and 61 deletions.
diff --git a/.github/workflows/test-aviary.yml b/.github/workflows/test-aviary.yml
@@ -12,14 +12,13 @@ jobs:
         matrix:
             python-version: ["3.10"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up environment with Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: test
           environment-file: aviary.yml
           python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
           auto-activate-base: false
           channels: conda-forge,bioconda
           channel-priority: true

diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,4 @@ aviary_genome.egg-info
 example/
 test/data/.conda
 test/data/wgsim.metaspades.assembly.fna.fai
+config.yaml
diff --git a/CITATION.cff b/CITATION.cff
@@ -20,6 +20,6 @@ authors:
     given-names: Ben J.
     orcid: https://orcid.org/0000-0003-0670-7480
 title: "Aviary: Hybrid assembly and genome recovery from metagenomes with Aviary"
-version: 0.8.3
-doi: 10.5281/zenodo.10158087
-date-released: 2023-11-20
+version: 0.9.0
+doi: 10.5281/zenodo.10806928
+date-released: 2024-03-12
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 ![](https://anaconda.org/bioconda/aviary/badges/version.svg)
 ![](https://anaconda.org/bioconda/aviary/badges/latest_release_relative_date.svg)
 ![](https://anaconda.org/bioconda/aviary/badges/platforms.svg)
-[![DOI](https://zenodo.org/badge/271448699.svg)](https://zenodo.org/doi/10.5281/zenodo.10158086)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10806928.svg)](https://doi.org/10.5281/zenodo.10806928)
 
 
 ![](docs/_include/images/aviary_logo.png)

diff --git a/aviary/modules/binning/binning.smk b/aviary/modules/binning/binning.smk
@@ -178,7 +178,7 @@ rule vamb:
         config["max_threads"]
     resources:
         mem_mb = lambda wildcards, attempt: min(int(config["max_memory"])*1024, 128*1024*attempt),
-        runtime = lambda wildcards, attempt: 24*60*attempt,
+        runtime = lambda wildcards, attempt: 48*60*attempt,
         gpus = 1 if config["request_gpu"] else 0
     output:
         "data/vamb_bins/done"

diff --git a/config.yaml b/config.yaml
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,4 @@
+[build-system]
+# XXX: If your project needs other packages to build properly, add them to this list.
+requires = ["setuptools >= 64"]
+build-backend = "setuptools.build_meta"