Check for new version snapshotting

.github/scripts/check_version_snapshot.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+# /// script
+# requires-python = ">=3.10"
+# dependencies = []
+# ///
+
+"""Check that versions are captured not hashed."""
+
+import argparse
+import re
+from pathlib import Path
+from typing import Optional, Sequence
+
+
+def check_snapshotting(lines: list[str], path: Path) -> None:
+    """Check each line for proper snapshotting."""
+    good_pattern = re.compile(
+        r'snapshot\(path\(process\.out\.versions\.get\(0\)\)\.yaml\)\.match\("versions"\)|path\(process\.out\.versions\.get\(0\)\)\.yaml'
+    )
+    bad_pattern = re.compile(r"process\.out\.versions|snapshot\(process\.out\)\.match\(\)")
+
+    for line_number, line in enumerate(lines, start=1):
+        if bad_pattern.search(line) and not good_pattern.search(line):
+            print(f"Improper snapshotting in {path} at line {line_number}: {line.strip()}")
+
+
+def main(argv: Optional[Sequence[str]] = None) -> None:
+    """Check that versions are captured not hashed."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument("paths", nargs="*", type=Path)
+    args = parser.parse_args(argv)
+    for path in args.paths:
+        with path.open() as f:
+            lines = f.readlines()
+            check_snapshotting(lines, path)
+
+
+if __name__ == "__main__":
+    main()

.github/scripts/conda_env_sorter.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# /// script
+# requires-python = ">=3.10"
+# dependencies = [
+#     "ruamel.yaml",
+# ]
+# ///
+
+"""Sort dependencies in conda environment files."""
+
+import argparse
+from pathlib import Path
+from typing import Optional, Sequence
+
+import ruamel.yaml
+
+yaml = ruamel.yaml.YAML()
+yaml.indent(mapping=2, sequence=2, offset=2)  # Set indentation to 2 spaces
+
+
+def main(argv: Optional[Sequence[str]] = None) -> None:
+    """Sort dependencies in conda environment files."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument("paths", nargs="*", type=Path)
+    args = parser.parse_args(argv)
+    for path in args.paths:
+        with path.open() as f:
+            lines = f.readlines()
+
+        # Define the schema lines to be added if missing
+        schema_lines = [
+            "---\n",
+            "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n",
+        ]
+
+        # Check if the first two lines match the expected schema lines
+        if lines[:2] == schema_lines:
+            header = lines[:2]
+            content = lines[2:]
+        else:
+            # Add schema lines if they are missing
+            header = schema_lines
+            content = lines
+
+        doc = yaml.load("".join(content))
+        dicts = []
+        others = []
+
+        for term in doc["dependencies"]:
+            if isinstance(term, dict):
+                dicts.append(term)
+            else:
+                others.append(term)
+        others.sort(key=str)
+        for dict_term in dicts:
+            for value in dict_term.values():
+                if isinstance(value, list):
+                    value.sort(key=str)
+        dicts.sort(key=str)
+        doc["dependencies"].clear()
+        doc["dependencies"].extend(others)
+        doc["dependencies"].extend(dicts)
+
+        with path.open("w") as f:
+            f.writelines(header)
+            yaml.dump(doc, f)
+
+
+if __name__ == "__main__":
+    main()

.pre-commit-config.yaml

@@ -1,4 +1,22 @@
 repos:
+  - 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"]
+  - repo: local
+    hooks:
+      - id: check-version-snapshot
+        name: Versions are captured not hashed
+        entry: ./.github/scripts/check_version_snapshot.py
+        language: python
+        files: \.nf\.test$
+        types: [file]
+        additional_dependencies: []
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"
     hooks:

modules/nf-core/bowtie/align/environment.yml

@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # renovate: datasource=conda depName=bioconda/bowtie
-  - bioconda::bowtie=1.3.1
   # renovate: datasource=conda depName=bioconda/samtools
   - bioconda::samtools=1.20
+  # renovate: datasource=conda depName=bioconda/bowtie
+  - bioconda::bowtie=1.3.1

modules/nf-core/ensemblvep/environment.yml

@@ -1,5 +1,3 @@
-# You can use this file to create a conda environment for this module:
-#   conda env create -f environment.yml
 channels:
   - conda-forge
   - bioconda

modules/nf-core/gatk4/variantstotable/environment.yml

@@ -1,6 +1,6 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda

modules/nf-core/hlala/preparegraph/environment.yml

@@ -1,3 +1,5 @@
 channels:
   - conda-forge
   - bioconda
+dependencies:
+  - bioconda::hla-la=1.0.4

modules/nf-core/regtools/junctionsextract/environment.yml

@@ -1,6 +1,5 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::regtools=1.0.0"
+  - bioconda::regtools=1.0.0

modules/nf-core/snpeff/environment.yml

@@ -1,5 +1,6 @@
-# You can use this file to create a conda environment for this module:
-#   conda env create -f environment.yml
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+
+---
 channels:
   - conda-forge
   - bioconda

modules/nf-core/trgt/merge/environment.yml

@@ -1,4 +1,6 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+
+---
 channels:
   - conda-forge
   - bioconda

modules/nf-core/trgt/plot/environment.yml

@@ -1,4 +1,6 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+
+---
 channels:
   - conda-forge
   - bioconda