Initial commit

.editorconfig

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+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[makefile]
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+indent_style = tab
+indent_size = 4

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: bug
+assignees: ""
+---
+
+<!-- Describe the bug -->
+
+## Description
+
+[TEXT HERE]
+
+<!-- To reproduce -->
+
+```python
+# Your code here
+```
+
+<!-- Put your Error output in this code block (if applicable, else delete the block): -->
+
+<details> <summary> Error output </summary>
+
+```pytb
+# Paste the error output here, if applicable
+```
+
+</details>
+
+## Versions
+
+<details> <summary> Versions </summary>
+
+```pytb
+# Paste the ouput of tradeseq.__version__ and all relevant versions here
+```
+
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: enhancement
+assignees: ""
+---
+
+## Description
+
+**Is your feature request related to a problem? Please describe.**
+
+<!-- A clear and concise description of what the problem is. For example: I need to do [...] which is not possible because [...]. -->
+
+**Describe the solution you are looking for.**
+
+<!-- A clear and concise description of what you want to happen. -->

.github/pull_request_template.md

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+## Changes
+
+<!-- Please remove section if this PR does change an existing feature -->
+
+-   ...
+
+## Bug fixes
+
+<!-- Please give section if this PR does not fix any bugs -->
+
+-   ...
+
+## New
+
+<!-- Please give section if this PR does not implement a new feature -->
+
+-   ...
+
+## Related issues
+
+<!-- Please list related issues. If none exist, open one and reference it here. -->
+
+Closes #

.github/workflows/book.yml

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+name: deploy-jupyter-book
+
+on:
+    push:
+        branches:
+            - main
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+    deploy-book:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+
+            # Install dependencies
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+
+            - name: Install dependencies
+              run: |
+                  pip install jupyter-book
+            # Build the book
+            - name: Build the book
+              run: |
+                  jupyter-book build notebooks
+            # Push the book's HTML to github-pages
+            - name: GitHub Pages action
+              uses: peaceiris/[email protected]
+              with:
+                  github_token: ${{ secrets.GITHUB_TOKEN }}
+                  publish_dir: notebooks/_build/html

.github/workflows/lint.yml

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+name: Lint
+
+on:
+    push:
+        branches: main
+    pull_request:
+        branches: main
+
+jobs:
+    linting:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v3
+            - name: Setup Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install pre-commit
+            - name: Check pre-commit compatibility
+              run: pre-commit run --all-files --show-diff-on-failure

.gitignore

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+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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
+
+# Pyre type checker
+.pyre/
+
+# patterns to prevent data and figures from being uploaded
+*.csv
+*.pickle
+*.h5ad
+*.RData
+*.loom
+*.pdf
+*.eps
+*.png
+*.jpg
+*.jpeg
+*.svg
+*.mtx
+*.txt
+*.rds
+*.npz
+*.h5
+*.txt.gz
+*.gmt
+*.gmx
+
+data/
+figures/
+
+# OS specifics
+**.DS_Store
+
+# R stuff
+*.Rhistory
+
+.vscode/*

.pre-commit-config.yaml

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+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/mwouts/jupytext
+      rev: v1.14.5
+      hooks:
+          - id: jupytext
+            args:
+                [--from, ipynb, --sync, --pipe, black, --pipe-fmt, "py:percent"]
+            additional_dependencies:
+                - black==23.1.0 # Matches hook
+    - repo: https://github.com/psf/black
+      rev: "23.1.0"
+      hooks:
+          - id: black-jupyter
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.4
+      hooks:
+          - id: prettier
+            # Newer versions of node don't work on systems that have an older version of GLIBC
+            # (in particular Ubuntu 18.04 and Centos 7)
+            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+            # https://github.com/jupyterlab/jupyterlab/issues/12675
+            language_version: "17.9.1"
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.253
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: detect-private-key
+          - id: check-ast
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+          - id: check-case-conflict
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'