feat: add plugin scaffolding

.gitattributes

@@ -1 +1,3 @@
 snakedeploy/_version.py export-subst
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/main.yml

@@ -13,42 +13,22 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup environments
-        run: |
-          conda create -c conda-forge --quiet --name black black>=22
-          conda create -c conda-forge --quiet --name pyflakes pyflakes
-
-      - name: Check formatting with black
-        run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate black
-          black --check snakedeploy
+      - uses: prefix-dev/setup-pixi@v0
 
-      - name: Check imports with pyflakes
+      - name: Test snakedeploy
         run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate pyflakes
-          pyflakes snakedeploy
+          pixi run format --check
+          pixi run check
 
   testing:
     needs: code-quality
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.8, 3.9]
 
     steps:
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
       - uses: actions/checkout@v4
 
-      - name: Setup test environment
-        run: |
-          pip install -e .
+      - uses: prefix-dev/setup-pixi@v0
 
       - name: Test snakedeploy
         run: |
-          /bin/bash tests/test_client.sh
+          pixi run test

.gitignore

@@ -5,3 +5,8 @@ build
 __pycache__
 dist
 .env
+
+# pixi environments
+.pixi
+*.egg-info
+pixi.lock

.python-version

@@ -0,0 +1 @@
+3.11

.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  commands:
+    - curl -fsSL https://pixi.sh/install.sh | sh
+    - $HOME/.pixi/bin/pixi run build-docs
+    - mkdir -p $READTHEDOCS_OUTPUT/html
+    - rm -rf $READTHEDOCS_OUTPUT/html && mv docs/_build/html $READTHEDOCS_OUTPUT/html
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt

docs/conf.py

@@ -13,17 +13,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
-import os
-from recommonmark.parser import CommonMarkParser
+from sphinxawesome_theme.postprocess import Icons
 
-source_parsers = {".md": CommonMarkParser}
-
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath("../"))
 
 # -- General configuration ------------------------------------------------
 
@@ -37,19 +28,20 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
-    "sphinxcontrib.napoleon",
     "sphinxarg.ext",
     "sphinx.ext.autosectionlabel",
 ]
 
 # Snakmake theme (made by SciAni).
-html_css_files = ["theme.css"]
+# html_css_files = ["theme.css"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
+html_permalinks_icon = Icons.permalinks_icon
+
 # The suffix of source filenames.
-source_suffix = [".rst", ".md"]
+# source_suffix = [".rst"]
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -61,23 +53,6 @@
 project = "Snakedeploy"
 copyright = "2020, Johannes Koester and Vanessa Sochat"
 
-import snakedeploy
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = snakedeploy.__version__
-
-if os.environ.get("READTHEDOCS") == "True":
-    # Because Read The Docs modifies conf.py, versioneer gives a "dirty"
-    # version like "5.10.0+0.g28674b1.dirty" that is cleaned here.
-    version = version.partition("+0.g")[0]
-
-# The full version, including alpha/beta/rc tags.
-release = version
-
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 # language = None
@@ -108,7 +83,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
+# pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -121,7 +96,18 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "sphinx_rtd_theme"
+html_theme = "sphinxawesome_theme"
+html_theme_options = {
+    "logo_light": "logo-snake.svg",
+    "logo_dark": "logo-snake.svg",
+    "main_nav_links": {
+        "Snakemake Homepage": "https://snakemake.github.io",
+        "Snakemake Documentation": "https://snakemake.readthedocs.io",
+    },
+    "awesome_external_links": True,
+    "awesome_headerlinks": True,
+    "show_prev_next": False,
+}
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -199,32 +185,11 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "Snakedeploydoc"
+# htmlhelp_basename = "Snakedeploydoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #'papersize': 'letterpaper',
-    # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
-    # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (
-        "index",
-        "Snakedeploy.tex",
-        "Snakedeploy Documentation",
-        "Johannes Koester",
-        "manual",
-    ),
-]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
@@ -249,51 +214,6 @@
 
 # -- Options for manual page output ---------------------------------------
 
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (
-        "index",
-        "snakedeploy",
-        "Snakedeploy Documentation",
-        ["Johannes Koester", "Vanessa Sochat"],
-        1,
-    )
-]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (
-        "index",
-        "Snakemake",
-        "Snakedeploy Documentation",
-        ["Johannes Koester", "Vanessa Sochat"],
-        "Snakedeploy",
-        "Easily deploy snakemake pipeline templates.",
-        "Miscellaneous",
-    ),
-]
-
-# Documents to append as an appendix to all manuals.
-# texinfo_appendices = []
-
-# If false, no module index is generated.
-# texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-# texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-# texinfo_no_detailmenu = False
-
-
-def setup(app):
-    app.add_stylesheet("sphinx-argparse.css")

docs/getting_started/installation.rst

@@ -4,7 +4,21 @@
 Installation
 ============
 
-Snakedeploy can be installed via conda, pypi or from source.
+Snakedeploy can be installed via pixi, conda, pypi or from source.
+
+Install via pixi
+================
+For global installation (recommended), run
+
+.. code:: console
+
+    $ pixi global install snakedeploy
+
+For local installation into an existing pixi workspace, run
+
+.. code:: console
+
+    $ pixi add snakedeploy
 
 Install via mamba/conda
 =======================
@@ -42,7 +56,7 @@ Install from source
 
     $ pip install -e .
 
-========================
+
 Testing the installation
 ========================
 

docs/index.rst

@@ -4,37 +4,50 @@
 Snakedeploy
 ============
 
-.. image:: https://img.shields.io/pypi/pyversions/snakedeploy.svg
+.. image:: https://img.shields.io/conda/dn/bioconda/snakedeploy.svg?label=Bioconda&color=%23064e3b
+    :target: https://bioconda.github.io/recipes/snakedeploy/README.html
+
+.. image:: https://img.shields.io/pypi/pyversions/snakedeploy.svg?color=%23065f46
     :target: https://www.python.org
 
-.. image:: https://img.shields.io/pypi/v/snakedeploy.svg
+.. image:: https://img.shields.io/pypi/v/snakedeploy.svg?color=%23047857
     :target: https://pypi.python.org/pypi/snakedeploy
 
-.. image:: https://github.com/snakemake/snakedeploy/workflows/CI/badge.svg?branch=main&label=CI
-    :target: https://github.com/snakemake/snakemake/actions?query=branch%3Amain+workflow%3ACI
+.. image:: https://img.shields.io/github/actions/workflow/status/snakemake/snakedeploy/main.yml?label=tests&color=%2310b981
+    :target: https://github.com/snakemake/snakedeploy/actions?query=branch%3Amain+workflow%3ACI
+
+.. image:: https://img.shields.io/badge/stack-overflow-orange.svg?color=%2334d399
+    :target: https://stackoverflow.com/questions/tagged/snakemake
 
-.. image:: https://img.shields.io/discord/753690260830945390?label=discord%20chat   
+.. image:: https://img.shields.io/discord/753690260830945390?label=discord%20chat&color=%23a7f3d0
     :alt: Discord
     :target: https://discord.gg/NUdMtmr
 
-.. image:: https://img.shields.io/github/stars/snakemake/snakedeploy?style=social
-    :alt: GitHub stars
-    :target: https://github.com/snakemake/snakemake/stargazers
+.. image:: https://img.shields.io/badge/bluesky-follow-%23d1fae5
+   :alt: Bluesky
+   :target: https://bsky.app/profile/johanneskoester.bsky.social
+
+.. image:: https://img.shields.io/badge/mastodon-follow-%23ecfdf5
+   :alt: Mastodon
+   :target: https://fosstodon.org/@johanneskoester
+
+
 
+Snakedeploy is a command line tool and Python library for automation of deployment and maintenance tasks around `Snakemake and Snakemake workflows <https://snakemake.github.io>`.
 
-SnakeDeploy is a command line tool and Python library
-to easily deploy Snakemake pipelines from version control like GitHub.
-To learn more about Snakemake, visit the `official documentation <https://snakemake.github.io/>`_
+* **Workflow users** can apply it to automatically :ref:`deploy (i.e. set up for use) <deploy>` public workflows for execution on their local machine or use it to :ref:`register input data <input_registration>` for their workflow configuration.
+* **Workflow developers** can use it to automatically :ref:`update conda environment files <update_conda_envs>` or :ref:`Snakemake wrapper versions <update_snakemake_wrappers>` and :ref:`pin/lock conda environments<pin_conda_envs>` in their workflows.
+* **Snakemake developers** can use it to :ref:`scaffold Snakemake plugins <scaffold_snakemake_plugins>` (i.e. to obtain a skeleton codebase as a starting point for each type of possible Snakemake plugin).
 
 .. _main-support:
 
 -------
 Support
 -------
 
-* In case of **questions**, please post on `stack overflow <https://stackoverflow.com/questions/tagged/snakemake>`_.
-* For **bugs and feature requests**, please use the `issue tracker <https://github.com/snakemake/snakedeploy/issues>`_.
-* For **contributions**, visit snakedeploy on `Github <https://github.com/snakemake/snakedeploy>`_.
+* In case of **questions**, please post on `stack overflow <https://stackoverflow.com/questions/tagged/snakemake>`__ or ask on `Discord <https://discord.gg/NUdMtmr>`_.
+* For **bugs and feature requests**, please use the `issue tracker <https://github.com/snakemake/snakedeploy/issues>`__.
+* For **contributions**, visit snakedeploy on `Github <https://github.com/snakemake/snakedeploy>`__.
 
 .. toctree::
    :caption: Getting started
@@ -43,7 +56,32 @@ Support
    :maxdepth: 1
 
    getting_started/installation
-   getting_started/tools
+
+.. toctree::
+   :caption: Workflow users
+   :name: workflow_users
+   :hidden:
+   :maxdepth: 1
+
+   workflow_users/workflow_deployment
+   workflow_users/input_registration
+
+.. toctree::
+   :caption: Workflow developers
+   :name: workflow_developers
+   :hidden:
+   :maxdepth: 1
+
+   workflow_developers/update_conda_envs
+   workflow_developers/update_snakemake_wrappers
+
+.. toctree::
+   :caption: Snakemake developers
+   :name: snakemake_developers
+   :hidden:
+   :maxdepth: 1
+
+   snakemake_developers/scaffold_plugins
 
 .. toctree::
     :caption: API Reference