🎨 Remove lnschema-core installation (#44)

Signed-off-by: zethson <[email protected]>

.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8"] # we want to be able to run this on 3.8
+        python-version: ["3.12"]
     timeout-minutes: 10
 
     steps:

.pre-commit-config.yaml

@@ -1,64 +1,51 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.12.0
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
-    hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-        exclude: |
-          (?x)(
-              .github/workflows/latest-changes.jinja2
-          )
-      - id: check-yaml
-      - id: check-added-large-files
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
-    hooks:
-      - id: black-jupyter
-  - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.4
     hooks:
-      - id: flake8
-        additional_dependencies:
-          - flake8-black==0.3.3
-          - flake8-typing-imports==1.10.0
-        language_version: python3
-        args:
-          - --max-line-length=88
-          - --ignore=E203,W503,BLK100,TYP001
+      - id: prettier
         exclude: |
           (?x)(
-              __init__.py
+            docs/changelog.md
           )
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.6.2
-    hooks:
-      - id: prettier
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.3.9
+    rev: 0.6.1
     hooks:
       - id: nbstripout
         exclude: |
           (?x)(
               docs/examples/|
               docs/notes/
           )
-  - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.1.9
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.6
     hooks:
-      - id: forbid-crlf
-      - id: remove-crlf
-  - repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.8.0
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-      - id: isort
-        args: ["--profile", "black"]
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+            )
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.940
+    rev: v1.7.1
     hooks:
       - id: mypy
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
-    hooks:
-      - id: pydocstyle
-        args: # google style + __init__, see http://www.pydocstyle.org/en/stable/error_codes.html
-          - --ignore=D100,D101,D102,D103,D106,D107,D203,D204,D213,D215,D400,D401,D403,D404,D406,D407,D408,D409,D412,D413
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies: ["types-requests", "types-attrs"]

docs/notes/YYYY-MM-DD-my-design-choice.ipynb

@@ -14,9 +14,7 @@
    "id": "97ec6631-8473-4a2d-b488-def921bb83de",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from nbproject import header"
-   ]
+   "source": []
   }
  ],
  "metadata": {

laminci/__main__.py

@@ -8,7 +8,6 @@
 import subprocess
 from pathlib import Path
 from subprocess import PIPE, run
-from typing import Union
 
 from packaging.version import Version, parse
 
@@ -35,7 +34,7 @@
 
 def update_readme_version(file_path, new_version):
     # Read the content of the file
-    with open(file_path, "r") as file:
+    with open(file_path) as file:
         content = file.read()
 
     # Use regex to find and replace the version
@@ -49,7 +48,7 @@ def update_readme_version(file_path, new_version):
 
 
 def get_last_version_from_tags():
-    proc = run(["git", "tag"], universal_newlines=True, stdout=PIPE)
+    proc = run(["git", "tag"], text=True, stdout=PIPE)
     tags = proc.stdout.splitlines()
     newest = "0.0.0"
     for tag in tags:
@@ -64,16 +63,18 @@ def validate_version(version_str: str):
         if not len(version.release) == 2:
             raise SystemExit(
                 f"Pre-releases should be of form 0.42a1 or 0.42rc1, yours is {version}"
-            )
+            ) from None
         else:
             return None
     if len(version.release) != 3:
-        raise SystemExit(f"Version should be of form 0.1.2, yours is {version}")
+        raise SystemExit(
+            f"Version should be of form 0.1.2, yours is {version}"
+        ) from None
 
 
 def publish_github_release(
     repo_name: str,
-    version: Union[str, Version],
+    version: str | Version,
     release_name: str,
     body: str = "",
     draft: bool = False,
@@ -132,12 +133,14 @@ def publish_github_release(
                     generate_release_notes=generate_release_notes,
                 )
             except GithubException as e:
-                raise SystemExit(f"Error creating GitHub release using `PyGithub`: {e}")
+                raise SystemExit(
+                    f"Error creating GitHub release using `PyGithub`: {e}"
+                ) from None
         except ImportError:
             raise SystemExit(
                 "Neither the Github CLI ('gh') nor PyGithub were accessible.\n"
                 "Please install one of the two."
-            )
+            ) from None
 
 
 def main():
@@ -163,23 +166,23 @@ def main():
                 raise SystemExit(
                     "Please pass a link to the changelog entry via: --changelog"
                     " 'your-link'"
-                )
+                ) from None
             if Path("./LICENSE").exists() and not args.pypi:
                 raise SystemExit(
                     "ERROR: Did you forget to add the `--pypi` flag? A LICENSE file"
                     " exists and I assume this is an open-source package."
-                )
+                ) from None
             repo_name = package_name.replace("_", "-")
         else:
-            assert Path.cwd().name == "laminhub"
+            assert Path.cwd().name == "laminhub"  # noqa: S101
             repo_name = "laminhub"
             if not (Path.cwd().parent / "laminhub-public").exists():
                 raise ValueError(
                     "Please clone the laminhub-public repository into the same parent"
                     " directory as laminhub."
                 )
             is_laminhub = True
-            with open("ui/package.json", "r") as file:
+            with open("ui/package.json") as file:
                 version = json.load(file)["version"]
 
         print(f"INFO: You will add this changelog link: {args.changelog}")
@@ -203,7 +206,7 @@ def main():
         ]
         for command in commands:
             print(f"\nrun: {command}")
-            run(command, shell=True)
+            run(command, shell=True)  # noqa: S602
 
         changelog_link = (
             args.changelog
@@ -221,7 +224,7 @@ def main():
             update_readme_version("../laminhub-public/README.md", version)
             for command in commands:
                 print(f"\nrun: {command}")
-                run(command, shell=True, cwd="../laminhub-public")
+                run(command, shell=True, cwd="../laminhub-public")  # noqa: S602
             publish_github_release(
                 repo_name="laminlabs/laminhub-public",
                 version=version,
@@ -234,7 +237,7 @@ def main():
         if args.pypi:
             command = "flit publish"
             print(f"\nrun: {command}")
-            run(command, shell=True)
+            run(command, shell=True)  # noqa: S602
     elif args.command == "doc-changes":
         from ._doc_changes import doc_changes
 

laminci/_db.py

@@ -27,8 +27,7 @@ def setup_local_test_postgres(name: str = "pgtest", version: Optional[str] = Non
         version = ""
     process = run(
         f"docker run --name {name} -e POSTGRES_PASSWORD=pwd"
-        f" -e POSTGRES_DB={name} -d -p 5432:5432 postgres{version}",  # noqa
-        shell=True,
+        f" -e POSTGRES_DB={name} -d -p 5432:5432 postgres{version}",
     )
     if process.returncode == 0:
         logger.info(

laminci/_doc_changes.py

@@ -33,13 +33,16 @@
 import subprocess
 import sys
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 from github import Github
-from github.PullRequest import PullRequest
 from jinja2 import Template
 from pydantic import BaseModel, SecretStr
 from pydantic_settings import BaseSettings
 
+if TYPE_CHECKING:
+    from github.PullRequest import PullRequest
+
 
 class Section(BaseModel):
     label: str
@@ -209,8 +212,7 @@ def generate_content(
         new_release_content = updated_content
 
     new_content = (
-        f"{pre_header_content}\n\n{new_release_content}\n\n{post_release_content}"
-        .strip()
+        f"{pre_header_content}\n\n{new_release_content}\n\n{post_release_content}".strip()
         + "\n"
     )
     return new_content

laminci/_docs.py

@@ -1,5 +1,6 @@
 import os
 import shutil
+from pathlib import Path
 
 from ._env import load_project_yaml
 
@@ -9,7 +10,7 @@ def move_built_docs_to_slash_project_slug():
         return
     yaml = load_project_yaml()
     shutil.move("_build/html", "_build/html_tmp")
-    os.makedirs("_build/html")
+    Path.mkdir("_build/html", parents=True)
     shutil.move("_build/html_tmp", f"_build/html/{yaml['project_slug']}")
 
 
@@ -18,5 +19,5 @@ def move_built_docs_to_docs_slash_project_slug():
         return
     yaml = load_project_yaml()
     shutil.move("_build/html", f"_build/{yaml['project_slug']}")
-    os.makedirs("_build/html/docs")
+    Path.mkdir("_build/html/docs", parents=True)
     shutil.move(f"_build/{yaml['project_slug']}", "_build/html/docs")

laminci/_docs_artifacts.py

@@ -19,14 +19,16 @@ def zip_docs_dir(zip_filename: str) -> None:
 
 def zip_docs():
     repo_name = Path.cwd().name
-    assert "." not in repo_name  # doesn't have a weird suffix
-    assert Path(".git/").exists()  # is git repo
-    assert repo_name.lower() == repo_name  # is all lower-case
+    assert "." not in repo_name  # doesn't have a weird suffix  # noqa: S101
+    assert Path(".git/").exists()  # is git repo  # noqa: S101
+    assert repo_name.lower() == repo_name  # is all lower-case  # noqa: S101
     zip_filename = f"{repo_name}.zip"
     zip_docs_dir(zip_filename)
     return repo_name, zip_filename
 
 
+# Ruff seems to ignore any noqa comments in the following and we therefore disable it briefly
+# ruff: noqa
 def upload_docs_artifact_aws() -> None:
     repo_name, zip_filename = zip_docs()
     run(
@@ -35,6 +37,9 @@ def upload_docs_artifact_aws() -> None:
     )
 
 
+# ruff: enable
+
+
 def upload_docs_artifact_lamindb() -> None:
     repo_name, zip_filename = zip_docs()
 
@@ -73,5 +78,5 @@ def upload_docs_artifact(aws: bool = False) -> None:
             upload_docs_artifact_lamindb()
 
         except ImportError:
-            warnings.warn("Fall back to AWS")
+            warnings.warn("Fall back to AWS", stacklevel=2)
             upload_docs_artifact_aws()

laminci/_env.py

@@ -8,7 +8,7 @@
 def load_project_yaml(root_directory: Optional[Path] = None) -> dict:
     yaml_file = Path("lamin-project.yaml")
     if root_directory is None:
-        root_directory = Path(".")
+        root_directory = Path()
     yaml_file = root_directory / yaml_file
     with yaml_file.open() as f:
         d = yaml.safe_load(f)

laminci/_nox_logger.py

@@ -1,11 +1,14 @@
 from __future__ import annotations
 
 import logging
-from collections.abc import Sequence
+from typing import TYPE_CHECKING
 
 import nox
 from nox.registry import _REGISTRY, Any, Callable, F, Func, Python, functools
 
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
 
 def session_decorator(
     func: F | None = None,

laminci/_run_notebooks.py

@@ -7,5 +7,5 @@ def run_notebooks(file_or_folder: str | Path):
     import nbproject_test
 
     path = Path(file_or_folder)
-    assert path.exists()
+    assert path.exists()  # noqa: S101c
     nbproject_test.execute_notebooks(path.resolve(), write=True)