switch to more basic pre-commit from pyrenew

CDCgov · Feb 10, 2025 · a91ef10 · a91ef10
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diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
@@ -5,6 +5,10 @@ on:
   push:
     branches: [main]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
@@ -13,10 +17,4 @@ jobs:
     - uses: actions/setup-python@v5
       with:
         python-version: "3.12"
-    - name: Set up Quarto
-      uses: quarto-dev/quarto-actions/setup@v2
-    - name: Install Poetry
-      run: pip install poetry
-    - name: Install packages
-      run: poetry install --with dev
     - uses: pre-commit/[email protected]
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,108 +1,39 @@
 repos:
-################################################################################
-# GENERAL
-################################################################################
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  #####
+  # Basic file cleanliness
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-    -   id: check-added-large-files
-        args: ["--maxkb=10000"]
-    -   id: check-yaml
-        args: ["--allow-multiple-documents"]
-    -   id: check-toml
-    -   id: end-of-file-fixer
-    -   id: mixed-line-ending
-    -   id: trailing-whitespace
-
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
-    hooks:
-    # prevent giant files from being committed.
-    -   id: check-added-large-files
-        args: ["--maxkb=10000"]
-    # simply check whether files parse as valid
-    # python
-    -   id: check-ast
-    # check for files with names that would
-    # conflict on a case-insensitive filesystem
-    # like MacOS HFS+ or Windows FAT.
-    -   id: check-case-conflict
-    # checks for a common error of placing
-    # code before the docstring.
-    -   id: check-docstring-first
-    # attempts to load all yaml files to
-    # verify syntax.
-    -   id: check-yaml
-        # allow yaml files which use the
-        # multi-document syntax
-        args: ["--allow-multiple-documents"]
-    # attempts to load all TOML files to
-    # verify syntax.
-    -   id: check-toml
-    # makes sure files end in a newline and
-    # only a newline.
-    -   id: end-of-file-fixer
-    # replaces or checks mixed line ending.
-    -   id: mixed-line-ending
-    # verifies that test files are named
-    # correctly.
-    -   id: name-tests-test
-        # ensure tests match test_.*\.py
-        args: ["--pytest-test-first"]
-    # trims trailing whitespace.
-    -   id: trailing-whitespace
-    # checks that non-binary executables have
-    # a proper shebang.
-    -   id: check-executables-have-shebangs
-        files: \.sh$
-################################################################################
-# QUARTO README RENDERING
-################################################################################
--   repo: local
-    hooks:
-    -   id: render-quarto-readme
-        name: "render README.qmd as README.md"
-        entry: "./scripts/hooks/render-quarto-readme.sh"
-        language: script
-        always_run: true
-        files: "README.(q|)md"
-################################################################################
-# PYTHON
-################################################################################
--   repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-    -   id: isort
-        args: ["--profile", "black", "--line-length", "79"]
--   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.3
-    hooks:
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+  #####
+  # Python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.1
+    hooks:
+      # Sort imports
       - id: ruff
-        args: ["--ignore=E741", "--ignore=E731", "--fix"]
-################################################################################
-# GITHUB ACTIONS
-################################################################################
--   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.4
-    hooks:
-    -   id: actionlint
-################################################################################
-# SPELLING
-################################################################################
--   repo: https://github.com/crate-ci/typos
-    rev: typos-dict-v0.11.37
-    hooks:
-    -   id: typos
-        args: ["--force-exclude"]
-################################################################################
-# COMMIT MESSAGES
-################################################################################
--   repo: https://github.com/commitizen-tools/commitizen
-    rev: v4.1.0
-    hooks:
-    -   id: commitizen
--   repo: https://github.com/jorisroovers/gitlint
-    rev:  v0.19.1
-    hooks:
-    -   id: gitlint
-################################################################################
+        args: ["check", "--select", "I", "--fix"]
+        # Run the linter
+      - id: ruff
+        # Run the formatter
+      - id: ruff-format
+        args: ["--line-length", "79"]
+  #####
+  # R
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3
+    hooks:
+      - id: style-files
+      - id: lintr
+  # Secrets
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.5.0
+    hooks:
+      - id: detect-secrets
+        args: ["--baseline", ".secrets.baseline"]
+        exclude: package.lock.json
diff --git a/.pre-commit-config_max.yaml b/.pre-commit-config_max.yaml
@@ -0,0 +1,108 @@
+repos:
+################################################################################
+# GENERAL
+################################################################################
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: check-added-large-files
+        args: ["--maxkb=10000"]
+    -   id: check-yaml
+        args: ["--allow-multiple-documents"]
+    -   id: check-toml
+    -   id: end-of-file-fixer
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    # prevent giant files from being committed.
+    -   id: check-added-large-files
+        args: ["--maxkb=10000"]
+    # simply check whether files parse as valid
+    # python
+    -   id: check-ast
+    # check for files with names that would
+    # conflict on a case-insensitive filesystem
+    # like MacOS HFS+ or Windows FAT.
+    -   id: check-case-conflict
+    # checks for a common error of placing
+    # code before the docstring.
+    -   id: check-docstring-first
+    # attempts to load all yaml files to
+    # verify syntax.
+    -   id: check-yaml
+        # allow yaml files which use the
+        # multi-document syntax
+        args: ["--allow-multiple-documents"]
+    # attempts to load all TOML files to
+    # verify syntax.
+    -   id: check-toml
+    # makes sure files end in a newline and
+    # only a newline.
+    -   id: end-of-file-fixer
+    # replaces or checks mixed line ending.
+    -   id: mixed-line-ending
+    # verifies that test files are named
+    # correctly.
+    -   id: name-tests-test
+        # ensure tests match test_.*\.py
+        args: ["--pytest-test-first"]
+    # trims trailing whitespace.
+    -   id: trailing-whitespace
+    # checks that non-binary executables have
+    # a proper shebang.
+    -   id: check-executables-have-shebangs
+        files: \.sh$
+################################################################################
+# QUARTO README RENDERING
+################################################################################
+-   repo: local
+    hooks:
+    -   id: render-quarto-readme
+        name: "render README.qmd as README.md"
+        entry: "./scripts/hooks/render-quarto-readme.sh"
+        language: script
+        always_run: true
+        files: "README.(q|)md"
+################################################################################
+# PYTHON
+################################################################################
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: ["--profile", "black", "--line-length", "79"]
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.3
+    hooks:
+      - id: ruff
+        args: ["--ignore=E741", "--ignore=E731", "--fix"]
+################################################################################
+# GITHUB ACTIONS
+################################################################################
+-   repo: https://github.com/rhysd/actionlint
+    rev: v1.7.4
+    hooks:
+    -   id: actionlint
+################################################################################
+# SPELLING
+################################################################################
+-   repo: https://github.com/crate-ci/typos
+    rev: typos-dict-v0.11.37
+    hooks:
+    -   id: typos
+        args: ["--force-exclude"]
+################################################################################
+# COMMIT MESSAGES
+################################################################################
+-   repo: https://github.com/commitizen-tools/commitizen
+    rev: v4.1.0
+    hooks:
+    -   id: commitizen
+-   repo: https://github.com/jorisroovers/gitlint
+    rev:  v0.19.1
+    hooks:
+    -   id: gitlint
+################################################################################
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -0,0 +1,112 @@
+{
+  "version": "1.4.0",
+  "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
+    {
+      "name": "AWSKeyDetector"
+    },
+    {
+      "name": "AzureStorageKeyDetector"
+    },
+    {
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
+    },
+    {
+      "name": "BasicAuthDetector"
+    },
+    {
+      "name": "CloudantDetector"
+    },
+    {
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3.0
+    },
+    {
+      "name": "IbmCloudIamDetector"
+    },
+    {
+      "name": "IbmCosHmacDetector"
+    },
+    {
+      "name": "JwtTokenDetector"
+    },
+    {
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
+    },
+    {
+      "name": "MailchimpDetector"
+    },
+    {
+      "name": "NpmDetector"
+    },
+    {
+      "name": "PrivateKeyDetector"
+    },
+    {
+      "name": "SendGridDetector"
+    },
+    {
+      "name": "SlackDetector"
+    },
+    {
+      "name": "SoftlayerDetector"
+    },
+    {
+      "name": "SquareOAuthDetector"
+    },
+    {
+      "name": "StripeDetector"
+    },
+    {
+      "name": "TwilioKeyDetector"
+    }
+  ],
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    }
+  ],
+  "results": {},
+  "generated_at": "2023-09-24T19:52:08Z"
+}
diff --git a/forecasttools/__init__.py b/forecasttools/__init__.py
@@ -32,7 +32,9 @@
     "location_table.parquet"
 )
 location_table = pl.read_parquet(location_table_path)
-united_states = location_table.filter(pl.col("is_state")).get_column("long_name").to_list()
+united_states = (
+    location_table.filter(pl.col("is_state")).get_column("long_name").to_list()
+)
 
 # load example flusight submission
 example_flusight_submission_path = importlib.resources.files(