TCY

Tsv → Conda YML

TCY is a lightweight tool for generating reproducible Conda environment .yml files from a documented .tsv (spreadsheet-style) input file. Instead of maintaining opaque YAML files, TCY lets you document the why, what, and where of every package—while still producing Conda-ready environment definitions.

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Why TCY?

Conda environment files are great for reproducibility, but they have limitations:

• ❓ Why was a package included?
• 📦 What does it do?
• 🖥️ Does it work on Linux, macOS, and Windows?
• ⚠️ Are there known platform-specific bugs?

Spreadsheet formats (like .tsv) are much better for documentation, annotations, and validation. TCY bridges this gap by letting you maintain a richly documented package list and exporting it into valid Conda .yml files.

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Recommended Workflow (Using This Repository as a Template)

The easiest way to use TCY is to create your own repository from this template.

Why use the template?

1. Your package documentation lives in a GitHub repository and is accessible from anywhere.
2. Conda environment solving can be slow. This workflow offloads that work to GitHub Actions, producing pre-solved environment files that you can create locally in seconds.

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Step-by-Step Setup

1. Create a new repository
   Click “Use this template” in the upper right of this repository.

2. Allow GitHub Actions to push changes
   Go to:
   Settings → Actions → General → Workflow permissions
   Enable “Read and write permissions”.

3. Clone your repository locally

4. Edit the package list
   Modify environments/packages.tsv.

5. Push your changes
   This triggers a GitHub Actions workflow that validates the TSV file and generates OS-specific solved .yml files.

6. Pull the generated files

7. Create your Conda environment

   conda env create -f ubuntu-latest_solved.yml
   

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What goes into the packages.tsv file?

The input spreadsheet file must contain the following columns:

Column name	Description
package_name	The official name of the package.
version	May be left empty, or may specify the package version using the package match specification syntax.
package_manager	Must be one of: pip, conda, or cran.
conda_channel	May be left empty if the package manager is pip or cran, but must contain the name of the conda channel to install from if the package manager is conda.
include	Must be either true or false.
language	Must be one of: python, r, or julia.
bug_flag	May be left empty, or must be one of: linux, windows, or cross_platform.

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🛠️🛠️ Only For Developers 🛠️🛠️

Installation

pip install tcy

TCY can be used both as a Python library and a command-line application.

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Using TCY as a Python Library

from tcy import run

The run function allows you to generate Conda .yml files programmatically inside your own codebase.

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Using TCY as a Command-Line Application

tcy {linux|windows} [OPTIONS]

Required positional argument

• {linux,windows}
  Target operating system for which the environment file is generated.
  Packages flagged as incompatible with this OS are excluded.
  Packages flagged as cross_platform are never included.

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CLI Options

Option	Description
--yml_name	Sets the name: field in the .yml file
--yml_file_name	Output filename (default: environment.yml)
--pip_requirements_file	Write pip packages to requirements.txt
--write_conda_channels	Inline channels (e.g. conda-forge::numpy)
--tsv_path	Path to .tsv file (default: packages.tsv)
--yml_dir	Output directory
--cran_installation_script	Generate install_cran_packages.sh
--cran_mirror	CRAN mirror URL (default: https://cloud.r-project.org)
--languages	Filter by python, r, julia, or all

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Automatic Validation of packages.tsv

This repository includes a testing pipeline that checks the integrity of, and the validity of entries in, the packages.tsv file. Which tests are executed is determined by the test_configs.json file. Each test corresponds to a key in this JSON file. If the corresponding value is set to null, the test is not executed.

Below is an explanation of each test and the rules for how the values should be provided if the test is enabled.

key	value	description
valid_columns	list of column names	The TSV file must contain only these columns, and they must appear in this exact order.
filled_out_columns	list of column names	Cells in these columns must not contain NaN values; every row in these columns must contain a value.
valid_options	dict with column names as keys and lists of valid options as values	Cells in these columns must contain only the one the specified valid options.
column_dependencies	dict with column names as keys and lists of other columns as values	If a cell in this column is filled, the corresponding cells in the specified other column(s) must also be filled.
conditional_column_dependencies	dict of dicts of lists	If a cell in this column has a specific value, the corresponding cells in the specified other column(s) must be filled.
multi_option_columns	dict with column names as keys and lists of valid options as values	Cells in these columns must contain only a set of these valid options, separated by commas.

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CRAN Packages (Experimental)

Some R packages are not available via Conda.

TCY can generate an install_cran_packages.sh script that should:

1. Activate the Conda environment
2. Start R
3. Install CRAN packages inside this environment using install.packages()