Merge branch 'main' into priority

GenomicMedLab · Mar 21, 2024 · e5d275f · e5d275f
2 parents 25fd49a + 8e9432c
commit e5d275f
Show file tree

Hide file tree

Showing 5 changed files with 92 additions and 46 deletions.
diff --git a/.github/workflows/checks.yml → .github/workflows/checks.yaml b/.github/workflows/checks.yml → .github/workflows/checks.yaml
@@ -1,6 +1,24 @@
 name: Checks
 on: [push, pull_request]
 jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version:  ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: python3 -m pip install ".[tests]"
+
+      - name: Run tests
+        run: python3 -m pytest tests/
   python-lint:
     runs-on: ubuntu-latest
     steps:
@@ -31,21 +49,3 @@ jobs:
         run: rustup component add rustfmt
 
       - run: cargo fmt -- --check
-  unit-tests:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version:  ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: python3 -m pip install ".[tests]"
-
-      - name: Run tests
-        run: python3 -m pytest tests/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,13 +1,13 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v1.4.0
   hooks:
   - id: check-added-large-files
   - id: detect-private-key
   - id: trailing-whitespace
   - id: end-of-file-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.13
+  rev: v0.2.0
   hooks:
     - id: ruff-format
     - id: ruff

diff --git a/README.md b/README.md
@@ -3,11 +3,13 @@
 [![image](https://img.shields.io/pypi/v/agct.svg)](https://pypi.python.org/pypi/agct)
 [![image](https://img.shields.io/pypi/l/agct.svg)](https://pypi.python.org/pypi/agct)
 [![image](https://img.shields.io/pypi/pyversions/agct.svg)](https://pypi.python.org/pypi/agct)
-[![Actions status](https://github.com/genomicmedlab/agct/workflows/CI/badge.svg)](https://github.com/genomicmedlab/agct/actions)
+[![Actions status](https://github.com/genomicmedlab/agct/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/agct/actions/checks.yaml)
 
 <!-- description -->
-A drop-in replacement for the [pyliftover](https://github.com/konstantint/pyliftover) tool, using the St. Jude's [chainfile](https://docs.rs/chainfile/latest/chainfile/) crate. Enables significantly faster chainfile loading from cold start (see `analysis/`).
-<!-- /description -->
+Drop-in replacement for the [pyliftover](https://github.com/konstantint/pyliftover) tool, using the St. Jude's [chainfile](https://docs.rs/chainfile/latest/chainfile/) crate.
+<!-- description -->
+
+Enables significantly faster chainfile loading from cold start (see `analysis/`).
 
 ## Installation
 
@@ -47,16 +49,16 @@ source venv/bin/activate
 python3 -m pip install -e '.[dev,tests]'
 ```
 
-Be sure to install pre-commit hooks:
+This installs Python code as editable, but after any changes to Rust code, run ``maturin develop`` to rebuild the Rust binary:
 
 ```shell
-pre-commit install
+maturin develop
 ```
 
-This installs Python code as editable, but after any changes to Rust code, ``maturin develop`` must be run:
+Be sure to install pre-commit hooks:
 
 ```shell
-maturin develop
+pre-commit install
 ```
 
 Check Python style with `ruff`:

diff --git a/pyproject.toml b/pyproject.toml
@@ -2,12 +2,10 @@
 name = "agct"
 version = "0.1.0-dev1"
 authors = [
-    {name = "James Stevenson"}
+    {name = "James Stevenson"},
+    {name = "Kori Kuzma"},
 ]
-description = "Another Genome Conversion Tool: Python frontend to Rust chainfile crate"
 readme = "README.md"
-license = {file = "LICENSE"}
-requires-python = ">=3.8"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Rust",
@@ -18,10 +16,14 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
 ]
+requires-python = ">=3.8"
+description = "Another Genome Conversion Tool: Python frontend to Rust chainfile crate"
+license = {file = "LICENSE"}
 dependencies = ["wags-tails"]
 
 [project.optional-dependencies]
@@ -31,7 +33,7 @@ tests = [
 ]
 dev = [
     "maturin",
-    "ruff>=0.1.12",
+    "ruff==0.2.0",
     "pre-commit",
 ]
 
@@ -60,15 +62,51 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
-# pycodestyle (E, W)
-# Pyflakes (F)
-# flake8-annotations (ANN)
-# pydocstyle (D)
-# pep8-naming (N)
-# isort (I)
-select = ["E", "W", "F", "ANN", "D", "N", "I"]
-fixable = ["I", "F401"]
 
+[tool.ruff.lint]
+select = [
+    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
+    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
+fixable = [
+    "I",
+    "F401",
+    "D",
+    "UP",
+    "ANN",
+    "B",
+    "C4",
+    "G",
+    "PIE",
+    "PT",
+    "RSE",
+    "SIM",
+    "RUF"
+]
 # ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
 # D203 - one-blank-line-before-class
@@ -83,16 +121,20 @@ fixable = ["I", "F401"]
 # E117 - over-indented*
 # E501 - line-too-long*
 # W191 - tab-indentation*
+# S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
     "ANN101", "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
-    "W191"
+    "W191",
+    "S321",
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
-# ANN102 - missing-type-cls
 # ANN2 - missing-return-type
-"tests/*" = ["ANN001", "ANN102", "ANN2"]
+# ANN102 - missing-type-cls
+# S101 - assert
+# B011 - assert-false
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
diff --git a/src/agct/converter.py b/src/agct/converter.py
@@ -57,10 +57,12 @@ def __init__(
         """
         if not chainfile:
             if from_db is None and to_db is None:
-                raise ValueError("Must provide both `from_db` and `to_db`")
+                msg = "Must provide both `from_db` and `to_db`"
+                raise ValueError(msg)
 
             if from_db == to_db:
-                raise ValueError("Liftover must be to/from different sources.")
+                msg = "Liftover must be to/from different sources."
+                raise ValueError(msg)
 
             data_handler = CustomData(
                 f"chainfile_{from_db.value}_to_{to_db.value}",