@@ -6,48 +6,7 @@ project adheres to [Semantic Versioning](https://semver.org/).
66
77## [ Unreleased]
88
9- ### Documentation
10-
11- - ** Second README pass: less lecturing.** The first pass moved caveats out of the reading path; this one
12- cuts explanation a reader does not act on. Gone: the decimal-vs-binary units lesson on the free-disk
13- bullet ("a volume sold as 100 GB is 93.1 GiB, so it fits with ~ 2 GiB spare"), ~ 15 lines on why conda envs
14- are large (pip hardlinking, ` du -sc ` semantics), a units note explaining an inconsistency in our own
15- tables, the provenance of an older audit's equivalence numbers, and the history of the background
16- downloader's previous fetch rule. Also removed five outright duplications — a comment-only BedGraph code
17- block that pointed at the real recipe, two ways to load the same genome, ` Core concepts ` re-defining
18- "Oracle" and "Track" from ` Key terms ` , ` Key terms ` re-defining "Conversational genomics" from the
19- paragraph three lines above it, and the credentials/conda-env rule stated in two places. Cumulatively
20- since 0.7.5: aside text ** 12,229 → 6,409 chars (−48%)** , longest aside 1,692 → 704, prose lines over 420
21- chars 17 → 8.
22-
23- One guard was deleted rather than satisfied: ` test_the_tldr_install_size_agrees_with_the_disk_table `
24- existed to keep the TLDR's install size in sync with the disk table, and the TLDR no longer states an
25- install size, so there was nothing left to keep in sync.
26- - ** README restructured to cut clutter.** It had accumulated ** 24 blockquote asides totalling 12,229
27- characters** , the longest 1,692 — caveats and per-release detail interrupting the reading path rather
28- than living somewhere findable. Now ** 6,793 characters** (−44%), longest 704. The changes are structural,
29- not just shorter: one ** Caveats** section holds the four things that can change a number (Enformer
30- cross-process variation, the pre-0.7.5 ` alphagenome_pt ` splice history, Cherimoya-vs-ChromBPNet
31- magnitude, hg38-only), with inline asides reduced to pointers; token plumbing moved from the quick start
32- into the installation section; and per-release detail is delegated to this changelog, so the README stops
33- growing by a line per release.
34- - ** Six documentation defects fixed** , found auditing notebooks, examples, docs and the nulls:
35- - ` examples/walkthroughs/README.md ` described Sei by its ** pre-0.7.4 scope** ("40 sequence classes") in a
36- table the README calls a "full side-by-side comparison" — which also covered only 6 of 8 oracles.
37- Corrected, with Cherimoya and EPInformer-seq added.
38- - ` docs/variant_analysis_framework.md ` still carried the ** "1–2 % fp32 noise"** backend-equivalence claim
39- that 0.7.5 corrected in the README: understated, and false for the ` SPLICE_SITES ` assay.
40- - ** ` describe_tracks() ` appeared zero times in ` docs/ ` ** , including the "Full Python API reference". Now
41- documented there with its signature, its load-free guarantees, and what it replaces.
42- - ` docs/BACKGROUND_NULL_PROTOCOL.md ` had ** no record that ` alphagenome_pt ` has no null of its own** and
43- ranks against ` alphagenome ` 's. New §8b states the alias, the premise, the test that enforces it, and
44- that the test must be extended before another oracle is aliased. Decision logged for 2026-08-18.
45- - ` examples/notebooks/README.md ` said each notebook "produces … outputs inline" while ** 16 code cells
46- across three ship blank** — the cells needing a second oracle env or ` coolbox ` . Now stated.
47- - The free-disk bullet still said a single-oracle install is "~ 13 GiB, not 85" after the total moved
48- to 87.
49- - Full findings, what was verified clean, and the guard/false-positive notes:
50- [ ` audits/2026-08-18_post_v075_docs_and_readme_audit.md ` ] ( audits/2026-08-18_post_v075_docs_and_readme_audit.md ) .
9+ _ Nothing yet._
5110
5211## [ 0.7.5] — 2026-08-18
5312### Fixed
@@ -145,6 +104,46 @@ project adheres to [Semantic Versioning](https://semver.org/).
145104- ` TrackRecord.has_background ` no longer promises more than it delivers: no oracle populates it, so
146105 the docstring now says so and explains why (` describe_tracks() ` stays download-free), pointing
147106 callers at ` NormalizationLoader.has_background ` .
107+ - ** README restructured to cut clutter.** It had accumulated ** 24 blockquote asides totalling 12,229
108+ characters** , the longest 1,692 — caveats and per-release detail interrupting the reading path rather
109+ than living somewhere findable. Now ** 6,793 characters** (−44%), longest 704. The changes are structural,
110+ not just shorter: one ** Caveats** section holds the four things that can change a number (Enformer
111+ cross-process variation, the pre-0.7.5 ` alphagenome_pt ` splice history, Cherimoya-vs-ChromBPNet
112+ magnitude, hg38-only), with inline asides reduced to pointers; token plumbing moved from the quick start
113+ into the installation section; and per-release detail is delegated to this changelog, so the README stops
114+ growing by a line per release.
115+ - ** Second README pass: less lecturing.** The first pass moved caveats out of the reading path; this one
116+ cuts explanation a reader does not act on. Gone: the decimal-vs-binary units lesson on the free-disk
117+ bullet ("a volume sold as 100 GB is 93.1 GiB, so it fits with ~ 2 GiB spare"), ~ 15 lines on why conda envs
118+ are large (pip hardlinking, ` du -sc ` semantics), a units note explaining an inconsistency in our own
119+ tables, the provenance of an older audit's equivalence numbers, and the history of the background
120+ downloader's previous fetch rule. Also removed five outright duplications — a comment-only BedGraph code
121+ block that pointed at the real recipe, two ways to load the same genome, ` Core concepts ` re-defining
122+ "Oracle" and "Track" from ` Key terms ` , ` Key terms ` re-defining "Conversational genomics" from the
123+ paragraph three lines above it, and the credentials/conda-env rule stated in two places. Cumulatively
124+ since 0.7.5: aside text ** 12,229 → 6,409 chars (−48%)** , longest aside 1,692 → 704, prose lines over 420
125+ chars 17 → 8.
126+
127+ One guard was deleted rather than satisfied: ` test_the_tldr_install_size_agrees_with_the_disk_table `
128+ existed to keep the TLDR's install size in sync with the disk table, and the TLDR no longer states an
129+ install size, so there was nothing left to keep in sync.
130+ - ** Six documentation defects fixed** , found auditing notebooks, examples, docs and the nulls:
131+ - ` examples/walkthroughs/README.md ` described Sei by its ** pre-0.7.4 scope** ("40 sequence classes") in a
132+ table the README calls a "full side-by-side comparison" — which also covered only 6 of 8 oracles.
133+ Corrected, with Cherimoya and EPInformer-seq added.
134+ - ` docs/variant_analysis_framework.md ` still carried the ** "1–2 % fp32 noise"** backend-equivalence claim
135+ that 0.7.5 corrected in the README: understated, and false for the ` SPLICE_SITES ` assay.
136+ - ** ` describe_tracks() ` appeared zero times in ` docs/ ` ** , including the "Full Python API reference". Now
137+ documented there with its signature, its load-free guarantees, and what it replaces.
138+ - ` docs/BACKGROUND_NULL_PROTOCOL.md ` had ** no record that ` alphagenome_pt ` has no null of its own** and
139+ ranks against ` alphagenome ` 's. New §8b states the alias, the premise, the test that enforces it, and
140+ that the test must be extended before another oracle is aliased. Decision logged for 2026-08-18.
141+ - ` examples/notebooks/README.md ` said each notebook "produces … outputs inline" while ** 16 code cells
142+ across three ship blank** — the cells needing a second oracle env or ` coolbox ` . Now stated.
143+ - The free-disk bullet still said a single-oracle install is "~ 13 GiB, not 85" after the total moved
144+ to 87.
145+ - Full findings, what was verified clean, and the guard/false-positive notes:
146+ [ ` audits/2026-08-18_post_v075_docs_and_readme_audit.md ` ] ( audits/2026-08-18_post_v075_docs_and_readme_audit.md ) .
148147
149148## [ 0.7.4] — 2026-08-17
150149
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