License

Apache-2.0 License File Conventions (Acid Genomics)

Applies to all repos under ~/git/personal/ and ~/.local/share/koopa/.

How GitHub detects licenses

GitHub uses the Ruby licensee gem. It normalizes the LICENSE file body (strips markdown, collapses whitespace, normalizes quote characters) and computes similarity against SPDX canonical texts. Detection requires ≥98% match — any abridged or substantively altered text drops below the threshold and the repo shows NOASSERTION in the sidebar.

Content is what matters, not filename or cosmetics. LICENSE, LICENSE.md, LICENSE.txt are all recognized equally. The normalizer makes these invisible to detection:

• format (plain text vs markdown headings/emphasis)
• straight " vs curly “” quotes
• trailing whitespace / extra blank lines

So only wording changes (missing clauses, swapped words) break detection.

Verify detection status — this is the ground truth, not the rendered sidebar:

gh api repos/acidgenomics/<repo> --jq '.license.spdx_id'
# Apache-2.0 = detected; NOASSERTION = not detected

Detection runs only on the repo's default branch. Pushing the fix to a non-default branch (e.g. koopa's develop) leaves the sidebar unchanged — the canonical LICENSE must reach main:

gh api repos/acidgenomics/<repo> --jq '.default_branch'

Canonical sources by repo type

Python packages + koopa + dotfiles → LICENSE (plain text)

Source: GitHub's own reference copy, guaranteed to match licensee exactly.

gh api /licenses/apache-2.0 --jq '.body' > LICENSE

Verify after writing:

grep -c 'consequential' LICENSE   # must be 1 (corrupted copies say "exemplary")

R packages → LICENSE.md (markdown-formatted)

Source: the usethis bundled template, which is the CRAN-expected format.

cp "$(Rscript -e 'cat(system.file("templates/license-apache-2.md", package="usethis"))')" LICENSE.md

Or locate it directly:

/Library/Frameworks/R.framework/Versions/4.6/Resources/site-library/usethis/templates/license-apache-2.md

LICENSE.md must appear in .Rbuildignore (CRAN prohibits bundling standard license text in the package tarball):

^LICENSE\.md$

DESCRIPTION field: License: Apache License (>= 2)

Verify:

grep -c 'consequential' LICENSE.md   # must be 1
grep 'LICENSE' .Rbuildignore         # must show ^LICENSE\.md$

The corruption that triggered this audit

All plaintext LICENSE files across koopa, dotfiles, and all py-* packages once shared an abridged variant (MD5 7216c64b041f0b8284981ca10dddaf1c, 193 lines, 10805 bytes). Key missing/altered content vs canonical:

• §8 "Limitation of Liability": said "exemplary damages", canonical says "consequential damages" — the single fastest check.
• §1 "Contribution" definition: truncated (dropped "any work of authorship, including the original version of the Work…").
• §1 "Derivative Works" definition: dropped "whether in Source or Object form".
• Several §4 redistribution clauses were abridged.

The R LICENSE.md files used the markdown-reflowed usethis format, which has canonical text. So R packages were already detected (Apache-2.0) while everything else was not (NOASSERTION).

Fixed 2026-06-20:

• 9 plaintext repos (real fix): koopa, dotfiles, all 7 py-* — replaced the abridged LICENSE with gh api /licenses/apache-2.0. This is what flips NOASSERTION → Apache-2.0.
• 24 R repos (cosmetic only): re-copied the installed usethis template into LICENSE.md. The sole diff was straight-quote → curly-quote typography, which licensee normalizes away — detection was already correct, so this commit is optional consistency, not a fix. Do not mistake an R LICENSE.md working-tree diff for a compliance problem; grep -c consequential was already 1.

Scope of repos affected

Repos	File	Source
koopa, dotfiles	LICENSE	gh api /licenses/apache-2.0
py-acidbase, py-acidgenomes, py-acidplyr, py-cellosaurus, py-goalie, py-pipette, py-syntactic	LICENSE	gh api /licenses/apache-2.0
all 24 r-*	LICENSE.md	usethis template

R packages do NOT have a plain LICENSE file — LICENSE.md + .Rbuildignore entry is the complete, correct setup.

Adding a license badge (README)

Dynamic badge — renders "Apache-2.0" once detection is working:

![License: Apache-2.0](https://img.shields.io/github/license/acidgenomics/<repo>)

koopa and dotfiles READMEs have this badge on the line after the lifecycle badge (added 2026-06-20). Python package READMEs do not currently carry a badge.