pydeps2env 1.4.1

A python helper to generate conda environment files from project dependencies.

pydeps2env

An easy way to create conda environment files from you python project dependencies.
Creates a conda environment.yml file from python package dependencies listed in on or multiple different source formats like pyproject.toml, setup.cfg, environment.yaml or requirements.txt files.

The project contains

• GitHub action
• python package
• command line script

flowchart LR
    pyproject.toml --> pydeps2env
    setup.cfg --> pydeps2env
    environment.yaml --> pydeps2env
    requirements.txt --> pydeps2env
    pydeps2env --> E2[environment.yaml]
    pydeps2env --> R2[requirements.txt]

basic usage (GitHub action)

By default, the action will parse a pyproject.toml file in your root directory into environment.yml. Here is an example of a simple setup:

steps:
  - uses: CagtayFabry/pydeps2env@v1.0.0

[project]
requires-python = ">=3.8,<3.10"
dependencies = [
    "numpy >=1.20",
    "pandas >=1.0",
    "IPython",
    "boltons",
]
[project.optional-dependencies]
test = ["pytest"]
pip_only = ["bidict"]

The default parameters will output this sorted environment.yml (note that the python dependency specification will always be the first item on the list):

channels:
  - defaults
dependencies:
  - python>=3.8,<3.10
  - boltons
  - IPython
  - numpy>=1.20
  - pandas>=1.0

A full output with options --build_system include --extras test pip_only --pip bidict

channels:
  - defaults
dependencies:
  - python>=3.8,<3.10
  - boltons
  - IPython
  - numpy>=1.20
  - pandas>=1.0
  - pytest
  - setuptools>=40.9.0
  - setuptools_scm
  - wheel
  - pip:
    - bidict

basic usage (python)

Create an Environment using Python and export it to an environment.yaml file.

from pydeps2env import Environment

env = Environment("./test/pyproject.toml[doc]")
env.export("my_environment.yaml")

basic usage (command line)

Combine multiple source files into a single environment file (including build dependencies). Install pandas using pip.

pydeps2env ./test/setup.cfg ./test/pyproject.toml[doc] ./test/environment.yaml ./test/requirements.txt -o output.yaml -c defaults --extras test -b include --pip pandas

advanced usage (definition file)

Users can store complex configurations in a single yaml file and create the desired output using create_from_definition. Example definition file:

# the target file to create
output: test-configuration.yaml
# default name of the environment
name: test-env
# conda channels to include
channels:
- conda-forge
- defaults
# list of source files that define sub environments
# these will be loaded as Environment()
sources:
- ./test/environment.yaml
- ./test/local.yaml
- ./test/pyproject.toml[doc]
- ./test/requirements.txt
- https://github.com/CagtayFabry/pydeps2env/blob/custom_deps/pyproject.toml
# extras to apply to all sources and packages
extras:
- test
# dependencies that should be removed after collection
remove:
- pyyaml
additional_requirements:
- urllib3
# include build system dependencies
# list of dependencies that must be pip installed (excluding auto-sorted depedencies like urls)
pip:
- urllib3
include_build_system: include

configuration options (GitHub action)

To customize the output the input options are available to the action:

files

Specify the location of the dependencies files to parse. (defaults to 'pyproject.toml') Multiple files can be listed. This will result in a combined environment file.

output:

Specify the location and name of the conda environment file to generate. (defaults to 'environment.yml')

channels:

List the conda channels to include in the environment file. (defaults to 'conda-forge') Separate a list of multiple channels by spaces (e.g. 'conda-forge defaults').

extras:

Specify one or more optional [extras_require] sections to add to all the environments (e.g. 'test' to include package that you would normally install with pip install pkg[test]). Note that for individual packages, the [extra]` syntax is also possible.

build_system:

If set to 'include' the dependencies listed under [build-system] (or [options:setup_requires] in setup.cfg) will be added to the environment (default is 'omit' so no setup dependencies will be installed).

pip

List of packages to install via pip instead of conda. The dependencies will be listed under the pip: section in the environment file. If a dependency is listed with its URN, it will always be installed via pip (e.g. pydeps2env @ git+https://github.com/CagtayFabry/pydeps2env)

example

steps:
  - uses: CagtayFabry/pydeps2env@v1.0.0
    with:
      files: ./test/pyproject.toml[doc] ./test/setup.cfg # comine both files, add [doc] only for pyproject.toml
      output: 'environment_test.yml'
      channels: 'conda-forge defaults'
      extras: 'test'
      build_system: 'include'
      pip: 'bidict'

[project]
requires-python = ">=3.8,<3.10"
dependencies = [
    "numpy >=1.20",
    "pandas >=1.0",
    "IPython",
    "boltons",
]
[project.optional-dependencies]
test = ["pytest"]
pip_only = ["bidict"]

channels:
  - conda-forge
  - defaults
dependencies:
  - python>=3.8,<3.10
  - boltons
  - IPython
  - numpy>=1.20
  - pandas>=1.0
  - pytest
  - setuptools>=40.9.0
  - setuptools_scm
  - sphinx
  - wheel
  - pip:
    - bidict