v0.4.10
What you can do now
The Genome tab is one page at a time, and it opens with findings. Seven
headings on one scroll — all open, the maintenance block above every conclusion,
and the same gene appearing in four of them without any of them saying so — are
now panes of one tab. The first is neither ClinVar nor polygenic nor longevity: it
is one list, ordered by how much a line can change and marked with the source each
came from. Clicking a gene anywhere on the tab gathers what every source holds
about it into a single card: the loci and their genotypes with coverage, what
ClinVar says at those positions, what the longevity layer and the lipid card say
about that gene. Nothing was removed — the sections are still there, one at a
time, and the service text each of them opened with is folded rather than first.
The documents inside the package open as pages, and the second opinion offers
the one written for a clinician. The product's own output names files — «see
PREPARING-THE-GENOME.md» — and after pip install the only way to read one was
scholion doc <name> at a terminal, which the person reading the interface may
not have open. The local server now serves the same nine documents at
/doc/<name>, each as a self-contained page that prints on paper and pulls
nothing from the network. «Second opinion» carries a button to the one-page
description for clinicians and researchers: what the program is, what it
computes, and where it refuses to answer — meant to be handed over at the
appointment.
The first screen is the person. It opened with the one experiment being run
this month and reached the reader before anything about the reader. The order is
now the order the questions come in: who the data belong to — sex, age, height,
body-mass index, the reference panel — then their own indicators, then the
targets they are aiming at, then the body systems and the figure, then what is
out of range right now, then what is worth measuring, and last the focus of
attention. Every block still names the tab that owns it and goes there on a
click.
The Profile tab is retired into that first block. It held four cards and two
forms, and the four cards were the ones a watch measures every day; as a tab of
its own it had become the emptiest page in the product. Nothing it could do was
lost — the profile form, the manual measurement form and the list of what the
profile is still missing all open at the top of the first screen.
The state of the genome is said in one place, including when it is not being
read. The tab used to show a grey badge and leave the reason unprinted; a
person whose folder held more than one candidate file met «not read» in six
places and the cause in none. The state now carries the file, the assembly, the
sample, what was set aside and why — and, where a choice is open, the names with
a button beside each. The choice is kept, so it is asked once
(scholion choose-genome at the command line).
«What to test» is part of the second opinion. Every row of it is a line for
the same conversation, and it was a tab that handed half of its own list back to
the tab beside it. The routine controls travel with it, folded.
The lifestyle brief's «needs review» can be answered. The flag is raised when
a marker a block watches is measured after the block's wording was last read, and
until now nothing in the product could lower it: it went up once and stayed up, at
the top of the tab, above the content. There is now one button — the wording still
holds — which records the date that has always been what the flag compares against
(scholion brief-reviewed <block>). It also moves down the page to sit beside the
wording it is about.
What is fixed
Accepting the reach baseline moved the whole file to whichever machine ran
it. A number in test_reach_baseline.json is not a property of the code
alone: it is what the suite reached on one interpreter, with one backend — the
two do not count a line identically — and, for at least one module, only where a
file the repository does not carry happens to sit. --strict had printed a
warning whenever the run and the recorded stamp disagreed; --accept rewrote
every number regardless, restamped the file, and reported it in one line.
There are three writing modes now, and only one of them moves the file.
--accept records the whole measurement and refuses when the baseline was taken
elsewhere — before measuring, since the answer never depended on the ninety
seconds. --accept-new records only modules that have no accepted number yet,
which is what the suite's own guard asks for when a module is added; it changes
no other number, not the overall, and not the stamp, and it does not run the
suite at all when there is nothing to add. --rebaseline is the deliberate
whole-file move and prints every number it lowers, old → new, before writing.
A document name was tolerant about spelling, which was free until a route
handed it one. DATA_LAYOUT, data-layout.md and data-layout are one
request, and refusing two of them teaches nothing but the exact spelling. While
the only caller was a person typing at their own prompt, that was the whole
story; a URL is composed by whoever holds it, and ../../../etc/passwd builds a
path outside the package as readily as a name builds one inside it. The
tolerance stays and the shape does not: a document name is one file name, or it
is nothing. Anything else opens the list of documents instead.
Seven of the thirteen rows of the goal table said «—» while the numbers sat in
the file. Weight, body-mass index, body fat, muscle mass, VO₂max, resting heart
rate and steps come from a wearable device, and five of the goal charts drew
nothing at all. The lifestyle layer stores a measurement together with the device
that made it — two watches do not measure resting heart rate the same way, and
one series built out of both shows a step on the month the second export was
loaded — and the goal reader had been written before that was true. It looked for
the metrics where they used to sit, found nothing, and returned an empty series.
Nothing failed and nothing was logged: «—» is what that table prints when there
is no data, and there was a decade of it.
Two things follow, and both are new behaviour rather than a repair. The reader
goes through the accessor that knows the file's shape, so a file written by an
older version answers exactly as a current one does. And a row with no number now
says which of three things is the matter — nothing carries this series, the
series is empty, or more than one device measures it and the goal has to say
whose. The last of those is refused rather than averaged, and a goal may name the
device (wear:garmin:RestingHeartRate) to answer it.
A number the watch already had was reported as missing, or as three weeks
old. Some indicators are kept twice: what a person types in, and what a device
records every day. Only the first was read. Steps stood at a single figure
entered in July and were called «below target», while the device series had the
month just gone above it; sleep showed nothing at all beside seventy-five months
of nightly data; a resting heart rate from December stood as the current one in
September. The two are joined now: the newest measurement is the one shown, each
card says which store it came from and on what date, and the other store is
printed beside it rather than instead of it. A tie goes to the hand-entered
reading — a monthly mean and a measurement taken on a day are not the same
statement. Neither file is written to.
The pairing is declared once, in the shipped wearable reference, and only where
the two are the same quantity. Where they are merely similar it is left out and
the row goes on saying it has nothing behind it: intensity minutes are not
«minutes of activity», and a pairing that is nearly true prints a number nobody
can act on.
The goal board was dated by one of the files behind it. The heading read
«data as of» the timestamp of the wearables file, while half the rows come from
the laboratory — so a table carrying a draw from the 3rd was headed with the 23rd
of the month before. Every row carries its own date now, and the heading carries
the newest of them.
A stored result was deciding what language the product speaks. Polygenic
risks and longevity markers printed in Russian while the interface was English.
Neither catalogue is missing a translation — both carry every name in both
languages. The names were coming from prs_results.json and
longevity_findings.json, which are stored RESULTS: each label is a copy of the
catalogue made on the day of the run, in whatever language that run was speaking.
The catalogue now decides what a thing is called and the file decides what the
number is; a trait or a marker the catalogue does not carry keeps the name it was
stored with, because a percentile with no name is worse than a name in one
language.
The longevity layer showed genotypes and explained none of them. Each row
printed a gene, an rsID, a genotype — and an explanation line that was always
empty, because the page asked for a field these rows do not carry. Everything
that says what a marker MEANS was in the catalogue, in both languages, unread: what
the allele is, what a second copy does, what it argues for, what population the
direction holds in, and the papers behind it. Rows now carry all of it, sorted so
that what was found comes first and what was checked-and-quiet folds away. The
verdict and the strength of the sources are written out as sentences rather than
as the internal words they are — and a word the catalogue does not recognise is
never turned into a message key, which is how «⟦longevity.verdict.…⟧» used to
reach a reader.
APOE says what APOE is. The card led with «APOE — status» over two rsID
numbers, which tells a reader nothing about the gene or about their own
combination. It now opens with what the gene is and what this particular pair
means, says plainly that it is a factor and not a diagnosis, and folds the two
positions it was computed from underneath.
A file carved out of a genome was counted as a second genome, and the whole
genomic layer went dark behind it. Files called from the same reads at a chosen
list of positions — the loci of the catalogue, the scoring sites of the polygenic
models — sit beside the main file by design. They were recognised by NAME, from a
list of four; an output written under a fifth name became a second candidate, the
choice became ambiguous, and a refusal to guess between two files means no locus is
read at all. Nothing failed and nothing was logged. Every genomic answer said «not
read» — including a card that named two positions and said they had not been read
while the reads sat in the file beside it.
What a file is called no longer decides anything. bcftools records its command in
the header, and a pileup restricted to a list of sites, or an annotation pass over
another file's rows, is an extraction rather than the genome it came from; files
this project writes stamp themselves besides. The rule may narrow the set of
candidates and may never empty it — a folder holding nothing but extractions still
holds the person's reads — and whatever it sets aside is named with its reason
rather than dropped in silence.
A card no longer blames the positions when the genome is not being read. «The
PCSK9 positions have not been read» is a statement about two rows of a file that is
open. With no genome connected there is no such file, and the sentence sent a
reader to look at their sequencing when the answer was in the folder beside it.
What is retracted
No stored value changes. Answers that said «not read» for the reason above will
now say what the reads say — which is not a retraction of a claim but the end of
a refusal.
One claim is retracted, and it was a claim about a person rather than a silence:
an indicator whose hand-entered point was older than the device series was judged
against its target on the old point. Where that judgement was «below target» and
the device disagrees, the flag changes with this version. Nothing was stored, so
nothing has to be undone — but a printed page or an exported summary made before
this version may carry the old flag.
What needs recomputing
Nothing has to be recomputed and nothing has to be re-imported. A profile whose
genome folder holds one file behaves exactly as before; one that holds several is
asked, once, which file is the genome, and everything that was silent answers
from it. The wearable series were on disk the whole time — they are read now, not
rebuilt — so the goal charts fill in on the first run with no export and no
ingest.