Run automated formatting and linters

.github/CODEOWNERS

@@ -1,3 +1,3 @@
-# automatically requests pull request reviews for files matching the given pattern; the last match takes precendence
+# automatically requests pull request reviews for files matching the given pattern; the last match takes precedence
 
 *       @spacetelescope/stcal-maintainers

.github/labeler.yml

@@ -1,46 +1,46 @@
 documentation:
-  - 'docs/**/*'
-  - any: [ '*.rst', '!CHANGES.rst' ]
-  - '*.md'
-  - '.readthedocs.yaml'
-  - 'LICENSE'
+  - "docs/**/*"
+  - any: ["*.rst", "!CHANGES.rst"]
+  - "*.md"
+  - ".readthedocs.yaml"
+  - "LICENSE"
 
 installation:
-  - 'pyproject.toml'
-  - 'setup.*'
-  - 'requirements-*.txt'
-  - 'MANIFEST.in'
+  - "pyproject.toml"
+  - "setup.*"
+  - "requirements-*.txt"
+  - "MANIFEST.in"
 
 # --------------------------------------- testing ---------------------------------------
 
 automation:
-  - '.github/**'
-  - '.bandit.yaml'
-  - '.codecov.yml'
+  - ".github/**"
+  - ".bandit.yaml"
+  - ".codecov.yml"
 
 testing:
-  - '**/tests/**'
-  - '.github/workflows/ci*.yml'
-  - 'conftest.py'
+  - "**/tests/**"
+  - ".github/workflows/ci*.yml"
+  - "conftest.py"
 
 # --------------------------------------- modules ---------------------------------------
 
 dark_current:
-  - '**/*dark_current*'
-  - '**/*dark_current*/**'
+  - "**/*dark_current*"
+  - "**/*dark_current*/**"
 
 jump:
-  - '**/*jump*'
-  - '**/*jump*/**'
+  - "**/*jump*"
+  - "**/*jump*/**"
 
 linearity:
-  - '**/*linearity*'
-  - '**/*linearity*/**'
+  - "**/*linearity*"
+  - "**/*linearity*/**"
 
 ramp_fitting:
-  - '**/*ramp_fitting*'
-  - '**/*ramp_fitting*/**'
+  - "**/*ramp_fitting*"
+  - "**/*ramp_fitting*/**"
 
 saturation:
-  - '**/*saturation*'
-  - '**/*saturation*/**'
+  - "**/*saturation*"
+  - "**/*saturation*/**"

.github/pull_request_template.md

@@ -1,15 +1,19 @@
-<!-- If this PR closes a JIRA ticket, make sure the title starts with the JIRA issue number, 
+<!-- If this PR closes a JIRA ticket, make sure the title starts with the JIRA issue number,
 for example JP-1234: <Fix a bug> -->
+
 Resolves [JP-nnnn](https://jira.stsci.edu/browse/JP-nnnn)
 Resolves [RCAL-nnnn](https://jira.stsci.edu/browse/RCAL-nnnn)
 
 <!-- If this PR closes a GitHub issue, reference it here by its number -->
+
 Closes #
 
 <!-- describe the changes comprising this PR here -->
+
 This PR addresses ...
 
 **Checklist**
+
 - [ ] added entry in `CHANGES.rst` (either in `Bug Fixes` or `Changes to API`)
 - [ ] updated relevant tests
 - [ ] updated relevant documentation

.github/workflows/build.yml

@@ -2,7 +2,7 @@ name: build
 
 on:
   release:
-    types: [ released ]
+    types: [released]
   pull_request:
   workflow_dispatch:
 
@@ -25,4 +25,3 @@ jobs:
       sdist: true
     secrets:
       pypi_token: ${{ secrets.PYPI_PASSWORD_STSCI_MAINTAINER }}
-

.github/workflows/ci.yml

@@ -4,9 +4,9 @@ on:
   push:
     branches:
       - main
-      - '*x'
+      - "*x"
     tags:
-      - '*'
+      - "*"
   pull_request:
     branches:
       - main
@@ -24,7 +24,6 @@ jobs:
     with:
       envs: |
         - linux: check-style
-        - linux: check-security
         - linux: check-build
   test:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
@@ -43,7 +42,7 @@ jobs:
       setenv: |
         CRDS_PATH: /tmp/crds_cache
         CRDS_CLIENT_RETRY_COUNT: 3
-        CRDS_CLIENT_RETRY_DELAY_SECONDS: 20 
+        CRDS_CLIENT_RETRY_DELAY_SECONDS: 20
       envs: |
         - linux: py311-jwst-cov-xdist
         - linux: py311-romancal-cov-xdist

.github/workflows/label_pull_request.yml

@@ -13,4 +13,4 @@ jobs:
       - uses: actions/labeler@v4
         if: github.event_name == 'pull_request_target' || github.event_name == 'pull_request'
         with:
-          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.gitignore

@@ -151,4 +151,4 @@ docs/source/api
 .DS_Store
 
 # VSCode stuff
-.vscode
+.vscode

.pre-commit-config.yaml

@@ -0,0 +1,69 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-yaml
+        args: ["--unsafe"]
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: text-unicode-replacement-char
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.5
+    hooks:
+      - id: codespell
+        args: ["--write-changes"]
+        additional_dependencies:
+          - tomli
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.5"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/MarcoGorelli/cython-lint
+    rev: v0.15.0
+    hooks:
+      - id: cython-lint
+      - id: double-quote-cython-strings
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (cython)
+        types: [cython]
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==22.12.0
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.1"
+    hooks:
+      - id: prettier
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2023.10.27
+    hooks:
+      - id: sp-repo-review
+        additional_dependencies: ["repo-review[cli]"]

CHANGES.rst

@@ -1,8 +1,13 @@
 1.4.5 (unreleased)
 ==================
 
+Other
+-----
+
 - Added ``alignment`` sub-package. [#179]
 
+- Enable automatic linting and code style checks [#187]
+
 ramp_fitting
 ------------
 
@@ -27,11 +32,6 @@ Bug Fixes
 
 -
 
-Other
------
-
-- 
-
 1.4.4 (2023-09-15)
 ==================
 
@@ -174,7 +174,7 @@ ramp_fitting
 - Correct the "averaging" of the final image slope by properly excluding
   variances as a part of the denominator from integrations with invalid slopes.
   [#167]
-- Removing the usage of ``numpy.where`` where possible for perfomance
+- Removing the usage of ``numpy.where`` where possible for performance
   reasons. [#169]
 
 1.3.7 (2023-04-26)
@@ -218,7 +218,7 @@ Other
 -----
 
 - Remove use of deprecated ``pytest-openfiles`` ``pytest`` plugin. This has been replaced by
-  catching ``ResourceWarning``s. [#159]
+  catching ``ResourceWarning``. [#159]
 
 
 1.3.5 (2023-03-30)
@@ -566,7 +566,7 @@ ramp_fitting
 jump
 ~~~~
 
-- Fix issue in jump detection that occured when there were only 2 usable
+- Fix issue in jump detection that occurred when there were only 2 usable
   differences with no other groups flagged. This PR also added tests and
   fixed some of the logging statements in twopoint difference. [#74]
 

CODE_OF_CONDUCT.md

@@ -2,7 +2,6 @@
 
 We expect all "spacetelescope" organization projects to adopt a code of conduct that ensures a productive, respectful environment for all open source contributors and participants. We are committed to providing a strong and enforced code of conduct and expect everyone in our community to follow these guidelines when interacting with others in all forums. Our goal is to keep ours a positive, inclusive, successful, and growing community. The community of participants in open source Astronomy projects is made up of members from around the globe with a diverse set of skills, personalities, and experiences. It is through these differences that our community experiences success and continued growth.
 
-
 As members of the community,
 
 - We pledge to treat all people with respect and provide a harassment- and bullying-free environment, regardless of sex, sexual orientation and/or gender identity, disability, physical appearance, body size, race, nationality, ethnicity, and religion. In particular, sexual language and imagery, sexist, racist, or otherwise exclusionary jokes are not appropriate.

README.md

@@ -12,21 +12,20 @@ STScI Calibration algorithms and tools.
 
 **STCAL requires Python 3.9 or above and a C compiler for dependencies.**
 
-**Linux and MacOS platforms are tested and supported.  Windows is not currently supported.**
-
-**If installing on MacOS Mojave 10.14, you must install 
-  into an environment with python 3.9. Installation will fail on python 3.10 due
-  to lack of a stable build for dependency ``opencv-python``.**
+**Linux and MacOS platforms are tested and supported. Windows is not currently supported.**
 
+**If installing on MacOS Mojave 10.14, you must install
+into an environment with python 3.9. Installation will fail on python 3.10 due
+to lack of a stable build for dependency `opencv-python`.**
 
 `STCAL` is intended to be used as a support package for calibration pipeline
-software, such as the `JWST` and `Roman` calibration pipelines.  `STCAL` is a
+software, such as the `JWST` and `Roman` calibration pipelines. `STCAL` is a
 separate package because it is also intended to be software that can be reused
-by multiple calibration pipelines.  Even though it is intended to be a support
+by multiple calibration pipelines. Even though it is intended to be a support
 package for calibration pipelines, it can be installed and used as a stand alone
-package.  This could make usage unwieldy as it is easier to use `STCAL` through
-calibration software.  The main use case for stand alone installation is for
-development purposes, such as bug fixes and feature additions.  When installing
+package. This could make usage unwieldy as it is easier to use `STCAL` through
+calibration software. The main use case for stand alone installation is for
+development purposes, such as bug fixes and feature additions. When installing
 calibration pipelines that depend on `STCAL` this package automatically gets
 installed as a dependency.
 
@@ -48,17 +47,18 @@ If desired, you can create multiple environments to allow for switching between
 versions of the `stcal` package (e.g. a released version versus the current development version).
 
 In all cases, the installation is generally a 3-step process:
-* Create a conda environment
-* Activate that environment
-* Install the desired version of the `stcal` package into that environment
+
+- Create a conda environment
+- Activate that environment
+- Install the desired version of the `stcal` package into that environment
 
 Details are given below on how to do this for different types of installations,
 including tagged releases and development versions.
 Remember that all conda operations must be done from within a bash/zsh shell.
 
 ### Installing latest releases
 
-You can install the latest released version via `pip`.  From a bash/zsh shell:
+You can install the latest released version via `pip`. From a bash/zsh shell:
 
     conda create -n <env_name> python
     conda activate <env_name>
@@ -100,7 +100,7 @@ fork and clone the `stcal` repo:
     git clone https://github.com/spacetelescope/stcal
     cd stcal
 
-*Note: `python setup.py install` and `python setup.py develop` commands do not work.*
+_Note: `python setup.py install` and `python setup.py develop` commands do not work._
 
 Install from your local checked-out copy as an "editable" install:
 
@@ -117,7 +117,6 @@ Need other useful packages in your development environment?
 
     pip install ipython jupyter matplotlib pylint ipdb
 
-
 ## Contributions and Feedback
 
 We welcome contributions and feedback on the project. Please follow the
@@ -131,7 +130,7 @@ at https://github.com/spacetelescope/stcal/issues.
 
 ## Unit Tests
 
-Unit tests can be run via `pytest`.  Within the top level of your local `stcal` repo checkout:
+Unit tests can be run via `pytest`. Within the top level of your local `stcal` repo checkout:
 
     pip install -e ".[test]"
     pytest

docs/Makefile

@@ -76,4 +76,3 @@ linkcheck:
 
 livehtml:
 	sphinx-autobuild -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-

docs/conf.py

@@ -26,14 +26,14 @@ def setup(app):
 
 # Read the package's `pyproject.toml` so that we can use relevant
 # values here:
-with open(REPO_ROOT / "pyproject.toml", "rb") as configuration_file:
+with (REPO_ROOT / "pyproject.toml").open("rb") as configuration_file:
     conf = tomllib.load(configuration_file)
 setup_metadata = conf["project"]
 
 project = setup_metadata["name"]
 primary_author = setup_metadata["authors"][0]
 author = f'{primary_author["name"]} <{primary_author["email"]}>'
-copyright = f'{datetime.now().year}, {primary_author["name"]}'
+copyright = f'{datetime.now().year}, {primary_author["name"]}'  # noqa: A001
 
 package = importlib.import_module(project)
 version = package.__version__.split("-", 1)[0]