✨ Support Posix Paths (#42)

* ✨ Support Posix Paths Signed-off-by: Lukas Heumos <[email protected]> * 🎨 Security Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]>
laminlabs · Jan 22, 2025 · d6bc4f1 · d6bc4f1
1 parent 8224f44
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -12,39 +12,43 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.12", "3.13"]
 
     steps:
       - name: Checkout main
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+
       - name: Checkout lndocs
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: laminlabs/lndocs
           ssh-key: ${{ secrets.READ_LNDOCS }}
           path: lndocs
           ref: main
+
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
-          cache-dependency-path: ".github/workflows/build.yml" # See dependencies below
+
       - name: Cache pre-commit
         uses: actions/cache@v3
         if: matrix.python-version == '3.12'
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+
       - name: Install Python dependencies
         run: |
           python -m pip install -U pip
           pip install -U laminci
+
       - run: nox -s lint
         if: matrix.python-version == '3.12'
       - run: nox -s build
+
       - name: Codecov
         if: matrix.python-version == '3.12'
         uses: codecov/codecov-action@v2

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,73 +1,51 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-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: 22.3.0
-    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.8
     hooks:
-      - id: flake8
-        additional_dependencies:
-          - flake8-black>=0.1.1
-          - flake8-typing-imports==1.10.0
-        language_version: python3
-        args:
-          - --max-line-length=88
-          - --ignore=E203
-          - --min-python-version=3.8.0
+      - 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/tasks/|
-              docs/examples/
+              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: v0.9.2
     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)(
-              __init__.py
-          )
+              .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: v1.14.1
     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,D105,D107,D203,D204,D213,D215,D400,D401,D402,D403,D404,D406,D407,D408,D409,D413
-        exclude: |
-          (?x)(
-              __init__.py
-          )
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies: ["types-requests", "types-attrs"]
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,23 +1,23 @@
 cff-version: 1.2.0
 title: "readfcs: Read FCS files"
 authors:
-- family-names: Sun
-  given-names: Sunny
-  orcid: https://orcid.org/0000-0002-2365-0888
-- family-names: Wolf
-  given-names: F. Alexander
-  orcid: https://orcid.org/0000-0002-8760-7838
-url: https://github.com/laminlabs/readfcs
-preferred-citation:
-  type: article
-  title: "readfcs: Read FCS files"
-  authors:
   - family-names: Sun
     given-names: Sunny
     orcid: https://orcid.org/0000-0002-2365-0888
   - family-names: Wolf
     given-names: F. Alexander
     orcid: https://orcid.org/0000-0002-8760-7838
+url: https://github.com/laminlabs/readfcs
+preferred-citation:
+  type: article
+  title: "readfcs: Read FCS files"
+  authors:
+    - family-names: Sun
+      given-names: Sunny
+      orcid: https://orcid.org/0000-0002-2365-0888
+    - family-names: Wolf
+      given-names: F. Alexander
+      orcid: https://orcid.org/0000-0002-8760-7838
   doi: 10.56528/rfcs
   journal: Lamin Reports
   year: 2022
diff --git a/pyproject.toml b/pyproject.toml
@@ -9,7 +9,6 @@ readme = "README.md"
 dynamic = ["version", "description"]
 classifiers = [
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -33,9 +32,6 @@ dev = [
     "laminci",
 ]
 
-[tool.black]
-preview = true
-
 [tool.pytest.ini_options]
 testpaths = [
     "tests",
@@ -46,3 +42,109 @@ testpaths = [
 omit = [
     "readfcs/*",
 ]
+
+[tool.ruff]
+src = ["src"]
+line-length = 88
+lint.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
+    "S"  # Security
+]
+lint.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",
+    # camcelcase imported as lowercase
+    "N813",
+    # module import not at top level of file
+    "E402",
+    # open()` should be replaced by `Path.open()
+    "PTH123",
+    # subprocess` call: check for execution of untrusted input - https://github.com/PyCQA/bandit/issues/333
+    "S603",
+    # Starting a process with a partial executable path
+    "S607",
+    # Audit URL open for permitted schemes. Allowing use of `file:` or custom schemes is often unexpected.
+    "S310"
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+"docs/*" = ["I", "S101"]
+"tests/**/*.py" = [
+    "D",  # docstrings are allowed to look a bit off
+    "S101", # asserts allowed in tests...
+    "ARG", # Unused function args -> fixtures nevertheless are functionally relevant...
+    "FBT", # Don't care about booleans as positional arguments in tests, e.g. via @pytest.mark.parametrize()
+    "PLR2004", # Magic value used in comparison, ...
+    "S311", # Standard pseudo-random generators are not suitable for cryptographic purposes
+]
+"*/__init__.py" = ["F401"]