Bulk sort environment yamls (#7372)

* fix: Remove second conda-env-sorter

* style: Run ruff

* style: Bulk update sort

In theory should:
- Sort dependencies
- Add yaml schema
- Remove quotes

.github/scripts/conda_env_sorter.py

@@ -11,15 +11,15 @@
 # uv run --with pytest -- pytest -v .github/scripts/conda_env_sorter.py
 
 import argparse
+import sys
 from pathlib import Path
 from typing import Optional, Sequence
+
 import ruamel.yaml
-import sys
 
 # Add pytest imports conditionally
-if 'pytest' in sys.modules:
+if "pytest" in sys.modules:
     import pytest
-    from tempfile import NamedTemporaryFile
 
 yaml = ruamel.yaml.YAML()
 yaml.indent(mapping=2, sequence=2, offset=2)  # Set indentation to 2 spaces
@@ -79,24 +79,19 @@ def main(argv: Optional[Sequence[str]] = None) -> None:
     main()
 
 # Pytest tests (only loaded when running pytest)
-if 'pytest' in sys.modules:
-    @pytest.mark.parametrize("input_content,expected", [
-        # Test basic sorting
-        (
-            "dependencies:\n  - zlib\n  - python\n",
-            ["python", "zlib"]
-        ),
-        # Test dict sorting
-        (
-            "dependencies:\n  - pip:\n    - b\n    - a\n  - python\n",
-            ["python", {"pip": ["a", "b"]}]
-        ),
-        # Test existing headers
-        (
-            "---\n# yaml-language-server: $schema=...\ndependencies:\n  - b\n  - a\n",
-            ["a", "b"]
-        )
-    ])
+if "pytest" in sys.modules:
+
+    @pytest.mark.parametrize(
+        "input_content,expected",
+        [
+            # Test basic sorting
+            ("dependencies:\n  - zlib\n  - python\n", ["python", "zlib"]),
+            # Test dict sorting
+            ("dependencies:\n  - pip:\n    - b\n    - a\n  - python\n", ["python", {"pip": ["a", "b"]}]),
+            # Test existing headers
+            ("---\n# yaml-language-server: $schema=...\ndependencies:\n  - b\n  - a\n", ["a", "b"]),
+        ],
+    )
     def test_conda_sorter(tmp_path, input_content, expected):
         test_file = tmp_path / "environment.yml"
         test_file.write_text(input_content)

.pre-commit-config.yaml

@@ -34,15 +34,6 @@ repos:
         args: ["--schemafile", "subworkflows/yaml-schema.json"]
       - id: check-github-workflows
       - id: check-github-actions
-  - repo: local
-    hooks:
-      - id: conda-env-sorter
-        name: Sort dependencies in conda environment files.
-        entry: ./.github/scripts/conda_env_sorter.py
-        language: python
-        files: environment
-        types: [yaml]
-        additional_dependencies: ["ruamel.yaml"]
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.7.3

modules/nf-core/abacas/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/abricate/run/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/abricate/summary/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/abritamr/run/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/adapterremoval/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/adapterremovalfixprefix/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/admixture/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/affy/justrma/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/agat/convertbed2gff/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::agat=1.4.2"
+  - bioconda::agat=1.4.2

modules/nf-core/agat/convertspgff2gtf/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/agat/convertspgff2tsv/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/agat/convertspgxf2gxf/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/agat/spaddintrons/environment.yml

@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::agat=1.4.2"
+  - bioconda::agat=1.4.2

modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::agat=1.4.2"
+  - bioconda::agat=1.4.2

modules/nf-core/agat/spmergeannotations/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::agat=1.4.2"
+  - bioconda::agat=1.4.2

modules/nf-core/agat/spstatistics/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/agat/sqstatbasic/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/agrvate/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ale/environment.yml

@@ -6,4 +6,4 @@ channels:
   - tanghaibao
 dependencies:
   # renovate: datasource=conda depName=bioconda/ale
-  - "bioconda::ale=20180904"
+  - bioconda::ale=20180904

modules/nf-core/allelecounter/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ampcombi/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ampcombi2/cluster/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=2.0.1"
+  - bioconda::ampcombi=2.0.1

modules/nf-core/ampcombi2/complete/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=2.0.1"
+  - bioconda::ampcombi=2.0.1

modules/nf-core/ampcombi2/parsetables/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=2.0.1"
+  - bioconda::ampcombi=2.0.1

modules/nf-core/ampir/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/amplify/predict/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/amps/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/amrfinderplus/run/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/amrfinderplus/update/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/angsd/contamination/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/angsd/docounts/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/angsd/gl/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::angsd=0.940"
-  - "bioconda::htslib=1.17"
+  - bioconda::angsd=0.940
+  - bioconda::htslib=1.17

modules/nf-core/anndata/barcodes/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/anndata/getsize/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/annotsv/annotsv/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/annotsv/installannotations/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/anota2seq/anota2seqrun/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::bioconductor-anota2seq=1.24.0"
+  - bioconda::bioconductor-anota2seq=1.24.0

modules/nf-core/antismash/antismashlite/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/arcashla/extract/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/argnorm/environment.yml

@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::argnorm=0.5.0"
+  - bioconda::argnorm=0.5.0

modules/nf-core/aria2/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ariba/getref/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ariba/run/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/arriba/download/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/art/illumina/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/artic/guppyplex/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/artic/minion/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ascat/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ashlar/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/assemblyscan/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ataqv/ataqv/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/ataqv/mkarv/environment.yml

@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda