Update skeleton

.github/workflows/docs-ci.yml

@@ -2,6 +2,7 @@ name: CI Documentation
 
 on: [push, pull_request]
 
+permissions: {}
 jobs:
   build:
     runs-on: ubuntu-24.04
@@ -13,10 +14,12 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+        with:
+          persist-credentials: false
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/zizmor.yml

@@ -0,0 +1,24 @@
+name: GitHub Actions Security Analysis with zizmor 🌈
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+permissions: {}
+
+jobs:
+  zizmor:
+    name: Run zizmor 🌈
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write # Required for upload-sarif (used by zizmor-action) to upload SARIF files.
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+
+      - name: Run zizmor 🌈
+        uses: zizmorcore/zizmor-action@b1d7e1fb5de872772f31590499237e7cce841e8e # v0.5.3

.gitignore

@@ -72,3 +72,5 @@ tcl
 
 # Ignore Jupyter Notebook related temp files
 .ipynb_checkpoints/
+/.ruff_cache/
+.env

.readthedocs.yml

@@ -26,4 +26,4 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - docs
+        - dev

MANIFEST.in

@@ -1,15 +1,25 @@
 graft src
+graft docs
+graft etc
 
 include *.LICENSE
 include NOTICE
 include *.ABOUT
 include *.toml
 include *.yml
 include *.rst
+include *.png
 include setup.*
 include configure*
 include requirements*
-include .git*
+include .dockerignore
+include .gitignore
+include .readthedocs.yml
+include manage.py
+include Dockerfile*
+include Makefile
+include MANIFEST.in
 
-global-exclude *.py[co] __pycache__ *.*~
+include .VERSION
 
+global-exclude *.py[co] __pycache__ *.*~

configure

@@ -29,13 +29,13 @@ CLI_ARGS=$1
 
 # Requirement arguments passed to pip and used by default or with --dev.
 REQUIREMENTS="--editable . "
-DOCS_REQUIREMENTS="--editable .[docs]"
+DOCS_REQUIREMENTS="--editable .[dev]"
 
 # where we create a virtualenv
 VIRTUALENV_DIR=venv
 
 # Cleanable files and directories to delete with the --clean option
-CLEANABLE="build dist venv .cache .eggs"
+CLEANABLE="build dist venv .cache .eggs *.egg-info docs/_build/ pip-selfcheck.json"
 
 # extra  arguments passed to pip
 PIP_EXTRA_ARGS=" "
@@ -110,7 +110,7 @@ create_virtualenv() {
         fi
 
         $PYTHON_EXECUTABLE "$VIRTUALENV_PYZ" \
-            --wheel embed --pip embed --setuptools embed \
+            --pip embed --setuptools embed \
             --seeder pip \
             --never-download \
             --no-periodic-update \
@@ -167,6 +167,7 @@ clean() {
     for cln in $CLEANABLE;
         do rm -rf "${CFG_ROOT_DIR:?}/${cln:?}";
     done
+    find . -type f -name '*.py[co]' -delete -o -type d -name __pycache__ -delete
     set +e
     exit
 }

configure.bat

@@ -27,7 +27,7 @@
 
 @rem # Requirement arguments passed to pip and used by default or with --dev.
 set "REQUIREMENTS=--editable . "
-set "DOCS_REQUIREMENTS=--editable .[docs]"
+set "DOCS_REQUIREMENTS=--editable .[dev]"
 
 @rem # where we create a virtualenv
 set "VIRTUALENV_DIR=venv"
@@ -110,7 +110,7 @@ if not exist "%CFG_BIN_DIR%\python.exe" (
 
     if exist "%CFG_ROOT_DIR%\etc\thirdparty\virtualenv.pyz" (
         %PYTHON_EXECUTABLE% "%CFG_ROOT_DIR%\etc\thirdparty\virtualenv.pyz" ^
-            --wheel embed --pip embed --setuptools embed ^
+            --pip embed --setuptools embed ^
             --seeder pip ^
             --never-download ^
             --no-periodic-update ^
@@ -126,7 +126,7 @@ if not exist "%CFG_BIN_DIR%\python.exe" (
             )
         )
         %PYTHON_EXECUTABLE% "%CFG_ROOT_DIR%\%VIRTUALENV_DIR%\virtualenv.pyz" ^
-            --wheel embed --pip embed --setuptools embed ^
+            --pip embed --setuptools embed ^
             --seeder pip ^
             --never-download ^
             --no-periodic-update ^

docs/Makefile

@@ -7,7 +7,7 @@ SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
 SPHINXAUTOBUILD = sphinx-autobuild
 SOURCEDIR     = source
-BUILDDIR      = build
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/source/conf.py

@@ -17,8 +17,8 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "aboutcode"
-copyright = "nexB Inc. and others."
+project = "nexb-skeleton"
+copyright = "nexB Inc., AboutCode and others."
 author = "AboutCode.org authors and contributors"
 
 
@@ -94,7 +94,8 @@
 html_show_sphinx = True
 
 # Define CSS and HTML abbreviations used in .rst files.  These are examples.
-# .. role:: is used to refer to styles defined in _static/theme_overrides.css and is used like this: :red:`text`
+# .. role:: is used to refer to styles defined in _static/theme_overrides.css
+# and is used like this: :red:`text`
 rst_prolog = """
 .. |psf| replace:: Python Software Foundation
 

docs/source/contributing/contrib_doc.rst

@@ -43,9 +43,9 @@ you can install the dependencies in a virtualenv::
 
 .. note::
 
-    In case of windows, run ``configure --docs`` instead of this.
+    In case of windows, run ``configure --dev``.
 
-Now, this will install the following prerequisites:
+This will install and configure all requirements foer development including for docs development.
 
 - Sphinx
 - sphinx_rtd_theme (the format theme used by ReadTheDocs)
@@ -57,21 +57,21 @@ These requirements are already present in setup.cfg and `./configure
 Now you can build the HTML documents locally::
 
     source venv/bin/activate
-    cd docs
-    make html
+    make docs
 
 Assuming that your Sphinx installation was successful, Sphinx should build
 a local instance of the documentation .html files::
 
-    open build/html/index.html
+    open docs/_build/index.html
 
-.. note::
 
     In case this command did not work, for example on Ubuntu 18.04 you may
     get a message like “Couldn’t get a file descriptor referring to the
     console”, try:
 
-    ::
+    source venv/bin/activate
+    make doc8
+    make docs-check
 
         see build/html/index.html
 
@@ -119,31 +119,26 @@ that common errors are avoided and documentation standards are enforced.
 Travis-CI presently checks for these 3 aspects of the documentation :
 
 1. Successful Builds (By using ``sphinx-build``)
-2. No Broken Links   (By Using ``link-check``)
-3. Linting Errors    (By Using ``Doc8``)
-
-So run these scripts at your local system before creating a Pull Request::
+2. No Broken Links   (By Using ``linkcheck``)
+3. Linting Errors    (By Using ``doc8``)
 
-    cd docs
-    ./scripts/sphinx_build_link_check.sh
-    ./scripts/doc8_style_check.sh
+You myst run these scripts locally before creating a pull request::
 
-If you don't have permission to run the scripts, run::
+    make doc8
+    make check-docs
 
-    chmod u+x ./scripts/doc8_style_check.sh
 
 .. _doc_style_docs8:
 
-Style Checks Using ``Doc8``
+Style Checks Using ``doc8``
 ---------------------------
 
 How To Run Style Tests
 ^^^^^^^^^^^^^^^^^^^^^^
 
 In the project root, run the following commands::
 
-    $ cd docs
-    $ ./scripts/doc8_style_check.sh
+    make doc8
 
 A sample output is::
 
@@ -168,6 +163,7 @@ A sample output is::
 Now fix the errors and run again till there isn't any style error in the
 documentation.
 
+
 What is Checked?
 ^^^^^^^^^^^^^^^^
 
@@ -259,6 +255,7 @@ create a link to the local label.
 For more information, refer this tutorial named `Using Intersphinx
 <https://my-favorite-documentation-test.readthedocs.io/en/latest/using_intersphinx.html>`_.
 
+
 .. _doc_style_conv:
 
 Style Conventions for the Documentaion
@@ -350,6 +347,7 @@ Style Conventions for the Documentaion
     and then included to eliminate redundancy, as these are frequently used
     in multiple files.
 
+
 Converting from Markdown
 ------------------------
 

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 50", "wheel", "setuptools_scm[toml] >= 6"]
+requires = ["setuptools >= 50", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
@@ -14,7 +14,6 @@ norecursedirs = [
    "dist",
    "build",
    "_build",
-   "dist",
    "etc",
    "local",
    "ci",
@@ -34,7 +33,9 @@ norecursedirs = [
    "thirdparty",
    "tmp",
    "venv",
+   ".venv",
    "tests/data",
+   "*/tests/test_data",
    ".eggs",
    "src/*/data",
    "tests/*/data"
@@ -50,3 +51,79 @@ addopts = [
     "--strict-markers",
     "--doctest-modules"
 ]
+
+[tool.ruff]
+line-length = 100
+extend-exclude = []
+target-version = "py310"
+include = [
+  "pyproject.toml",
+  "src/**/*.py",
+  "etc/**/*.py",
+  "test/**/*.py",
+  "tests/**/*.py",
+  "doc/**/*.py",
+  "docs/**/*.py",
+  "*.py",
+  "."
+
+]
+# ignore test data and testfiles: they should never be linted nor formatted 
+exclude = [
+# main style
+  "**/tests/data/**/*",
+# scancode-toolkit
+  "**/tests/*/data/**/*",
+# dejacode, purldb
+  "**/tests/testfiles/**/*",
+# vulnerablecode, fetchcode
+  "**/tests/*/test_data/**/*",
+  "**/tests/test_data/**/*",
+# django migrations
+  "**/migrations/**/*"
+]
+
+[tool.ruff.lint]
+# Rules: https://docs.astral.sh/ruff/rules/
+select = [
+#    "E",  # pycodestyle
+#    "W",  # pycodestyle warnings
+    "D",  # pydocstyle
+#    "F",  # Pyflakes
+#    "UP", # pyupgrade
+#    "S",  # flake8-bandit
+    "I",  # isort
+#    "C9", # McCabe complexity
+]
+ignore = ["D1", "D200", "D202", "D203", "D205", "D212", "D400", "D415", "I001"]
+
+
+[tool.ruff.lint.isort]
+force-single-line = true
+lines-after-imports = 1
+default-section = "first-party"
+known-first-party = ["src", "tests", "etc/scripts/**/*.py"]
+known-third-party = ["click", "pytest"]
+
+sections = { django = ["django"] }
+section-order = [
+    "future",
+    "standard-library",
+    "django",
+    "third-party",
+    "first-party",
+    "local-folder",
+]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 10
+
+[tool.ruff.lint.per-file-ignores]
+# Place paths of files to be ignored by ruff here
+"tests/*" = ["S101"]
+"test_*.py" = ["S101"]
+
+
+[tool.doc8]
+ignore-path = ["docs/build", "doc/build", "docs/_build", "doc/_build"]
+max-line-length=100