v0.4.9

What you can do now

The Overview draws the body beside the radar. The same systems, twice:
the radar as before, and a figure on which every system with a place on a body is
lit by its score. Around each mark a ring shows how much of that system was
actually measured, which is the number the radar has never been able to show. A liver scoring 100 out of 100 on one marker of three is a full
point at the edge of the radar and a ring closed a third of the way on the body.
Picking a system on either picture marks it on the other.

The endocrine system is four systems, and each is scored on the panel a
laboratory actually issues. One domain called «Hormones», averaged from
testosterone, IGF-1 and TSH, is gone. In its place the radar carries the thyroid
axis (TSH, free T4, free T3, anti-TPO), the adrenals (cortisol, DHEA-S), the
gonads (testosterone, DHT, estradiol) and the growth axis (IGF-1, growth
hormone). The ring beside each now says how much of that panel exists, instead of
how much of a mixture of three markers nobody orders together; a system with
nothing measured is not drawn at all rather than averaged into the picture.

A hormone is marked at the gland that makes it, not at the organ it is read
for: TSH and growth hormone at the pituitary that secretes them, free T4, free T3
and anti-TPO at the thyroid, cortisol and DHEA-S at the adrenals, IGF-1 at the
liver that writes it, testosterone at the gonads. Each mark carries the score of
what is made there — the average of a whole axis would print the same number in
two places and mean it in neither. Two hormones answer instead that there is no
one place to mark: DHT is converted in the tissues that respond to it, and
estradiol comes from the ovary in one person and from adipose tissue in another.
An antibody is the one named exception to the rule — anti-TPO is made by
lymphocytes, which are everywhere and mean nothing as a place, so it is marked at
the gland it is raised against. A reason is recorded beside every placement, and
beside every refusal to place.

The pancreas is on the map. It is a system of its own now — amylase, its
pancreatic fraction, lipase and C-peptide, the acinar cell and the beta cell
together — and insulin, which stays in the carbohydrate panel because HOMA-IR is
computed from it, is marked at the gland that secretes it. Nothing else about
carbohydrate metabolism moves: glucose, HbA1c and the index itself say plainly
that they are made nowhere in particular.

A reference interval that belongs to one sex is no longer lent to the other.
Six markers carry both corridors and were already handled. Every other marker
carries one, transcribed from the forms of one person — and it was borrowed by
anybody whose own laboratory printed no range. HDL's floor of 1.0 mmol/L is a
man's; so are AST's ceiling of 40 U/L, GGT's of 60, and the intervals for DHEA-S,
DHT and estradiol. Borrowed for a woman, none of them failed: each produced a
verdict, and the wrong one. Every marker a body system is scored on now declares
whether its corridor depends on sex — silence was what made the class invisible,
so silence now fails the build — and a corridor is withheld, with the reason
printed, rather than lent across that boundary. A person's own form is unaffected:
it is always preferred, and this only ever governed what fills a hole.

A number with no reference interval beside it no longer costs its system
points. Such a marker scored 55 out of 100 — the score for «a deviation whose
size cannot be assessed» — when there is no deviation, because there is nothing to
deviate from; and it was counted among the system's deviations, while the marker
list on the same screen said, correctly, that it was not one. It is now left out
of the score and out of that count, and still counted as measured: a system whose
only measured markers carry no corridor reports no score rather than a mediocre
one.

The five systems with no place on a body say so rather than being drawn on an
organ they do not belong to; which is which is recorded with a reason beside each
entry, and a system added to the radar without one now fails the build. The figure
is drawn male or female from the profile; where the profile does not say, it is
not drawn at all and the radar answers alone.

Windows is a supported platform. The package, the command line, the local
web application and the assistant skill run there, and a cell of the test matrix
now says so on every commit rather than leaving it to hope. The promise and the
check are tied together: a platform named in the package metadata with no runner
behind it, or a runner with no promise in front of it, now fails the suite.

Two things stay Unix-only and both are optional. The crossread wrapper is a
shell script — on Windows the installed scholion command is the same core, so
nothing is lost but the second name. Building a genome from raw reads drives
external alignment and coverage tools through shell scripts; every such tool is
looked for before it is used, so where one is missing the answer names it
instead of failing. The data directory on Windows is %USERPROFILE%\.scholion,
and SCHOLION_REPO_DIR overrides it as everywhere else.

The suite can be started without a shell. Until now the only way to run it
was a bash script, including the run the release procedure requires INSIDE the
unpacked package. There is now a second entry point written in Python that does
the same run, so a person who received the package can check it on a machine
that has no shell at all. The build carries it, and a check makes sure of that:
every way of starting the suite that the project's own automation uses must be
present in the package a recipient receives, or the build fails.

Any gene can be asked about, not only one in the curated catalogue. scholion genome --gene CASR used to answer "Gene CASR is not in the coordinate reference"
— true about loci.json, which is a book of pharmacogenetic loci, and easily read
as a statement about the genome, whose reads were there the whole time. The gene
name is now resolved to coordinates from a local Ensembl annotation (or from
Ensembl live, cached afterwards), the interval is cut out of the personal VCF,
coding variants are separated from the rest by the coding exons of the canonical
transcript, and what each one does to the protein is computed against the same
reference the genome was called against — no web service is asked, and no
coordinate leaves the machine.

A gene report prints coverage before it prints findings. Every reassuring
thing such a report can say has the form "no such variant", and that sentence is
empty until the region is known to have been read. Read depth is computed
directly from the alignment, without samtools or pysam, and it reproduces the
project's own native callability run exactly — mean and every threshold, to the
last base, on four genes across three chromosomes. Where a piece is missing the
report names it and what would supply it: coverage without an alignment prints as
"not measured — because", and "changing the protein: 0" is replaced by "not
computed" wherever the reference was absent, because a zero and an uncomputed
number look identical on the page and mean opposite things. The two blind spots
of short reads — large exon-level deletions, and deep intronic or regulatory
variants — are printed on every answer, not only on the reassuring ones.

Three analytes the dictionary did not know are now recognised. A urine
albumin-to-creatinine ratio, a urine microalbumin and a total T3 went through
ingest-labs without a word: an unrecognised line is skipped, and a skipped line is
indistinguishable from a line that was never on the form. All three sit on real forms
of an ordinary laboratory, and the ratio is one of the two axes of KDIGO staging — a
value whose absence changes what may be said about the kidneys. Total T3 gets its own
table rather than joining free T3: the two are reported in different units (ng/dL
against pg/mL) and the same number under the wrong one is out by an order of
magnitude. The unit table learned mg/g, so the ratio prints with a unit rather than
a code.

A polygenic percentile is printed with two quantities beside it: how stable
the number is, and how informative the model is. A bare percentile looked
equally convincing for coronary artery disease and for intelligence, and it is
not: for the second, the choice of reference population moves the number by
some fifty points while the model's whole range separates the outcome by a
few. The two are different properties and are shown as such, under every
percentile in the prs report and in its JSON. Stability belongs to the
measurement — the spread of the percentile across the five reference
populations, its spread across the models scored for the trait, and the share
of the model your file actually covers. Informativeness belongs to the model —
its discrimination (AUROC), and what the score's range from the 10th to the
90th percentile does to the outcome, read per standard deviation as the
catalogue reports it. A figure that is not on the machine is named as «not
recorded» rather than left out, because a line with one number and a line
with three look alike only when the missing two are silent. The two are not
folded into one «signal to method» ratio: the effect size cancels out of such
a ratio, and what remains is the population spread written in other letters.

What is fixed

A corridor transcribed at one age was lent at every age, and most corridors
did not say whose they were. The rule that keeps one sex's interval from the
other covered only the markers the body systems score; the other three hundred
and forty held a corridor and were silent about it, so a man's prolactin or
LH interval could still be borrowed for a woman whose form printed no range.
And age was not modelled at all: IGF-1 and DHEA-S depend on it more than on
sex, every laboratory bands them, and the dictionary held one corridor each.
Every corridor now declares both — whose it is, and whether age governs it —
with three states for age: independent, banded with the band on record
unknown (lent to nobody), or a band in years (lent inside it; an unrecorded
age is not lent a band). A corridor that could not be checked against a form
or a standard interval says so in a word — unreviewed — and is lent to
nobody until it is; nine are marked so, the estrogen-metabolite panel among
them, and that number may only shrink. PSA is a different case again: not a
man's interval but a test that exists for the male sex only, and for a woman's
profile the value is shown with that sentence rather than with a borrowed or
withheld corridor. The reason is printed beside the value in each case, and it
names what would supply the corridor: the range on the person's own form, or
the birth year in the profile.

A value was judged by a range its own form did not print. The rule that
the range on the person's own form wins held only at the level of the marker,
which keeps the first range it met and is not rewritten by later forms; no
stored value carried the range printed beside it. A September draw was then
judged by a corridor recorded in December, or by one entered by hand. An ionised
calcium the form called a hair under its 1.10–1.35 read as deeply low against
a 1.16–1.32 recorded months before; a DHT five per cent under one corridor was
twenty-three per cent under the other. The range printed on the form now
travels with the value and the verdict stands on it; where a value has none,
the marker's recorded range answers and the report says so; and a series whose
corridor changed between draws says that its values compare and its flags do
not.

A bound printed instead of a number lost its sign. A laboratory that
cannot quantify a value prints the limit — «< 0.09 nmol/L» — and the ordinary
form reader stored the number without the sign, as if 0.09 had been measured.
The engine has carried a censoring mark for such values all along, and two
special readers (flora, titres) supplied it; the common path did not, and a
series of «below the limit» results read as a level that later rose. The sign
is now read from the text immediately before the value — <, >, ≤, ≥
and their spelled-out forms — so a bound in a reference column further along
the row cannot be mistaken for it.

Calcium measured by two methods was filed as one series. Elemental
analysis (ICP) prints calcium in mg/L; a biochemistry panel prints total
calcium in mmol/L; one marker caught both and converted the second into the
first by molar mass. The two methods disagree beyond rounding — thirteen per
cent on the same person two months apart — and a series that holds both
presents a change of method as a trend. Total calcium is now a marker of its
own, the elemental one no longer reads a biochemistry form, and the rule is
written where the next mineral will meet it: a series belongs to a method, not
to a substance — a unit conversion is legitimate within a method and not
across methods. Magnesium and the other minerals have not been checked yet.

A form that printed «HOMA-IR» in the Cyrillic alphabet was not read. The
dictionary knew the index by its Latin spelling only; the file was refused
with an honest reason and the value had to be entered by hand. Both alphabets
are recognised now, and «insulin resistance index» as well.

A report could not be redirected to a file. scholion labs > labs.txt, and
every other command whose output was piped or saved rather than read on screen,
ended in a crash partway through — thirteen of sixteen commands measured. The
reports are written with arrows, dashes and guillemets, and the encoding a
redirected stream inherits from the system cannot always carry them. Output is
now written as UTF-8 whatever the system would have chosen, so a saved report is
the report. A character that still cannot be written appears as its own escape
rather than as a question mark, so what was lost is visible.

Files were read in whatever encoding the machine assumed. A genotype table,
a cached answer or an export written as UTF-8 and read back through a national
code page does not fail — it decodes, wrongly, and where the read also asked for
replacement characters the wrongness was silent by construction. Every text read
and write in the package now states its encoding, and a check over the source
refuses a new one that does not. Twenty-nine places were corrected; six of them
were never reached by any test, which is why the check reads the source rather
than watching a run.

Two programs writing the profile at once could lose a change. Where the
system offers no lock between processes — Windows has none — the local web
application and a command line each read a file, changed one field and wrote it
back; whoever finished last erased the other, with no error anywhere. A lock the
program takes itself now covers that case, and where it is already held the
second writer says who holds it and stops rather than writing over them. A lock
left behind by a run that died is taken over after a minute.

The update button reached for a shell that need not exist. On a machine
without one it now says so in a sentence, instead of showing the failure of a
program it tried to start. The search path it builds is also joined the way the
platform joins it, rather than always with a colon.

The monthly reanalysis stopped at its first step. The ClinVar annotation
(annotate_clinvar.sh) died with «GEN: unbound variable» on the first scheduled
run: the branch that looks for a reference FASTA named a variable that belongs
to the orchestrator calling it, not to the script itself, and set -u stopped
it at the first of three such places. All three now use the script's own
GENOME_DIR. The annotation has not yet been re-run against the fresh ClinVar
release; until it is, findings stand on the release recorded in the profile.

A profile that spelled its sex «f» or «m» could be measured against the wrong
reference row. Several spellings of sex are accepted when a profile is
written — «f», «female», «woman» and their male counterparts — but the reader
that picks the applicable row of a multi-row reference interval compared the
raw spelling with «male»/«female», so for any other spelling the sex half of
that choice was silently off: a men-only row could fit a woman, a women-only
row a man. The reader now recognises sex the way everything else does. A
profile created by scholion init was never affected — it can only write the
two spellings; the demonstration profile and imported or hand-edited profiles
were.

The version shown could be another installation's. With any scholion
distribution installed on the machine — an older one from the registry, kept
for comparison — a copy run from its source tree reported the installed
number rather than its own, in the server's header and in --version. The tree
now answers for itself; an installed copy still answers from its metadata.

The polygenic-score layer could stop starting on a machine that had run it
the week before. The scoring sidecar is fetched into an isolated environment
on first use, and its own dependency declaration left one library unbounded; a
newer major version of that library reached the index in August, and any fresh
cache took it — the sidecar then died at start-up, before the first request,
and prs, its page in the web application and the monthly reanalysis all
reported a server that «exited without an answer». The resolution is now pinned
below that major version wherever the sidecar is launched, from the application
and from the setup script alike; a constraint already set in the environment
by whoever runs it is respected rather than overruled. The message for a server that
exits without answering now carries its exit code and names this cause and the
pin, so a recurrence reads as «the pin was not applied» rather than as silence.

Every polygenic-score computation went to the server twice. Two optional
settings of the report — a wider pool of candidate models, and the models of
child traits — are not accepted by the pinned sidecar; they were sent with every
trait, refused with every trait, and each trait was computed again without them,
so a full panel cost double for a setting that was never in force. A refusal is
now remembered for the rest of the run and the panel pays it once. The two
settings are honoured only by a newer sidecar than the pinned one, and the help
says so.

Three models were computed for a trait and one was shown. The client asked
the server to score several models per trait and then to return only its
favourite, so the spread between them — for a trait whose score explains five
per cent of the variance, half of the answer to «how much of a number is
this» — never reached the page. Every scored model now comes back, the spread
is stored with the panel and printed as part of the percentile's stability.
And the count of candidate models left unscored — eighty-five of eighty-eight
for coronary artery disease — travelled without its rule; the rule is the
report's own --models limit, and the count now says so wherever it appears.

A panel entered by hand and then re-imported from its form stood twice in
every series. The form prints the draw hour, so the re-import arrived with a
finer date than the day entered by hand; the two did not match as strings, and
the second point joined the series beside the first — identical values, one
draw, nothing reported. Trends were then computed against a «previous point»
that was the same blood. A point now stands in for every point of the same day
whatever precision either carries, the more precise date is the one kept
whichever order the two arrived in, and what the earlier entry recorded about
the draw — its context, its source — travels to the replacement instead of
being erased on every re-import. The importer names each replacement. The one
case that cannot be decided — a bare day arriving against two timed draws of
that day — is still reported and left to the person.

One file the reader could not handle stopped ingest-labs for the whole
folder. A traceback, every form after it unread, and no indication of which
file was at fault. Each file is now read on its own: a file that raises is
listed among the files nothing was taken from, with the exception's type and
text, the rest of the folder is processed, and the command exits with a
non-zero status so that a partial run is not mistaken for a clean one. The
failed file is tried again on the next run rather than remembered as done.

The list of files already read was shared by every profile on the
machine. ingest-labs and ingest-studies remembered what they had read in
the application-wide cache rather than beside the profile, so anyone working
with more than one profile — a family member's, a temporary one — shared a
single list, and a form already read for one profile could be silently skipped
for another. The list now lives in the profile directory, one per profile
(ingest_labs_manifest.json, ingest_studies_manifest.json); on the first run
after upgrading the old list is carried over from the cache and the run says so
once, so no form is read as new because of the move. Both loaders report the
carry-over as a manifest_moved field in --json.

The reach baseline could not be accepted for a commit that added a module.
The suite fails when a module of the package has no accepted reach, and its
message says to run --accept; --accept in turn refused to record a suite
that had failed. Adding any module therefore closed a circle the tool could not
be talked out of, and the only exit was to seed the new module in
test_reach_baseline.json by hand. --accept now enters missing modules at
0.0 before the suite is measured, drops entries whose file is gone, says which
it did, and records the measured numbers over the seeds. When the suite fails
anyway the file is put back exactly as it was. --strict is unchanged and
still fails on a module nobody has reviewed.

A series break

knowledge/lab_markers.json now records whose reference interval each scored
marker holds, and a corridor that belongs to one sex is no longer lent to
another. On unchanged input that changes the verdict in one place: a profile
whose sex differs from the corridor's, for a marker whose own laboratory form
printed no range, used to receive a flag and now receives the value together with
the reason no corridor is shown. Thirty-six markers can be affected — the six the
body systems score (HDL, AST, GGT, DHEA-S, DHT, estradiol) and thirty more
whose adult interval is sex-specific: the red cell count and ESR, iron and
transferrin saturation, the gonadal and pituitary hormones, calcitonin,
osteocalcin, leptin, PSA, urine creatinine and the estrogen metabolites — and
only where the range was borrowed: a person's own form has always been
preferred, and this governs nothing but the hole it filled. The remedy is the
form itself, or a range recorded by hand.

Age is the same line, one axis over. Four markers whose interval every
laboratory bands by age — IGF-1, DHEA-S, inhibin B and total PSA — held one corridor
each, transcribed at one age, and lent it to everybody. The band on record is
not known, so the corridor is now lent to nobody and the reason is printed; a
value that used to receive a verdict against it receives the value alone. The
same remedy applies. Every corridor in the dictionary now states both — whose
it is, and whether age governs it — and a marker that does not fails the suite,
because absence was how the question used to be spelled.

A verdict now stands on the range printed beside the value rather than on the
range first recorded for the marker. For a value whose own form printed a
different range from the one on record, the flag can change either way; the
value does not. Which ruler each flag stands on is printed, so the two can be
told apart on the page.

The score of a body system also moves where a measured marker had no corridor:
such a marker used to take 45 points off its system and no longer takes any. The
overall health index is a mean over systems, so it moves with them. Values from
either side of this line belong on one chart only with a note.

What is retracted

No stored value changes and no conclusion is revisited. One correction above —
the spelling of sex — is to how a reference row is chosen for a profile spelled
other than «male»/«female»; what that asks of such a profile is under the next
heading. The rest are to how reports are written and how files are read.

What needs recomputing

For a profile whose sex is spelled other than «male»/«female» and which has
ingested forms carrying sex-specific reference rows: the reference intervals
stored from those forms may have been picked without the sex filter, and
ingest-labs --force on the same folder rewrites them. For every other profile,
nothing on that account. A report saved from an earlier version may be truncated at the point
its first unwritable character appeared — running the command again produces the
whole one.

A form that carried a urine albumin-to-creatinine ratio, a urine microalbumin or
a total T3 was ingested without those lines, and nothing in the profile says so.
ingest-labs --force on the folder that holds such forms reads them again and
adds the three analytes; every value already stored stays as it is.

A series that already holds a hand-entered day beside the same draw's timed
re-import keeps both until that day is written again: the same
ingest-labs --force collapses each such pair into one point, keeps the timed
date, and names every collapse it made.

A value stored by an earlier version carries no range of its own: until the
folder is read again with ingest-labs --force, it is judged by the marker's
recorded range and the report marks it so; after, by the range its form
printed. A value stored from a form that printed a bound («< 0.09») carries no
sign until the same re-read; points entered by
hand before the form was read keep whatever was typed. A biochemistry total
calcium ingested by an earlier version sits in the elemental series converted
to mg/L: reading the folder again files it under total calcium, but the
converted point is not removed from the elemental series — that is done by
hand, and the report until then shows a method change as a trend.

A polygenic panel computed by an earlier version carries no spread across
models and no AUROC: the report prints «not recorded» in their place until the
panel is recomputed (python3 -m scholion.prs report) and rebuilt with the
panel-build step of the genome guide. The spread across reference populations
comes from the ancestry-sensitivity step of the same guide, run once per panel.