pyproject2conda 0.23.1

A script to convert a Python project declared on a pyproject.toml to a conda environment.

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

• Automatic creation of environment.yamland requirements.txt files from pyproject.toml.
• Simple remapping of pypi package name to conda package name when creating environment.yaml files.
• pre-commit hooks to automatically keep dependency files up to data.

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!

Pre-commit hooks

pyproject2conda works with pre-commit. Hooks are available for the project, yaml, and requirements subcommands described below:

- repo: https://github.com/usnistgov/pyproject2conda
  rev: { version } # replace with current version
  hooks:
    - id: pyproject2conda-project
    - id: pyproject2conda-yaml
    - id: pyproject2conda-requirements

For yaml and requirements, you can override the default behavior (of creating environment/requirement files from the dependency-group dev) by passing in args. For example, you could use the following to create an environment file with the extra dev-complete

- repo: https://github.com/usnistgov/pyproject2conda
  rev: { version } # replace with current version
  hooks:
    - id: pyproject2conda-yaml
      args: ["-e", "dev-complete", "-o", "environment-dev.yaml", "-w", "force"]

Note that if called from pre-commit (detected by the presence of PRE_COMMIT environment variable), the default is to set --custom-command="pre-commit". You can explicitly pass in --custom-command to override this.

Installation

Use one of the following to install pyproject2conda:

$ pip/pipx/uvx install pyproject2conda

or

$ conda/condax install -c conda-forge pyproject2conda

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

$ pip/pipx/uvx 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 --pyproject 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 --pyproject tests/data/test-pyproject.toml \
    --python-include infer
channels:
  - conda-forge
dependencies:
  - python<3.11,>=3.8
  - 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 --pyproject 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 --pyproject 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 --pyproject 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 --pyproject tests/data/test-pyproject.toml --python \
    3.10
channels:
  - conda-forge
dependencies:
  - python=3.10
  - bthing-conda
  - pip
  - pip:
      - athing

Passing --python="default" will extract the python version from .python-version file. Passing --python value "lowest" or "highest" will extract the lowest or highest python version, respectively, from the project.classifiers table of the pyproject.toml file. Using the option python="all" in pyproject.toml will include all python versions in the project.classifiers table.

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 --pyproject 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 --pyproject 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 --pyproject 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 --pyproject 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",
]
optional-opt1 = [ "hello[opt1]" ]
optional-opt2 = [ "hello[opt2]" ]
optional-all = [ "hello[all]" ]

# ...

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

$ pyproject2conda yaml --pyproject 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 --pyproject tests/data/test-pyproject.toml --header
#
# This file is autogenerated by pyproject2conda
# with the following command:
#
#     $ pyproject2conda yaml --pyproject 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

You can customize the command in the header with the --custom-command option.

Usage within python

pyproject2conda can also be used within python:

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

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

# Environment with extras
>>> print(p.to_conda_yaml(extras="test", channels="conda-forge").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" ]
# 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 --pyproject tests/data/test-pyproject.toml -e dist-pypi \
    --skip-package
channels:
  - conda-forge
dependencies:
  - setuptools
  - pip
  - pip:
      - build

or

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

# Basic environment
>>> print(p.to_conda_yaml(extras="dist-pypi", skip_package=True).strip())
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" ]
# 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 --pyproject 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. For example, specify template-python = ... in the config file instead of passing --template-python. You can optionally replace all dashes with underscores in config file option names, but this will be deprecated in future versions. 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-groups, 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 subsequent 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.

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.

What's new?

See changelog.

License

This is free software. See LICENSE.

Contact

The author can be reached at [e-mail].

Credits

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