Add documentation for all scripts: bootstrap_setup, buildnote, most_recent_note, notetaker, kaggle_manager, promodoro, promodoro_menu, setup_crontab, add_ipykernel, get_app_id, setup_macos_dock

docs/add_ipykernel/Usage.md

@@ -0,0 +1,59 @@
+## [add_ipykernel](../../scripts/add_ipykernel)
+
+Adds Python virtual environments as Jupyter ipykernel options.
+
+## Description
+
+This script automates the creation and registration of Python environments as Jupyter kernels. It supports both conda and pip virtual environments.
+
+## Usage
+
+```bash
+./add_ipykernel.sh ENV_NAME [--create] [--verbose] [pkg1 pkg2 ...]
+```
+
+## Arguments
+
+- `ENV_NAME`: Name of the environment/kernel to create or use
+- `--create`: Create a new environment if it doesn't exist
+- `--verbose`: Enable detailed output
+- `pkg1 pkg2 ...`: Additional packages to install
+
+## Examples
+
+```bash
+# Create new conda environment and register as kernel
+./add_ipykernel.sh ds_env --create python=3.11 pandas
+
+# Use existing environment
+./add_ipykernel.sh ds_env --verbose
+
+# Create pip venv with specific packages
+./add_ipykernel.sh myproject --create numpy scipy matplotlib
+```
+
+## Package Manager Detection
+
+The script automatically detects the appropriate package manager:
+
+- **conda**: Used if environment exists in conda or if `environment.yml`/`conda.yaml` is present
+- **pip**: Used if `requirements.txt` or `pyproject.toml` exists, or if already in a virtual environment
+
+## What It Does
+
+1. Detects package manager (conda or pip)
+2. Creates environment if `--create` flag is used
+3. Activates the environment
+4. Installs `ipykernel` if not present
+5. Registers the environment as a Jupyter kernel with display name `Python (ENV_NAME)`
+
+## Requirements
+
+- conda (for conda environments) OR python3 with venv (for pip environments)
+- Jupyter installed (for kernel registration)
+
+## Notes
+
+- Kernels are registered in user space (`--user` flag)
+- After registration, the kernel appears in Jupyter as "Python (ENV_NAME)"
+- If environment already exists, just registers it without modifying packages

docs/bootstrap_setup/Usage.md

@@ -0,0 +1,54 @@
+## [bootstrap_setup](../../scripts/bootstrap_setup)
+
+Bootstraps a new development machine by installing essential tools and setting up the development environment.
+
+## Description
+
+This script automates the initial setup of a new development machine by:
+- Installing essential tools (git, stow, curl)
+- Installing package manager (Homebrew on macOS)
+- Cloning the dotfiles repository
+- Setting up development scripts
+
+**Platform Support:** macOS (Homebrew), Linux (apt)
+
+## Usage
+
+```bash
+./bootstrap_setup.sh [--dry-run]
+```
+
+## Options
+
+- `--dry-run`: Enable dry run mode. Commands will be echoed but not executed.
+
+## What It Does
+
+1. **Installs essential tools:**
+   - Linux: `apt update && apt install -y git stow curl`
+   - macOS: Installs Xcode Command Line Tools, Homebrew, then `brew install stow git curl`
+
+2. **Clones dotfiles repository:**
+   - Clones `https://github.com/jfrays/dotfiles.git` to `~/.dotfiles`
+   - Runs the dotfiles setup script
+
+3. **Sets up development scripts:**
+   - Creates `~/.local/bin/scripts` directory
+   - Clones scripts repository to the scripts directory
+   - Runs `setup_dev_env.sh` to complete the environment setup
+
+## Example
+
+```bash
+# Run the bootstrap normally
+./bootstrap_setup.sh
+
+# Preview what would happen without making changes
+./bootstrap_setup.sh --dry-run
+```
+
+## Notes
+
+- The script uses `set -e` to exit immediately if any command fails
+- Ensure you have sudo access on Linux systems
+- On macOS, you may need to approve Xcode license after command line tools installation

docs/buildnote/Usage.md

@@ -0,0 +1,55 @@
+## [buildnote](../../scripts/buildnote)
+
+Converts markdown notes to PDF using pandoc with xelatex engine.
+
+## Description
+
+This script generates professionally formatted PDF documents from markdown files. It uses pandoc with the xelatex PDF engine and applies syntax highlighting, custom fonts, and margins.
+
+## Dependencies
+
+- pandoc
+- xelatex (TeX Live)
+- DejaVu fonts (DejaVuSerif, DejaVuSans, DejaVuSansMono)
+
+## Usage
+
+```bash
+./buildnote.sh <input_file> <output_file>
+```
+
+## Arguments
+
+- `input_file`: Path to the markdown file to convert
+- `output_file`: Path for the generated PDF file
+
+## Features
+
+- **PDF Engine**: xelatex for Unicode and custom font support
+- **Syntax Highlighting**: pygments style for code blocks
+- **Fonts**:
+  - Main: DejaVuSerif (with Bold, Italic, BoldItalic variants)
+  - Sans: DejaVuSans
+  - Mono: DejaVuSansMono
+- **Margins**: 1 inch on all sides
+- **Links**: NavyBlue color for URLs
+
+## Example
+
+```bash
+# Convert a markdown note to PDF
+./buildnote.sh notes.md output.pdf
+
+# The script runs in background and prints the output path
+./buildnote.sh ~/notes/daily.md ~/notes/daily.pdf
+```
+
+## Integration with Neovim
+
+The script is designed to work with Neovim. It prints the output file path on the last line, which can be captured by editor integrations.
+
+## Notes
+
+- The conversion runs in the background (using `&`)
+- Ensure all dependencies are installed before running
+- The script validates that the input file exists before processing

docs/get_app_id/Usage.md

@@ -0,0 +1,62 @@
+## [get_app_id](../../scripts/get_app_id)
+
+Retrieves macOS application bundle identifiers.
+
+## Description
+
+This script extracts the code-signing identifier (bundle ID) from macOS application bundles. Useful for automation, scripting, and identifying applications programmatically.
+
+## Platform
+
+**macOS only** - Uses `codesign` command which is macOS-specific
+
+## Usage
+
+```bash
+./get_app_id.sh [app_name|app_path]
+```
+
+## Arguments
+
+- `app_name`: Name of the app (e.g., "Safari" or "Safari.app")
+- `app_path`: Full path to the .app bundle (e.g., "/Applications/Safari.app")
+
+## Examples
+
+```bash
+# Interactive mode - select from all applications using fzf
+./get_app_id.sh
+
+# Get bundle ID by app name
+./get_app_id.sh Safari
+
+# Get bundle ID by full path
+./get_app_id.sh /Applications/Safari.app
+
+# Output: com.apple.Safari
+```
+
+## Interactive Mode
+
+When run without arguments, the script:
+1. Lists all applications in `/Applications`
+2. Opens an fzf picker with live preview showing the bundle ID
+3. Returns the selected app's identifier
+
+## Requirements
+
+- macOS with `codesign` command (included in Xcode Command Line Tools)
+- fzf (for interactive mode): `brew install fzf`
+
+## How It Works
+
+The script extracts the identifier from the code signature using:
+```bash
+codesign -dr - "/Applications/AppName.app" | grep identifier
+```
+
+## Notes
+
+- Apps must be code-signed to have a bundle identifier
+- Some apps may not have code signatures (returns error)
+- The interactive preview shows "No code signature found" for unsigned apps

docs/kaggle_manager/Usage.md

@@ -0,0 +1,63 @@
+## [kaggle_manager](../../scripts/kaggle_manager)
+
+Manages Kaggle datasets and notebooks via the Kaggle API.
+
+## Description
+
+This script provides command-line access to Kaggle functionality including:
+- Downloading datasets
+- Fetching notebooks
+- Submitting competition entries
+
+## Prerequisites
+
+You must have a `kaggle.json` file at `~/.kaggle/kaggle.json` containing your Kaggle credentials:
+```json
+{
+  "username": "your_username",
+  "key": "your_api_key"
+}
+```
+
+## Usage
+
+```bash
+./kaggle_manager.sh [options]
+```
+
+## Options
+
+- `-d, --dataset <name>`: Download a dataset (format: `username/dataset-name`)
+- `-n, --notebook <name>`: Download a notebook (format: `username/notebook-name`)
+- `-s, --submit <file>`: Submit a notebook file to a competition
+- `-c, --competition <name>`: Specify competition name for submission
+- `-g, --git`: Add and commit changes to Git after operation
+- `-v, --verbose`: Enable verbose output
+- `-h, --help`: Display help message
+
+## Examples
+
+```bash
+# Download a dataset
+./kaggle_manager.sh -d "zillow/zecon"
+
+# Download a notebook
+./kaggle_manager.sh -n "jfraeys/my-notebook"
+
+# Submit to competition
+./kaggle_manager.sh -s submission.csv -c "titanic"
+
+# Download with Git commit
+./kaggle_manager.sh -d "zillow/zecon" -g
+```
+
+## Directory Structure
+
+- Datasets: Stored in `data/raw/`
+- Notebooks: Stored in `notebooks/`
+
+## Notes
+
+- The script uses curl to interact with the Kaggle API
+- Credentials are extracted from kaggle.json using jq
+- Git commits use the message: "Added dataset or notebook"

docs/most_recent_note/Usage.md

@@ -0,0 +1,29 @@
+## [most_recent_note](../../scripts/most_recent_note)
+
+Opens the most recently created PDF note from the Google Drive notes folder.
+
+## Description
+
+This script finds the most recently modified PDF file in `~/Google Drive/My Drive/notes/pdf` and opens it with zathura PDF viewer.
+
+## Dependencies
+
+- zathura (PDF viewer)
+
+## Usage
+
+```bash
+./most_recent_note.sh
+```
+
+## How It Works
+
+1. Searches for all PDF files in `~/Google Drive/My Drive/notes/pdf`
+2. Sorts them by modification time (newest first)
+3. Opens the most recent PDF with zathura
+
+## Notes
+
+- Requires Google Drive to be synced to the local machine
+- Assumes notes are stored in the specific path: `~/Google Drive/My Drive/notes/pdf`
+- zathura must be installed and available in PATH

docs/notetaker/Usage.md

@@ -0,0 +1,44 @@
+## [notetaker](../../scripts/notetaker)
+
+Creates and opens daily markdown notes with YAML frontmatter in Neovim.
+
+## Description
+
+This script automates the creation of daily notes by:
+- Creating a markdown file for the current date if it doesn't exist
+- Adding YAML frontmatter with title, author, and date
+- Opening the file in Neovim with automatic timestamp insertion
+
+## Usage
+
+```bash
+./notetaker.sh
+```
+
+## File Location
+
+Notes are stored in: `~/Google Drive/My Drive/notes/src/note-YYYY-MM-DD.md`
+
+## YAML Frontmatter
+
+New notes are created with the following frontmatter:
+```yaml
+---
+title: "Notes"
+author: "Jeremie Fraeys"
+date: YYYY-MM-DD
+---
+```
+
+## Neovim Integration
+
+When opening the note, Neovim is configured to:
+- Jump to the end of the file
+- Insert a timestamped subtitle (e.g., `## 14:30`)
+- Enter insert mode ready for typing
+
+## Notes
+
+- Google Drive sync is required for notes to be backed up
+- The script creates the note file if it doesn't exist, or opens the existing one
+- Requires Neovim to be installed and available in PATH

docs/promodoro/Usage.md

@@ -0,0 +1,29 @@
+## [promodoro](../../scripts/promodoro)
+
+Pomodoro timer script for productivity tracking.
+
+## Description
+
+A simple Pomodoro timer implementation that helps track work sessions using the Pomodoro Technique - alternating focused work periods with short breaks.
+
+## Usage
+
+```bash
+./promodoro.sh [options]
+```
+
+## Features
+
+- Customizable work and break durations
+- Visual/audible notifications when sessions end
+- Tracks completed pomodoros
+- Session logging
+
+## Integration
+
+Use with `promodoro_menu.sh` for an interactive menu interface.
+
+## Notes
+
+- Designed to run in terminal or tmux status bar
+- Can be customized for different work/break ratios

docs/promodoro_menu/Usage.md

@@ -0,0 +1,29 @@
+## [promodoro_menu](../../scripts/promodoro_menu)
+
+Interactive menu interface for the Pomodoro timer.
+
+## Description
+
+Provides a user-friendly menu interface for controlling the Pomodoro timer, allowing easy start, stop, and configuration of work sessions.
+
+## Usage
+
+```bash
+./promodoro_menu.sh
+```
+
+## Features
+
+- Interactive menu for Pomodoro timer control
+- Options to start/stop/reset timer
+- Configuration of work and break durations
+- Status display
+
+## Integration
+
+Works with `promodoro.sh` for the actual timing functionality.
+
+## Notes
+
+- Provides a more user-friendly interface than the command-line timer
+- Can be run in terminal or integrated with dmenu/rofi for desktop environments

docs/setup_crontab/Usage.md

@@ -0,0 +1,63 @@
+## [setup_crontab](../../scripts/setup_crontab)
+
+Sets up automated cron jobs from a configuration file.
+
+## Description
+
+This script manages cron jobs by reading from `mycronjobs.txt` and merging them into the system crontab. It intelligently avoids duplicate entries and ensures the cron service is running.
+
+## Usage
+
+```bash
+./setup_crontab.sh
+```
+
+## Configuration File
+
+The script expects a cron job definition file at:
+`~/.local/bin/mycronjobs.txt`
+
+Example `mycronjobs.txt`:
+```
+# Daily backup at 2 AM
+0 2 * * * /home/user/.local/bin/backup.sh
+
+# Weekly cleanup on Sundays
+0 0 * * 0 /home/user/.local/bin/cleanup.sh
+```
+
+## Features
+
+- **Smart Merging**: Only adds new jobs, skips existing duplicates
+- **Comments Support**: Lines starting with `#` are ignored
+- **Service Management**: Automatically starts cron service on Linux
+- **Cross-Platform**: Works on Linux (systemd) and macOS (launchd)
+
+## Platform Behavior
+
+### Linux
+- Starts cron via `systemctl` if not running
+- Uses standard crontab
+
+### macOS
+- Uses launchd (cron runs automatically)
+- No additional service management needed
+
+## Example Output
+
+```
+✅  Added 2 new cron job(s):
+   + 0 2 * * * /home/user/.local/bin/backup.sh
+   + 0 0 * * 0 /home/user/.local/bin/cleanup.sh
+```
+
+Or if jobs already exist:
+```
+ℹ️  No new cron jobs to add; all jobs already present.
+```
+
+## Notes
+
+- The script uses `set -euo pipefail` for strict error handling
+- Existing crontab entries are preserved
+- Empty lines are ignored during processing

docs/setup_macos_dock/Usage.md

@@ -0,0 +1,58 @@
+## [setup_macos_dock](../../scripts/setup_macos_dock)
+
+Configures macOS Dock settings and populates it with preferred applications.
+
+## Platform
+
+**macOS only** - Uses `defaults` and `dockutil`
+
+## Description
+
+This script automates the configuration of the macOS Dock by:
+- Setting visual preferences (auto-hide, size, magnification)
+- Removing all existing Dock items
+- Adding a curated list of frequently used applications
+- Restarting the Dock to apply changes
+
+## Usage
+
+```bash
+./setup_macos_dock.sh
+```
+
+## Dock Settings Applied
+
+| Setting | Value | Description |
+|---------|-------|-------------|
+| autohide | true | Dock hides automatically |
+| tilesize | 50 | Icon size (pixels) |
+| largesize | 64 | Magnified icon size |
+| magnification | false | Disable icon magnification |
+| orientation | bottom | Dock position |
+| mineffect | "" | Minimize effect (none) |
+| NSAutomaticWindowAnimationsEnabled | false | Disable window animations |
+
+## Default Applications
+
+The script adds these apps to the Dock (in order):
+1. Mail.app
+2. Messages.app
+3. WezTerm.app
+4. Obsidian.app
+5. Zen.app
+6. System Settings.app
+
+## Requirements
+
+- macOS
+- dockutil: `brew install dockutil` (script auto-installs if missing)
+
+## Warning
+
+**This script removes ALL existing Dock items** before adding the preferred applications. Your current Dock configuration will be replaced.
+
+## Notes
+
+- The Dock automatically restarts after configuration
+- System Settings may be called "System Preferences" on older macOS versions
+- Edit the script to customize the list of applications