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A cookiecutter template for conda packages using Python

License: BSD 3-Clause "New" or "Revised" License

Python 100.00%

cookiecutter-conda-python's Introduction

Conda is a cross-platform, language-agnostic binary package manager. It is the package manager used by Anaconda installations, but it may be used for other systems as well. Conda makes environments first-class citizens, making it easy to create independent environments even for C libraries. Conda is written entirely in Python, and is BSD licensed open source.

Conda is enhanced by organizations, tools, and repositories created and managed by the amazing members of the conda community. Some of them can be found here.

Installation

Conda is a part of the Anaconda Distribution. Use Miniconda to bootstrap a minimal installation that only includes conda and its dependencies.

Updating conda

To update conda to the newest version, use the following command:

$ conda update -n base conda

Tip

It is possible that conda update does not install the newest version if the existing conda version is far behind the current release. In this case, updating needs to be done in stages.

For example, to update from conda 4.12 to conda 23.10.0, conda 22.11.1 needs to be installed first:

$ conda install -n base conda=22.11.1
$ conda update conda

Getting Started

If you install the Anaconda Distribution, you will already have hundreds of packages installed. You can see what packages are installed by running:

$ conda list

to see all the packages that are available, use:

$ conda search

and to install a package, use

$ conda install <package-name>

The real power of conda comes from its ability to manage environments. In conda, an environment can be thought of as a completely separate installation. Conda installs packages into environments efficiently using hard links by default when it is possible, so environments are space efficient, and take seconds to create.

The default environment, which conda itself is installed into, is called base. To create another environment, use the conda create command. For instance, to create an environment with PyTorch, you would run:

$ conda create --name ml-project pytorch

This creates an environment called ml-project with the latest version of PyTorch, and its dependencies.

We can now activate this environment:

$ conda activate ml-project

This puts the bin directory of the ml-project environment in the front of the PATH, and sets it as the default environment for all subsequent conda commands.

To go back to the base environment, use:

$ conda deactivate

Building Your Own Packages

You can easily build your own packages for conda, and upload them to anaconda.org, a free service for hosting packages for conda, as well as other package managers. To build a package, create a recipe. Package building documentation is available here. See AnacondaRecipes for the recipes that make up the Anaconda Distribution and defaults channel. Conda-forge and Bioconda are community-driven conda-based distributions.

To upload to anaconda.org, create an account. Then, install the anaconda-client and login:

$ conda install anaconda-client
$ anaconda login

Then, after you build your recipe:

$ conda build <recipe-dir>

you will be prompted to upload to anaconda.org.

To add your anaconda.org channel, or other's channels, to conda so that conda install will find and install their packages, run:

$ conda config --add channels https://conda.anaconda.org/username

(replacing username with the username of the person whose channel you want to add).

Getting Help

Contributing

Contributions to conda are welcome. See the contributing documentation for instructions on setting up a development environment.

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cookiecutter-conda-python's Issues

Failed CLI test

============================= test session starts ==============================
platform darwin -- Python 3.8.5, pytest-6.1.0, py-1.9.0, pluggy-0.13.1
rootdir: $SRC_DIR
plugins: cov-2.10.1
collected 1 item

tests/test_cli.py F [100%]

=================================== FAILURES ===================================
______________________________ test_cli_template _______________________________

def test_cli_template():

  assert cli.cli() is None

tests/test_cli.py:4:

../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.8/site-packages/pieparty/cli.py:16: in cli
args = p.parse_args(args)
../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.8/argparse.py:1771: in parse_args
self.error(msg % ' '.join(argv))
../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.8/argparse.py:2521: in error
self.exit(2, _('%(prog)s: error: %(message)s\n') % args)

self = ArgumentParser(prog='pytest', usage=None, description='scRNA visualization tool', formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='resolve', add_help=True)
status = 2, message = 'pytest: error: unrecognized arguments: tests\n'

def exit(self, status=0, message=None):
    if message:
        self._print_message(message, _sys.stderr)

  _sys.exit(status)

E SystemExit: 2

../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.8/argparse.py:2508: SystemExit
----------------------------- Captured stderr call -----------------------------
usage: pytest [-h] [-V]
pytest: error: unrecognized arguments: tests
=========================== short test summary info ============================
FAILED tests/test_cli.py::test_cli_template - SystemExit: 2
============================== 1 failed in 0.17s ===============================

Add selectable license?

Should this cookiecutter add a selectable license similar to audreyr/cookiecutter-pypackage? It would be easy enough for me to fabricate the necessary template.

TypeError: 'NoneType' object is not callable

While building the package using 'conda build' command, i am getting error as below:

Traceback (most recent call last):
File "/home/lovekesh/anaconda3/bin/conda-build", line 11, in
sys.exit(main())
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 469, in main
execute(sys.argv[1:])
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 460, in execute
verify=args.verify, variants=args.variants)
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/api.py", line 209, in build
notest=notest, need_source_download=need_source_download, variants=variants)
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/build.py", line 2322, in build_tree
bypass_env_check=True)
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/render.py", line 785, in render_recipe
m = MetaData(recipe_dir, config=config)
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/metadata.py", line 863, in init
self.parse_again(permit_undefined_jinja=True, allow_no_other_outputs=True)
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/metadata.py", line 940, in parse_again
bypass_env_check=bypass_env_check),
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/conda_build/metadata.py", line 1528, in _get_contents
rendered = template.render(environment=env)
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/jinja2/environment.py", line 1090, in render
self.environment.handle_exception()
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/jinja2/environment.py", line 832, in handle_exception
reraise(*rewrite_traceback_stack(source=source))
File "/home/lovekesh/anaconda3/lib/python3.7/site-packages/jinja2/_compat.py", line 28, in reraise
raise value.with_traceback(tb)
File "/home/lovekesh/repository_name/conda.recipe/meta.yaml", line 45, in top-level template code
requires:
TypeError: 'NoneType' object is not callable

Here's a list of my installed packages.

packages in environment at /home/lovekesh/.conda/envs/test-env:

Thanks

failing to setup

I am unable to setup this project with after installed using conda 2 and python 2.7

after running the below, its just returning back to the prompt, please suggest
$ cookiecutter https://github.com/drivendata/cookiecutter-data-science

zainmdm@DESKTOP-D0AN22H MINGW64 /d/zain_python/gitcode (master)
$ echo $?
1

Unable to install cookiecutter-conda-python template

Unable to install cookiecutter-conda-python template :
subprocess.CalledProcessError: Command '['git', 'clone', 'https://github.com/conda/cookiecutter-conda-python.git']' returned non-zero exit status 1.

(keras) ninjawarrior@ninjas-MBP mymodules % cookiecutter https://github.com/conda/cookiecutter-conda-python.git
Traceback (most recent call last):
File "/Users/ninjawarrior/miniconda3/envs/keras/bin/cookiecutter", line 11, in
sys.exit(main())
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/cookiecutter/cli.py", line 120, in main
password=os.environ.get('COOKIECUTTER_REPO_PASSWORD')
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/cookiecutter/main.py", line 63, in cookiecutter
password=password
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/cookiecutter/repository.py", line 103, in determine_repo_dir
no_input=no_input,
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/site-packages/cookiecutter/vcs.py", line 99, in clone
stderr=subprocess.STDOUT,
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/subprocess.py", line 395, in check_output
**kwargs).stdout
File "/Users/ninjawarrior/miniconda3/envs/keras/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['git', 'clone', 'https://github.com/conda/cookiecutter-conda-python.git']' returned non-zero exit status 1.

Example entry point outputs to stderr and returns an error to the OS

The file cli.py implements the one entry point which returns a string.

See: https://setuptools.readthedocs.io/en/latest/setuptools.html#automatic-script-creation

… their return value is passed to sys.exit(), so you can return an errorlevel or message to print to stderr.

Thus the affect of calling the command from a terminal is to print to stderr rather than stdout and also return an error level of 1.

Since this is the only example with no indication that it is supposed to constitute an error, I propose something more like this:

def cli():
    print("CLI template")
    # Return a value of 1 or higher to signify an error; 0 or None means good.
    return  # See https://docs.python.org/3/library/sys.html#sys.exit

main.py is broken

__main__.py imports the module {{cookiecutter.package_name}}.cli and then attempts to call the module rather than the function inside.

The name "cli" is both the name of a module and the name of a function inside that model.

Instead __main__.py should do this:

from temp.cli import cli

cli()

Here is a transcript of the problem and a hotfix:

dev$ cookiecutter cookiecutter-conda-python
full_name [Walker Hale]: 
email [[email protected]]: 
github_username [walkerh]: 
repo_name [repository_name]: temp
package_name [temp]: 
project_short_description [Short description]: 
version [0.1.1-a0]: 
dev$ cd temp
temp$ python -m temp
Traceback (most recent call last):
  File "/anaconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/anaconda3/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/Users/hale/Documents/HGSC/dev/repo/third-party/temp/temp/__main__.py", line 3, in <module>
    cli()
TypeError: 'module' object is not callable
temp$ 
temp$ # And now a hotfix...
temp$ 
temp$ cat <<EOD > temp/__main__.py
> from temp.cli import cli
> 
> cli()
> EOD
temp$ 
temp$ # Test it.
temp$ python -m temp
CLI template
temp$

Issues with CLI and tests

Hello,
When I specify to have a CLI, I'm getting the error do conda build. Do I need to configure something else prior to doing the build?

=================================== FAILURES ===================================
______________________________ test_cli_template _______________________________

    def test_cli_template():
>       assert cli.cli() is None

tests/test_cli.py:4:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.9/site-packages/plpquantum/cli.py:16: in cli
    args = p.parse_args(args)
../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.9/argparse.py:1821: in parse_args
    self.error(msg % ' '.join(argv))
../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.9/argparse.py:2575: in error
    self.exit(2, _('%(prog)s: error: %(message)s\n') % args)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = ArgumentParser(prog='pytest', usage=None, description='PLP-Quantum Computing Integration', formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='resolve', add_help=True)
status = 2, message = 'pytest: error: unrecognized arguments: tests\n'

    def exit(self, status=0, message=None):
        if message:
            self._print_message(message, _sys.stderr)
>       _sys.exit(status)
E       SystemExit: 2

../_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.9/argparse.py:2562: SystemExit
----------------------------- Captured stderr call -----------------------------
usage: pytest [-h] [-V]
pytest: error: unrecognized arguments: tests
=========================== short test summary info ============================
FAILED tests/test_cli.py::test_cli_template - SystemExit: 2
============================== 1 failed in 0.22s ===============================
Tests failed for plpquantum-0+unknown-py_0.tar.bz2 - moving package to /home/jhellmers/anaconda3/conda-bld/broken
WARNING:conda_build.build:Tests failed for plpquantum-0+unknown-py_0.tar.bz2 - moving package to /home/jhellmers/anaconda3/conda-bld/broken
WARNING conda_build.build:tests_failed(2895): Tests failed for plpquantum-0+unknown-py_0.tar.bz2 - moving package to /home/jhellmers/anaconda3/conda-bld/broken
TESTS FAILED: plpquantum-0+unknown-py_0.tar.bz2