v5 compatibility

.github/workflows/condabot.yml

@@ -0,0 +1,16 @@
+name: Condabot
+
+on:
+  schedule:
+    - cron: '0 2 * * 1'
+  workflow_dispatch:
+
+jobs:
+  run-condabot:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+            fetch-depth: 0
+      - uses: sunbeam-labs/condabot@v1

.github/workflows/tests.yml

@@ -1,74 +1,31 @@
 name: Tests
 
 on:
+  workflow_dispatch:
+
   pull_request:
-    branches: [ master, main ]
+    branches: [ main, master ]
   push:
-    branches: [ master, main ]
-  workflow_call:
-  workflow_dispatch:
-  schedule:
-    - cron: "0 13 * * 1"
+    branches: [ main, master ]
 
 jobs:
-  lint:
-    name: Lint Code
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-            python-version: 3.12
-
-      - name: Install Dependencies
-        run: pip install black snakefmt
-
-      - name: Run Linter
-        run: |
-          black --check .
-          snakefmt --check *.smk
-
-  test-unit:
-    name: Run Extension Unit Tests
+  test:
+    name: Test
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout Code
         uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        with:
-            python-version: 3.12
-
-      - name: Install Dependencies
-        run: pip install pytest pandas
-
-      - name: Run Unit Tests
-        run: pytest .tests/unit/
-
-  test-e2e:
-    name: Test Extension with Sunbeam
-    runs-on: ubuntu-latest
-    needs:
-      - test-unit
-      - lint
-
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-
-      - name: Test with Sunbeam
+      - name: Sunbeam tests
         uses: sunbeam-labs/sbx_test_action@v1
 
       - name: Dump Logs
         shell: bash
         if: always()
-        run: tail -n +1 logs/*
+        run: tail -n +1 logs/* || true
 
       - name: Dump Stats
         shell: bash
         if: always()
-        run: cat stats/*
+        run: cat stats/* || true

.tests/e2e/test_dry_run.py

@@ -1,3 +1,4 @@
+import os
 import pytest
 import shutil
 import subprocess as sp
@@ -6,14 +7,8 @@
 
 
 @pytest.fixture
-def setup(monkeypatch):
+def setup():
     temp_dir = Path(tempfile.mkdtemp())
-    monkeypatch.setenv(
-        "SUNBEAM_EXTENSIONS", str(Path(__file__).parent.parent.parent.parent.resolve())
-    )
-    print(
-        "SUNBEAM_EXTENSIONS:", str(Path(__file__).parent.parent.parent.parent.resolve())
-    )
 
     reads_fp = Path(".tests/data/reads/").resolve()
 
@@ -22,8 +17,6 @@ def setup(monkeypatch):
     sp.check_output(["sunbeam", "init", "--data_fp", reads_fp, project_dir])
 
     config_fp = project_dir / "sunbeam_config.yml"
-    with open(config_fp, "r") as f:
-        print("Initial config file content:", f.read())
 
     config_str = f"sbx_sga: {{mash_ref: '{temp_dir}/dummy.msh'}}"
     Path(temp_dir / "dummy.msh").touch()
@@ -94,15 +87,12 @@ def run_sunbeam(setup):
     print("STDOUT: ", sbx_proc.stdout)
     print("STDERR: ", sbx_proc.stderr)
 
-    try:
-        shutil.copytree(log_fp, "logs/")
-        shutil.copytree(stats_fp, "stats/")
-    except FileNotFoundError:
-        print("No logs or stats directory found.")
-        Path("logs/").mkdir(parents=True, exist_ok=True)
-        Path("stats/").mkdir(parents=True, exist_ok=True)
-        Path("logs/file").touch()
-        Path("stats/file").touch()
+    if os.getenv("GITHUB_ACTIONS") == "true":
+        try:
+            shutil.copytree(log_fp, "logs/")
+            shutil.copytree(stats_fp, "stats/")
+        except FileNotFoundError:
+            print("No logs or stats directory found.")
 
     output_fp = project_dir / "sunbeam_output"
     benchmarks_fp = project_dir / "stats/"

README.md

@@ -4,44 +4,20 @@
 
 <!-- Badges start -->
 [![Tests](https://github.com/sunbeam-labs/sbx_sga/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_sga/actions/workflows/tests.yml)
+![Condabot](https://img.shields.io/badge/condabot-active-purple)
 [![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_sga)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_sga/)
 <!-- Badges end -->
 
 ## Introduction
 
 sbx_sga (Single Genome Assembly) is a [sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for isolate QC, assembly, and classification. This pipeline uses [Mash](https://github.com/marbl/mash) for quality control, [Shovill](https://github.com/tseemann/shovill) for bacterial isolate assembly, [CheckM2](https://github.com/chklovski/CheckM2) and [QUAST](https://github.com/ablab/quast) for assembly QC, [MLST](https://github.com/tseemann/mlst) for typing, [Bakta](https://github.com/oschwengers/bakta) for annotation, [abriTAMR](https://github.com/MDU-PHL/abritamr) for AMR profiling, and [Sylph](https://github.com/bluenote-1577/sylph) for taxonomic classification.
 
-## Installation
-
-Extension install is as simple as passing the extension's URL on GitHub to `sunbeam extend`:
-
-    sunbeam extend https://github.com/sunbeam-labs/sbx_sga
-
-Any user-modifiable parameters specified in `config.yml` are automatically added on `sunbeam init`. If you're installing an extension in a project where you already have a config file, run the following to add the options for your newly added extension to your config (the `-i` flag means in-place config file modification; remove the `-i` flag to see the new config in stdout):
-
-    sunbeam config update -i /path/to/project/sunbeam_config.yml
-
-Installation instructions for older versions of Sunbeam are included at the end of this README.
-
-## Running
-
-To run an extension, simply run Sunbeam as usual with your extension's target rule specified:
-
-    sunbeam run --profile /path/to/project/ example_rule
-
-### Options for config.yml
+## Config
 
   - mash_ref: the reference file for running Mash (should be a file ending in `.msh`)
   - checkm_ref: the diamond database for running CheckM2 (should be a file ending in `.dmnd`)
   - bakta_ref: the bakta reference database (should be a directory similar to `.../bakta_db/db/`)
 
-## Installing an extension (legacy instructions for sunbeam <3.0)
-
-Installing an extension is as simple as cloning (or moving) your extension directory into the sunbeam/extensions/ folder, installing requirements through Conda, and adding the new options to your existing configuration file: 
-
-    git clone https://github.com/sunbeam-labs/sbx_sga/ sunbeam/extensions/sbx_sga
-    cat sunbeam/extensions/sbx_sga/config.yml >> sunbeam_config.yml
-
-## Issues with pipeline
+## Docs
 
-Please post any issues with this extension [here](https://github.com/sunbeam-labs/sbx_sga/issues).
+More [docs](https://sunbeam.readthedocs.io/en/stable/extensions.html).

envs/abritamr.yml

@@ -2,91 +2,5 @@ name: sga_abritamr
 channels:
   - conda-forge
   - bioconda
-  - defaults
-  - r
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - abritamr=1.0.11
-  - blast=2.15.0
-  - bzip2=1.0.8
-  - c-ares=1.28.1
-  - ca-certificates=2024.2.2
-  - curl=7.88.1
-  - entrez-direct=21.6
-  - gettext=0.22.5
-  - gettext-tools=0.22.5
-  - hmmer=3.4
-  - keyutils=1.6.1
-  - krb5=1.20.1
-  - ld_impl_linux-64=2.40
-  - libasprintf=0.22.5
-  - libasprintf-devel=0.22.5
-  - libblas=3.9.0
-  - libcblas=3.9.0
-  - libcurl=7.88.1
-  - libedit=3.1.20191231
-  - libev=4.33
-  - libffi=3.4.2
-  - libgcc-ng=13.2.0
-  - libgettextpo=0.22.5
-  - libgettextpo-devel=0.22.5
-  - libgfortran-ng=13.2.0
-  - libgfortran5=13.2.0
-  - libgomp=13.2.0
-  - libidn2=2.3.7
-  - liblapack=3.9.0
-  - libnghttp2=1.58.0
-  - libnsl=2.0.1
-  - libopenblas=0.3.27
-  - libsqlite=3.45.3
-  - libssh2=1.11.0
-  - libstdcxx-ng=13.2.0
-  - libunistring=0.9.10
-  - libxcrypt=4.4.36
-  - libzlib=1.2.13
-  - ncbi-amrfinderplus=3.10.16
-  - ncbi-vdb=3.1.1
-  - ncurses=6.5
-  - numpy=1.21.6
-  - openssl=3.3.0
-  - pandas=1.3.5
-  - pcre=8.45
-  - perl=5.32.1
-  - perl-archive-tar=2.40
-  - perl-carp=1.50
-  - perl-common-sense=3.75
-  - perl-compress-raw-bzip2=2.201
-  - perl-compress-raw-zlib=2.202
-  - perl-encode=3.21
-  - perl-exporter=5.74
-  - perl-exporter-tiny=1.002002
-  - perl-extutils-makemaker=7.70
-  - perl-io-compress=2.201
-  - perl-io-zlib=1.14
-  - perl-json=4.10
-  - perl-json-xs=2.34
-  - perl-list-moreutils=0.430
-  - perl-list-moreutils-xs=0.430
-  - perl-parent=0.241
-  - perl-pathtools=3.75
-  - perl-scalar-list-utils=1.63
-  - perl-storable=3.15
-  - perl-types-serialiser=1.01
-  - pip=24.0
-  - python=3.7.12
-  - python-dateutil=2.9.0
-  - python_abi=3.7
-  - pytz=2024.1
-  - readline=8.2
-  - setuptools=59.8.0
-  - six=1.16.0
-  - sqlite=3.45.3
-  - tk=8.6.13
-  - wget=1.21.4
-  - wheel=0.34.2
-  - xlsxwriter=3.1.9
-  - xz=5.2.6
-  - zlib=1.2.13
-  - zstd=1.5.6
-
+  - abritamr