✨Modernize repository (#26)

Signed-off-by: zethson <[email protected]>
laminlabs · Oct 22, 2024 · 8731025 · 8731025
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commit 8731025
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     timeout-minutes: 20
 
     steps:
@@ -29,7 +29,7 @@ jobs:
           ssh-key: ${{ secrets.READ_LNDOCS }}
           path: lndocs
           ref: main
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,70 +1,56 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
 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,E501,W503,BLK100
+      - 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/static/
+              docs/static/|
+              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: v0.1.7
     hooks:
-      - id: forbid-crlf
-      - id: remove-crlf
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+      - 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
-        name: isort (python)
-        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
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-      - id: pyupgrade
-        description: Automatically upgrade syntax for newer versions.
-        args: [--py38-plus]
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies: ["types-requests", "types-attrs"]
+        exclude: |
+          (?x)(
+              test_notebooks.py
+          )
diff --git a/docs/vitessce.ipynb b/docs/vitessce.ipynb
@@ -261,7 +261,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "lamindb",
    "language": "python",
    "name": "python3"
   },
@@ -275,7 +275,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/noxfile.py b/noxfile.py
@@ -1,6 +1,13 @@
 import nox
 from laminci import upload_docs_artifact
-from laminci.nox import build_docs, login_testuser1, run_pre_commit
+from laminci.nox import (
+    SYSTEM,
+    build_docs,
+    install_lamindb,
+    login_testuser1,
+    run,
+    run_pre_commit,
+)
 
 nox.options.default_venv_backend = "none"
 
@@ -12,22 +19,9 @@ def lint(session: nox.Session) -> None:
 
 @nox.session
 def build(session):
-    session.run(
-        "uv",
-        "pip",
-        "install",
-        "--system",
-        "lamindb[bionty] @ git+https://github.com/laminlabs/lamindb@main",
-    )
-    session.run(*"uv pip install --system -r requirements.txt".split())
-    session.run(
-        "uv",
-        "pip",
-        "install",
-        "--system",
-        "lamindb_setup @ git+https://github.com/laminlabs/lamindb-setup@main",
-    )
+    install_lamindb(session, branch="release", extras="bionty,aws,gcp,jupyter")
+    run(session, f"uv pip install {SYSTEM} .[dev,use_case]")
     login_testuser1(session)
-    session.run(*"pytest -s tests".split())
+    run(session, "pytest -s tests")
     build_docs(session, strict=True)
     upload_docs_artifact(aws=True)
diff --git a/pyproject.toml b/pyproject.toml
@@ -3,7 +3,7 @@ requires = ["flit_core >=3.2,<4"]
 build-backend = "flit_core.buildapi"
 
 [project]
-name = "rxrx_lamin"
+name = "lamin_spatial"
 authors = [{name = "Lamin Labs", email = "[email protected]"}]
 readme = "README.md"
 dynamic = ["version", "description"]
@@ -20,11 +20,112 @@ dev = [
     "pytest-cov",
     "nbproject_test",
 ]
-
-[tool.black]
-preview = true
+use_case = [
+    "wetlab",
+    "findrefs",
+    "vitessce",
+    "starlette",
+    "duckdb",
+    "s3fs>=2024.10.0"  # gets downgraded by vitessce/starlette but needs to be recent
+]
 
 [tool.pytest.ini_options]
 testpaths = [
     "tests",
 ]
+
+[tool.ruff]
+src = ["src"]
+line-length = 88
+select = [
+    "F",  # Errors detected by Pyflakes
+    "E",  # Error detected by Pycodestyle
+    "W",  # Warning detected by Pycodestyle
+    "I",  # isort
+    "D",  # pydocstyle
+    "B",  # flake8-bugbear
+    "TID",  # flake8-tidy-imports
+    "C4",  # flake8-comprehensions
+    "BLE",  # flake8-blind-except
+    "UP",  # pyupgrade
+    "RUF100",  # Report unused noqa directives
+    "TCH",  # Typing imports
+    "NPY",  # Numpy specific rules
+    "PTH"  # Use pathlib
+]
+ignore = [
+    # Do not catch blind exception: `Exception`
+    "BLE001",
+    # Errors from function calls in argument defaults. These are fine when the result is immutable.
+    "B008",
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    "E501",
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    "E731",
+    # allow I, O, l as variable names -> I is the identity matrix
+    "E741",
+    # Missing docstring in public module
+    "D100",
+    # undocumented-public-class
+    "D101",
+    # Missing docstring in public method
+    "D102",
+    # Missing docstring in public function
+    "D103",
+    # Missing docstring in public package
+    "D104",
+    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    "D105",
+    # Missing docstring in public nested class
+    "D106",
+    # Missing docstring in __init__
+    "D107",
+    ## Disable one in each pair of mutually incompatible rules
+    # We don’t want a blank line before a class docstring
+    "D203",
+    # 1 blank line required after class docstring
+    "D204",
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    # We want docstrings to start immediately after the opening triple quote
+    "D213",
+    # Section underline is over-indented ("{name}")
+    "D215",
+    # First line should end with a period
+    "D400",
+    # First line should be in imperative mood; try rephrasing
+    "D401",
+    # First word of the first line should be capitalized: {} -> {}
+    "D403",
+    # First word of the docstring should not be "This"
+    "D404",
+    # Section name should end with a newline ("{name}")
+    "D406",
+    # Missing dashed underline after section ("{name}")
+    "D407",
+    # Section underline should be in the line following the section's name ("{name}")
+    "D408",
+    # Section underline should match the length of its name ("{name}")
+    "D409",
+    # No blank lines allowed between a section header and its content ("{name}")
+    "D412",
+    # Missing blank line after last section ("{name}")
+    "D413",
+    # Missing argument description
+    "D417",
+    # Imports unused
+    "F401",
+    # camcelcase imported as lowercase
+    "N813",
+    # module import not at top level of file
+    "E402",
+    # open()` should be replaced by `Path.open()
+    "PTH123",
+]
+
+[tool.ruff.pydocstyle]
+convention = "google"
+
+[tool.ruff.per-file-ignores]
+"docs/*" = ["I"]
+"tests/*" = ["D"]
+"*/__init__.py" = ["F401"]
diff --git a/requirements.txt b/requirements.txt