copier.yml.backup

_subdirectory: template

# Post-generation tasks
_tasks:
  - command: git init
    description: "Initialize Git repository"
  - command: |
      if [ "{{ author_name }}" != "Your Name" ]; then
        git config user.name "{{ author_name }}"
      fi
      if [ "{{ author_email }}" != "your.email@example.com" ]; then
        git config user.email "{{ author_email }}"
      fi
    description: "Configure Git user information"
  - command: git add .
    description: "Stage all files for initial commit"
  - command: git commit -m "Initial commit from template-analysis-and-writeup"
    description: "Create initial commit with project metadata"

# Basic Project Information
project_name:
  type: str
  help: What is your project name?
  validator: >-
    {% if not project_name %}
    Project name is required
    {% endif %}

short_name:
  type: str
  help: What is your project's short name? (used for file naming)
  validator: >-
    {% if not short_name %}
    Short name is required
    {% elif ' ' in short_name %}
    Short name cannot contain spaces
    {% endif %}

description:
  type: str
  help: Brief description of the project
  default: A comprehensive data science analysis project

# Author Information
author_name:
  type: str
  help: Your name or team name
  default: "Your Name"

author_email:
  type: str
  help: Contact email for the project
  default: "your.email@example.com"

# === PROJECT STRUCTURE SELECTION ===
project_type:
  type: str
  help: What type of project are you creating?
  choices:
    - Minimal Starter (notebooks + basic writeup)
    - Full Academic Project (analysis + writeup)
    - Analysis Only (data science pipeline)
    - Manuscript Only (writing and publications)
    - Package Development (software/library)
    - Custom (choose components manually)
  default: Minimal Starter (notebooks + basic writeup)

# === PRINCIPAL FOLDER SELECTION ===
# These will be auto-calculated based on project_type
include_analysis:
  type: bool
  help: Include analysis folder (notebooks, scripts, data pipeline)
  default: true
  when: "{{ project_type == 'Custom (choose components manually)' }}"

include_writeup:
  type: bool
  help: Include writeup folder (manuscripts, presentations, grants, reports)
  default: true
  when: "{{ project_type == 'Custom (choose components manually)' }}"

include_infrastructure:
  type: bool
  help: Include infrastructure folder (Docker, cloud deployment, CI/CD)
  default: true
  when: "{{ project_type == 'Custom (choose components manually)' }}"

include_misc:
  type: bool
  help: Include misc folder (utilities, legacy code, experimental features)
  default: true
  when: "{{ project_type == 'Custom (choose components manually)' }}"

# Project Configuration
programming_language:
  type: str
  help: Primary programming language
  choices:
    - Python
    - R
    - Both
  default: Python

python_version:
  type: str
  help: Python version to use
  default: "3.11"
  when: "{{ programming_language in ['Python', 'Both'] }}"

# Analysis Components
include_eda_templates:
  type: bool
  help: Include exploratory data analysis templates
  default: true

include_statistical_analysis:
  type: bool
  help: Include statistical analysis templates
  default: true

include_ml_components:
  type: bool
  help: Include machine learning workflow templates
  default: true

# Data Management
data_versioning:
  type: bool
  help: Include DVC setup for data versioning
  default: false

data_validation:
  type: bool
  help: Include data validation frameworks (Great Expectations, Pandera)
  default: false

# Documentation and Reporting
documentation_format:
  type: str
  help: Primary documentation format
  choices:
    - Markdown
    - Jupyter Notebooks
    - Quarto
    - RMarkdown
  default: Jupyter Notebooks

include_publication_templates:
  type: bool
  help: Include academic publication templates
  default: false

# Experiment Tracking
experiment_tracking:
  type: str
  help: Experiment tracking platform
  choices:
    - None
    - MLflow
    - Weights & Biases
    - Neptune
  default: None

# CI/CD and Automation
github_actions:
  type: bool
  help: Add GitHub Actions workflows
  default: false

pre_commit_hooks:
  type: bool
  help: Configure pre-commit hooks for code quality
  default: false

# Deployment Options
include_deployment_templates:
  type: bool
  help: Include deployment templates (Docker, FastAPI, etc.)
  default: false

module_name:
  type: str
  help: Python module name (auto-generated from short_name)
  default: "{{ short_name|lower|replace(' ', '_')|replace('-', '_') }}"
  when: false  # Auto-generated, not user input

# === SUBCOMPONENT SELECTION FOR ANALYSIS ===
include_notebooks:
  type: bool
  help: Include structured notebook workflow (00-scratch to 10-iteration)
  default: true
  when: "{{ include_analysis }}"

include_scripts:
  type: bool
  help: Include production scripts directory (Python, R, shells)
  default: true
  when: "{{ include_analysis }}"

include_data_pipeline:
  type: bool
  help: Include data pipeline structure (01_raw to 08_reporting)
  default: true
  when: "{{ include_analysis }}"

include_testing:
  type: bool
  help: Include testing framework for data and models
  default: true
  when: "{{ include_analysis }}"

include_packages:
  type: bool
  help: Include local package development structure
  default: true
  when: "{{ include_analysis }}"

# === SUBCOMPONENT SELECTION FOR WRITEUP ===
include_manuscript:
  type: bool
  help: Include manuscript writing capabilities
  default: true
  when: "{{ include_writeup }}"

include_presentations:
  type: bool
  help: Include presentation templates and management
  default: true
  when: "{{ include_writeup }}"

include_grants:
  type: bool
  help: Include grant application management
  default: true
  when: "{{ include_writeup }}"

include_abstracts:
  type: bool
  help: Include abstract submission management
  default: true
  when: "{{ include_writeup }}"

include_posters:
  type: bool
  help: Include poster creation and management
  default: true
  when: "{{ include_writeup }}"

include_reports:
  type: bool
  help: Include technical report templates
  default: true
  when: "{{ include_writeup }}"

include_blog:
  type: bool
  help: Include blog post templates for informal writing
  default: true
  when: "{{ include_writeup }}"

# === INFRASTRUCTURE SUBCOMPONENTS ===
include_docker:
  type: bool
  help: Include Docker configuration
  default: true
  when: "{{ include_infrastructure }}"

include_cloud_deployment:
  type: bool
  help: Include cloud deployment templates (AWS, GCP, Azure)
  default: true
  when: "{{ include_infrastructure }}"

include_virtualization:
  type: bool
  help: Include VM and container orchestration
  default: true
  when: "{{ include_infrastructure }}"

include_automation:
  type: bool
  help: Include automation tools (GitHub Actions, etc.)
  default: true
  when: "{{ include_infrastructure }}"

# === VERSION CONTROL ENHANCEMENT ===
include_jujutsu:
  type: bool
  help: Include Jujutsu (jj) version control with Git backend for enhanced academic workflows
  default: false

include_fossil:
  type: bool
  help: Include Fossil SCM for self-contained archives and manuscript versioning
  default: false

use_hybrid_vcs:
  type: bool
  help: Use hybrid version control (Jujutsu + Fossil) for comprehensive research management
  default: false
  when: "{{ include_jujutsu and include_fossil }}"

# === AUTO-CONFIGURATION BASED ON PROJECT TYPE ===
# These variables auto-configure components based on the selected project_type

_computed_include_analysis:
  type: bool
  default: >
    {%- if project_type in ['Minimal Starter (notebooks + basic writeup)', 'Full Academic Project (analysis + writeup)', 'Analysis Only (data science pipeline)', 'Package Development (software/library)'] -%}
    true
    {%- elif project_type == 'Manuscript Only (writing and publications)' -%}
    false
    {%- else -%}
    {{ include_analysis }}
    {%- endif -%}
  when: false

_computed_include_writeup:
  type: bool
  default: >
    {%- if project_type in ['Minimal Starter (notebooks + basic writeup)', 'Full Academic Project (analysis + writeup)', 'Manuscript Only (writing and publications)'] -%}
    true
    {%- elif project_type in ['Analysis Only (data science pipeline)', 'Package Development (software/library)'] -%}
    false
    {%- else -%}
    {{ include_writeup }}
    {%- endif -%}
  when: false

_computed_include_infrastructure:
  type: bool
  default: >
    {%- if project_type == 'Full Academic Project (analysis + writeup)' -%}
    true
    {%- elif project_type in ['Minimal Starter (notebooks + basic writeup)', 'Analysis Only (data science pipeline)', 'Manuscript Only (writing and publications)', 'Package Development (software/library)'] -%}
    false
    {%- else -%}
    {{ include_infrastructure }}
    {%- endif -%}
  when: false

# === MINIMAL CONFIGURATION OVERRIDES ===
# For Minimal Starter, override complex features to be simpler

_minimal_notebooks_only:
  type: bool
  default: >
    {%- if project_type == 'Minimal Starter (notebooks + basic writeup)' -%}
    true
    {%- else -%}
    false
    {%- endif -%}
  when: false

_minimal_writeup_only:
  type: bool
  default: >
    {%- if project_type == 'Minimal Starter (notebooks + basic writeup)' -%}
    true
    {%- else -%}
    false
    {%- endif -%}
  when: false