pyproject2conda

A script to convert pyproject.toml dependencies to environment.yaml files.

Overview

The main goal of pyproject2conda is to provide a means to keep all basic dependency information, for both pip based and conda based environments, in pyproject.toml. I often use a mix of pip and conda when developing packages, and in my everyday workflow. Some packages just aren't available on both. If you use poetry, I'd highly recommend poetry2conda.

Features

• Simple comment based syntax to add information to dependencies when creating environment.yaml

Status

This package is actively used by the author, but is still very much a work in progress. Please feel free to create a pull request for wanted features and suggestions!

Quick start

Use one of the following to install pyproject2conda:

$ pip install pyproject2conda

or

$ conda install -c conda-forge pyproject2conda

If using pip, to install with rich and shellingham support, either install them your self, or use:

$ pip install pyproject2conda[all]

The conda-forge distribution of typer (which pyproject2conda uses) installs rich and shellingham by default.

Example usage

Basic usage

Consider the toml file test-pyproject.toml.

[project]
name = "hello"
requires-python = ">=3.8,<3.11"
dependencies = [
"athing", #
"bthing",
"cthing; python_version < '3.10'",
]

[project.optional-dependencies]
test = [
"pandas", #
"pytest",
]
dev-extras = ["matplotlib"]
dev = ["hello[test]", "hello[dev-extras]"]
dist-pypi = [
# this is intended to be parsed with --skip-package option
"setuptools",
"build",
]

[tool.pyproject2conda.dependencies]
athing = { pip = true }
bthing = { skip = true, packages = "bthing-conda" }
cthing = { channel = "conda-forge" }
pytest = { channel = "conda-forge" }
matplotlib = { skip = true, packages = [
"additional-thing; python_version < '3.9'",
"conda-matplotlib"
] }
build = { channel = "pip" }

# ...

Note the table [tool.pyproject2conda.dependencies]. This table takes as keys the dependency names from project.dependencies or project.optional-dependencies, and as values a mapping with keys:

• pip: if true, specify install via pip in environment.yaml file
• skip: if true, skip the dependency
• channel: conda-channel to use for this dependency
• packages: Additional packages to include in environment.yaml file

So, if we run the following, we get:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml
channels:
  - conda-forge
dependencies:
  - bthing-conda
  - conda-forge::cthing
  - pip
  - pip:
      - athing

By default, the python version is not included in the resulting conda output. To include the specification from pyproject.toml, use --python-include infer option:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml --python-include infer
channels:
  - conda-forge
dependencies:
  - python>=3.8,<3.11
  - bthing-conda
  - conda-forge::cthing
  - pip
  - pip:
      - athing

Specify python version

To specify a specific value of python in the output, pass a value with:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml --python-include \
    python=3.9
channels:
  - conda-forge
dependencies:
  - python=3.9
  - bthing-conda
  - conda-forge::cthing
  - pip
  - pip:
      - athing

Note that this is for including python in the resulting environment file.

You can also constrain packages by the python version using the standard pyproject.toml syntax "...; python_version < 'some-version-number'". For is parsed for both the pip packages and conda packages:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml --python-version 3.10
channels:
  - conda-forge
dependencies:
  - bthing-conda
  - pip
  - pip:
      - athing

It is common to want to specify the python version and include it in the resulting environment file. You could, for example use:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml --python-version 3.10 \
    --python-include python=3.10
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bthing-conda
  - pip
  - pip:
      - athing

Because this is common, you can also just pass the option -p/--python:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml --python 3.10
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bthing-conda
  - pip
  - pip:
      - athing

Adding extra conda dependencies and pip requirements

You can also add additional conda and pip dependencies with the flags -d/--deps and -r/--reqs, respectively. Adding the last example:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml -d dep -r req
channels:
  - conda-forge
dependencies:
  - bthing-conda
  - conda-forge::cthing
  - dep
  - pip
  - pip:
      - athing
      - req

These will also obey dependencies like dep:python_version<={version}. Pass the flags multiple times to pass multiple dependencies.

Command "aliases"

The name pyproject2conda can be a bit long to type. For this reason, the package also ships with the alias p2c, which has the exact same functionality. Additionally, the subcommands can be shortened to a unique match:

$ p2c y -f tests/data/test-pyproject.toml --python 3.10
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bthing-conda
  - pip
  - pip:
      - athing

You can also call with python -m pyproject2conda.

Installing extras

Given the extra dependency:

# ...
[project.optional-dependencies]
test = [
"pandas", #
"pytest",
]
dev-extras = ["matplotlib"]
dev = ["hello[test]", "hello[dev-extras]"]
dist-pypi = [
# this is intended to be parsed with --skip-package option
"setuptools",
"build",
]

# ...

and running the following gives:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml -e test
channels:
  - conda-forge
dependencies:
  - bthing-conda
  - conda-forge::cthing
  - conda-forge::pytest
  - pandas
  - pip
  - pip:
      - athing

pyproject2conda also works with self referenced dependencies:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml -e dev
channels:
  - conda-forge
dependencies:
  - additional-thing
  - bthing-conda
  - conda-forge::cthing
  - conda-forge::pytest
  - conda-matplotlib
  - pandas
  - pip
  - pip:
      - athing

Installing from dependency-groups

pyproject2conda also support the PEP 735 dependency-groups table. For example, if we have the follinging

# ...
[dependency-groups]
test = ["pandas", "pytest"]
dev-extras = ["matplotlib"]
dev = [{ include-group = "test" }, { include-group = "dev-extras" }]
dist-pypi = [
# this is intended to be parsed with --skip-package option
"setuptools",
"build",
]

# ...

Then, we can build a requirement file, specifying groups with -g/--group flag.

$ pyproject2conda yaml -f tests/data/test-pyproject-groups.toml --group dev
channels:
  - conda-forge
dependencies:
  - additional-thing
  - bthing-conda
  - conda-forge::cthing
  - conda-forge::pytest
  - conda-matplotlib
  - pandas
  - pip
  - pip:
      - athing

The advantage of using dependency-groups as opposed to package.optional-dependencies is that they work for non-package projects, and are not included in the metadata of distributed packages.

Header in output

By default, pyproject2conda includes a header in most output files to note that the files are auto generated. No header is included by default when writing to standard output. To override this behavior, pass --header/--noheader:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml --header
#
# This file is autogenerated by pyproject2conda
# with the following command:
#
#     $ pyproject2conda yaml -f tests/data/test-pyproject.toml --header
#
# You should not manually edit this file.
# Instead edit the corresponding pyproject.toml file.
#
channels:
  - conda-forge
dependencies:
  - bthing-conda
  - conda-forge::cthing
  - pip
  - pip:
      - athing

Usage within python

pyproject2conda can also be used within python:

>>> from pyproject2conda.requirements import ParseDepends
>>> p = ParseDepends.from_path("./tests/data/test-pyproject.toml")

# Basic environment
>>> print(p.to_conda_yaml(python_include="infer").strip())
channels:
  - conda-forge
dependencies:
  - python>=3.8,<3.11
  - bthing-conda
  - conda-forge::cthing
  - pip
  - pip:
      - athing

# Environment with extras
>>> print(p.to_conda_yaml(extras="test").strip())
channels:
  - conda-forge
dependencies:
  - bthing-conda
  - conda-forge::cthing
  - conda-forge::pytest
  - pandas
  - pip
  - pip:
      - athing

Configuration

pyproject2conda can be configured with a [tool.pyproject2conda] section in pyproject.toml. To specify conda channels use:

# ...
[tool.pyproject2conda]
channels = ['conda-forge']
# these are the same as the default values of `p2c project`
template_python = "py{py}-{env}"
template = "{env}"
style = "yaml"
# options
python = ["3.10"]
# Note that this is relative to the location of pyproject.toml
user_config = "config/userconfig.toml"
# These environments will be created with the package, package dependencies, and
# dependencies from groups or extras with environment name so the below is the
# same as
#
# [tool.pyproject2conda.envs.test]
# extras_or_groups = "test"
#
default_envs = ["test", "dev", "dist-pypi"]

[tool.pyproject2conda.envs.base]
style = ["requirements"]

# This will have no extras or groups
#
# A value of `extras = true` will would be equivalent to
# passing extras_or_groups = <env-name>
[tool.pyproject2conda.envs."test-extras"]
extras = ["test"]
style = ["yaml", "requirements"]

[[tool.pyproject2conda.overrides]]
envs = ['test-extras', "dist-pypi"]
skip_package = true

[[tool.pyproject2conda.overrides]]
envs = ["test", "test-extras"]
python = ["3.10", "3.11"]

Note that specifying channels at the command line overrides tool.pyproject2conda.channels.

You can also specify environments without the package dependences (those under project.dependencies) by passing the --skip-package flag. This is useful for defining environments for build, etc, that do not require the package be installed. For example:

# ...
dist-pypi = [
# this is intended to be parsed with --skip-package option
"setuptools",
"build",
]

[tool.pyproject2conda.dependencies]
athing = { pip = true }
bthing = { skip = true, packages = "bthing-conda" }
cthing = { channel = "conda-forge" }
pytest = { channel = "conda-forge" }
matplotlib = { skip = true, packages = [
"additional-thing; python_version < '3.9'",
"conda-matplotlib"
] }
build = { channel = "pip" }

# ...

These can be accessed using either of the following:

$ pyproject2conda yaml -f tests/data/test-pyproject.toml -e dist-pypi --skip- \
    package
channels:
  - conda-forge
dependencies:
  - setuptools
  - pip
  - pip:
      - build

or

>>> from pyproject2conda.requirements import ParseDepends
>>> p = ParseDepends.from_path("./tests/data/test-pyproject.toml")

# Basic environment
>>> print(p.to_conda_yaml(extras="dist-pypi", skip_package=True).strip())
channels:
  - conda-forge
dependencies:
  - setuptools
  - pip
  - pip:
      - build

Creating multiple environments from pyproject.toml

pyproject2conda provides a means to create all needed environment/requirement files in one go. We configure the environments using the pyproject.toml files in the [tool.pyproject2conda] section. For example, example the configuration:

# ...
[tool.pyproject2conda]
channels = ['conda-forge']
# these are the same as the default values of `p2c project`
template_python = "py{py}-{env}"
template = "{env}"
style = "yaml"
# options
python = ["3.10"]
# Note that this is relative to the location of pyproject.toml
user_config = "config/userconfig.toml"
# These environments will be created with the package, package dependencies, and
# dependencies from groups or extras with environment name so the below is the
# same as
#
# [tool.pyproject2conda.envs.test]
# extras_or_groups = "test"
#
default_envs = ["test", "dev", "dist-pypi"]

[tool.pyproject2conda.envs.base]
style = ["requirements"]

# This will have no extras or groups
#
# A value of `extras = true` will would be equivalent to
# passing extras_or_groups = <env-name>
[tool.pyproject2conda.envs."test-extras"]
extras = ["test"]
style = ["yaml", "requirements"]

[[tool.pyproject2conda.overrides]]
envs = ['test-extras', "dist-pypi"]
skip_package = true

[[tool.pyproject2conda.overrides]]
envs = ["test", "test-extras"]
python = ["3.10", "3.11"]

run through the command pyproject2conda project (or p2c project):

$ p2c project -f tests/data/test-pyproject.toml --dry
# --------------------
# Creating requirements base.txt
athing
bthing
cthing;python_version<"3.10"
# --------------------
# Creating yaml py310-test-extras.yaml
channels:
  - conda-forge
dependencies:
  - python=3.10
  - conda-forge::pytest
  - pandas
# --------------------
# Creating yaml py311-test-extras.yaml
channels:
  - conda-forge
dependencies:
  - python=3.11
  - conda-forge::pytest
  - pandas
# --------------------
# Creating requirements test-extras.txt
pandas
pytest
# --------------------
# Creating yaml py310-test.yaml
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bthing-conda
  - conda-forge::pytest
  - pandas
  - pip
  - pip:
      - athing
# --------------------
# Creating yaml py311-test.yaml
channels:
  - conda-forge
dependencies:
  - python=3.11
  - bthing-conda
  - conda-forge::pytest

 ...

Note that here, we have used the --dry option to just print the output. In production, you'd omit this flag, and files according to --template and --template-python would be used.

The options under [tool.pyproject2conda] follow the command line options (replace - with _). To specify an environment, you can either use the [tool.pyproject.envs."environment-name"] method, or, if the environment is the same as an project.optional-dependencies or dependency-grroups, you can just specify it under tool.pyproject2conda.default_envs:

[tool.pyproject2conda]
# ...
default_envs = ["test"]

is equivalent to

[tool.pyproject2conda.envs.test]
extras = ["tests"]

To specify a conda environment (yaml) file, pass style = "yaml" (the default). To specify a requirements file, pass style = "requirements". You can specify both to make both.

Options in a given tool.pyproject2conda.envs."environment-name" section override those at the tool.pyproject2conda level. So, for example:

# ...
[tool.pyproject2conda.envs."test-extras"]
extras = ["test"]
style = ["yaml", "requirements"]

# ...

will override use the two styles instead of the default of yaml.

You can also override options for multiple environments using the [[tools.pyproject2conda.overrides]] list. Just specify the override option(s) and the environments to apply them to. For example, above we specify that the base option is False for envs test-extras and dist-pypi, and that the python version should be 3.10 and 3.11 for envs test and test-extras. Note that each "overrides" table must specify the options to be overridden, and the environments that these overrides apply to. Also, note that subsequenct overrides override previous overrides/options (last option wins).

So in all, options are picked up, in order, from the overrides list, then the environment definition, and finally, from the default options.

You can also define "user defined" configurations. This can be done through the option --user-config. This allows you to define your own environments outside of the (most likely source controlled) pyproject.toml file. For example, we have the option user_config=config/userconfig.toml.

[tool.pyproject2conda.envs."user-dev"]
extras_or_groups = ["dev", "dist-pypi"]
deps = ["extra-dep"]
reqs = ["extra-req"]
name = "hello"

Note that the full path of this file is note that the path of the user_conifg file is relative to thempyproject.toml file. So, if the pyproject.toml file is at a/path/pyproject.toml, the path of user configuration files will be a/path/config/userconfig.toml. We then can run the following:

$ p2c project -f tests/data/test-pyproject.toml --dry --envs user-dev
# --------------------
# Creating yaml py310-user-dev.yaml
name: hello
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bthing-conda
  - conda-forge::pytest
  - conda-matplotlib
  - extra-dep
  - pandas
  - setuptools
  - pip
  - pip:
      - athing
      - build
      - extra-req

CLI options

See command line interface documentation for details on the commands and options.

Related work

The application pyproject2conda is used in the development of the following packages:

• cmomy
• thermoextrap
• tmmc-lnpy
• module-utilities
• analphipy
• pyproject2conda itself!

Documentation

See the documentation for a look at pyproject2conda in action.

License

This is free software. See LICENSE.

Contact

The author can be reached at [email protected].

Credits

This package was created using Cookiecutter with the usnistgov/cookiecutter-nist-python template.