Merge pull request #2199 from nf-core/rm-mulled

refactor: remove the mulled command and all related code

CHANGELOG.md

@@ -23,6 +23,7 @@
 ### Modules
 
 - Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
+- Removed the `nf-core modules mulled` command and all its code dependencies ([2199](https://github.com/nf-core/tools/pull/2199)).
 
 ### Subworkflows
 

README.md

@@ -42,7 +42,6 @@ A python package with helper tools for the nf-core community.
   - [`modules lint` - Check a module against nf-core guidelines](#check-a-module-against-nf-core-guidelines)
   - [`modules test` - Run the tests for a module](#run-the-tests-for-a-module-using-pytest)
   - [`modules bump-versions` - Bump software versions of modules](#bump-bioconda-and-container-versions-of-modules-in)
-  - [`modules mulled` - Generate the name for a multi-tool container image](#generate-the-name-for-a-multi-tool-container-image)
 
 - [`nf-core subworkflows` - commands for dealing with subworkflows](#subworkflows)
   - [`subworkflows list` - List available subworkflows](#list-subworkflows)
@@ -972,17 +971,6 @@ bump-versions:
   star/align: "2.6.1d"
 ```
 
-### Generate the name for a multi-tool container image
-
-When you want to use an image of a multi-tool container and you know the specific dependencies and their versions of that container, for example, by looking them up in the [BioContainers hash.tsv](https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv), you can use the `nf-core modules mulled` helper tool. This tool generates the name of a BioContainers mulled image.
-
-<!-- RICH-CODEX
-working_dir: tmp/modules
-after_command: cd ../../ && rm -rf tmp
--->
-
-![`nf-core modules mulled pysam==0.16.0.1 biopython==1.78`](docs/images/nf-core-modules-mulled.svg)
-
 ## Subworkflows
 
 After the launch of nf-core modules, we can provide now also nf-core subworkflows to fully utilize the power of DSL2 modularization.

nf_core/__main__.py

@@ -52,7 +52,7 @@
         },
         {
             "name": "Developing new modules",
-            "commands": ["create", "create-test-yml", "lint", "bump-versions", "mulled", "test"],
+            "commands": ["create", "create-test-yml", "lint", "bump-versions", "test"],
         },
     ],
     "nf-core subworkflows": [
@@ -875,49 +875,6 @@ 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
-
-    try:
-        image_name = MulledImageNameGenerator.generate_image_name(
-            MulledImageNameGenerator.parse_targets(specifications), build_number=build_number
-        )
-    except ValueError as e:
-        log.error(e)
-        sys.exit(1)
-    if not MulledImageNameGenerator.image_exists(image_name):
-        log.error("The generated multi-tool container image name does not seem to exist yet.")
-        log.info(
-            "Please double check that your provided combination of tools and versions exists in the file: "
-            "[link=https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv]BioContainers/multi-package-containers 'combinations/hash.tsv'[/link]"
-        )
-        log.info(
-            "If it does not, please add your desired combination as detailed at: "
-            "https://github.com/BioContainers/multi-package-containers"
-        )
-        sys.exit(1)
-    log.info("Mulled container hash:")
-    stdout.print(image_name)
-
-
 # nf-core modules test
 @modules.command("test")
 @click.pass_context

nf_core/modules/__init__.py

@@ -8,7 +8,6 @@
 from .modules_repo import ModulesRepo
 from .modules_test import ModulesTest
 from .modules_utils import ModuleException
-from .mulled import MulledImageNameGenerator
 from .patch import ModulePatch
 from .remove import ModuleRemove
 from .test_yml_builder import ModulesTestYmlBuilder

requirements.txt

@@ -1,6 +1,5 @@
 click
 filetype
-galaxy-tool-util
 GitPython
 jinja2
 jsonschema>=3.0