From d1165cde454e5be0278c759cbce22deb8619d730 Mon Sep 17 00:00:00 2001 From: kert Date: Tue, 27 Oct 2026 14:23:42 -0400 Subject: [PATCH] =?UTF-8?q?docs(cli):=20regenerate=20the=20CLI=20reference?= =?UTF-8?q?=20=E2=80=94=20typer=200.27=20help=20format,=20new=20nlm=20and?= =?UTF-8?q?=20zot=20fetch=20pages?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/docs/cli/api-serve.md | 11 ++-- docs/docs/cli/bcda-adopt.md | 14 ++--- docs/docs/cli/bcda-auth.md | 6 +- docs/docs/cli/bcda-cancel.md | 10 ++-- docs/docs/cli/bcda-errors.md | 8 +-- docs/docs/cli/bcda-export.md | 20 +++---- docs/docs/cli/bcda-jobs.md | 8 +-- docs/docs/cli/bcda-preflight.md | 6 +- docs/docs/cli/bcda-resume.md | 10 ++-- docs/docs/cli/bcda-ui.md | 10 ++-- docs/docs/cli/bib-attach-iom.md | 6 +- docs/docs/cli/bib-backfill-comments.md | 8 +-- docs/docs/cli/bib-cfr-jump.md | 18 +++--- docs/docs/cli/bib-code-tags.md | 25 ++++----- docs/docs/cli/bib-discover-pfs-rules.md | 6 +- docs/docs/cli/bib-fetch-docket-comments.md | 10 ++-- docs/docs/cli/bib-fetch-pfs-comments.md | 10 ++-- docs/docs/cli/bib-fr-grab.md | 8 +-- docs/docs/cli/bib-fr-jump.md | 20 +++---- docs/docs/cli/bib-import-zotero.md | 26 ++++----- docs/docs/cli/bib-ingest-iom.md | 6 +- docs/docs/cli/bib-ingest-mail.md | 16 +++--- docs/docs/cli/bib-ingest-oig.md | 6 +- docs/docs/cli/bib-query.md | 4 +- docs/docs/cli/bib-refresh-iom.md | 15 ++--- docs/docs/cli/bib-sync-zotero.md | 65 +++++++++++----------- docs/docs/cli/bib-tag.md | 4 +- docs/docs/cli/bls-ces.md | 16 +++--- docs/docs/cli/bls-oews.md | 10 ++-- docs/docs/cli/comments-extract-ocr.md | 10 ++-- docs/docs/cli/comments-extract.md | 43 +++++++------- docs/docs/cli/comments-seal.md | 8 +-- docs/docs/cli/comments-stats.md | 4 +- docs/docs/cli/comments-unseal.md | 4 +- docs/docs/cli/db-inspect.md | 4 +- docs/docs/cli/docs-serve.md | 6 +- docs/docs/cli/lake-deploy.md | 14 ++--- docs/docs/cli/lake-load.md | 11 ++-- docs/docs/cli/lake-parity.md | 4 +- docs/docs/cli/lake-validate.md | 8 +-- docs/docs/cli/llm-eval-tags.md | 12 ++-- docs/docs/cli/llm-index.md | 23 ++++---- docs/docs/cli/llm-restamp.md | 12 ++-- docs/docs/cli/llm-serve.md | 6 +- docs/docs/cli/llm-stamp-themes.md | 10 ++-- docs/docs/cli/llm-tag.md | 10 ++-- docs/docs/cli/llm-vocab.md | 8 +-- docs/docs/cli/load-bcda.md | 12 ++-- docs/docs/cli/load-cclf.md | 8 +-- docs/docs/cli/load-cms.md | 20 ++++--- docs/docs/cli/load-seed.md | 10 ++-- docs/docs/cli/mail-attach-smarthost.md | 2 +- docs/docs/cli/mail-dkim-export.md | 2 +- docs/docs/cli/mail-dns.md | 2 +- docs/docs/cli/mail-down.md | 2 +- docs/docs/cli/mail-provision.md | 8 +-- docs/docs/cli/mail-rotate-creds.md | 8 +-- docs/docs/cli/mail-seed-mailboxes.md | 2 +- docs/docs/cli/mail-status.md | 2 +- docs/docs/cli/mail-up.md | 6 +- docs/docs/cli/mail-wire-git.md | 2 +- docs/docs/cli/mail.md | 2 +- docs/docs/cli/nlm-fetch.md | 18 ++++++ docs/docs/cli/nlm-releases.md | 17 ++++++ docs/docs/cli/nlm-vsac.md | 24 ++++++++ docs/docs/cli/nlm.md | 21 +++++++ docs/docs/cli/perf-show.md | 7 +-- docs/docs/cli/pfs-cpt-ingest.md | 8 +-- docs/docs/cli/pfs-elements.md | 18 +++--- docs/docs/cli/pfs-exposure.md | 25 ++++----- docs/docs/cli/pfs-guidance.md | 4 +- docs/docs/cli/pfs-lineage.md | 16 +++--- docs/docs/cli/pfs-reaction.md | 18 +++--- docs/docs/cli/pfs-review.md | 4 +- docs/docs/cli/pfs-utilization.md | 18 +++--- docs/docs/cli/prisma-eligible.md | 52 ++++++++--------- docs/docs/cli/prisma-export.md | 14 ++--- docs/docs/cli/prisma-extract.md | 42 +++++++------- docs/docs/cli/prisma-fetch.md | 47 ++++++++-------- docs/docs/cli/prisma-flow.md | 14 ++--- docs/docs/cli/prisma-init.md | 14 ++--- docs/docs/cli/prisma-ping-llm.md | 2 +- docs/docs/cli/prisma-run.md | 21 ++++--- docs/docs/cli/prisma-screen.md | 38 ++++++------- docs/docs/cli/prisma-vpn.md | 2 +- docs/docs/cli/prisma.md | 2 +- docs/docs/cli/rec-opps.md | 12 ++-- docs/docs/cli/rec-pfs.md | 12 ++-- docs/docs/cli/run.md | 16 +++--- docs/docs/cli/stack.md | 1 + docs/docs/cli/validate.md | 10 ++-- docs/docs/cli/zot-dump-schema.md | 10 ++-- docs/docs/cli/zot-fetch.md | 43 ++++++++++++++ docs/docs/cli/zot-fix-dates.md | 6 +- docs/docs/cli/zot-fix-fields.md | 6 +- docs/docs/cli/zot-fix-keys.md | 8 +-- docs/docs/cli/zot-verify-parity.md | 4 +- docs/docs/cli/zot.md | 1 + 98 files changed, 682 insertions(+), 560 deletions(-) create mode 100644 docs/docs/cli/nlm-fetch.md create mode 100644 docs/docs/cli/nlm-releases.md create mode 100644 docs/docs/cli/nlm-vsac.md create mode 100644 docs/docs/cli/nlm.md create mode 100644 docs/docs/cli/zot-fetch.md diff --git a/docs/docs/cli/api-serve.md b/docs/docs/cli/api-serve.md index 0c67627..0e02fe6 100644 --- a/docs/docs/cli/api-serve.md +++ b/docs/docs/cli/api-serve.md @@ -11,11 +11,10 @@ Usage: stack api serve [OPTIONS] Start the stack API server. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --host TEXT Bind address. │ -│ --port INTEGER Port number. │ -│ --workers INTEGER Number of workers. │ -│ --reload --no-reload Enable auto-reload. │ -│ [default: no-reload] │ -│ --help Show this message and exit. │ +│ --host Bind address. │ +│ --port Port number. │ +│ --workers Number of workers. │ +│ --reload --no-reload Enable auto-reload. [default: no-reload] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-adopt.md b/docs/docs/cli/bcda-adopt.md index ea01c5c..63d6ca2 100644 --- a/docs/docs/cli/bcda-adopt.md +++ b/docs/docs/cli/bcda-adopt.md @@ -6,18 +6,18 @@ sidebar_position: 16 # `stack bcda adopt` ``` -Usage: stack bcda adopt [OPTIONS] JOB_ID +Usage: stack bcda adopt [OPTIONS] {job_id} Download a completed job this store did not start. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * job_id TEXT Server job id (see `stack bcda jobs`). [required] │ +│ * job_id Server job id (see `stack bcda jobs`). [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │ -│ [default: Large Model Entity] │ -│ --type -t TEXT Resource type(s) the job holds, for the store │ -│ record. │ -│ --help Show this message and exit. │ +│ --preset Public sandbox entity when BCDA_CLIENT_ID is unset. │ +│ [default: Large Model Entity] │ +│ --type -t Resource type(s) the job holds, for the store │ +│ record. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-auth.md b/docs/docs/cli/bcda-auth.md index 3fc839c..092f150 100644 --- a/docs/docs/cli/bcda-auth.md +++ b/docs/docs/cli/bcda-auth.md @@ -11,8 +11,8 @@ Usage: stack bcda auth [OPTIONS] Issue a token and show attribution status. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │ -│ [default: Large Model Entity] │ -│ --help Show this message and exit. │ +│ --preset Public sandbox entity when BCDA_CLIENT_ID is unset. │ +│ [default: Large Model Entity] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-cancel.md b/docs/docs/cli/bcda-cancel.md index b69a25a..f4f2aa9 100644 --- a/docs/docs/cli/bcda-cancel.md +++ b/docs/docs/cli/bcda-cancel.md @@ -6,16 +6,16 @@ sidebar_position: 18 # `stack bcda cancel` ``` -Usage: stack bcda cancel [OPTIONS] JOB_ID +Usage: stack bcda cancel [OPTIONS] {job_id} Cancel an in-progress job. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * job_id TEXT Server job id. [required] │ +│ * job_id Server job id. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │ -│ [default: Large Model Entity] │ -│ --help Show this message and exit. │ +│ --preset Public sandbox entity when BCDA_CLIENT_ID is unset. │ +│ [default: Large Model Entity] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-errors.md b/docs/docs/cli/bcda-errors.md index d9ecc96..336eebb 100644 --- a/docs/docs/cli/bcda-errors.md +++ b/docs/docs/cli/bcda-errors.md @@ -6,15 +6,15 @@ sidebar_position: 20 # `stack bcda errors` ``` -Usage: stack bcda errors [OPTIONS] KEY +Usage: stack bcda errors [OPTIONS] {key} OperationOutcome issues from a job's error files (a partial export). ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * key TEXT Store job key. [required] │ +│ * key Store job key. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --limit INTEGER Issues to print. [default: 50] │ -│ --help Show this message and exit. │ +│ --limit Issues to print. [default: 50] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-export.md b/docs/docs/cli/bcda-export.md index e7ebbd7..c6c662d 100644 --- a/docs/docs/cli/bcda-export.md +++ b/docs/docs/cli/bcda-export.md @@ -11,37 +11,37 @@ Usage: stack bcda export [OPTIONS] Run an export through the store (blocks until downloaded). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when │ +│ --preset Public sandbox entity when │ │ BCDA_CLIENT_ID is unset. │ │ [default: Large Model Entity] │ -│ --type -t TEXT Resource type(s); default all │ +│ --type -t Resource type(s); default all │ │ three. │ -│ --endpoint TEXT Group/all, Group/runout or │ +│ --endpoint Group/all, Group/runout or │ │ Patient. │ │ [default: Group/all] │ -│ --since TEXT FHIR instant │ +│ --since FHIR instant │ │ (2026-10-01T00:00:00+00:00) │ │ or 'auto' = the per-type │ │ watermark. │ │ --force Start even when the _since │ │ checks say block. │ -│ --system-type TEXT _typeFilter System-Type │ +│ --system-type _typeFilter System-Type │ │ tag(s). │ -│ --outcome TEXT _typeFilter outcome: partial │ +│ --outcome _typeFilter outcome: partial │ │ and/or complete. │ -│ --service-date-from TEXT _typeFilter earliest │ +│ --service-date-from _typeFilter earliest │ │ service-date (YYYY[-MM[-DD]], │ │ optional gt/ge/eq prefix). │ -│ --service-date-to TEXT _typeFilter latest │ +│ --service-date-to _typeFilter latest │ │ service-date (optional lt/le │ │ prefix). │ │ --per-type --one-job One job per type (survives │ │ sandbox sweeps). │ │ [default: per-type] │ -│ --cancel-retries INTEGER Restarts after server-side │ +│ --cancel-retries Restarts after server-side │ │ cancellation. │ │ [default: 6] │ -│ --poll-interval FLOAT Seconds between status polls. │ +│ --poll-interval Seconds between status polls. │ │ [default: 15.0] │ │ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ diff --git a/docs/docs/cli/bcda-jobs.md b/docs/docs/cli/bcda-jobs.md index 21f95c8..d5965b3 100644 --- a/docs/docs/cli/bcda-jobs.md +++ b/docs/docs/cli/bcda-jobs.md @@ -11,9 +11,9 @@ Usage: stack bcda jobs [OPTIONS] Server job history for the entity (shared on the sandbox). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │ -│ [default: Large Model Entity] │ -│ --limit INTEGER Newest N jobs. [default: 25] │ -│ --help Show this message and exit. │ +│ --preset Public sandbox entity when BCDA_CLIENT_ID is unset. │ +│ [default: Large Model Entity] │ +│ --limit Newest N jobs. [default: 25] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-preflight.md b/docs/docs/cli/bcda-preflight.md index 16c5c93..6f73c8c 100644 --- a/docs/docs/cli/bcda-preflight.md +++ b/docs/docs/cli/bcda-preflight.md @@ -11,8 +11,8 @@ Usage: stack bcda preflight [OPTIONS] /_version, /_health and metadata — no token needed. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │ -│ [default: Large Model Entity] │ -│ --help Show this message and exit. │ +│ --preset Public sandbox entity when BCDA_CLIENT_ID is unset. │ +│ [default: Large Model Entity] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-resume.md b/docs/docs/cli/bcda-resume.md index e4b1593..7814341 100644 --- a/docs/docs/cli/bcda-resume.md +++ b/docs/docs/cli/bcda-resume.md @@ -6,16 +6,16 @@ sidebar_position: 17 # `stack bcda resume` ``` -Usage: stack bcda resume [OPTIONS] KEY +Usage: stack bcda resume [OPTIONS] {key} Finish a store job: re-poll, download missing files, record the manifest. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * key TEXT Store job key (see `stack bcda store`). [required] │ +│ * key Store job key (see `stack bcda store`). [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │ -│ [default: Large Model Entity] │ -│ --help Show this message and exit. │ +│ --preset Public sandbox entity when BCDA_CLIENT_ID is unset. │ +│ [default: Large Model Entity] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bcda-ui.md b/docs/docs/cli/bcda-ui.md index 7eb7344..5bc32ca 100644 --- a/docs/docs/cli/bcda-ui.md +++ b/docs/docs/cli/bcda-ui.md @@ -11,10 +11,10 @@ Usage: stack bcda ui [OPTIONS] Launch the BCDA manager (Streamlit; /metrics when STACK_TELEMETRY is on). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --port INTEGER Port for the Streamlit server. │ -│ [default: 8501] │ -│ --headless --no-headless Do not open a browser. │ -│ [default: headless] │ -│ --help Show this message and exit. │ +│ --port Port for the Streamlit server. │ +│ [default: 8501] │ +│ --headless --no-headless Do not open a browser. │ +│ [default: headless] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-attach-iom.md b/docs/docs/cli/bib-attach-iom.md index 52f8070..d3e7c14 100644 --- a/docs/docs/cli/bib-attach-iom.md +++ b/docs/docs/cli/bib-attach-iom.md @@ -14,8 +14,8 @@ Usage: stack bib attach-iom [OPTIONS] CMS since the last run. Safe to schedule on a timer. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --pub -p TEXT Limit to specific pub numbers. Repeat for multiple. │ -│ --force Re-download even if local SHA-256 matches. │ -│ --help Show this message and exit. │ +│ --pub -p Limit to specific pub numbers. Repeat for multiple. │ +│ --force Re-download even if local SHA-256 matches. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-backfill-comments.md b/docs/docs/cli/bib-backfill-comments.md index e2cd687..1b2f44d 100644 --- a/docs/docs/cli/bib-backfill-comments.md +++ b/docs/docs/cli/bib-backfill-comments.md @@ -21,19 +21,19 @@ Usage: stack bib backfill-comments [OPTIONS] (#662): no API key, no cap, and mirror-only comments get created. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --docket TEXT Limit to one docket (e.g. CMS-2026-2377). Without │ +│ --docket Limit to one docket (e.g. CMS-2026-2377). Without │ │ it the walk covers every un-enriched stub in the │ │ store — a multi-day crawl at the reg.gov rate │ │ cap. │ -│ --limit -n INTEGER Cap items processed this run. 0 = no cap │ +│ --limit -n Cap items processed this run. 0 = no cap │ │ (multi-day crawl). │ │ [default: 0] │ -│ --sleep FLOAT Seconds between API calls. 3.7s ≈ 970/hr — just │ +│ --sleep Seconds between API calls. 3.7s ≈ 970/hr — just │ │ under the 1000/hr reg.gov hourly cap (the binding │ │ limit; the 50/min burst cap is looser). CDN │ │ downloads are concurrent and don't count. │ │ [default: 3.7] │ -│ --log PATH Append-only progress log (survives restarts). │ +│ --log Append-only progress log (survives restarts). │ │ [default: /tmp/bib-backfill-comments.log] │ │ --mirror Pull from the Mirrulations S3 mirror instead of │ │ the reg.gov API — bulk speed, no rate cap, also │ diff --git a/docs/docs/cli/bib-cfr-jump.md b/docs/docs/cli/bib-cfr-jump.md index 5c68ff4..b79712c 100644 --- a/docs/docs/cli/bib-cfr-jump.md +++ b/docs/docs/cli/bib-cfr-jump.md @@ -6,20 +6,20 @@ sidebar_position: 46 # `stack bib cfr-jump` ``` -Usage: stack bib cfr-jump [OPTIONS] [REF] +Usage: stack bib cfr-jump [OPTIONS] [ref] Bidirectional CFR cite ↔ eCFR URL (#640); optionally place the link. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ ref [REF] CFR cite: "42 CFR 425.400(c)(1)(iv)" or "42 CFR Part 425". │ +│ ref CFR cite: "42 CFR 425.400(c)(1)(iv)" or "42 CFR Part 425". │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --url TEXT Reverse mode: print the cite for an eCFR URL. │ -│ --md Print a markdown link. │ -│ --place Attach the link to its bib regulation item (fr_links) │ -│ so the next zotero sync carries it as a child link │ -│ attachment. │ -│ --label TEXT Label for the placed link. │ -│ --help Show this message and exit. │ +│ --url Reverse mode: print the cite for an eCFR URL. │ +│ --md Print a markdown link. │ +│ --place Attach the link to its bib regulation item (fr_links) │ +│ so the next zotero sync carries it as a child link │ +│ attachment. │ +│ --label Label for the placed link. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-code-tags.md b/docs/docs/cli/bib-code-tags.md index 13cf021..087231e 100644 --- a/docs/docs/cli/bib-code-tags.md +++ b/docs/docs/cli/bib-code-tags.md @@ -28,18 +28,17 @@ Usage: stack bib code-tags [OPTIONS] merged pass. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --collection TEXT Which collection: all | comments | │ -│ rules | corpus. │ -│ [default: all] │ -│ --anchors-only Rules only, straight from fr_anchors │ -│ text — skip pgvector entirely. │ -│ --dry-run Compute the merged item→codes mapping │ -│ and report what would be tagged; write │ -│ nothing. │ -│ --max-codes-per-item INTEGER Items with more distinct codes get │ -│ family: tags only (+ hand-family │ -│ codes). │ -│ [default: 200] │ -│ --help Show this message and exit. │ +│ --collection Which collection: all | comments | rules │ +│ | corpus. │ +│ [default: all] │ +│ --anchors-only Rules only, straight from fr_anchors text │ +│ — skip pgvector entirely. │ +│ --dry-run Compute the merged item→codes mapping and │ +│ report what would be tagged; write │ +│ nothing. │ +│ --max-codes-per-item Items with more distinct codes get │ +│ family: tags only (+ hand-family codes). │ +│ [default: 200] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-discover-pfs-rules.md b/docs/docs/cli/bib-discover-pfs-rules.md index a6aa291..b84c2f7 100644 --- a/docs/docs/cli/bib-discover-pfs-rules.md +++ b/docs/docs/cli/bib-discover-pfs-rules.md @@ -16,9 +16,9 @@ Usage: stack bib discover-pfs-rules [OPTIONS] (~20 rules since 2017). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --since TEXT [default: 2017-01-01] │ -│ --until TEXT │ +│ --since [default: 2017-01-01] │ +│ --until │ │ --dry-run │ -│ --help Show this message and exit. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-fetch-docket-comments.md b/docs/docs/cli/bib-fetch-docket-comments.md index 1570acf..0fca322 100644 --- a/docs/docs/cli/bib-fetch-docket-comments.md +++ b/docs/docs/cli/bib-fetch-docket-comments.md @@ -6,7 +6,7 @@ sidebar_position: 31 # `stack bib fetch-docket-comments` ``` -Usage: stack bib fetch-docket-comments [OPTIONS] DOCKET +Usage: stack bib fetch-docket-comments [OPTIONS] {docket} Walk one docket's comments from its stored watermark; upsert as Source items. @@ -15,15 +15,15 @@ Usage: stack bib fetch-docket-comments [OPTIONS] DOCKET Sealed dockets are skipped unless --force. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * docket TEXT reg.gov docket id, e.g. CMS-2026-2377 [required] │ +│ * docket reg.gov docket id, e.g. CMS-2026-2377 [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --cms-id TEXT Associate comments with a specific CMS rule │ +│ --cms-id Associate comments with a specific CMS rule │ │ tag. │ -│ --limit -n INTEGER Stop after N comments. 0 = all. [default: 0] │ +│ --limit -n Stop after N comments. 0 = all. [default: 0] │ │ --attachments Also download each comment's PDF/DOCX │ │ attachments. │ -│ --sleep FLOAT Seconds between API calls (rate budget). │ +│ --sleep Seconds between API calls (rate budget). │ │ [default: 1.3] │ │ --force Walk from page 1 even if sealed / │ │ watermarked. Never unseals. │ diff --git a/docs/docs/cli/bib-fetch-pfs-comments.md b/docs/docs/cli/bib-fetch-pfs-comments.md index ba9666c..1a4636f 100644 --- a/docs/docs/cli/bib-fetch-pfs-comments.md +++ b/docs/docs/cli/bib-fetch-pfs-comments.md @@ -18,14 +18,14 @@ Usage: stack bib fetch-pfs-comments [OPTIONS] even under `--docket`: see that option's help. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --since TEXT [default: 2017-01-01] │ -│ --until TEXT │ +│ --since [default: 2017-01-01] │ +│ --until │ │ --attachments │ -│ --per-docket-limit INTEGER Cap comments fetched per docket. 0 = │ +│ --per-docket-limit Cap comments fetched per docket. 0 = │ │ unlimited. │ │ [default: 0] │ -│ --sleep FLOAT [default: 1.3] │ -│ --docket TEXT Only pull this reg.gov docket (e.g. │ +│ --sleep [default: 1.3] │ +│ --docket Only pull this reg.gov docket (e.g. │ │ CMS-2026-2377). Filtered before any API │ │ call ONLY once the docket is known (a │ │ `dockets` row already exists for its CMS │ diff --git a/docs/docs/cli/bib-fr-grab.md b/docs/docs/cli/bib-fr-grab.md index 10922aa..f685575 100644 --- a/docs/docs/cli/bib-fr-grab.md +++ b/docs/docs/cli/bib-fr-grab.md @@ -14,9 +14,9 @@ Usage: stack bib fr-grab [OPTIONS] ``fr_anchor_docs`` for offline jump-link resolution. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --key TEXT Grab one rule item by bib key. │ -│ --all Backfill every rule item with an FR URL. │ -│ --force Re-grab even if an anchor map already exists. │ -│ --help Show this message and exit. │ +│ --key Grab one rule item by bib key. │ +│ --all Backfill every rule item with an FR URL. │ +│ --force Re-grab even if an anchor map already exists. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-fr-jump.md b/docs/docs/cli/bib-fr-jump.md index e786a3b..0e8e127 100644 --- a/docs/docs/cli/bib-fr-jump.md +++ b/docs/docs/cli/bib-fr-jump.md @@ -6,21 +6,21 @@ sidebar_position: 45 # `stack bib fr-jump` ``` -Usage: stack bib fr-jump [OPTIONS] REF +Usage: stack bib fr-jump [OPTIONS] {ref} Resolve an FR citation to its web jump link (#637); optionally place it. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * ref TEXT FR reference: "91 FR 44218", "91 FR 44218 ¶3", "p-3600", │ -│ or a quote. │ -│ [required] │ +│ * ref FR reference: "91 FR 44218", "91 FR 44218 ¶3", │ +│ "p-3600", or a quote. │ +│ [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --key TEXT Bib item key to scope resolution. │ -│ --md Print a markdown link. │ -│ --place Record the link in fr_links so the next zotero sync │ -│ carries it as a child link attachment. │ -│ --label TEXT Label for the placed link. │ -│ --help Show this message and exit. │ +│ --key Bib item key to scope resolution. │ +│ --md Print a markdown link. │ +│ --place Record the link in fr_links so the next zotero sync │ +│ carries it as a child link attachment. │ +│ --label Label for the placed link. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-import-zotero.md b/docs/docs/cli/bib-import-zotero.md index 10f565b..6d8716a 100644 --- a/docs/docs/cli/bib-import-zotero.md +++ b/docs/docs/cli/bib-import-zotero.md @@ -21,18 +21,18 @@ Usage: stack bib import-zotero [OPTIONS] applies. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ * --collection TEXT Zotero collection name to pull │ -│ from. │ -│ [required] │ -│ --with-files --no-with-files Only import items that have at │ -│ least one attachment file. │ -│ [default: no-with-files] │ -│ --only TEXT Title substring filter │ -│ (case-insensitive). │ -│ --tag TEXT Tag every imported item with │ -│ this. Repeat for multiple. │ -│ --dry-run Report what would happen without │ -│ writing. │ -│ --help Show this message and exit. │ +│ * --collection Zotero collection name to pull │ +│ from. │ +│ [required] │ +│ --with-files --no-with-files Only import items that have at │ +│ least one attachment file. │ +│ [default: no-with-files] │ +│ --only Title substring filter │ +│ (case-insensitive). │ +│ --tag Tag every imported item with │ +│ this. Repeat for multiple. │ +│ --dry-run Report what would happen │ +│ without writing. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-ingest-iom.md b/docs/docs/cli/bib-ingest-iom.md index 782eef4..30598d6 100644 --- a/docs/docs/cli/bib-ingest-iom.md +++ b/docs/docs/cli/bib-ingest-iom.md @@ -15,8 +15,8 @@ Usage: stack bib ingest-iom [OPTIONS] advertises. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --pub -p TEXT Limit to specific pub numbers (e.g. 100-02). Repeat │ -│ for multiple. │ -│ --help Show this message and exit. │ +│ --pub -p Limit to specific pub numbers (e.g. 100-02). Repeat │ +│ for multiple. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-ingest-mail.md b/docs/docs/cli/bib-ingest-mail.md index 6718736..5191380 100644 --- a/docs/docs/cli/bib-ingest-mail.md +++ b/docs/docs/cli/bib-ingest-mail.md @@ -16,13 +16,13 @@ Usage: stack bib ingest-mail [OPTIONS] tagged ``source:email`` into the appropriate Zotero collection. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --user TEXT Mailbox address to poll (must have a password in │ -│ .state/mail/credentials.json). │ -│ [default: cmsupdates@mail.fhirworx.io] │ -│ --host TEXT [default: mail.fhirworx.io] │ -│ --port INTEGER [default: 993] │ -│ --folder TEXT [default: INBOX] │ -│ --limit -n INTEGER [default: 0] │ -│ --help Show this message and exit. │ +│ --user Mailbox address to poll (must have a password in │ +│ .state/mail/credentials.json). │ +│ [default: cmsupdates@mail.fhirworx.io] │ +│ --host [default: mail.fhirworx.io] │ +│ --port [default: 993] │ +│ --folder [default: INBOX] │ +│ --limit -n [default: 0] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-ingest-oig.md b/docs/docs/cli/bib-ingest-oig.md index caa38d6..bcac479 100644 --- a/docs/docs/cli/bib-ingest-oig.md +++ b/docs/docs/cli/bib-ingest-oig.md @@ -11,8 +11,8 @@ Usage: stack bib ingest-oig [OPTIONS] Crawl OIG Compliance Program Guidance + fraud alerts indexes. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --kind -k TEXT Restrict to a subset: 'cpg' and/or 'alerts'. Repeat │ -│ for multiple. │ -│ --help Show this message and exit. │ +│ --kind -k Restrict to a subset: 'cpg' and/or 'alerts'. Repeat │ +│ for multiple. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-query.md b/docs/docs/cli/bib-query.md index 2d8c480..d914be9 100644 --- a/docs/docs/cli/bib-query.md +++ b/docs/docs/cli/bib-query.md @@ -6,12 +6,12 @@ sidebar_position: 29 # `stack bib query` ``` -Usage: stack bib query [OPTIONS] TERM +Usage: stack bib query [OPTIONS] {term} Search the bibliography store. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * term TEXT Search term. [required] │ +│ * term Search term. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ │ --help Show this message and exit. │ diff --git a/docs/docs/cli/bib-refresh-iom.md b/docs/docs/cli/bib-refresh-iom.md index 74f47d8..680820a 100644 --- a/docs/docs/cli/bib-refresh-iom.md +++ b/docs/docs/cli/bib-refresh-iom.md @@ -19,12 +19,13 @@ Usage: stack bib refresh-iom [OPTIONS] Zotero is held (stopped) during the sync phase only. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --pub -p TEXT │ -│ --file-issue --no-file-issue When watch-iom detects a │ -│ futurepdf.pdf change, auto-file a │ -│ Gitea issue tagged 'cms-update'. │ -│ Disable for local/dev runs. │ -│ [default: file-issue] │ -│ --help Show this message and exit. │ +│ --pub -p │ +│ --file-issue --no-file-issue When watch-iom detects a │ +│ futurepdf.pdf change, auto-file │ +│ a Gitea issue tagged │ +│ 'cms-update'. Disable for │ +│ local/dev runs. │ +│ [default: file-issue] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-sync-zotero.md b/docs/docs/cli/bib-sync-zotero.md index 6b596c6..fd8bbfc 100644 --- a/docs/docs/cli/bib-sync-zotero.md +++ b/docs/docs/cli/bib-sync-zotero.md @@ -15,37 +15,38 @@ Usage: stack bib sync-zotero [OPTIONS] duration of the sync and start it again afterward. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --tag TEXT Only sync items matching a │ -│ tag. │ -│ --type TEXT Only sync one item_type. │ -│ --hold-zotero --no-hold Stop the 'zotero' container │ -│ during sync so Zotero │ -│ releases its exclusive │ -│ SQLite lock; restart │ -│ afterwards. │ -│ [default: hold-zotero] │ -│ --dedupe-collection TEXT DEPRECATED — use │ -│ --merge-dupes instead, │ -│ which merges rather than │ -│ deletes. After the push, │ -│ remove title+date │ -│ duplicates from this Zotero │ -│ collection (and from bib, │ -│ so the next sync can't │ -│ resurrect them). CMS │ -│ listservs re-send identical │ -│ mail with fresh │ -│ Message-IDs, so duplicates │ -│ otherwise accumulate — e.g. │ -│ 'Cmsupdates'. │ -│ --merge-dupes --no-merge-dupes After the push, merge │ -│ same-URL duplicate items │ -│ library-wide (union │ -│ tags/collections/notes/att… │ -│ keep-earliest). Supersedes │ -│ --dedupe-collection, which │ -│ deletes without merging. │ -│ [default: no-merge-dupes] │ -│ --help Show this message and exit. │ +│ --tag Only sync items matching a │ +│ tag. │ +│ --type Only sync one item_type. │ +│ --hold-zotero --no-hold Stop the 'zotero' │ +│ container during sync so │ +│ Zotero releases its │ +│ exclusive SQLite lock; │ +│ restart afterwards. │ +│ [default: hold-zotero] │ +│ --dedupe-collection DEPRECATED — use │ +│ --merge-dupes instead, │ +│ which merges rather than │ +│ deletes. After the push, │ +│ remove title+date │ +│ duplicates from this │ +│ Zotero collection (and │ +│ from bib, so the next sync │ +│ can't resurrect them). CMS │ +│ listservs re-send │ +│ identical mail with fresh │ +│ Message-IDs, so duplicates │ +│ otherwise accumulate — │ +│ e.g. 'Cmsupdates'. │ +│ --merge-dupes --no-merge-dupes After the push, merge │ +│ same-URL duplicate items │ +│ library-wide (union │ +│ tags/collections/notes/at… │ +│ keep-earliest). Supersedes │ +│ --dedupe-collection, which │ +│ deletes without merging. │ +│ [default: no-merge-dupes] │ +│ --help Show this message and │ +│ exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bib-tag.md b/docs/docs/cli/bib-tag.md index 95f833e..8a667ae 100644 --- a/docs/docs/cli/bib-tag.md +++ b/docs/docs/cli/bib-tag.md @@ -6,12 +6,12 @@ sidebar_position: 28 # `stack bib tag` ``` -Usage: stack bib tag [OPTIONS] [PATTERN] +Usage: stack bib tag [OPTIONS] [pattern] List or search bibliography tags. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ pattern [PATTERN] Tag namespace or pattern to filter. │ +│ pattern Tag namespace or pattern to filter. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ │ --help Show this message and exit. │ diff --git a/docs/docs/cli/bls-ces.md b/docs/docs/cli/bls-ces.md index e4e64d4..6d357bc 100644 --- a/docs/docs/cli/bls-ces.md +++ b/docs/docs/cli/bls-ces.md @@ -14,13 +14,13 @@ Usage: stack bls ces [OPTIONS] the per-request limits), one bib Source per series. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --series TEXT CES series id(s) to print; default all in the │ -│ registry. │ -│ --start INTEGER First year to pull with --write. [default: 2006] │ -│ --end INTEGER Last year to pull with --write. [default: 2025] │ -│ --annual Print annual means instead of months. │ -│ --write Pull the registry's series, load bls.ces, cite, │ -│ republish. │ -│ --help Show this message and exit. │ +│ --series CES series id(s) to print; default all in the │ +│ registry. │ +│ --start First year to pull with --write. [default: 2006] │ +│ --end Last year to pull with --write. [default: 2025] │ +│ --annual Print annual means instead of months. │ +│ --write Pull the registry's series, load bls.ces, cite, │ +│ republish. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/bls-oews.md b/docs/docs/cli/bls-oews.md index f377066..4178f2c 100644 --- a/docs/docs/cli/bls-oews.md +++ b/docs/docs/cli/bls-oews.md @@ -14,10 +14,10 @@ Usage: stack bls oews [OPTIONS] cms.ingest_log. --occ prints the series. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --year INTEGER Release year(s); default 2013–. │ -│ --occ TEXT SOC code(s) to print, e.g. 31-9092. │ -│ --write Download, load bls.oews, cite, republish. │ -│ --offline With --write: use the cached zips. │ -│ --help Show this message and exit. │ +│ --year Release year(s); default 2013–. │ +│ --occ SOC code(s) to print, e.g. 31-9092. │ +│ --write Download, load bls.oews, cite, republish. │ +│ --offline With --write: use the cached zips. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/comments-extract-ocr.md b/docs/docs/cli/comments-extract-ocr.md index 9d5285e..3a7c603 100644 --- a/docs/docs/cli/comments-extract-ocr.md +++ b/docs/docs/cli/comments-extract-ocr.md @@ -18,10 +18,10 @@ Usage: stack comments extract-ocr [OPTIONS] uv run --with rapidocr-onnxruntime stack comments extract-ocr ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --root PATH Comments root dir. [default: .state/comments] │ -│ --docket TEXT Limit to one docket (e.g. CMS-2023-0121). │ -│ --limit INTEGER Cap comment dirs processed this run. 0 = no cap. │ -│ [default: 0] │ -│ --help Show this message and exit. │ +│ --root Comments root dir. [default: .state/comments] │ +│ --docket Limit to one docket (e.g. CMS-2023-0121). │ +│ --limit Cap comment dirs processed this run. 0 = no cap. │ +│ [default: 0] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/comments-extract.md b/docs/docs/cli/comments-extract.md index 2a03b59..a32a08c 100644 --- a/docs/docs/cli/comments-extract.md +++ b/docs/docs/cli/comments-extract.md @@ -11,27 +11,26 @@ Usage: stack comments extract [OPTIONS] Walk comment dirs and write combined.md (PDF/DOCX → text). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --root PATH Comments root dir. │ -│ [default: .state/comments] │ -│ --docket TEXT Limit to one docket (e.g. │ -│ CMS-2023-0121). │ -│ --limit INTEGER Cap dirs processed this run. 0 = no │ -│ cap. │ -│ [default: 0] │ -│ --workers INTEGER Concurrent extraction threads. │ -│ [default: 8] │ -│ --force Re-extract dirs that already have │ -│ combined.md. │ -│ --bib --no-bib Look up inline body from bib.sqlite │ -│ items.abstract. │ -│ [default: bib] │ -│ --attach --no-attach Attach combined.md back to its bib │ -│ item (so it flows to Zotero via `bib │ -│ sync`). Implies --bib; no-op when │ -│ --no-bib. │ -│ [default: attach] │ -│ --reattach Also attach combined.md notes for dirs │ -│ that were already current (repair). │ -│ --help Show this message and exit. │ +│ --root Comments root dir. │ +│ [default: .state/comments] │ +│ --docket Limit to one docket (e.g. │ +│ CMS-2023-0121). │ +│ --limit Cap dirs processed this run. 0 = no │ +│ cap. │ +│ [default: 0] │ +│ --workers Concurrent extraction threads. │ +│ [default: 8] │ +│ --force Re-extract dirs that already have │ +│ combined.md. │ +│ --bib --no-bib Look up inline body from bib.sqlite │ +│ items.abstract. │ +│ [default: bib] │ +│ --attach --no-attach Attach combined.md back to its bib item │ +│ (so it flows to Zotero via `bib sync`). │ +│ Implies --bib; no-op when --no-bib. │ +│ [default: attach] │ +│ --reattach Also attach combined.md notes for dirs │ +│ that were already current (repair). │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/comments-seal.md b/docs/docs/cli/comments-seal.md index ff5fe35..286e18f 100644 --- a/docs/docs/cli/comments-seal.md +++ b/docs/docs/cli/comments-seal.md @@ -6,15 +6,15 @@ sidebar_position: 56 # `stack comments seal` ``` -Usage: stack comments seal [OPTIONS] DOCKET +Usage: stack comments seal [OPTIONS] {docket} Mark a docket complete: every stage skips it until unsealed or --force. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * docket TEXT reg.gov docket id [required] │ +│ * docket reg.gov docket id [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --reason TEXT [default: manual] │ -│ --help Show this message and exit. │ +│ --reason [default: manual] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/comments-stats.md b/docs/docs/cli/comments-stats.md index b1a6998..3d184a5 100644 --- a/docs/docs/cli/comments-stats.md +++ b/docs/docs/cli/comments-stats.md @@ -11,7 +11,7 @@ Usage: stack comments stats [OPTIONS] Rebuild the index and print per-status counts. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --root PATH Comments root dir. [default: .state/comments] │ -│ --help Show this message and exit. │ +│ --root Comments root dir. [default: .state/comments] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/comments-unseal.md b/docs/docs/cli/comments-unseal.md index fab72b0..7663129 100644 --- a/docs/docs/cli/comments-unseal.md +++ b/docs/docs/cli/comments-unseal.md @@ -6,12 +6,12 @@ sidebar_position: 57 # `stack comments unseal` ``` -Usage: stack comments unseal [OPTIONS] DOCKET +Usage: stack comments unseal [OPTIONS] {docket} Reopen a sealed docket. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * docket TEXT reg.gov docket id [required] │ +│ * docket reg.gov docket id [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ │ --help Show this message and exit. │ diff --git a/docs/docs/cli/db-inspect.md b/docs/docs/cli/db-inspect.md index f9a2780..ec1b950 100644 --- a/docs/docs/cli/db-inspect.md +++ b/docs/docs/cli/db-inspect.md @@ -6,12 +6,12 @@ sidebar_position: 75 # `stack db inspect` ``` -Usage: stack db inspect [OPTIONS] [TABLE] +Usage: stack db inspect [OPTIONS] [table] Inspect DuckDB table schema and stats. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ table [TABLE] Table name (schema.table). │ +│ table Table name (schema.table). │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ │ --help Show this message and exit. │ diff --git a/docs/docs/cli/docs-serve.md b/docs/docs/cli/docs-serve.md index c096693..eccad2b 100644 --- a/docs/docs/cli/docs-serve.md +++ b/docs/docs/cli/docs-serve.md @@ -11,8 +11,8 @@ Usage: stack docs serve [OPTIONS] Serve documentation locally with hot reload. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --port INTEGER Port to serve on. [default: 3000] │ -│ --skip-generate Skip content generation. │ -│ --help Show this message and exit. │ +│ --port Port to serve on. [default: 3000] │ +│ --skip-generate Skip content generation. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/lake-deploy.md b/docs/docs/cli/lake-deploy.md index b758820..b088d8d 100644 --- a/docs/docs/cli/lake-deploy.md +++ b/docs/docs/cli/lake-deploy.md @@ -11,12 +11,12 @@ Usage: stack lake deploy [OPTIONS] Create schemas and tables from SQLTable models. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --target TEXT Target: iceberg (nessie/polaris) or databricks. │ -│ [default: iceberg] │ -│ --catalog-type TEXT Catalog type: nessie or polaris. │ -│ [default: nessie] │ -│ --schema TEXT Only deploy these schemas. │ -│ --dry-run Report without creating. │ -│ --help Show this message and exit. │ +│ --target Target: iceberg (nessie/polaris) or databricks. │ +│ [default: iceberg] │ +│ --catalog-type Catalog type: nessie or polaris. │ +│ [default: nessie] │ +│ --schema Only deploy these schemas. │ +│ --dry-run Report without creating. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/lake-load.md b/docs/docs/cli/lake-load.md index caf1e15..b29792a 100644 --- a/docs/docs/cli/lake-load.md +++ b/docs/docs/cli/lake-load.md @@ -11,10 +11,11 @@ Usage: stack lake load [OPTIONS] Populate Iceberg tables with data from DuckDB. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --catalog-type TEXT Catalog type: nessie or polaris. │ -│ [default: nessie] │ -│ --schema TEXT Only load these schemas. │ -│ --mode TEXT Write mode: append or replace. [default: append] │ -│ --help Show this message and exit. │ +│ --catalog-type Catalog type: nessie or polaris. │ +│ [default: nessie] │ +│ --schema Only load these schemas. │ +│ --mode Write mode: append or replace. │ +│ [default: append] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/lake-parity.md b/docs/docs/cli/lake-parity.md index 7ee9cfa..09806aa 100644 --- a/docs/docs/cli/lake-parity.md +++ b/docs/docs/cli/lake-parity.md @@ -11,7 +11,7 @@ Usage: stack lake parity [OPTIONS] Compare pipeline outputs between DuckDB and Databricks. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --schema TEXT Only check these schemas. │ -│ --help Show this message and exit. │ +│ --schema Only check these schemas. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/lake-validate.md b/docs/docs/cli/lake-validate.md index d690b52..bfc26b9 100644 --- a/docs/docs/cli/lake-validate.md +++ b/docs/docs/cli/lake-validate.md @@ -11,9 +11,9 @@ Usage: stack lake validate [OPTIONS] Validate Iceberg tables match SQLTable model definitions. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --catalog-type TEXT Catalog type: nessie or polaris. │ -│ [default: nessie] │ -│ --schema TEXT Only validate these schemas. │ -│ --help Show this message and exit. │ +│ --catalog-type Catalog type: nessie or polaris. │ +│ [default: nessie] │ +│ --schema Only validate these schemas. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/llm-eval-tags.md b/docs/docs/cli/llm-eval-tags.md index 7542e53..955ddad 100644 --- a/docs/docs/cli/llm-eval-tags.md +++ b/docs/docs/cli/llm-eval-tags.md @@ -15,17 +15,17 @@ Usage: stack llm eval-tags [OPTIONS] re-tags each golden comment now. Exit 1 when the gate fails. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --golden TEXT Golden YAML (comment ids with expected │ +│ --golden Golden YAML (comment ids with expected │ │ themes). │ │ [default: tests/llm/golden_themes.yaml] │ │ --live Re-tag through the model instead of scoring │ │ what is stored on the items. │ -│ --limit INTEGER Score only the first N golden entries. │ +│ --limit Score only the first N golden entries. │ │ [default: 0] │ -│ --top INTEGER [default: 8] │ -│ --max-tags INTEGER [default: 3] │ -│ --min-confidence FLOAT [default: 0.6] │ -│ --dump TEXT With --live: write every comment's │ +│ --top [default: 8] │ +│ --max-tags [default: 3] │ +│ --min-confidence [default: 0.6] │ +│ --dump With --live: write every comment's │ │ shortlist, verdicts and confidences to this │ │ JSON file. │ │ --help Show this message and exit. │ diff --git a/docs/docs/cli/llm-index.md b/docs/docs/cli/llm-index.md index ae6588b..51d9c83 100644 --- a/docs/docs/cli/llm-index.md +++ b/docs/docs/cli/llm-index.md @@ -15,17 +15,16 @@ Usage: stack llm index [OPTIONS] corpus = every non-comment bib item incl. Zotero-only storage PDFs. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --collection TEXT Which collection: comments | rules | │ -│ corpus | all. │ -│ [default: comments] │ -│ --docket TEXT Limit comments to one docket id. │ -│ --key TEXT Limit rules/corpus to these item │ -│ keys. │ -│ --force --no-force Re-embed even when unchanged. │ -│ [default: no-force] │ -│ --limit INTEGER Stop after N docs per collection (0 = │ -│ all). │ -│ [default: 0] │ -│ --help Show this message and exit. │ +│ --collection Which collection: comments | rules | │ +│ corpus | all. │ +│ [default: comments] │ +│ --docket Limit comments to one docket id. │ +│ --key Limit rules/corpus to these item keys. │ +│ --force --no-force Re-embed even when unchanged. │ +│ [default: no-force] │ +│ --limit Stop after N docs per collection (0 = │ +│ all). │ +│ [default: 0] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/llm-restamp.md b/docs/docs/cli/llm-restamp.md index 68890d7..2fc462a 100644 --- a/docs/docs/cli/llm-restamp.md +++ b/docs/docs/cli/llm-restamp.md @@ -21,11 +21,11 @@ Usage: stack llm restamp [OPTIONS] under `--dry-run`. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --collection TEXT Which collection: comments | rules | corpus | │ -│ all. │ -│ [default: comments] │ -│ --batch INTEGER Rows per transaction. [default: 2000] │ -│ --dry-run Scan and report without writing. │ -│ --help Show this message and exit. │ +│ --collection Which collection: comments | rules | corpus | │ +│ all. │ +│ [default: comments] │ +│ --batch Rows per transaction. [default: 2000] │ +│ --dry-run Scan and report without writing. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/llm-serve.md b/docs/docs/cli/llm-serve.md index 3a6a6fb..08c5f8e 100644 --- a/docs/docs/cli/llm-serve.md +++ b/docs/docs/cli/llm-serve.md @@ -11,8 +11,8 @@ Usage: stack llm serve [OPTIONS] Serve the SSO-guarded chat UI (llm.api:app). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --host TEXT Bind address. [default: 127.0.0.1] │ -│ --port INTEGER Port. [default: 8000] │ -│ --help Show this message and exit. │ +│ --host Bind address. [default: 127.0.0.1] │ +│ --port Port. [default: 8000] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/llm-stamp-themes.md b/docs/docs/cli/llm-stamp-themes.md index ff7dbaf..f2f17f3 100644 --- a/docs/docs/cli/llm-stamp-themes.md +++ b/docs/docs/cli/llm-stamp-themes.md @@ -15,12 +15,12 @@ Usage: stack llm stamp-themes [OPTIONS] them. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --collection TEXT comments | rules | corpus. [default: corpus] │ -│ --doctype TEXT Only chunks of this doctype ('' = every chunk). │ +│ --collection comments | rules | corpus. [default: corpus] │ +│ --doctype Only chunks of this doctype ('' = every chunk). │ │ [default: manual] │ -│ --key TEXT Only this item key. │ -│ --top INTEGER Themes kept per chunk. [default: 2] │ -│ --min-score FLOAT Cosine similarity a theme must reach. │ +│ --key Only this item key. │ +│ --top Themes kept per chunk. [default: 2] │ +│ --min-score Cosine similarity a theme must reach. │ │ [default: 0.6] │ │ --force Re-stamp chunks already on the current │ │ vocabulary version. │ diff --git a/docs/docs/cli/llm-tag.md b/docs/docs/cli/llm-tag.md index 673cc71..738e7d3 100644 --- a/docs/docs/cli/llm-tag.md +++ b/docs/docs/cli/llm-tag.md @@ -15,21 +15,21 @@ Usage: stack llm tag [OPTIONS] skipped unless --force. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ * --docket TEXT regulations.gov docket id, e.g. │ +│ * --docket regulations.gov docket id, e.g. │ │ CMS-2026-2377. │ │ [required] │ -│ --limit INTEGER Stop after N comments (newest first; 0 = │ +│ --limit Stop after N comments (newest first; 0 = │ │ all). │ │ [default: 0] │ │ --force Re-tag comments whose stored state is │ │ current. │ │ --dry-run Compute and print, write nothing. │ -│ --top INTEGER Themes shortlisted per comment before │ +│ --top Themes shortlisted per comment before │ │ judging. │ │ [default: 8] │ -│ --max-tags INTEGER Most themes written per comment. │ +│ --max-tags Most themes written per comment. │ │ [default: 3] │ -│ --min-confidence FLOAT Shortlist similarity below which a │ +│ --min-confidence Shortlist similarity below which a │ │ judged yes is not written. │ │ [default: 0.0] │ │ --verbose Print every comment's tags. │ diff --git a/docs/docs/cli/llm-vocab.md b/docs/docs/cli/llm-vocab.md index c02f11d..1408b43 100644 --- a/docs/docs/cli/llm-vocab.md +++ b/docs/docs/cli/llm-vocab.md @@ -13,9 +13,9 @@ Usage: stack llm vocab [OPTIONS] it was seeded from. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --path TEXT A vocabulary file to validate instead of the packaged │ -│ one. │ -│ --slug TEXT Show one theme in full. │ -│ --help Show this message and exit. │ +│ --path A vocabulary file to validate instead of the packaged │ +│ one. │ +│ --slug Show one theme in full. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/load-bcda.md b/docs/docs/cli/load-bcda.md index 58e9b9a..f6e6518 100644 --- a/docs/docs/cli/load-bcda.md +++ b/docs/docs/cli/load-bcda.md @@ -16,11 +16,11 @@ Usage: stack load bcda [OPTIONS] resource type under the BCDA store (a v3 pull is three jobs). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --ndjson-dir PATH Directory containing FHIR ndjson files. │ -│ --database TEXT DuckDB database path (default: config). │ -│ --skip-flatten Skip flattening, load existing Parquet. │ -│ --run-pipeline Also run the bcda connector pipeline into │ -│ input_layer.* │ -│ --help Show this message and exit. │ +│ --ndjson-dir Directory containing FHIR ndjson files. │ +│ --database DuckDB database path (default: config). │ +│ --skip-flatten Skip flattening, load existing Parquet. │ +│ --run-pipeline Also run the bcda connector pipeline into │ +│ input_layer.* │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/load-cclf.md b/docs/docs/cli/load-cclf.md index 410eec9..e82dd39 100644 --- a/docs/docs/cli/load-cclf.md +++ b/docs/docs/cli/load-cclf.md @@ -15,9 +15,9 @@ Usage: stack load cclf [OPTIONS] pipeline to produce ``input_layer`` tables. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ * --path PATH Directory containing CCLF files. [required] │ -│ --database TEXT DuckDB database path (default: config). │ -│ --no-pipeline Load raw tables only, skip CCLF pipeline. │ -│ --help Show this message and exit. │ +│ * --path Directory containing CCLF files. [required] │ +│ --database DuckDB database path (default: config). │ +│ --no-pipeline Load raw tables only, skip CCLF pipeline. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/load-cms.md b/docs/docs/cli/load-cms.md index 4d32158..3402cf3 100644 --- a/docs/docs/cli/load-cms.md +++ b/docs/docs/cli/load-cms.md @@ -17,14 +17,16 @@ Usage: stack load cms [OPTIONS] claims or ``cms.aco_participant_tin`` know it. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --table -t TEXT cms. (default: the institutional │ -│ universe). │ -│ --database TEXT DuckDB database path (default: config). │ -│ --refresh Re-download even if the CSV is on disk. │ -│ --derive --no-derive Rebuild institutional_provider / │ -│ ccn_crosswalk / provider_tin_observed / │ -│ ccn_tin. │ -│ [default: derive] │ -│ --help Show this message and exit. │ +│ --table -t cms.
(default: the │ +│ institutional universe). │ +│ --database DuckDB database path (default: │ +│ config). │ +│ --refresh Re-download even if the CSV is on │ +│ disk. │ +│ --derive --no-derive Rebuild institutional_provider / │ +│ ccn_crosswalk / provider_tin_observed │ +│ / ccn_tin. │ +│ [default: derive] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/load-seed.md b/docs/docs/cli/load-seed.md index 18a7501..b083cec 100644 --- a/docs/docs/cli/load-seed.md +++ b/docs/docs/cli/load-seed.md @@ -11,10 +11,10 @@ Usage: stack load seed [OPTIONS] Load seed/reference data (CSV, Excel, Parquet) into DuckDB. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --seed-dir PATH Directory containing seed files. │ -│ --database TEXT DuckDB database path (default: config). │ -│ --schema TEXT Target DuckDB schema for seed tables. │ -│ [default: reference_data] │ -│ --help Show this message and exit. │ +│ --seed-dir Directory containing seed files. │ +│ --database DuckDB database path (default: config). │ +│ --schema Target DuckDB schema for seed tables. │ +│ [default: reference_data] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/mail-attach-smarthost.md b/docs/docs/cli/mail-attach-smarthost.md index 043b0ee..f0082ec 100644 --- a/docs/docs/cli/mail-attach-smarthost.md +++ b/docs/docs/cli/mail-attach-smarthost.md @@ -1,6 +1,6 @@ --- title: stack mail attach-smarthost -sidebar_position: 122 +sidebar_position: 123 --- # `stack mail attach-smarthost` diff --git a/docs/docs/cli/mail-dkim-export.md b/docs/docs/cli/mail-dkim-export.md index 867d1da..c777600 100644 --- a/docs/docs/cli/mail-dkim-export.md +++ b/docs/docs/cli/mail-dkim-export.md @@ -1,6 +1,6 @@ --- title: stack mail dkim-export -sidebar_position: 121 +sidebar_position: 122 --- # `stack mail dkim-export` diff --git a/docs/docs/cli/mail-dns.md b/docs/docs/cli/mail-dns.md index 893943c..d17840a 100644 --- a/docs/docs/cli/mail-dns.md +++ b/docs/docs/cli/mail-dns.md @@ -1,6 +1,6 @@ --- title: stack mail dns -sidebar_position: 120 +sidebar_position: 121 --- # `stack mail dns` diff --git a/docs/docs/cli/mail-down.md b/docs/docs/cli/mail-down.md index 27dc331..b263ea9 100644 --- a/docs/docs/cli/mail-down.md +++ b/docs/docs/cli/mail-down.md @@ -1,6 +1,6 @@ --- title: stack mail down -sidebar_position: 118 +sidebar_position: 119 --- # `stack mail down` diff --git a/docs/docs/cli/mail-provision.md b/docs/docs/cli/mail-provision.md index 11cf506..d6145d2 100644 --- a/docs/docs/cli/mail-provision.md +++ b/docs/docs/cli/mail-provision.md @@ -1,6 +1,6 @@ --- title: stack mail provision -sidebar_position: 116 +sidebar_position: 117 --- # `stack mail provision` @@ -11,8 +11,8 @@ Usage: stack mail provision [OPTIONS] End-to-end idempotent: up → wait → DNS → DKIM → smarthost → git env. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --region TEXT DO region slug (one your ISP can reach). │ -│ [default: nyc3] │ -│ --help Show this message and exit. │ +│ --region DO region slug (one your ISP can reach). │ +│ [default: nyc3] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/mail-rotate-creds.md b/docs/docs/cli/mail-rotate-creds.md index a6489e0..f1b1e49 100644 --- a/docs/docs/cli/mail-rotate-creds.md +++ b/docs/docs/cli/mail-rotate-creds.md @@ -1,18 +1,18 @@ --- title: stack mail rotate-creds -sidebar_position: 123 +sidebar_position: 124 --- # `stack mail rotate-creds` ``` -Usage: stack mail rotate-creds [OPTIONS] USER +Usage: stack mail rotate-creds [OPTIONS] {user} Mint a new password for *user*@fhirworx.io and push to droplet. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * user TEXT Mailbox to rotate (e.g. git, postmaster, cmsupdates). │ -│ [required] │ +│ * user Mailbox to rotate (e.g. git, postmaster, cmsupdates). │ +│ [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ │ --help Show this message and exit. │ diff --git a/docs/docs/cli/mail-seed-mailboxes.md b/docs/docs/cli/mail-seed-mailboxes.md index 8051a29..0d25928 100644 --- a/docs/docs/cli/mail-seed-mailboxes.md +++ b/docs/docs/cli/mail-seed-mailboxes.md @@ -1,6 +1,6 @@ --- title: stack mail seed-mailboxes -sidebar_position: 124 +sidebar_position: 125 --- # `stack mail seed-mailboxes` diff --git a/docs/docs/cli/mail-status.md b/docs/docs/cli/mail-status.md index e135886..6afa950 100644 --- a/docs/docs/cli/mail-status.md +++ b/docs/docs/cli/mail-status.md @@ -1,6 +1,6 @@ --- title: stack mail status -sidebar_position: 119 +sidebar_position: 120 --- # `stack mail status` diff --git a/docs/docs/cli/mail-up.md b/docs/docs/cli/mail-up.md index fcd5b90..7424680 100644 --- a/docs/docs/cli/mail-up.md +++ b/docs/docs/cli/mail-up.md @@ -1,6 +1,6 @@ --- title: stack mail up -sidebar_position: 117 +sidebar_position: 118 --- # `stack mail up` @@ -11,7 +11,7 @@ Usage: stack mail up [OPTIONS] Adopt-or-create the mail droplet. Idempotent. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --region TEXT DO region slug. [default: nyc3] │ -│ --help Show this message and exit. │ +│ --region DO region slug. [default: nyc3] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/mail-wire-git.md b/docs/docs/cli/mail-wire-git.md index 72df4c5..43198d4 100644 --- a/docs/docs/cli/mail-wire-git.md +++ b/docs/docs/cli/mail-wire-git.md @@ -1,6 +1,6 @@ --- title: stack mail wire-git -sidebar_position: 125 +sidebar_position: 126 --- # `stack mail wire-git` diff --git a/docs/docs/cli/mail.md b/docs/docs/cli/mail.md index a663dba..e8f11cf 100644 --- a/docs/docs/cli/mail.md +++ b/docs/docs/cli/mail.md @@ -1,6 +1,6 @@ --- title: stack mail -sidebar_position: 115 +sidebar_position: 116 --- # `stack mail` diff --git a/docs/docs/cli/nlm-fetch.md b/docs/docs/cli/nlm-fetch.md new file mode 100644 index 0000000..0618104 --- /dev/null +++ b/docs/docs/cli/nlm-fetch.md @@ -0,0 +1,18 @@ +--- +title: stack nlm fetch +sidebar_position: 129 +--- + +# `stack nlm fetch` + +``` +Usage: stack nlm fetch [OPTIONS] + + Download the current file of every (or each named) release stream. + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│ --stream Only these streams. │ +│ --dest Root directory (default nlm.dir). │ +│ --help Show this message and exit. │ +╰──────────────────────────────────────────────────────────────────────────────╯ +``` diff --git a/docs/docs/cli/nlm-releases.md b/docs/docs/cli/nlm-releases.md new file mode 100644 index 0000000..61437d0 --- /dev/null +++ b/docs/docs/cli/nlm-releases.md @@ -0,0 +1,17 @@ +--- +title: stack nlm releases +sidebar_position: 128 +--- + +# `stack nlm releases` + +``` +Usage: stack nlm releases [OPTIONS] + + List the current file of every release stream. + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│ --stream Only these streams. │ +│ --help Show this message and exit. │ +╰──────────────────────────────────────────────────────────────────────────────╯ +``` diff --git a/docs/docs/cli/nlm-vsac.md b/docs/docs/cli/nlm-vsac.md new file mode 100644 index 0000000..9314be0 --- /dev/null +++ b/docs/docs/cli/nlm-vsac.md @@ -0,0 +1,24 @@ +--- +title: stack nlm vsac +sidebar_position: 130 +--- + +# `stack nlm vsac` + +``` +Usage: stack nlm vsac [OPTIONS] + + Save every VSAC value-set definition, then expand each one. + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│ --dest Root directory (default │ +│ nlm.dir). │ +│ --definitions-only │ +│ --workers [1<=x<=16] [default: 4] │ +│ --limit Expand at most N (0 = │ +│ all). │ +│ [default: 0] │ +│ --help Show this message and │ +│ exit. │ +╰──────────────────────────────────────────────────────────────────────────────╯ +``` diff --git a/docs/docs/cli/nlm.md b/docs/docs/cli/nlm.md new file mode 100644 index 0000000..69f0024 --- /dev/null +++ b/docs/docs/cli/nlm.md @@ -0,0 +1,21 @@ +--- +title: stack nlm +sidebar_position: 127 +--- + +# `stack nlm` + +``` +Usage: stack nlm [OPTIONS] COMMAND [ARGS]... + + NLM terminology releases and VSAC value sets. + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│ --help Show this message and exit. │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│ releases List the current file of every release stream. │ +│ fetch Download the current file of every (or each named) release stream. │ +│ vsac Save every VSAC value-set definition, then expand each one. │ +╰──────────────────────────────────────────────────────────────────────────────╯ +``` diff --git a/docs/docs/cli/perf-show.md b/docs/docs/cli/perf-show.md index 5a65b6f..16064e0 100644 --- a/docs/docs/cli/perf-show.md +++ b/docs/docs/cli/perf-show.md @@ -11,9 +11,8 @@ Usage: stack perf show [OPTIONS] Pretty-print spans from the local JSONL trace file. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --path TEXT Path to JSONL span file. │ -│ [default: traces/spans.jsonl] │ -│ --last INTEGER Show last N spans. [default: 20] │ -│ --help Show this message and exit. │ +│ --path Path to JSONL span file. [default: traces/spans.jsonl] │ +│ --last Show last N spans. [default: 20] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-cpt-ingest.md b/docs/docs/cli/pfs-cpt-ingest.md index 27b76c8..ee95f08 100644 --- a/docs/docs/cli/pfs-cpt-ingest.md +++ b/docs/docs/cli/pfs-cpt-ingest.md @@ -13,9 +13,9 @@ Usage: stack pfs cpt-ingest [OPTIONS] 2026-09-09-cpt-canonical-schema-design.md §3). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --edition INTEGER CPT edition year to ingest (repeatable). │ -│ --all Every CPT EPUB edition found in bib (source:ama). │ -│ --dry-run Parse and report counts; write nothing. │ -│ --help Show this message and exit. │ +│ --edition CPT edition year to ingest (repeatable). │ +│ --all Every CPT EPUB edition found in bib (source:ama). │ +│ --dry-run Parse and report counts; write nothing. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-elements.md b/docs/docs/cli/pfs-elements.md index f7b0cba..69287f4 100644 --- a/docs/docs/cli/pfs-elements.md +++ b/docs/docs/cli/pfs-elements.md @@ -11,14 +11,14 @@ Usage: stack pfs elements [OPTIONS] Extract typed elements for codes into pfs.code_element (+ review queue). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --code TEXT HCPCS/CPT code (repeatable). │ -│ --family TEXT Expand a registered family (CCM, APCM, …); │ -│ repeatable. │ -│ --all-payable Every A/R/T code in the newest RVU year, one │ -│ inverted pass over fr_anchors. │ -│ --no-llm Skip the local-model classifier (unknown lines go │ -│ to review). │ -│ --dry-run Extract and report; write nothing. │ -│ --help Show this message and exit. │ +│ --code HCPCS/CPT code (repeatable). │ +│ --family Expand a registered family (CCM, APCM, …); │ +│ repeatable. │ +│ --all-payable Every A/R/T code in the newest RVU year, one │ +│ inverted pass over fr_anchors. │ +│ --no-llm Skip the local-model classifier (unknown lines │ +│ go to review). │ +│ --dry-run Extract and report; write nothing. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-exposure.md b/docs/docs/cli/pfs-exposure.md index 468634f..794f1c4 100644 --- a/docs/docs/cli/pfs-exposure.md +++ b/docs/docs/cli/pfs-exposure.md @@ -18,18 +18,17 @@ Usage: stack pfs exposure [OPTIONS] calendar); --code/--family only filter what is printed. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --code TEXT Filter to a code; repeatable. │ -│ --family TEXT Filter to a family key (CCM, APCM, …); │ -│ repeatable. │ -│ --controls INTEGER With one --code and --year: list up to N │ -│ never-treated control codes (same status + RVU │ -│ band, no exposure within --window years). │ -│ [default: 0] │ -│ --year INTEGER The exposure year --controls refers to. │ -│ [default: 0] │ -│ --window INTEGER ±years a control must be quiet for. [default: 2] │ -│ --write Rebuild the whole calendar into pfs.code_exposure │ -│ and republish. │ -│ --help Show this message and exit. │ +│ --code Filter to a code; repeatable. │ +│ --family Filter to a family key (CCM, APCM, …); repeatable. │ +│ --controls With one --code and --year: list up to N │ +│ never-treated control codes (same status + RVU │ +│ band, no exposure within --window years). │ +│ [default: 0] │ +│ --year The exposure year --controls refers to. │ +│ [default: 0] │ +│ --window ±years a control must be quiet for. [default: 2] │ +│ --write Rebuild the whole calendar into pfs.code_exposure │ +│ and republish. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-guidance.md b/docs/docs/cli/pfs-guidance.md index cb43089..b63bc65 100644 --- a/docs/docs/cli/pfs-guidance.md +++ b/docs/docs/cli/pfs-guidance.md @@ -13,8 +13,8 @@ Usage: stack pfs guidance [OPTIONS] CPT manual cite, with FR provenance. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --family TEXT Family key (CCM, APCM, …); repeatable. │ +│ --family Family key (CCM, APCM, …); repeatable. │ │ --write │ -│ --help Show this message and exit. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-lineage.md b/docs/docs/cli/pfs-lineage.md index 5e19ef9..34e7d29 100644 --- a/docs/docs/cli/pfs-lineage.md +++ b/docs/docs/cli/pfs-lineage.md @@ -14,13 +14,13 @@ Usage: stack pfs lineage [OPTIONS] fr_anchors instead of one query per code. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --code TEXT │ -│ --all-payable Every A/R/T code in the newest RVU year, one │ -│ inverted pass over fr_anchors. │ -│ --limit INTEGER Only the first N target codes (sorted) — for │ -│ smoke runs with --all-payable. │ -│ [default: 0] │ -│ --write Persist to pfs.code_event and republish. │ -│ --help Show this message and exit. │ +│ --code │ +│ --all-payable Every A/R/T code in the newest RVU year, one │ +│ inverted pass over fr_anchors. │ +│ --limit Only the first N target codes (sorted) — for │ +│ smoke runs with --all-payable. │ +│ [default: 0] │ +│ --write Persist to pfs.code_event and republish. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-reaction.md b/docs/docs/cli/pfs-reaction.md index 3c1d008..4c35c7c 100644 --- a/docs/docs/cli/pfs-reaction.md +++ b/docs/docs/cli/pfs-reaction.md @@ -16,15 +16,15 @@ Usage: stack pfs reaction [OPTIONS] persisting the result. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --family TEXT Family key (CCM, APCM, …); repeatable. │ -│ --code TEXT A single code as its own pseudo-family, │ -│ keyed by the code; repeatable. │ -│ --stance-sample INTEGER Classify the newest N commenters per docket │ -│ into support/oppose/modify/unclear via the │ -│ self-hosted classifier (0 = skip; no stance │ -│ sample means no LLM call at all). │ -│ [default: 0] │ +│ --family Family key (CCM, APCM, …); repeatable. │ +│ --code A single code as its own pseudo-family, keyed │ +│ by the code; repeatable. │ +│ --stance-sample Classify the newest N commenters per docket │ +│ into support/oppose/modify/unclear via the │ +│ self-hosted classifier (0 = skip; no stance │ +│ sample means no LLM call at all). │ +│ [default: 0] │ │ --write │ -│ --help Show this message and exit. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-review.md b/docs/docs/cli/pfs-review.md index 5a57f76..21d4ce7 100644 --- a/docs/docs/cli/pfs-review.md +++ b/docs/docs/cli/pfs-review.md @@ -11,7 +11,7 @@ Usage: stack pfs review [OPTIONS] Element lines the classifier could not place. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --code TEXT │ -│ --help Show this message and exit. │ +│ --code │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/pfs-utilization.md b/docs/docs/cli/pfs-utilization.md index b4a42c0..22a4ff9 100644 --- a/docs/docs/cli/pfs-utilization.md +++ b/docs/docs/cli/pfs-utilization.md @@ -18,14 +18,14 @@ Usage: stack pfs utilization [OPTIONS] republishes the replica; --code prints series from the replica. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --year INTEGER Calendar year(s) to ingest with --write; default │ -│ all 2013–. │ -│ --code TEXT Print the per-year series for these codes │ -│ (repeatable). │ -│ --write Fetch from data.cms.gov, load pfs.utilization, │ -│ cite, republish. │ -│ --offline With --write: load from the cached JSON instead of │ -│ the API. │ -│ --help Show this message and exit. │ +│ --year Calendar year(s) to ingest with --write; default all │ +│ 2013–. │ +│ --code Print the per-year series for these codes │ +│ (repeatable). │ +│ --write Fetch from data.cms.gov, load pfs.utilization, cite, │ +│ republish. │ +│ --offline With --write: load from the cached JSON instead of │ +│ the API. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-eligible.md b/docs/docs/cli/prisma-eligible.md index c906274..267c0b6 100644 --- a/docs/docs/cli/prisma-eligible.md +++ b/docs/docs/cli/prisma-eligible.md @@ -1,41 +1,41 @@ --- title: stack prisma eligible -sidebar_position: 109 +sidebar_position: 110 --- # `stack prisma eligible` ``` -Usage: stack prisma eligible [OPTIONS] NAME +Usage: stack prisma eligible [OPTIONS] {name} Stage 3 — LLM-driven full-text eligibility pass. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug. [required] │ +│ * name Project slug. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --limit -n INTEGER [default: 0] │ -│ --max-chars INTEGER Cap per-item markdown (full text) │ -│ at N chars so bounded-context local │ -│ models keep the criteria in window. │ -│ 0 = no cap. │ -│ [default: 0] │ -│ --db PATH [default: │ -│ data/zotero/data/zotero.sqlite] │ -│ --storage PATH [default: data/zotero/data/storage] │ -│ --hold --no-hold [default: hold] │ -│ --hosts TEXT Comma-separated Ollama base URLs — │ -│ fleet mode (#655): parallel │ -│ eligibility via native /api/chat │ -│ with per-request num_ctx; bypasses │ -│ PRISMA_LLM_* env config. │ -│ --fleet-model TEXT Model name on every fleet host. │ -│ [default: qwen2.5:14b] │ -│ --num-ctx INTEGER Context window per fleet request. │ -│ [default: 8192] │ -│ --per-host INTEGER Max in-flight requests per fleet │ -│ host. │ -│ [default: 1] │ -│ --help Show this message and exit. │ +│ --limit -n [default: 0] │ +│ --max-chars Cap per-item markdown (full text) at │ +│ N chars so bounded-context local │ +│ models keep the criteria in window. │ +│ 0 = no cap. │ +│ [default: 0] │ +│ --db [default: │ +│ data/zotero/data/zotero.sqlite] │ +│ --storage [default: data/zotero/data/storage] │ +│ --hold --no-hold [default: hold] │ +│ --hosts Comma-separated Ollama base URLs — │ +│ fleet mode (#655): parallel │ +│ eligibility via native /api/chat │ +│ with per-request num_ctx; bypasses │ +│ PRISMA_LLM_* env config. │ +│ --fleet-model Model name on every fleet host. │ +│ [default: qwen2.5:14b] │ +│ --num-ctx Context window per fleet request. │ +│ [default: 8192] │ +│ --per-host Max in-flight requests per fleet │ +│ host. │ +│ [default: 1] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-export.md b/docs/docs/cli/prisma-export.md index ca54166..df9768c 100644 --- a/docs/docs/cli/prisma-export.md +++ b/docs/docs/cli/prisma-export.md @@ -1,23 +1,23 @@ --- title: stack prisma export -sidebar_position: 106 +sidebar_position: 107 --- # `stack prisma export` ``` -Usage: stack prisma export [OPTIONS] ZOT_ID +Usage: stack prisma export [OPTIONS] {zot_id} Dump one Zotero item as the LLM-ready markdown snapshot. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * zot_id INTEGER Zotero itemID to export. [required] │ +│ * zot_id Zotero itemID to export. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ │ --fulltext │ -│ --db PATH [default: data/zotero/data/zotero.sqlite] │ -│ --storage PATH [default: data/zotero/data/storage] │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --db [default: data/zotero/data/zotero.sqlite] │ +│ --storage [default: data/zotero/data/storage] │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-extract.md b/docs/docs/cli/prisma-extract.md index d58d124..3042bc2 100644 --- a/docs/docs/cli/prisma-extract.md +++ b/docs/docs/cli/prisma-extract.md @@ -1,36 +1,36 @@ --- title: stack prisma extract -sidebar_position: 110 +sidebar_position: 111 --- # `stack prisma extract` ``` -Usage: stack prisma extract [OPTIONS] NAME +Usage: stack prisma extract [OPTIONS] {name} Stage 3+ — structured data extraction on included studies. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug. [required] │ +│ * name Project slug. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --limit -n INTEGER [default: 0] │ -│ --db PATH [default: │ -│ data/zotero/data/zotero.sqlite] │ -│ --storage PATH [default: data/zotero/data/storage] │ -│ --hold --no-hold [default: hold] │ -│ --hosts TEXT Comma-separated Ollama base URLs — │ -│ fleet mode (#655): parallel │ -│ extraction via native /api/chat │ -│ with per-request num_ctx; bypasses │ -│ PRISMA_LLM_* env config. │ -│ --fleet-model TEXT Model name on every fleet host. │ -│ [default: qwen2.5:14b] │ -│ --num-ctx INTEGER Context window per fleet request. │ -│ [default: 8192] │ -│ --per-host INTEGER Max in-flight requests per fleet │ -│ host. │ -│ [default: 1] │ -│ --help Show this message and exit. │ +│ --limit -n [default: 0] │ +│ --db [default: │ +│ data/zotero/data/zotero.sqlite] │ +│ --storage [default: data/zotero/data/storage] │ +│ --hold --no-hold [default: hold] │ +│ --hosts Comma-separated Ollama base URLs — │ +│ fleet mode (#655): parallel │ +│ extraction via native /api/chat with │ +│ per-request num_ctx; bypasses │ +│ PRISMA_LLM_* env config. │ +│ --fleet-model Model name on every fleet host. │ +│ [default: qwen2.5:14b] │ +│ --num-ctx Context window per fleet request. │ +│ [default: 8192] │ +│ --per-host Max in-flight requests per fleet │ +│ host. │ +│ [default: 1] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-fetch.md b/docs/docs/cli/prisma-fetch.md index b7a1a03..994d762 100644 --- a/docs/docs/cli/prisma-fetch.md +++ b/docs/docs/cli/prisma-fetch.md @@ -1,12 +1,12 @@ --- title: stack prisma fetch -sidebar_position: 112 +sidebar_position: 113 --- # `stack prisma fetch` ``` -Usage: stack prisma fetch [OPTIONS] NAME +Usage: stack prisma fetch [OPTIONS] {name} Fetch PDFs for every non-excluded item lacking an attachment. @@ -21,29 +21,28 @@ Usage: stack prisma fetch [OPTIONS] NAME the duration of the fetch and closes it on exit. No sudo required. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug. [required] │ +│ * name Project slug. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --limit -n INTEGER [default: 0] │ -│ --workers -w INTEGER Concurrent fetch workers (fallback │ -│ tier stays serialized). │ -│ [default: 8] │ -│ --db PATH [default: │ -│ data/zotero/data/zotero.sqlite] │ -│ --storage PATH [default: data/zotero/data/storage] │ -│ --scratch PATH [default: .state/prisma-fetch] │ -│ --proxy TEXT Override PRISMA_FETCH_PROXY (else │ -│ env). │ -│ --vpn --no-vpn Auto-open an SSH tunnel to the │ -│ provisioned droplet when one exists. │ -│ --no-vpn skips the tunnel and uses │ -│ only the unproxied sources. │ -│ [default: vpn] │ -│ --verify --no-verify Curl through the proxy once before │ -│ fetching and confirm egress is │ -│ non-US. │ -│ [default: verify] │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --limit -n [default: 0] │ +│ --workers -w Concurrent fetch workers (fallback │ +│ tier stays serialized). │ +│ [default: 8] │ +│ --db [default: │ +│ data/zotero/data/zotero.sqlite] │ +│ --storage [default: data/zotero/data/storage] │ +│ --scratch [default: .state/prisma-fetch] │ +│ --proxy Override PRISMA_FETCH_PROXY (else │ +│ env). │ +│ --vpn --no-vpn Auto-open an SSH tunnel to the │ +│ provisioned droplet when one exists. │ +│ --no-vpn skips the tunnel and uses │ +│ only the unproxied sources. │ +│ [default: vpn] │ +│ --verify --no-verify Curl through the proxy once before │ +│ fetching and confirm egress is non-US. │ +│ [default: verify] │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-flow.md b/docs/docs/cli/prisma-flow.md index 79ceb38..468b9f0 100644 --- a/docs/docs/cli/prisma-flow.md +++ b/docs/docs/cli/prisma-flow.md @@ -1,22 +1,22 @@ --- title: stack prisma flow -sidebar_position: 111 +sidebar_position: 112 --- # `stack prisma flow` ``` -Usage: stack prisma flow [OPTIONS] NAME +Usage: stack prisma flow [OPTIONS] {name} Emit the PRISMA 2020 flow diagram from current tag counts. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug. [required] │ +│ * name Project slug. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --mermaid --text [default: mermaid] │ -│ --db PATH [default: data/zotero/data/zotero.sqlite] │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --mermaid --text [default: mermaid] │ +│ --db [default: data/zotero/data/zotero.sqlite] │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-init.md b/docs/docs/cli/prisma-init.md index 574f139..20909fa 100644 --- a/docs/docs/cli/prisma-init.md +++ b/docs/docs/cli/prisma-init.md @@ -1,23 +1,23 @@ --- title: stack prisma init -sidebar_position: 105 +sidebar_position: 106 --- # `stack prisma init` ``` -Usage: stack prisma init [OPTIONS] NAME +Usage: stack prisma init [OPTIONS] {name} Create (or re-load) the project's three Zotero anchor items: criteria, extraction-template, and the reasons codebook. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug, e.g. skin-subs. [required] │ +│ * name Project slug, e.g. skin-subs. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --db PATH Zotero SQLite path. │ -│ [default: data/zotero/data/zotero.sqlite] │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --db Zotero SQLite path. │ +│ [default: data/zotero/data/zotero.sqlite] │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-ping-llm.md b/docs/docs/cli/prisma-ping-llm.md index 0f6cbc5..01cc9bd 100644 --- a/docs/docs/cli/prisma-ping-llm.md +++ b/docs/docs/cli/prisma-ping-llm.md @@ -1,6 +1,6 @@ --- title: stack prisma ping-llm -sidebar_position: 107 +sidebar_position: 108 --- # `stack prisma ping-llm` diff --git a/docs/docs/cli/prisma-run.md b/docs/docs/cli/prisma-run.md index ce18493..96dbd39 100644 --- a/docs/docs/cli/prisma-run.md +++ b/docs/docs/cli/prisma-run.md @@ -1,12 +1,12 @@ --- title: stack prisma run -sidebar_position: 113 +sidebar_position: 114 --- # `stack prisma run` ``` -Usage: stack prisma run [OPTIONS] NAME +Usage: stack prisma run [OPTIONS] {name} Orchestrate all PRISMA stages in order. @@ -15,18 +15,17 @@ Usage: stack prisma run [OPTIONS] NAME exclusions are terminal by design. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug. [required] │ +│ * name Project slug. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --limit -n INTEGER Same limit applied to every stage. │ -│ [default: 0] │ +│ --limit -n Same limit applied to every stage. │ +│ [default: 0] │ │ --skip-fetch │ │ --skip-extract │ -│ --db PATH [default: │ -│ data/zotero/data/zotero.sqlite] │ -│ --storage PATH [default: │ -│ data/zotero/data/storage] │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --db [default: │ +│ data/zotero/data/zotero.sqlite] │ +│ --storage [default: data/zotero/data/storage] │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-screen.md b/docs/docs/cli/prisma-screen.md index 1e5d76f..bef43ae 100644 --- a/docs/docs/cli/prisma-screen.md +++ b/docs/docs/cli/prisma-screen.md @@ -1,34 +1,34 @@ --- title: stack prisma screen -sidebar_position: 108 +sidebar_position: 109 --- # `stack prisma screen` ``` -Usage: stack prisma screen [OPTIONS] NAME +Usage: stack prisma screen [OPTIONS] {name} Stage 2 — LLM-driven title/abstract screening pass. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Project slug. [required] │ +│ * name Project slug. [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --limit -n INTEGER 0 = screen every unscreened item. │ -│ [default: 0] │ -│ --db PATH [default: │ -│ data/zotero/data/zotero.sqlite] │ -│ --storage PATH [default: data/zotero/data/storage] │ -│ --hold --no-hold [default: hold] │ -│ --hosts TEXT Comma-separated Ollama base URLs — │ -│ fleet mode (#655): parallel │ -│ screening via native /api/chat with │ -│ per-request num_ctx; bypasses │ -│ PRISMA_LLM_* env config. │ -│ --fleet-model TEXT Model name on every fleet host. │ -│ [default: qwen2.5:14b] │ -│ --num-ctx INTEGER Context window per fleet request. │ -│ [default: 8192] │ -│ --help Show this message and exit. │ +│ --limit -n 0 = screen every unscreened item. │ +│ [default: 0] │ +│ --db [default: │ +│ data/zotero/data/zotero.sqlite] │ +│ --storage [default: data/zotero/data/storage] │ +│ --hold --no-hold [default: hold] │ +│ --hosts Comma-separated Ollama base URLs — │ +│ fleet mode (#655): parallel │ +│ screening via native /api/chat with │ +│ per-request num_ctx; bypasses │ +│ PRISMA_LLM_* env config. │ +│ --fleet-model Model name on every fleet host. │ +│ [default: qwen2.5:14b] │ +│ --num-ctx Context window per fleet request. │ +│ [default: 8192] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/prisma-vpn.md b/docs/docs/cli/prisma-vpn.md index e9a6001..20ec797 100644 --- a/docs/docs/cli/prisma-vpn.md +++ b/docs/docs/cli/prisma-vpn.md @@ -1,6 +1,6 @@ --- title: stack prisma vpn -sidebar_position: 114 +sidebar_position: 115 --- # `stack prisma vpn` diff --git a/docs/docs/cli/prisma.md b/docs/docs/cli/prisma.md index 076fab0..4b801fa 100644 --- a/docs/docs/cli/prisma.md +++ b/docs/docs/cli/prisma.md @@ -1,6 +1,6 @@ --- title: stack prisma -sidebar_position: 104 +sidebar_position: 105 --- # `stack prisma` diff --git a/docs/docs/cli/rec-opps.md b/docs/docs/cli/rec-opps.md index 89a270f..c787b0b 100644 --- a/docs/docs/cli/rec-opps.md +++ b/docs/docs/cli/rec-opps.md @@ -11,11 +11,11 @@ Usage: stack rec opps [OPTIONS] Reconcile OPPS calculated rates against Addendum B. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --year -y INTEGER Year to reconcile; omit for all. │ -│ --format -f TEXT Output format: md | json. [default: md] │ -│ --output -o PATH Write to file instead of stdout. │ -│ --tolerance -t INTEGER Cents of tolerance for an 'exact' match. │ -│ [default: 0] │ -│ --help Show this message and exit. │ +│ --year -y Year to reconcile; omit for all. │ +│ --format -f Output format: md | json. [default: md] │ +│ --output -o Write to file instead of stdout. │ +│ --tolerance -t Cents of tolerance for an 'exact' match. │ +│ [default: 0] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/rec-pfs.md b/docs/docs/cli/rec-pfs.md index ff85848..18d5145 100644 --- a/docs/docs/cli/rec-pfs.md +++ b/docs/docs/cli/rec-pfs.md @@ -11,11 +11,11 @@ Usage: stack rec pfs [OPTIONS] Reconcile PFS calculated fees against carrier_locality. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --year -y INTEGER Year to reconcile; omit for all. │ -│ --format -f TEXT Output format: md | json. [default: md] │ -│ --output -o PATH Write to file instead of stdout. │ -│ --tolerance -t INTEGER Cents of tolerance for an 'exact' match. │ -│ [default: 0] │ -│ --help Show this message and exit. │ +│ --year -y Year to reconcile; omit for all. │ +│ --format -f Output format: md | json. [default: md] │ +│ --output -o Write to file instead of stdout. │ +│ --tolerance -t Cents of tolerance for an 'exact' match. │ +│ [default: 0] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/run.md b/docs/docs/cli/run.md index 2c62f55..447b44e 100644 --- a/docs/docs/cli/run.md +++ b/docs/docs/cli/run.md @@ -6,19 +6,19 @@ sidebar_position: 2 # `stack run` ``` -Usage: stack run [OPTIONS] NAME +Usage: stack run [OPTIONS] {name} Execute a named pipeline against the chosen target context. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ * name TEXT Pipeline name (e.g. readmissions). [required] │ +│ * name Pipeline name (e.g. readmissions). [required] │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --target TEXT Target context: local, lake, trino, databricks, │ -│ spark. │ -│ --catalog TEXT Unity Catalog name (overrides config). Implies │ -│ target=spark. │ -│ --save Save pipeline outputs back to the database. │ -│ --help Show this message and exit. │ +│ --target Target context: local, lake, trino, databricks, │ +│ spark. │ +│ --catalog Unity Catalog name (overrides config). Implies │ +│ target=spark. │ +│ --save Save pipeline outputs back to the database. │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/stack.md b/docs/docs/cli/stack.md index addf063..04f8f2e 100644 --- a/docs/docs/cli/stack.md +++ b/docs/docs/cli/stack.md @@ -37,5 +37,6 @@ Usage: stack [OPTIONS] COMMAND [ARGS]... │ zot Zotero database maintenance. │ │ prisma LLM-driven PRISMA screening workflow. │ │ mail Maddy mail server (DO + Resend smarthost). │ +│ nlm NLM terminology releases and VSAC value sets. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/validate.md b/docs/docs/cli/validate.md index 53e345d..b36ed2c 100644 --- a/docs/docs/cli/validate.md +++ b/docs/docs/cli/validate.md @@ -6,7 +6,7 @@ sidebar_position: 3 # `stack validate` ``` -Usage: stack validate [OPTIONS] [PIPELINE] +Usage: stack validate [OPTIONS] [pipeline] Verify pipeline output contracts against SQLTable models. @@ -15,11 +15,11 @@ Usage: stack validate [OPTIONS] [PIPELINE] without saving anything. ╭─ Arguments ──────────────────────────────────────────────────────────────────╮ -│ pipeline [PIPELINE] Pipeline name to validate (all if omitted). │ +│ pipeline Pipeline name to validate (all if omitted). │ ╰──────────────────────────────────────────────────────────────────────────────╯ ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --target TEXT Target context: local, lake, trino, databricks. │ -│ [default: local] │ -│ --help Show this message and exit. │ +│ --target Target context: local, lake, trino, databricks. │ +│ [default: local] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/zot-dump-schema.md b/docs/docs/cli/zot-dump-schema.md index 0e1e5ee..3cc3b9d 100644 --- a/docs/docs/cli/zot-dump-schema.md +++ b/docs/docs/cli/zot-dump-schema.md @@ -14,10 +14,10 @@ Usage: stack zot dump-schema [OPTIONS] FIELD_MAP, and CREATOR_TYPES in ``src/zot/db.py`` verbatim. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --db PATH Default: data/zotero/data/zotero.sqlite │ -│ --python --json Emit paste-ready Python literals for zot/db.py │ -│ (default) or JSON. │ -│ [default: python] │ -│ --help Show this message and exit. │ +│ --db Default: data/zotero/data/zotero.sqlite │ +│ --python --json Emit paste-ready Python literals for zot/db.py │ +│ (default) or JSON. │ +│ [default: python] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/zot-fetch.md b/docs/docs/cli/zot-fetch.md new file mode 100644 index 0000000..c37d00f --- /dev/null +++ b/docs/docs/cli/zot-fetch.md @@ -0,0 +1,43 @@ +--- +title: stack zot fetch +sidebar_position: 104 +--- + +# `stack zot fetch` + +``` +Usage: stack zot fetch [OPTIONS] + + Attach an open-access PDF to items that lack a full text. + + Per item: every Unpaywall location, then Semantic Scholar, PMC and + Europe PMC — open-access copies only (no DOI? a Crossref title match + first). Items with a PDF/EPUB, deleted items and ``document`` items + are skipped. Every attempt is a ledger line; a miss waits 30 days + unless --retry. + + Environment: UNPAYWALL_EMAIL — the contact address Unpaywall requires + (default dev@fhirworx.io). + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│ --collection Collection name. │ +│ --tag Tag name. │ +│ --type Item type, e.g. journalArticle, book. │ +│ --item One item key. │ +│ --all Every eligible item. │ +│ --limit Stop after N attempts (0 = all). │ +│ [default: 0] │ +│ --dry-run Show the DOI and open-access locations │ +│ per item; write nothing. Reads only, so │ +│ the Zotero desktop keeps running. │ +│ --retry Retry items the ledger marked as │ +│ misses. │ +│ --db │ +│ --ledger [default: │ +│ data/zotero/fetch_ledger.jsonl] │ +│ --hold --no-hold Stop the zotero container while │ +│ writing. │ +│ [default: hold] │ +│ --help Show this message and exit. │ +╰──────────────────────────────────────────────────────────────────────────────╯ +``` diff --git a/docs/docs/cli/zot-fix-dates.md b/docs/docs/cli/zot-fix-dates.md index 7f7c441..d1654e5 100644 --- a/docs/docs/cli/zot-fix-dates.md +++ b/docs/docs/cli/zot-fix-dates.md @@ -11,8 +11,8 @@ Usage: stack zot fix-dates [OPTIONS] Normalize item timestamps to ISO 8601 + install auto-fix triggers. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --db PATH │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --db │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/zot-fix-fields.md b/docs/docs/cli/zot-fix-fields.md index ce3750a..167e7a8 100644 --- a/docs/docs/cli/zot-fix-fields.md +++ b/docs/docs/cli/zot-fix-fields.md @@ -11,8 +11,8 @@ Usage: stack zot fix-fields [OPTIONS] Remap base-field rows to type-specific fieldIDs; drop orphans. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --db PATH │ -│ --hold --no-hold [default: hold] │ -│ --help Show this message and exit. │ +│ --db │ +│ --hold --no-hold [default: hold] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/zot-fix-keys.md b/docs/docs/cli/zot-fix-keys.md index 1af82a4..e5f68d5 100644 --- a/docs/docs/cli/zot-fix-keys.md +++ b/docs/docs/cli/zot-fix-keys.md @@ -11,9 +11,9 @@ Usage: stack zot fix-keys [OPTIONS] Replace invalid Zotero object keys (0/1/O/lowercase → valid). ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --db PATH │ -│ --hold --no-hold [default: hold] │ -│ --backup --no-backup [default: backup] │ -│ --help Show this message and exit. │ +│ --db │ +│ --hold --no-hold [default: hold] │ +│ --backup --no-backup [default: backup] │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/zot-verify-parity.md b/docs/docs/cli/zot-verify-parity.md index cdddbdf..3179fcf 100644 --- a/docs/docs/cli/zot-verify-parity.md +++ b/docs/docs/cli/zot-verify-parity.md @@ -15,7 +15,7 @@ Usage: stack zot verify-parity [OPTIONS] bumps Zotero without regenerating the maps. ╭─ Options ────────────────────────────────────────────────────────────────────╮ -│ --db PATH │ -│ --help Show this message and exit. │ +│ --db │ +│ --help Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ``` diff --git a/docs/docs/cli/zot.md b/docs/docs/cli/zot.md index 354c651..7b53079 100644 --- a/docs/docs/cli/zot.md +++ b/docs/docs/cli/zot.md @@ -21,5 +21,6 @@ Usage: stack zot [OPTIONS] COMMAND [ARGS]... │ fix-fields Remap base-field rows to type-specific fieldIDs; drop │ │ orphans. │ │ verify-parity Check that ``zot.db`` constants match the live Zotero schema. │ +│ fetch Attach an open-access PDF to items that lack a full text. │ ╰──────────────────────────────────────────────────────────────────────────────╯ ```