Refactoring

.bumpversion.cfg

@@ -0,0 +1,14 @@
+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:src/TRIPs/__init__.py]
+
+[bumpversion:file:tests/__init__.py]
+
+[bumpversion:file:pyproject.toml]
+

.copier-answers.yml

@@ -0,0 +1,19 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: '9030931'
+_src_path: git@tanuki-data.pnnl.gov:ciemss/ceda-project-copier.git
+author: Jeremy Zucker
+copyright_date: '2025'
+copyright_holder: Jeremy Zucker
+coverage: true
+deptry: true
+email: Jeremy.Zucker@pnnl.gov
+include_gitlab_ci: true
+mkdocs: true
+namespace: jeremy.zucker
+open_source_license: MIT License
+package_manager: uv
+project_description: This repo contains code for pre-processing, cycle analysis, promoter
+    distance analysis, and trip analysis for bacterium.
+project_name: TRIPs
+project_slug: TRIPs
+type_checker: mypy

.editorconfig

@@ -0,0 +1,8 @@
+[*]
+max_line_length = 88
+
+[*.md]
+trim_trailing_whitespace = true
+insert_final_newline = true
+indent_style = space
+indent_size = 4

.gitignore

@@ -0,0 +1,147 @@
+
+# MkDocs documentation
+docs/source
+public/
+
+
+# SLURM logs
+logs/
+
+# Based on https://raw.githubusercontent.com/github/gitignore/main/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# PEP 582
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# basedpyright/pyright
+.pyright_cache/
+pyrightconfig.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Vscode config files
+.vscode/
+
+# Exclude .DS_Store files from being added
+.DS_Store

.gitlab-ci.yml

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+stages:
+  - quality
+  - test
+  - docs
+  - deploy
+
+variables:
+  PRE_COMMIT_KEY: pre-commit-$CI_COMMIT_REF_SLUG
+  PRE_COMMIT_HOME: $CI_PROJECT_DIR/.cache/pre-commit
+  UV_CACHE_DIR: .uv-cache
+  UV_VERSION: 0.6
+  PYTHON_VERSION: 3.12 # Default Python version; others are tested in the test job
+  BASE_LAYER: bookworm
+
+default:
+
+  cache: &global_cache
+    key:
+      files:
+        - uv.lock
+    paths:
+      - $UV_CACHE_DIR
+  image: ghcr.io/astral-sh/uv:$UV_VERSION-python$PYTHON_VERSION-$BASE_LAYER
+  before_script:
+    - uv sync --frozen # Environment syncing common to all jobs
+  after_script:
+    - uv cache prune --ci # Cache pruning common to all jobs
+
+
+# Default trigger rules: push to default branch or merge request. Do not trigger on
+# tags.
+.default_rules: &default_rules
+  - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+  - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+  - if: $CI_COMMIT_TAG
+    when: never
+
+# Testing trigger rules: to avoid unnecessary testing on simple changes to the default
+# branch (e.g. fixing typos in documentation), we only test on the default branch if the
+# changes are made to package files or testing files
+.testing_rules: &testing_rules
+  - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PIPELINE_SOURCE != "merge_request_event"
+    changes:
+      - pyproject.toml
+      - uv.lock
+
+      - "src/TRIPs/**/*"
+  - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+  - if: $CI_COMMIT_TAG
+    when: never
+
+# Trigger rules for semantic version tags of the type (v)x(.x)(.x) used for deployment
+.tag_rules: &tag_rules
+  - if: $CI_COMMIT_TAG =~ /^v?(\d+\.)?(\d+\.)?(\*|\d+)$/
+
+quality:
+  cache:
+    <<: *global_cache # Inherit global cache settings
+    key: $PRE_COMMIT_KEY
+    paths:
+      - .cache/pre-commit
+  stage: quality
+  rules: *default_rules
+  script:
+
+    - uvx --from go-task-bin task check
+
+
+
+mypy:
+  stage: test
+  rules: *testing_rules
+  script:
+
+    - uvx --from go-task-bin task mypy
+
+  allow_failure: true
+
+
+
+
+test:
+  stage: test
+  rules: *testing_rules
+
+  parallel:
+    matrix:
+      - PYTHON_VERSION: ["3.10", "3.11", "3.12", "3.13"]
+  script:
+    - uvx --from go-task-bin task test
+
+
+  coverage: /TOTAL.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+
+
+
+docs:
+  stage: docs
+  rules: *default_rules
+  script:
+
+    - uvx --from go-task-bin task docs
+
+
+deploy-pages:
+  stage: deploy
+  rules: *tag_rules
+  script:
+
+    - uvx --from go-task-bin task docs
+
+  pages: true
+

.gitleaks.toml

@@ -0,0 +1,14 @@
+# See https://github.com/gitleaks/gitleaks?tab=readme-ov-file#configuration
+
+[extend]
+useDefault = true
+
+[[rules]]
+id = "SLURM account"
+description = "SLURM account"
+regex = '''#SBATCH --account=(\w+)'''
+
+[[rules]]
+id = "SLURM email"
+description = "SLURM email"
+regex = '''#SBATCH --mail-user=(\w+)'''

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.0
+    hooks:
+      - id: ruff
+        args: [--exit-non-zero-on-fix, --config=pyproject.toml]
+      - id: ruff-format
+        args: [--config=pyproject.toml]
+
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.24.0
+    hooks:
+      - id: gitleaks