Merge pull request #416 from sunbeam-labs/415-update-sunbeamlib-setup

Replace setup.py with pyproject.toml

.circleci/config.yml

@@ -6,7 +6,7 @@ version: 2
 jobs:
   build:
     docker:
-      - image: cimg/python:3.10
+      - image: continuumio/miniconda3
 
     steps:
       - checkout

.github/workflows/check_conda_envs.yml

@@ -0,0 +1,27 @@
+name: Check Conda Envs
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  workflow_dispatch:
+    inputs:
+      envs:
+        description: 'Regex for envs'     
+        required: false
+        default: './,workflow/envs/'
+
+jobs:
+  check_conda_envs:
+    name: Check Conda Envs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Check Conda Envs
+        uses: Ulthran/conda_env_check@v0
+        with:
+          envs: "./,workflow/envs/"

MANIFEST.in

@@ -1,2 +1,2 @@
-include sunbeamlib/data/*.yml
-include sunbeamlib/data/*.yaml
+include src/sunbeamlib/*.yml
+include src/sunbeamlib/*.yaml

Readme.md → README.md

@@ -2,7 +2,11 @@
 
 # Sunbeam: a robust, extensible metagenomic sequencing pipeline 
 
-[![CircleCI](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main.svg?style=shield)](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main) [![Super-Linter](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml) [![Documentation Status](https://readthedocs.org/projects/sunbeam/badge/?version=stable)](https://sunbeam.readthedocs.io/en/stable/?badge=stable) [![DOI:10.1186/s40168-019-0658-x](https://img.shields.io/badge/Published%20in-Microbiome-1abc9c.svg)](https://doi.org/10.1186/s40168-019-0658-x)
+[![CircleCI](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main.svg?style=shield)](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main)
+[![Super-Linter](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml)
+[![Conda Envs Status](https://byob.yarr.is/sunbeam-labs/sunbeam/env_check)](https://github.com/sunbeam-labs/sunbeam/actions/workflows/check_conda_envs.yml)
+[![Documentation Status](https://readthedocs.org/projects/sunbeam/badge/?version=stable)](https://sunbeam.readthedocs.io/en/stable/?badge=stable)
+[![DOI:10.1186/s40168-019-0658-x](https://img.shields.io/badge/Published%20in-Microbiome-1abc9c.svg)](https://doi.org/10.1186/s40168-019-0658-x)
 
 Sunbeam is a pipeline written in [snakemake](http://snakemake.readthedocs.io)
 that simplifies and automates many of the steps in metagenomic sequencing

dev_scripts/reformat.sh

@@ -5,4 +5,4 @@ cd $SUNBEAM_DIR
 snakefmt workflow/rules/
 snakefmt workflow/Snakefile
 
-black workflow/scripts/ sunbeamlib/ tests/
+black workflow/scripts/ src/sunbeamlib/ tests/e2e/*.py tests/unit/rules/*.py tests/unit/sunbeamlib/*.py tests/*.py

docs/install.rst

@@ -48,14 +48,6 @@ code under the 'sunbeamlib/' directory. If you have major or incompatible
 changes to make to the environment you should consider creating a new one under a 
 different name so that you always have a working version installed.
 
--m/--no_mamba
-++++++++++++++++
-
-Don't use mamba in base environment as dependency solver. It is the default 
-option to use mamba because it is considerably faster than conda in solving new 
-environments. However it can also sometimes be a pain to install, especially 
-with crowded 'base' environments.
-
 -v/--verbose
 +++++++++++++++
 

environment.yml

@@ -3,7 +3,5 @@ channels:
   - bioconda
 dependencies:
   - snakemake
-  - ruamel.yaml
-  - semantic_version
   - git # Ensure sunbeam extend works even with tar installation of main pipeline
   - python>=3.10

install.sh

@@ -9,7 +9,6 @@ read -r -d '' __usage <<-'EOF'
   -s --sunbeam_dir  [arg] Location of Sunbeam source code. Default: this directory
   -c --conda  [arg]       Location of Conda installation. Default: $CONDA_PREFIX
   -u --update [arg]       Update sunbeam [lib]rary, conda [env], or [all].
-  -m --no_mamba           Don't use mamba in base environment as dependency solver.
   -v --verbose            Show subcommand output.
   -d --debug              Run in debug mode.
   -h --help               Display this message and exit.
@@ -67,18 +66,13 @@ __sunbeam_dir="${arg_s:-$(readlink -f ${__dir})}"
 __sunbeam_env="${arg_e:-sunbeam${__version_tag}}"
 __update_lib=false
 __update_env=false
-__install_mamba=true
 if [[ "${arg_u}" = "all" || "${arg_u}" = "env" ]]; then
     __update_lib=true
     __update_env=true
 elif [[ "${arg_u}" = "lib" ]]; then
     __update_lib=true
 fi
 
-if [[ "${arg_m:?}" = "1" ]]; then
-    __install_mamba=false
-fi
-
 __old_path=$PATH
 PATH=$PATH:${__conda_path}/bin
 
@@ -94,10 +88,6 @@ function __test_conda() {
     command -v conda &> /dev/null && echo true || echo false
 }
 
-function __test_mamba() {
-    command -v mamba &> /dev/null && echo true || echo false
-}
-
 function __detect_conda_install() {
     local discovered=$(__test_conda)
     if [[ $discovered = true ]]; then
@@ -160,12 +150,7 @@ function install_conda () {
 }
 
 function install_environment () {
-    if [[ $(__test_mamba) = true ]]; then
-        cmd=mamba
-    else
-        cmd=conda
-    fi
-    debug_capture $cmd env create --name=$__sunbeam_env \
+    debug_capture conda env create --name=$__sunbeam_env \
               --quiet --file environment.yml
     if [[ $(__test_env) != true ]]; then
 	installation_error "Environment creation"
@@ -198,8 +183,6 @@ info "    Sunbeam env:  '${__sunbeam_env}'"
 debug "Components detected:"
 __conda_installed=$(__test_conda)
 debug "    Conda:       ${__conda_installed}"
-__mamba_installed=$(__test_mamba)
-debug "    Mamba:       ${__mamba_installed}"
 __env_exists=$(__test_env)
 debug "    Environment: ${__env_exists}"
 __sunbeam_installed=$(__test_sunbeam)
@@ -221,16 +204,6 @@ else
     __env_changed=true
 fi
 
-# Install mamba
-if [[ $__mamba_installed = true ]]; then
-    info "Mamba already installed."
-else
-    if [[ $__install_mamba = true ]]; then
-        info "Installing mamba..."
-        conda install --yes --quiet -n base -c conda-forge mamba || (info "Mamba failed to install, this is usually because you have too many packages already installed to your base environment. Install again without mamba (--no_mamba) or try to fix conflicts in base env." && exit 1)
-    fi
-fi
-
 conda config --set channel_priority strict # Set channel priority on new install
 
 # Create Conda environment for Sunbeam

pyproject.toml

@@ -0,0 +1,160 @@
+[project]
+# This is the name of your project. The first time you publish this
+# package, this name will be registered for you. It will determine how
+# users can install this project, e.g.:
+#
+# $ pip install sampleproject
+#
+# And where it will live on PyPI: https://pypi.org/project/sampleproject/
+#
+# There are some restrictions on what makes a valid project name
+# specification here:
+# https://packaging.python.org/specifications/core-metadata/#name
+name = "sunbeamlib"  # Required
+
+# Versions should comply with PEP 440:
+# https://www.python.org/dev/peps/pep-0440/
+#
+# For a discussion on single-sourcing the version, see
+# https://packaging.python.org/guides/single-sourcing-package-version/
+#version = "0.0.0"  # Required
+dynamic = ["version"]
+
+# This is a one-line description or tagline of what your project does. This
+# corresponds to the "Summary" metadata field:
+# https://packaging.python.org/specifications/core-metadata/#summary
+description = "A helper package for running the sunbeam pipeline"  # Optional
+
+# This is an optional longer description of your project that represents
+# the body of text which users will see when they visit PyPI.
+#
+# Often, this is the same as your README, so you can just read it in from
+# that file directly (as we have already done above)
+#
+# This field corresponds to the "Description" metadata field:
+# https://packaging.python.org/specifications/core-metadata/#description-optional
+readme = "README.md" # Optional
+
+# Specify which Python versions you support. In contrast to the
+# 'Programming Language' classifiers above, 'pip install' will check this
+# and refuse to install the project if the version does not match. See
+# https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
+requires-python = ">=3.7"
+
+# This is either text indicating the license for the distribution, or a file
+# that contains the license
+# https://packaging.python.org/en/latest/specifications/core-metadata/#license
+# license = {file = "LICENSE.txt"}
+
+# This field adds keywords for your project which will appear on the
+# project page. What does your project relate to?
+#
+# Note that this is a list of additional keywords, separated
+# by commas, to be used to assist searching for the distribution in a
+# larger catalog.
+#keywords = ["bioinformatics", "metagenomics"]  # Optional
+
+# This should be your name or the name of the organization who originally
+# authored the project, and a valid email address corresponding to the name
+# listed.
+# authors = [
+#   {name = "A. Random Developer", email = "[email protected]" } # Optional
+# ]
+
+# This should be your name or the names of the organization who currently
+# maintains the project, and a valid email address corresponding to the name
+# listed.
+maintainers = [
+  {name = "Charlie Bushman", email = "[email protected]" } # Optional
+]
+
+# Classifiers help users find your project by categorizing it.
+#
+# For a list of valid classifiers, see https://pypi.org/classifiers/
+classifiers = [  # Optional
+  # How mature is this project? Common values are
+  #   3 - Alpha
+  #   4 - Beta
+  #   5 - Production/Stable
+  "Development Status :: 5 - Production/Stable",
+
+  # Indicate who your project is intended for
+  # "Intended Audience :: Developers",
+  #"Topic :: Bioinformatics",
+
+  # Pick your license as you wish
+  "License :: OSI Approved :: MIT License",
+
+  # Specify the Python versions you support here. In particular, ensure
+  # that you indicate you support Python 3. These classifiers are *not*
+  # checked by "pip install". See instead "python_requires" below.
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3 :: Only",
+]
+
+# This field lists other packages that your project depends on to run.
+# Any package you put here will be installed by pip when your project is
+# installed, so they must be valid existing projects.
+#
+# For an analysis of this field vs pip's requirements files see:
+# https://packaging.python.org/discussions/install-requires-vs-requirements/
+dependencies = [ # Optional
+  "more-itertools",
+  "pyyaml",
+]
+
+# List additional groups of dependencies here (e.g. development
+# dependencies). Users will be able to install these using the "extras"
+# syntax, for example:
+#
+#   $ pip install sampleproject[dev]
+#
+# Similar to `dependencies` above, these must be valid existing
+# projects.
+[project.optional-dependencies] # Optional
+dev = ["black"]
+test = ["pytest"]
+
+# List URLs that are relevant to your project
+#
+# This field corresponds to the "Project-URL" and "Home-Page" metadata fields:
+# https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
+# https://packaging.python.org/specifications/core-metadata/#home-page-optional
+#
+# Examples listed include a pattern for specifying where the package tracks
+# issues, where the source is hosted, where to say thanks to the package
+# maintainers, and where to support the project financially. The key is
+# what's used to render the link text on PyPI.
+[project.urls]  # Optional
+"Homepage" = "https://github.com/sunbeam-labs/sunbeam"
+"Bug Reports" = "https://github.com/sunbeam-labs/sunbeam/issues"
+"Docs" = "https://sunbeam.readthedocs.io/en/stable/"
+# "Funding" = "https://donate.pypi.org"
+# "Say Thanks!" = "http://saythanks.io/to/example"
+"Source" = "https://github.com/sunbeam-labs/sunbeam"
+
+# The following would provide a command line executable called `sample`
+# which executes the function `main` from this package when invoked.
+[project.scripts]  # Optional
+sunbeam = "sunbeamlib.script_sunbeam:main"
+
+# This is configuration specific to the `setuptools` build backend.
+# If you are using a different build backend, you will need to change this.
+[tool.setuptools]
+# If there are data files included in your packages that need to be
+# installed, specify them here.
+#package-data = {"sunbeamlib" = ["*.yml", "*.yaml"]}
+
+[build-system]
+# These are the assumed default build requirements from pip:
+# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "sunbeamlib.__version__"}