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Acid Genomics Python package release — python.acidgenomics.com PEP 503 S3+CloudFront index, koopa app python publish/reindex, quality gate, CHANGELOG format, smoke test. Use when releasing or publishing an Acid Genomics Python package.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Acid Genomics R package development conventions — per-project air.toml, global ~/.lintr only, roxygen2 8.x @importFrom split, S4 linter tuning, AcidDevTools::check() gate. Use when writing or checking an acidgenomics R package, configuring air/lintr, or fixing roxygen/lint failures.
koopa R package release — cloud-native S3 + CloudFront, acidgenomics profile, koopa app r publish/reindex/archive, sonoma-arm64 binaries, pre-release AcidDevTools::check() gate. Use when releasing, publishing, reindexing, or archiving an Acid Genomics R package.
PowerShell (pwsh 7+) activation architecture, starship integration, and color-mode sync in koopa. Use when writing or debugging lang/powershell/ files, editing activate-*.ps1 functions, adding prompt-tool support (starship, zoxide), integrating OS appearance detection, or porting shell logic from bash/zsh/fish to PowerShell.
koopa AWS environment configuration — the gitignored <koopa-root>/.env, load_dotenv()/aws_account_id()/koopa_s3_bucket() helpers in aws.py, required vars, bucket naming, lazy-eval rule. Use when adding an AWS secret, wiring a bucket/CloudFront ID, or debugging a missing AWS env var in release tooling.
How koopa manages home dotfiles via chezmoi — source-of-truth layout, the explicit --source flag, template-vs-generator ordering, XDG path derivation in templates, symlink_ source files for App Support bridges, diagnosing chezmoi status contamination from stale env, and the correct re-run command. Use when editing a dotfile, working in opt/dotfiles/chezmoi/, debugging a file that reverts on chezmoi apply, wiring a chezmoi template, or bridging XDG paths to macOS Library/Application Support.
How koopa propagates and applies dark/light color mode across SSH, tmux, shells, and chezmoi-rendered theme files. Use when debugging wrong-palette or stale-theme symptoms after a dark↔light flip, working on color-mode sync jobs or watchers, editing the chezmoi color-mode apply path, or investigating why bat/starship/delta renders the wrong theme while fzf/LS_COLORS look correct.
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| name | koopa-python-release |
| description | Acid Genomics Python package release — python.acidgenomics.com PEP 503 S3+CloudFront index, koopa app python publish/reindex, quality gate, CHANGELOG format, smoke test. Use when releasing or publishing an Acid Genomics Python package. |
Python packages are hosted at python.acidgenomics.com — a private PEP 503
"simple" index backed by S3 (bucket in _BUCKET in lang/python/src/koopa/pypi.py) and served
via CloudFront. Packages are NOT published to public pypi.org.
s3://…/packages/<file>/) — index.html + <name>/index.htmlkoopa app python publish <package-dir> (calls koopa.pypi.publish)koopa app python reindexlang/python/src/koopa/pypi.py# one-off
uv pip install --index-url 'https://python.acidgenomics.com/' syntactic
# project pyproject.toml
[[tool.uv.index]]
url = "https://python.acidgenomics.com/"
py-syntactic)Applies to any package in ~/git/personal/py-<name> that uses bumpver +
uv_build. Adapt as needed for other projects.
pyproject.toml (version = "X.Y.Z" and
current_version = "vX.Y.Z" under [tool.bumpver]).ruff format --check src/ tests/ docs/
ruff check src/ tests/ docs/
pyright
ty check
pytest
bumpver is configured with tag = false, push = false, commit = true.
Running bumpver update --patch (or --minor/--major) bumps two lines in
pyproject.toml and creates a single commit — no tag, no push. The user owns
tagging and pushing.
pyright and ty check must exclude tests/ (test files import pytest,
a PATH dev tool not in the venv). Add to pyproject.toml:
[tool.pyright]
exclude = ["tests", ".venv"]
[tool.ty.src]
exclude = [".venv", "**/__pycache__", "**/.*", "tests"]
ty check can fail with Invalid VIRTUAL_ENV if the shell has a stale env
var (e.g. after moving the repo). Fix with:
[tool.ty.environment]
python = ".venv"
VIRTUAL_ENV and points ty directly at the local venv.pytest needs pythonpath = ["src"] in [tool.pytest.ini_options] for
src-layout packages to be importable without a venv install.koopa app python publish ~/git/personal/py-syntactic
This runs uv build, uploads wheel + sdist to S3, regenerates the PEP 503
index HTML at the bucket root, syncs it (with --exclude "packages/*" to
protect wheels from --delete), and invalidates CloudFront /*.
Requires: AWS profile acidgenomics configured; AWS_CLOUDFRONT_DISTRIBUTION_ID_PYTHON
set (or AWS_CLOUDFRONT_DISTRIBUTION_ID as fallback) — loaded from
<koopa-root>/.env if not already in the environment.
git tag vX.Y.Z
git push origin main
git push origin vX.Y.Z
Merging develop→main via PR before tagging is the standard flow.
After publish, confirm the package is installable:
tmp=$(mktemp -d)
uv venv --quiet "$tmp/venv"
uv pip install --python "$tmp/venv/bin/python" \
--index-url 'https://python.acidgenomics.com/' \
syntactic
"$tmp/venv/bin/python" -c "import syntactic; print(syntactic.__all__)"
rm -rf "$tmp"
The index is served at the domain root (not /simple/). The S3 bucket
structure is:
packages/ ← wheels + sdists (never touched by reindex sync)
index.html ← root listing: <a href="syntactic/">syntactic</a>
syntactic/index.html ← per-package: links to ../packages/<file>#sha256=…
_sync_index_to_s3 uses --exclude "packages/*" with --delete so that
reindexing never wipes uploaded artifacts.
Keep-a-Changelog style, version at top. Example heading:
## 0.1.0 (2026-06-19)
Sections: ### Features, ### Bug Fixes, ### Changes, ### Tests.
Omit empty sections.
Rendered Sphinx docs are hosted at python-docs.acidgenomics.com — a separate S3 bucket + CloudFront distribution from the package index, so the two are fully independent (reindex never touches docs).
https://python-docs.acidgenomics.com/<name>/python-docs → python-docs-<acct>-us-east-1-an
(via koopa_s3_bucket("python-docs") in aws.py)AWS_CLOUDFRONT_DISTRIBUTION_ID_PYTHON_DOCS
(fallback: AWS_CLOUDFRONT_DISTRIBUTION_ID)koopa app python publish-docs <package-dir>
(calls koopa.pypi.publish_docs)lang/python/src/koopa/pypi.py — publish_docs()koopa app python publish-docs ~/git/personal/py-syntactic
This:
[project] name from pyproject.toml, PEP 503-normalises it.uv run --extra docs sphinx-build -W -b html docs/ <tmp>/html.<tmp>/html/ → s3://python-docs-<acct>-us-east-1-an/syntactic/
with --delete (scoped to that package's subtree only)./* on the docs distribution.Requires: AWS profile acidgenomics configured;
AWS_CLOUDFRONT_DISTRIBUTION_ID_PYTHON_DOCS set in <koopa-root>/.env.
python-docs-<acct>-us-east-1-an (same region/account as the
package index bucket).python-docs.acidgenomics.com, ACM cert, default root object index.html.python-docs.acidgenomics.com → CloudFront distribution.AWS_CLOUDFRONT_DISTRIBUTION_ID_PYTHON_DOCS to <koopa-root>/.env.# Dry-run docs build locally (no AWS required):
cd ~/git/personal/py-syntactic
uv run --extra docs sphinx-build -W -b html docs/ /tmp/docs-test
# After publish-docs:
curl -sI https://python-docs.acidgenomics.com/syntactic/ | head -5
# Confirm package index is unaffected:
koopa app python reindex
curl -sI https://python-docs.acidgenomics.com/syntactic/ | head -5
R packages are hosted at r.acidgenomics.com via a drat repo in
~/git/personal/r-acidgenomics-com, using the same AWS account/profile/
CloudFront pattern. The Python index reuses that infra with a hand-rolled
PEP 503 generator in place of drat.