Update dependencies (#45)

* update everything

* version bump

* fix a typo

.pre-commit-config.yaml

@@ -48,7 +48,7 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.2
+    rev: v0.3.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.pyproject_generation/pyproject_custom.toml

@@ -1,12 +1,12 @@
 [project]
 name = "ghga_datasteward_kit"
-version = "1.2.1"
+version = "2.0.0"
 description = "GHGA Data Steward Kit - A utils package for GHGA data stewards."
 dependencies = [
     "crypt4gh >=1.6, <2",
-    "hexkit[s3]~=1.0.0",
-    "ghga-transpiler~=1.4.0",
-    "metldata~=1.1.0",
+    "hexkit[s3] >=2.1.1, <3",
+    "ghga-transpiler >=2, <3",
+    "metldata~=1.2.1",
 ]
 
 [project.urls]

lock/requirements-dev-template.in

@@ -28,6 +28,7 @@ jsonschema2md>=1.0.0
 setuptools>=69.1.0
 
 # required since switch to pyproject.toml and pip-tools
-pip-tools>=7.4.0
 tomli>=2.0.1
 tomli_w>=1.0.0
+
+uv>=0.1.21

pyproject.toml

@@ -22,13 +22,13 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "ghga_datasteward_kit"
-version = "1.2.1"
+version = "2.0.0"
 description = "GHGA Data Steward Kit - A utils package for GHGA data stewards."
 dependencies = [
     "crypt4gh >=1.6, <2",
-    "hexkit[s3]~=1.0.0",
-    "ghga-transpiler~=1.4.0",
-    "metldata~=1.1.0",
+    "hexkit[s3] >=2.1.1, <3",
+    "ghga-transpiler >=2, <3",
+    "metldata~=1.2.1",
 ]
 
 [project.license]

scripts/update_lock.py

@@ -23,6 +23,7 @@
 import os
 import re
 import subprocess
+from itertools import zip_longest
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -63,22 +64,25 @@ def fix_temp_dir_comments(file_path: Path):
 def is_file_outdated(old_file: Path, new_file: Path) -> bool:
     """Compares two lock files and returns True if there is a difference, else False"""
 
-    header_comment = "#    pip-compile"
     outdated = False
 
     with open(old_file, encoding="utf-8") as old:
         with open(new_file, encoding="utf-8") as new:
-            old_lines = old.readlines()
-            new_lines = new.readlines()
-            if len(old_lines) != len(new_lines):
-                outdated = True
-            if not outdated:
-                for old_line, new_line in zip(old_lines, new_lines):
-                    if old_line.startswith(header_comment):
-                        continue
-                    if old_line != new_line:
-                        outdated = True
-                        break
+            outdated = any(
+                old_line != new_line
+                for old_line, new_line in zip_longest(
+                    (
+                        line
+                        for line in (line.strip() for line in old)
+                        if line and not line.startswith("#")
+                    ),
+                    (
+                        line
+                        for line in (line.strip() for line in new)
+                        if line and not line.startswith("#")
+                    ),
+                )
+            )
     if outdated:
         cli.echo_failure(f"{str(old_file)} is out of date!")
     return outdated
@@ -97,10 +101,11 @@ def compile_lock_file(
     print(f"Updating '{output.name}'...")
 
     command = [
-        "pip-compile",
-        "--rebuild",
+        "uv",
+        "pip",
+        "compile",
+        "--refresh",
         "--generate-hashes",
-        "--annotate",
     ]
 
     if upgrade:

src/ghga_datasteward_kit/metadata.py

@@ -214,7 +214,7 @@ def transform_metadata(*, config: MetadataConfig) -> None:
         run_workflow_on_all_source_events(
             event_config=config,
             workflow_definition=GHGA_ARCHIVE_WORKFLOW,
-            worflow_config=config.workflow_config,
+            workflow_config=config.workflow_config,
             original_model=config.metadata_model,
         )
     )