Merge pull request #1519 from nf-core/feat-mulled

feat: add a modules mulled command

CHANGELOG.md

@@ -21,6 +21,7 @@
 ### Modules
 
 - Escaped test run output before logging it, to avoid a rich ` MarkupError`
+- Add a new command `nf-core modules mulled` which can generate the name for a multi-tool container image.
 
 ## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24]
 

nf_core/__main__.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 """ nf-core: Helper tools for use with nf-core Nextflow pipelines. """
-
 from rich import print
 import logging
 import os
@@ -49,7 +48,7 @@
         },
         {
             "name": "Developing new modules",
-            "commands": ["create", "create-test-yml", "lint", "bump-versions"],
+            "commands": ["create", "create-test-yml", "lint", "bump-versions", "mulled"],
         },
     ],
 }
@@ -674,6 +673,42 @@ def bump_versions(ctx, tool, dir, all, show_all):
         sys.exit(1)
 
 
+# nf-core modules mulled
+@modules.command()
+@click.argument("specifications", required=True, nargs=-1, metavar="<tool==version> <...>")
+@click.option(
+    "--build-number",
+    type=int,
+    default=0,
+    show_default=True,
+    metavar="<number>",
+    help="The build number for this image. This is an incremental value that starts at zero.",
+)
+def mulled(specifications, build_number):
+    """
+    Generate the name of a BioContainers mulled image version 2.
+
+    When you know the specific dependencies and their versions of a multi-tool container image and you need the name of
+    that image, this command can generate it for you.
+
+    """
+    from nf_core.modules.mulled import MulledImageNameGenerator
+
+    image_name = MulledImageNameGenerator.generate_image_name(
+        MulledImageNameGenerator.parse_targets(specifications), build_number=build_number
+    )
+    print(image_name)
+    if not MulledImageNameGenerator.image_exists(image_name):
+        log.error(
+            "The generated multi-tool container image name does not seem to exist yet. Please double check that your "
+            "provided combination of tools and versions exists in the file:\n"
+            "https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv\n"
+            "If it does not, please add your desired combination as detailed at:\n"
+            "https://github.com/BioContainers/multi-package-containers\n"
+        )
+        sys.exit(1)
+
+
 # nf-core schema subcommands
 @nf_core_cli.group()
 def schema():

nf_core/modules/__init__.py

@@ -9,3 +9,4 @@
 from .update import ModuleUpdate
 from .remove import ModuleRemove
 from .info import ModuleInfo
+from .mulled import MulledImageNameGenerator

nf_core/modules/mulled.py

@@ -0,0 +1,67 @@
+"""Generate the name of a BioContainers mulled image version 2."""
+
+
+import logging
+import re
+from packaging.version import Version, InvalidVersion
+from typing import Iterable, Tuple, List
+
+import requests
+from galaxy.tool_util.deps.mulled.util import build_target, v2_image_name
+
+
+log = logging.getLogger(__name__)
+
+
+class MulledImageNameGenerator:
+    """
+    Define a service class for generating BioContainers version 2 mulled image names.
+
+    Adapted from https://gist.github.com/natefoo/19cefeedd1942c30f9d88027a61b3f83.
+
+    """
+
+    _split_pattern = re.compile(r"==?")
+
+    @classmethod
+    def parse_targets(cls, specifications: Iterable[str]) -> List[Tuple[str, str]]:
+        """
+        Parse tool, version pairs from specification strings.
+
+        Args:
+            specifications: An iterable of strings that contain tools and their versions.
+
+        """
+        result = []
+        for spec in specifications:
+            try:
+                tool, version = cls._split_pattern.split(spec, maxsplit=1)
+            except ValueError:
+                raise ValueError(
+                    f"The specification {spec} does not have the expected format <tool==version> or <tool=version>."
+                ) from None
+            try:
+                Version(version)
+            except InvalidVersion:
+                raise ValueError(f"{version} in {spec} is not a PEP440 compliant version specification.") from None
+            result.append((tool.strip(), version.strip()))
+        return result
+
+    @classmethod
+    def generate_image_name(cls, targets: Iterable[Tuple[str, str]], build_number: int = 0) -> str:
+        """
+        Generate the name of a BioContainers mulled image version 2.
+
+        Args:
+            targets: One or more tool, version pairs of the multi-tool container image.
+            build_number: The build number for this image. This is an incremental value that starts at zero.
+
+        """
+        return v2_image_name([build_target(name, version) for name, version in targets], image_build=str(build_number))
+
+    @classmethod
+    def image_exists(cls, image_name: str) -> bool:
+        """Check whether a given BioContainers image name exists via a call to the quay.io API."""
+        response = requests.get(f"https://quay.io/biocontainers/{image_name}/", allow_redirects=True)
+        log.debug(response.text)
+        return response.status_code == 200

requirements.txt

@@ -1,4 +1,5 @@
 click
+galaxy-tool-util
 GitPython
 jinja2
 jsonschema>=3.0

tests/test_mullled.py

@@ -0,0 +1,65 @@
+"""Test the mulled BioContainers image name generation."""
+
+import pytest
+
+from nf_core.modules import MulledImageNameGenerator
+
+
+@pytest.mark.parametrize(
+    "specs, expected",
+    [
+        (["foo==0.1.2", "bar==1.1"], [("foo", "0.1.2"), ("bar", "1.1")]),
+        (["foo=0.1.2", "bar=1.1"], [("foo", "0.1.2"), ("bar", "1.1")]),
+    ],
+)
+def test_target_parsing(specs, expected):
+    """Test that valid specifications are correctly parsed into tool, version pairs."""
+    assert MulledImageNameGenerator.parse_targets(specs) == expected
+
+
+@pytest.mark.parametrize(
+    "specs",
+    [
+        ["foo<0.1.2", "bar==1.1"],
+        ["foo=0.1.2", "bar>1.1"],
+    ],
+)
+def test_wrong_specification(specs):
+    """Test that unexpected version constraints fail."""
+    with pytest.raises(ValueError, match="expected format"):
+        MulledImageNameGenerator.parse_targets(specs)
+
+
+@pytest.mark.parametrize(
+    "specs",
+    [
+        ["foo==0a.1.2", "bar==1.1"],
+        ["foo==0.1.2", "bar==1.b1b"],
+    ],
+)
+def test_noncompliant_version(specs):
+    """Test that version string that do not comply with PEP440 fail."""
+    with pytest.raises(ValueError, match="PEP440"):
+        MulledImageNameGenerator.parse_targets(specs)
+
+
+@pytest.mark.parametrize(
+    "specs, expected",
+    [
+        (
+            [("chromap", "0.2.1"), ("samtools", "1.15")],
+            "mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0",
+        ),
+        (
+            [("pysam", "0.16.0.1"), ("biopython", "1.78")],
+            "mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0",
+        ),
+        (
+            [("samclip", "0.4.0"), ("samtools", "1.15")],
+            "mulled-v2-d057255d4027721f3ab57f6a599a2ae81cb3cbe3:13051b049b6ae536d76031ba94a0b8e78e364815-0",
+        ),
+    ],
+)
+def test_generate_image_name(specs, expected):
+    """Test that a known image name is generated from given targets."""
+    assert MulledImageNameGenerator.generate_image_name(specs) == expected