jarvisplot 2.1.9__tar.gz → 2.1.11__tar.gz

jarvisplot-2.1.11/CHANGELOG.md

@@ -0,0 +1,61 @@
+# Changelog
+
+Release history of the `JarvisPLOT` distribution (import package `jarvisplot`,
+CLI `jplot`). Design documents, specifications and the roadmap live in
+[Jarvis-Books `Docs/Jarvis-PLOT/`](https://github.com/Pengxuan-Zhu-Phys/Jarvis-Books/blob/main/Docs/Jarvis-PLOT/README.md).
+
+## 2.1.11 — 2026-10-18
+
+- Exclude maintainer release helpers, local configuration, credentials, and
+  generated files from distribution archives.
+
+- `./jprel X.Y.Z` now completes PyPI upload, local editable install, Git tag,
+  and GitHub release. `--dry` checks inputs without changing the checkout.
+- Remove private research cards and scripts under `bin/` from version control
+  and distribution archives; public examples remain under `Example/`.
+- Cache cleanup removes empty registered cache directories whose marker is
+  missing, while retaining unmarked directories containing files.
+- Font card: `jplot fonts show|list|resolve|check|set|reset` and
+  `jplot man fonts`. Normal YAML rendering applies the bundled role card
+  (Helvetica sans, STIXGeneral serif, STIX MathText); explicit YAML fonts and
+  sizes take precedence. Personal overrides live in
+  `~/.jarvis/plot-fonts.json` (`JARVIS_HOME` overrides the directory).
+- When Helvetica is absent, the first installed of Arial, Liberation Sans,
+  Nimbus Sans and DejaVu Sans is used; `check` and `resolve` report the actual
+  font and the substitution reason.
+- Cut descriptions take their MathText font from the font card by default.
+- Documentation moved to Jarvis-Books; the repository keeps only `README.md`,
+  `CHANGELOG.md` and the example READMEs. The source distribution ships
+  `CHANGELOG.md` instead of a `docs/` tree, and `tools/check_release.py` checks
+  the latest `CHANGELOG.md` entry instead of the old release-note files.
+
+## 2.1.10 — 2026-10-13
+
+- Native forest figures read multi-interval CSV sources and mappings,
+  intervals-only rows, box/scatter coexistence and literal CSV value
+  annotations. Values are plotted as supplied, never computed.
+- Explicit shared x ticks, independent of grid divisions.
+- MathText needs `math: true`; formula fonts are STIX by default with DejaVu
+  Sans as an alternative, selected separately for legends and cut
+  descriptions. Header notes, paragraphs and formulas are preserved, and
+  layout uses the actual font, glyph and annotation bounds.
+- TTC faces keep their weight and slant; an explicit font size governs
+  measurement.
+- CLI, manuals, render reports and image metadata read the version from
+  `jarvisplot/version.py`. SVG output carries Dublin Core metadata; export
+  retries only on a backend's unsupported-metadata error and reports drawing
+  and I/O failures.
+- Packaged AI README (`jplot man agent-readme --json`), schema, manual and
+  example updates.
+- `tools/check_release.py` source, tag and wheel gates; the sdist includes the
+  native forest examples; CI runs Linux Python 3.10–3.13 and macOS 3.13.
+
+Existing forest YAML needs no migration. Custom export metadata must use keys
+the selected backend supports; invalid SVG keys are now reported.
+
+## Earlier releases
+
+See the [PyPI release history](https://pypi.org/project/JarvisPLOT/#history)
+and [GitHub Releases](https://github.com/Pengxuan-Zhu-Phys/Jarvis-PLOT/releases).
+Earlier release notes are archived in Jarvis-Books
+`Docs/archive/Jarvis-PLOT/2026-10-17/docs/release/`.

jarvisplot-2.1.11/Example/forest/README.md

@@ -0,0 +1,69 @@
+# Native forest examples
+
+- `interval.yaml`: generic supplied estimates/bounds, string IDs with leading zeros.
+- `box.yaml`: generic supplied quartiles/whiskers and observations, including a point-only row.
+- `multi-interval.yaml`: two supplied boxes, ten original points per row, three interval classes,
+  field-based values, lane offsets, a black common mean ± SD legend key, explicit ticks,
+  MathText row/cut labels and a caller-supplied header note.
+- `intervals-only.yaml`: row IDs/labels plus three intervals per row; no primary glyph or scatter source.
+- `real-demo.yaml`: producer-exported generic tables, 97 rows/241 points. This fixture preserves supplied box coordinates, classification and annotations. Producer-specific metadata in CSV is inspectable and never used by the renderer.
+
+Run `jplot validate Example/forest/real-demo.yaml --json`, `jplot doctor Example/forest/real-demo.yaml --json`, then `jplot Example/forest/real-demo.yaml --report`. Outputs go to `Workshop/forest_native/`; each native PNG/SVG has a `.layout.json` receipt with shared limits/ticks, physical positions, annotations, styles and verification. Generated images/reports are not package assets.
+
+The two multi-interval examples write PNG/PDF and receipts only to
+`/tmp/jarvisplot-forest-examples`. They select the commonly installed DejaVu Sans font;
+the original examples retain the Swiss card's Helvetica default. Run with the official package:
+
+```sh
+jplot validate Example/forest/multi-interval.yaml --json
+jplot doctor Example/forest/multi-interval.yaml --json
+jplot Example/forest/multi-interval.yaml --report
+jplot validate Example/forest/intervals-only.yaml --json
+jplot doctor Example/forest/intervals-only.yaml --json
+jplot Example/forest/intervals-only.yaml --report
+```
+
+`summary-rows.csv` supplies the already formatted box values; `summary-intervals.csv`
+supplies interval endpoints and already formatted mean ± SD values. The examples are
+illustrative supplied data, not a statistical reconstruction from the scatter sample.
+Class names are arbitrary. `interval_fields` can map noncanonical CSV headers without
+renaming files. `glyph_offset_mm` shifts the box and its points together; overlay `offset_mm`
+sets independent interval lanes. A positive `value_column_mm` reserves a right-hand values
+strip; zero keeps the full numerical width and requires room beside every interval.
+Long annotations or marks near a boundary fail explicitly when their measured ink does not fit.
+
+`multi-interval.yaml` gives the primary box/points and the three summary intervals equal
+5 mm halves of the 10 mm mark band. Its plot centre is 7.5 mm, primary offset -2.5 mm,
+and summary offsets 0.85/2.5/4.15 mm. This puts the primary distribution higher and the
+summary group lower with equal allocated vertical space. Legend formulas default to
+STIX; `frame.ax.legend.prop.math_fontfamily: dejavusans` restores the previous look.
+`jplot man legend --json` documents formula and ordinary legend font controls.
+The cut description explicitly sets `description.math: true` and
+`description.math_fontfamily: stix`; legend font settings do not change cut fonts.
+
+Use `jplot man forest --json`, `jplot template show forest --json`, and `jplot config expand Example/forest/real-demo.yaml --figure forest-all-97 --json` for discovery/inspection. Config expansion preserves the native high-level type and returns its solved scene in `data.forests`.
+
+The real demo declares Bin/W/P/E/n/CV columns. Column names and units appear only at the top; body cells contain values, with n formatted .0f and CV .1f. title/description are standard text blocks. The 20 mm footer has three sections: the glyph sample starts at reference column 2, point classes at column 5, and the unchanged YAML description at column 8. Description wraps in the last five reference columns; the header is now 20 mm. The standard Jarvis-HEP icon stays at bottom left, sharing height with the point column; the full figure is 82.5 x 573.5 mm.
+
+Columns use role: row_name/left/right. Bin is the row name; W/P/E form the compact left group; n/CV form the right group. Widths follow actual header/body font metrics, with no manual width declarations. Text sits near the top of each row; the full-width common numerical band below it contains the distributions and observations, extending horizontally beneath both text groups.
+
+Swiss style: installed Helvetica regular/bold; 9 pt title; 12 reference columns; compact left-aligned left cells and right-aligned right cells; black, white, Jarvis blue and red #DA291C. Widths follow actual text metrics without grid rounding; default gaps are 0.8 mm. `real-demo-debug.yaml` enables the separate grid/baseline/band overlay. `meta` controls the optional number/year/place.
+
+The normal chart shows a shared top numerical axis and continuous vertical grid; row rules/per-row axes are removed. `x.ticks` supplies explicit short marks and top/bottom labels. `forest.grid` independently controls numerical lines and deduplicates coincident coordinates; divisions do not add ticks. `debug.forest_grid` controls the separate design overlay.
+
+The default canvas is white, with no row shading, numbered metadata or legend heading. Point legend markers and their labels are left aligned using compact keys.
+
+For a study previously using `jarvis_forest_preview`, install the formal project in the same
+Python environment (`python -m pip install -e .` from the Jarvis-PLOT repository root),
+remove its preview path from the shell/launcher PYTHONPATH, and call the formal `jplot` on
+the existing YAML. The native interface accepts the established `intervals`, annotation,
+MathText, header_note and geometry keys; no task-specific names or data conversion are needed.
+For a one-off check use `env -u PYTHONPATH jplot validate <existing.yaml> --json`, followed
+by doctor and rendering in that clean environment. Verify `jplot --version` in that environment.
+To preserve existing study figures during verification, use a temporary YAML with only
+`project.workdir` and `output.dir` redirected to a temporary directory; retain the absolute
+source paths and all Figures/coordinates/statistical strings. Normal image output is governed
+by YAML `output.dir`, not the CLI `-o` flag.
+
+AI agents should read `jplot man agent-readme --json` before authoring YAML or reporting a
+missing feature; it includes the installed-version and feature-request feedback requirements.

jarvisplot-2.1.11/Example/forest/box.yaml

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+version: '0.3'
+DataSet:
+- name: rows
+  path: ./data/box.csv
+  type: csv
+- name: observations
+  path: ./data/points.csv
+  type: csv
+Figures:
+- name: forest-box
+  type: forest
+  data: rows
+  glyph: box
+  title:
+    text: Generic box comparison
+  x:
+    label: Supplied coordinates
+    reference: 0
+  points: observations
+output:
+  dir: ../../Workshop/forest_native
+  formats:
+  - png
+  - svg
+  dpi: 220

jarvisplot-2.1.11/Example/forest/data/box.csv

@@ -0,0 +1,3 @@
+row,label,detail,stats,lower,q1,median,q3,upper
+01,A,Treated,n=3,-2,-1,0,1,2
+02,B,Control,n=1,,,,,

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jarvisplot-2.1.11/Example/forest/data/forest-rows.csv

@@ -0,0 +1,98 @@
+row,label,detail,stats,estimate,lower,q1,median,q3,upper,n,cv,W,P,E,target,cell,raw_mean
+B001,B001,"W[160,170)  P[16,24)  E[70,80)",n 11   CV 9.7%,0,-11.89931350114416,-6.8649885583523975,-1.8306636155606357,4.462242562929067,8.237986270022889,11,9.673302374472604,"[160, 170)","[16, 24)","[70, 80)",y16,"[160, 170) | [16, 24) | [70, 80)",794.5454545454545
+B002,B002,"W[140,150)  P[8,16)  E[60,70)",n 9   CV 13.4%,0,-15.79754601226994,-13.036809815950921,2.1472392638036792,6.288343558282207,21.47239263803681,9,13.402924843830837,"[140, 150)","[8, 16)","[60, 70)",y16,"[140, 150) | [8, 16) | [60, 70)",724.4444444444445
+B003,B003,"W[150,160)  P[8,16)  E[70,80)",n 9   CV 7.9%,0,-9.090909090909092,-5.194805194805195,-2.5974025974025974,5.194805194805195,16.883116883116884,9,7.899691597789896,"[150, 160)","[8, 16)","[70, 80)",y16,"[150, 160) | [8, 16) | [70, 80)",770.0
+B004,B004,"W[120,130)  P[8,16)  E[50,60)",n 8   CV 20.8%,0,-29.508196721311474,-10.655737704918032,-3.278688524590164,15.573770491803279,29.508196721311474,8,20.810173200489984,"[120, 130)","[8, 16)","[50, 60)",y16,"[120, 130) | [8, 16) | [50, 60)",610.0
+B005,B005,"W[160,170)  P[16,24)  E[60,70)",n 8   CV 8.7%,0,-11.608391608391608,-4.335664335664336,-1.5384615384615385,2.097902097902098,6.293706293706293,8,8.747689941880779,"[160, 170)","[16, 24)","[60, 70)",y16,"[160, 170) | [16, 24) | [60, 70)",893.75
+B006,B006,"W[170,180)  P[16,24)  E[70,80)",n 8   CV 13.7%,0,-22.693997071742313,-6.295754026354318,4.24597364568082,7.759882869692533,18.301610541727673,8,13.744553034008797,"[170, 180)","[16, 24)","[70, 80)",y16,"[170, 180) | [16, 24) | [70, 80)",853.75
+B007,B007,"W[150,160)  P[16,24)  E[60,70)",n 6   CV 13.6%,0,-18.620689655172413,-8.96551724137931,1.3793103448275863,7.586206896551723,18.620689655172413,6,13.59163203428967,"[150, 160)","[16, 24)","[60, 70)",y16,"[150, 160) | [16, 24) | [60, 70)",725.0
+B008,B008,"W[160,170)  P[8,16)  E[60,70)",n 6   CV 7.2%,0,-11.242603550295858,-2.662721893491124,-0.591715976331361,5.029585798816568,8.875739644970414,6,7.208256725605236,"[160, 170)","[8, 16)","[60, 70)",y16,"[160, 170) | [8, 16) | [60, 70)",845.0
+B009,B009,"W[170,180)  P[16,24)  E[80,90)",n 6   CV 4.6%,0,0.5347593582887701,0.5347593582887701,1.0695187165775402,2.406417112299465,3.7433155080213902,6,4.624972900628802,"[170, 180)","[16, 24)","[80, 90)",y16,"[170, 180) | [16, 24) | [80, 90)",935.0
+B010,B010,"W[120,130)  P[8,16)  E[60,70)",n 5   CV 14.3%,0,,,,,,5,14.285714285714286,"[120, 130)","[8, 16)","[60, 70)",y16,"[120, 130) | [8, 16) | [60, 70)",770.0
+B011,B011,"W[160,170)  P[8,16)  E[70,80)",n 5   CV 9.7%,0,,,,,,5,9.713935052636915,"[160, 170)","[8, 16)","[70, 80)",y16,"[160, 170) | [8, 16) | [70, 80)",806.0
+B012,B012,"W[170,180)  P[8,16)  E[70,80)",n 5   CV 17.5%,0,,,,,,5,17.53096434152445,"[170, 180)","[8, 16)","[70, 80)",y16,"[170, 180) | [8, 16) | [70, 80)",880.0
+B013,B013,"W[180,190)  P[8,16)  E[70,80)",n 5   CV 10.8%,0,,,,,,5,10.756578002296004,"[180, 190)","[8, 16)","[70, 80)",y16,"[180, 190) | [8, 16) | [70, 80)",907.4557968835221
+B014,B014,"W[190,200)  P[16,24)  E[80,90)",n 5   CV 9.4%,0,,,,,,5,9.405415786845467,"[190, 200)","[16, 24)","[80, 90)",y16,"[190, 200) | [16, 24) | [80, 90)",922.0
+B015,B015,"W[130,140)  P[8,16)  E[60,70)",n 4   CV 6.3%,0,,,,,,4,6.332299533013858,"[130, 140)","[8, 16)","[60, 70)",y16,"[130, 140) | [8, 16) | [60, 70)",670.0
+B016,B016,"W[150,160)  P[16,24)  E[50,60)",n 4   CV 17.7%,0,,,,,,4,17.69383737069914,"[150, 160)","[16, 24)","[50, 60)",y16,"[150, 160) | [16, 24) | [50, 60)",750.3522242580038
+B017,B017,"W[150,160)  P[8,16)  E[60,70)",n 4   CV 9.5%,0,,,,,,4,9.543466530324071,"[150, 160)","[8, 16)","[60, 70)",y16,"[150, 160) | [8, 16) | [60, 70)",770.0
+B018,B018,"W[150,160)  P[8,16)  E[80,90)",n 4   CV 8.6%,0,,,,,,4,8.628170010875014,"[150, 160)","[8, 16)","[80, 90)",y16,"[150, 160) | [8, 16) | [80, 90)",782.5
+B019,B019,"W[170,180)  P[16,24)  E[60,70)",n 4   CV 10.6%,0,,,,,,4,10.61986604886756,"[170, 180)","[16, 24)","[60, 70)",y16,"[170, 180) | [16, 24) | [60, 70)",885.0
+B020,B020,"W[180,190)  P[8,16)  E[80,90)",n 4   CV 6.7%,0,,,,,,4,6.702334859269557,"[180, 190)","[8, 16)","[80, 90)",y16,"[180, 190) | [8, 16) | [80, 90)",992.5
+B021,B021,"W[190,200)  P[16,24)  E[70,80)",n 4   CV 7.0%,0,,,,,,4,7.007237029167781,"[190, 200)","[16, 24)","[70, 80)",y16,"[190, 200) | [16, 24) | [70, 80)",977.5
+B022,B022,"W[200,210)  P[8,16)  E[110,120)",n 4   CV 12.2%,0,,,,,,4,12.201435085467145,"[200, 210)","[8, 16)","[110, 120)",y16,"[200, 210) | [8, 16) | [110, 120)",1037.5
+B023,B023,"W[140,150)  P[8,16)  E[50,60)",n 3   CV 9.2%,0,,,,,,3,9.162836860292744,"[140, 150)","[8, 16)","[50, 60)",y16,"[140, 150) | [8, 16) | [50, 60)",726.6666666666666
+B024,B024,"W[150,160)  P[16,24)  E[80,90)",n 3   CV 9.0%,0,,,,,,3,8.97078107505793,"[150, 160)","[16, 24)","[80, 90)",y16,"[150, 160) | [16, 24) | [80, 90)",836.6666666666666
+B025,B025,"W[150,160)  P[8,16)  E[50,60)",n 3   CV 2.8%,0,,,,,,3,2.8386354538174534,"[150, 160)","[8, 16)","[50, 60)",y16,"[150, 160) | [8, 16) | [50, 60)",733.3333333333334
+B026,B026,"W[160,170)  P[16,24)  E[80,90)",n 3   CV 9.3%,0,,,,,,3,9.25244535041673,"[160, 170)","[16, 24)","[80, 90)",y16,"[160, 170) | [16, 24) | [80, 90)",796.6666666666666
+B027,B027,"W[160,170)  P[8,16)  E[50,60)",n 3   CV 2.2%,0,,,,,,3,2.2224192165118857,"[160, 170)","[8, 16)","[50, 60)",y16,"[160, 170) | [8, 16) | [50, 60)",936.6666666666666
+B028,B028,"W[170,180)  P[8,16)  E[60,70)",n 3   CV 2.9%,0,,,,,,3,2.9149939904520266,"[170, 180)","[8, 16)","[60, 70)",y16,"[170, 180) | [8, 16) | [60, 70)",863.3333333333334
+B029,B029,"W[170,180)  P[8,16)  E[90,100)",n 3   CV 9.7%,0,,,,,,3,9.689794727658056,"[170, 180)","[8, 16)","[90, 100)",y16,"[170, 180) | [8, 16) | [90, 100)",953.3333333333334
+B030,B030,"W[180,190)  P[16,24)  E[60,70)",n 3   CV 14.6%,0,,,,,,3,14.606741573033707,"[180, 190)","[16, 24)","[60, 70)",y16,"[180, 190) | [16, 24) | [60, 70)",890.0
+B031,B031,"W[190,200)  P[8,16)  E[100,110)",n 3   CV 9.3%,0,,,,,,3,9.310909692745154,"[190, 200)","[8, 16)","[100, 110)",y16,"[190, 200) | [8, 16) | [100, 110)",1090.0
+B032,B032,"W[190,200)  P[8,16)  E[80,90)",n 3   CV 8.4%,0,,,,,,3,8.358634967049253,"[190, 200)","[8, 16)","[80, 90)",y16,"[190, 200) | [8, 16) | [80, 90)",1003.3333333333334
+B033,B033,"W[210,220)  P[8,16)  E[100,110)",n 3   CV 7.3%,0,,,,,,3,7.335128644553427,"[210, 220)","[8, 16)","[100, 110)",y16,"[210, 220) | [8, 16) | [100, 110)",1143.3333333333333
+B034,B034,"W[110,120)  P[8,16)  E[60,70)",n 2   CV 7.3%,0,,,,,,2,7.252377242938949,"[110, 120)","[8, 16)","[60, 70)",y16,"[110, 120) | [8, 16) | [60, 70)",780.0
+B035,B035,"W[120,130)  P[8,16)  E[40,50)",n 2   CV 7.2%,0,,,,,,2,7.190916418846245,"[120, 130)","[8, 16)","[40, 50)",y16,"[120, 130) | [8, 16) | [40, 50)",590.0
+B036,B036,"W[130,140)  P[16,24)  E[60,70)",n 2   CV 4.9%,0,,,,,,2,4.876598490941707,"[130, 140)","[16, 24)","[60, 70)",y16,"[130, 140) | [16, 24) | [60, 70)",580.0
+B037,B037,"W[130,140)  P[8,16)  E[50,60)",n 2   CV 12.4%,0,,,,,,2,12.405382126079783,"[130, 140)","[8, 16)","[50, 60)",y16,"[130, 140) | [8, 16) | [50, 60)",570.0
+B038,B038,"W[140,150)  P[16,24)  E[70,80)",n 2   CV 1.8%,0,,,,,,2,1.8130943107347373,"[140, 150)","[16, 24)","[70, 80)",y16,"[140, 150) | [16, 24) | [70, 80)",780.0
+B039,B039,"W[140,150)  P[8,16)  E[70,80)",n 2   CV 6.0%,0,,,,,,2,5.975550263548288,"[140, 150)","[8, 16)","[70, 80)",y16,"[140, 150) | [8, 16) | [70, 80)",710.0
+B040,B040,"W[160,170)  P[0,8)  E[60,70)",n 2   CV 14.7%,0,,,,,,2,14.731391274719742,"[160, 170)","[0, 8)","[60, 70)",y16,"[160, 170) | [0, 8) | [60, 70)",960.0
+B041,B041,"W[160,170)  P[8,16)  E[90,100)",n 2   CV 1.5%,0,,,,,,2,1.5371886547533642,"[160, 170)","[8, 16)","[90, 100)",y16,"[160, 170) | [8, 16) | [90, 100)",920.0
+B042,B042,"W[170,180)  P[24,32)  E[60,70)",n 2   CV 2.7%,0,,,,,,2,2.668327476175651,"[170, 180)","[24, 32)","[60, 70)",y16,"[170, 180) | [24, 32) | [60, 70)",795.0
+B043,B043,"W[170,180)  P[8,16)  E[80,90)",n 2   CV 11.3%,0,,,,,,2,11.313708498984761,"[170, 180)","[8, 16)","[80, 90)",y16,"[170, 180) | [8, 16) | [80, 90)",1000.0
+B044,B044,"W[180,190)  P[0,8)  E[90,100)",n 2   CV 11.4%,0,,,,,,2,11.43406710003779,"[180, 190)","[0, 8)","[90, 100)",y16,"[180, 190) | [0, 8) | [90, 100)",1175.0
+B045,B045,"W[180,190)  P[24,32)  E[60,70)",n 2   CV 7.5%,0,,,,,,2,7.542472332656507,"[180, 190)","[24, 32)","[60, 70)",y16,"[180, 190) | [24, 32) | [60, 70)",750.0
+B046,B046,"W[180,190)  P[24,32)  E[70,80)",n 2   CV 6.0%,0,,,,,,2,6.017930052651469,"[180, 190)","[24, 32)","[70, 80)",y16,"[180, 190) | [24, 32) | [70, 80)",940.0
+B047,B047,"W[180,190)  P[8,16)  E[100,110)",n 2   CV 2.9%,0,,,,,,2,2.8569970957032225,"[180, 190)","[8, 16)","[100, 110)",y16,"[180, 190) | [8, 16) | [100, 110)",990.0
+B048,B048,"W[180,190)  P[8,16)  E[90,100)",n 2   CV 8.9%,0,,,,,,2,8.931875130777442,"[180, 190)","[8, 16)","[90, 100)",y16,"[180, 190) | [8, 16) | [90, 100)",950.0
+B049,B049,"W[190,200)  P[8,16)  E[90,100)",n 2   CV 4.0%,0,,,,,,2,4.002491214263476,"[190, 200)","[8, 16)","[90, 100)",y16,"[190, 200) | [8, 16) | [90, 100)",1060.0
+B050,B050,"W[100,110)  P[0,8)  E[40,50)",n 1   CV —,0,,,,,,1,,"[100, 110)","[0, 8)","[40, 50)",y16,"[100, 110) | [0, 8) | [40, 50)",580.0
+B051,B051,"W[100,110)  P[8,16)  E[50,60)",n 1   CV —,0,,,,,,1,,"[100, 110)","[8, 16)","[50, 60)",y16,"[100, 110) | [8, 16) | [50, 60)",650.0
+B052,B052,"W[110,120)  P[0,8)  E[40,50)",n 1   CV —,0,,,,,,1,,"[110, 120)","[0, 8)","[40, 50)",y16,"[110, 120) | [0, 8) | [40, 50)",510.0
+B053,B053,"W[110,120)  P[8,16)  E[40,50)",n 1   CV —,0,,,,,,1,,"[110, 120)","[8, 16)","[40, 50)",y16,"[110, 120) | [8, 16) | [40, 50)",720.0
+B054,B054,"W[120,130)  P[0,8)  E[50,60)",n 1   CV —,0,,,,,,1,,"[120, 130)","[0, 8)","[50, 60)",y16,"[120, 130) | [0, 8) | [50, 60)",630.0
+B055,B055,"W[120,130)  P[16,24)  E[50,60)",n 1   CV —,0,,,,,,1,,"[120, 130)","[16, 24)","[50, 60)",y16,"[120, 130) | [16, 24) | [50, 60)",700.0
+B056,B056,"W[130,140)  P[0,8)  E[60,70)",n 1   CV —,0,,,,,,1,,"[130, 140)","[0, 8)","[60, 70)",y16,"[130, 140) | [0, 8) | [60, 70)",530.0
+B057,B057,"W[130,140)  P[8,16)  E[40,50)",n 1   CV —,0,,,,,,1,,"[130, 140)","[8, 16)","[40, 50)",y16,"[130, 140) | [8, 16) | [40, 50)",630.0
+B058,B058,"W[130,140)  P[8,16)  E[70,80)",n 1   CV —,0,,,,,,1,,"[130, 140)","[8, 16)","[70, 80)",y16,"[130, 140) | [8, 16) | [70, 80)",650.0
+B059,B059,"W[140,150)  P[16,24)  E[60,70)",n 1   CV —,0,,,,,,1,,"[140, 150)","[16, 24)","[60, 70)",y16,"[140, 150) | [16, 24) | [60, 70)",750.0
+B060,B060,"W[140,150)  P[8,16)  E[80,90)",n 1   CV —,0,,,,,,1,,"[140, 150)","[8, 16)","[80, 90)",y16,"[140, 150) | [8, 16) | [80, 90)",680.0
+B061,B061,"W[150,160)  P[0,8)  E[60,70)",n 1   CV —,0,,,,,,1,,"[150, 160)","[0, 8)","[60, 70)",y16,"[150, 160) | [0, 8) | [60, 70)",760.0
+B062,B062,"W[150,160)  P[0,8)  E[70,80)",n 1   CV —,0,,,,,,1,,"[150, 160)","[0, 8)","[70, 80)",y16,"[150, 160) | [0, 8) | [70, 80)",773.543758830446
+B063,B063,"W[150,160)  P[0,8)  E[80,90)",n 1   CV —,0,,,,,,1,,"[150, 160)","[0, 8)","[80, 90)",y16,"[150, 160) | [0, 8) | [80, 90)",441.5759247750045
+B064,B064,"W[150,160)  P[16,24)  E[70,80)",n 1   CV —,0,,,,,,1,,"[150, 160)","[16, 24)","[70, 80)",y16,"[150, 160) | [16, 24) | [70, 80)",820.0
+B065,B065,"W[150,160)  P[24,32)  E[50,60)",n 1   CV —,0,,,,,,1,,"[150, 160)","[24, 32)","[50, 60)",y16,"[150, 160) | [24, 32) | [50, 60)",670.0
+B066,B066,"W[150,160)  P[24,32)  E[60,70)",n 1   CV —,0,,,,,,1,,"[150, 160)","[24, 32)","[60, 70)",y16,"[150, 160) | [24, 32) | [60, 70)",700.0
+B067,B067,"W[150,160)  P[8,16)  E[100,110)",n 1   CV —,0,,,,,,1,,"[150, 160)","[8, 16)","[100, 110)",y16,"[150, 160) | [8, 16) | [100, 110)",850.0
+B068,B068,"W[160,170)  P[0,8)  E[100,110)",n 1   CV —,0,,,,,,1,,"[160, 170)","[0, 8)","[100, 110)",y16,"[160, 170) | [0, 8) | [100, 110)",950.0
+B069,B069,"W[160,170)  P[16,24)  E[50,60)",n 1   CV —,0,,,,,,1,,"[160, 170)","[16, 24)","[50, 60)",y16,"[160, 170) | [16, 24) | [50, 60)",810.0
+B070,B070,"W[160,170)  P[16,24)  E[90,100)",n 1   CV —,0,,,,,,1,,"[160, 170)","[16, 24)","[90, 100)",y16,"[160, 170) | [16, 24) | [90, 100)",780.0
+B071,B071,"W[160,170)  P[24,32)  E[50,60)",n 1   CV —,0,,,,,,1,,"[160, 170)","[24, 32)","[50, 60)",y16,"[160, 170) | [24, 32) | [50, 60)",740.0
+B072,B072,"W[160,170)  P[24,32)  E[70,80)",n 1   CV —,0,,,,,,1,,"[160, 170)","[24, 32)","[70, 80)",y16,"[160, 170) | [24, 32) | [70, 80)",810.0
+B073,B073,"W[160,170)  P[8,16)  E[100,110)",n 1   CV —,0,,,,,,1,,"[160, 170)","[8, 16)","[100, 110)",y16,"[160, 170) | [8, 16) | [100, 110)",960.0
+B074,B074,"W[170,180)  P[0,8)  E[100,110)",n 1   CV —,0,,,,,,1,,"[170, 180)","[0, 8)","[100, 110)",y16,"[170, 180) | [0, 8) | [100, 110)",850.0
+B075,B075,"W[170,180)  P[16,24)  E[50,60)",n 1   CV —,0,,,,,,1,,"[170, 180)","[16, 24)","[50, 60)",y16,"[170, 180) | [16, 24) | [50, 60)",900.0
+B076,B076,"W[170,180)  P[16,24)  E[90,100)",n 1   CV —,0,,,,,,1,,"[170, 180)","[16, 24)","[90, 100)",y16,"[170, 180) | [16, 24) | [90, 100)",880.0
+B077,B077,"W[170,180)  P[24,32)  E[70,80)",n 1   CV —,0,,,,,,1,,"[170, 180)","[24, 32)","[70, 80)",y16,"[170, 180) | [24, 32) | [70, 80)",701.2549765309261
+B078,B078,"W[170,180)  P[24,32)  E[80,90)",n 1   CV —,0,,,,,,1,,"[170, 180)","[24, 32)","[80, 90)",y16,"[170, 180) | [24, 32) | [80, 90)",820.0
+B079,B079,"W[170,180)  P[32,40]  E[60,70)",n 1   CV —,0,,,,,,1,,"[170, 180)","[32, 40]","[60, 70)",y16,"[170, 180) | [32, 40] | [60, 70)",830.0
+B080,B080,"W[170,180)  P[8,16)  E[100,110)",n 1   CV —,0,,,,,,1,,"[170, 180)","[8, 16)","[100, 110)",y16,"[170, 180) | [8, 16) | [100, 110)",810.0
+B081,B081,"W[170,180)  P[8,16)  E[110,120)",n 1   CV —,0,,,,,,1,,"[170, 180)","[8, 16)","[110, 120)",y16,"[170, 180) | [8, 16) | [110, 120)",970.0
+B082,B082,"W[180,190)  P[16,24)  E[100,110)",n 1   CV —,0,,,,,,1,,"[180, 190)","[16, 24)","[100, 110)",y16,"[180, 190) | [16, 24) | [100, 110)",1090.0
+B083,B083,"W[180,190)  P[16,24)  E[70,80)",n 1   CV —,0,,,,,,1,,"[180, 190)","[16, 24)","[70, 80)",y16,"[180, 190) | [16, 24) | [70, 80)",907.3383471852242
+B084,B084,"W[180,190)  P[16,24)  E[80,90)",n 1   CV —,0,,,,,,1,,"[180, 190)","[16, 24)","[80, 90)",y16,"[180, 190) | [16, 24) | [80, 90)",930.0
+B085,B085,"W[180,190)  P[32,40]  E[70,80)",n 1   CV —,0,,,,,,1,,"[180, 190)","[32, 40]","[70, 80)",y16,"[180, 190) | [32, 40] | [70, 80)",870.0
+B086,B086,"W[180,190)  P[8,16)  E[50,60)",n 1   CV —,0,,,,,,1,,"[180, 190)","[8, 16)","[50, 60)",y16,"[180, 190) | [8, 16) | [50, 60)",860.0
+B087,B087,"W[180,190)  P[8,16)  E[60,70)",n 1   CV —,0,,,,,,1,,"[180, 190)","[8, 16)","[60, 70)",y16,"[180, 190) | [8, 16) | [60, 70)",880.0
+B088,B088,"W[190,200)  P[16,24)  E[100,110)",n 1   CV —,0,,,,,,1,,"[190, 200)","[16, 24)","[100, 110)",y16,"[190, 200) | [16, 24) | [100, 110)",880.0
+B089,B089,"W[190,200)  P[16,24)  E[110,120)",n 1   CV —,0,,,,,,1,,"[190, 200)","[16, 24)","[110, 120)",y16,"[190, 200) | [16, 24) | [110, 120)",1150.0
+B090,B090,"W[190,200)  P[16,24)  E[90,100)",n 1   CV —,0,,,,,,1,,"[190, 200)","[16, 24)","[90, 100)",y16,"[190, 200) | [16, 24) | [90, 100)",980.0
+B091,B091,"W[190,200)  P[24,32)  E[80,90)",n 1   CV —,0,,,,,,1,,"[190, 200)","[24, 32)","[80, 90)",y16,"[190, 200) | [24, 32) | [80, 90)",900.0
+B092,B092,"W[190,200)  P[8,16)  E[120,130]",n 1   CV —,0,,,,,,1,,"[190, 200)","[8, 16)","[120, 130]",y16,"[190, 200) | [8, 16) | [120, 130]",990.0
+B093,B093,"W[190,200)  P[8,16)  E[70,80)",n 1   CV —,0,,,,,,1,,"[190, 200)","[8, 16)","[70, 80)",y16,"[190, 200) | [8, 16) | [70, 80)",780.0
+B094,B094,"W[200,210)  P[0,8)  E[110,120)",n 1   CV —,0,,,,,,1,,"[200, 210)","[0, 8)","[110, 120)",y16,"[200, 210) | [0, 8) | [110, 120)",1290.0
+B095,B095,"W[200,210)  P[16,24)  E[80,90)",n 1   CV —,0,,,,,,1,,"[200, 210)","[16, 24)","[80, 90)",y16,"[200, 210) | [16, 24) | [80, 90)",1228.4976127923678
+B096,B096,"W[200,210)  P[8,16)  E[100,110)",n 1   CV —,0,,,,,,1,,"[200, 210)","[8, 16)","[100, 110)",y16,"[200, 210) | [8, 16) | [100, 110)",990.0
+B097,B097,"W[210,220)  P[16,24)  E[110,120)",n 1   CV —,0,,,,,,1,,"[210, 220)","[16, 24)","[110, 120)",y16,"[210, 220) | [16, 24) | [110, 120)",1160.0

jarvisplot-2.1.11/Example/forest/data/interval.csv

@@ -0,0 +1,3 @@
+row,label,estimate,lower,upper
+001,Study A,0.8,0.6,1.0
+002,Study B,1.1,0.9,1.3

jarvisplot-2.1.11/Example/forest/data/points.csv

@@ -0,0 +1,5 @@
+row,id,x,class
+01,001,-2,normal
+01,002,0,normal
+01,003,7,outlier
+02,004,1,singleton

jarvisplot-2.1.11/Example/forest/data/summary-intervals.csv

@@ -0,0 +1,7 @@
+row,id,estimate,lower,upper,class,stats
+01,a,0.611,0.608,0.614,cohort_a,0.611 ± 0.003
+01,b,0.613,0.608,0.618,cohort_b,0.613 ± 0.005
+01,r,0.616,0.611,0.621,repeat,0.616 ± 0.005
+02,a,0.621,0.618,0.624,cohort_a,0.621 ± 0.003
+02,b,0.623,0.618,0.628,cohort_b,0.623 ± 0.005
+02,r,0.626,0.621,0.631,repeat,0.626 ± 0.005

jarvisplot-2.1.11/Example/forest/data/summary-labels.csv

@@ -0,0 +1,3 @@
+row,label,N
+01,$S_1$,3
+02,$S_2$,4

jarvisplot-2.1.11/Example/forest/data/summary-points.csv

@@ -0,0 +1,21 @@
+row,id,x,class
+01,001,0.605,cohort_a
+01,002,0.608,cohort_a
+01,003,0.610,cohort_a
+01,004,0.611,cohort_a
+01,005,0.612,cohort_a
+01,006,0.613,cohort_a
+01,007,0.614,cohort_a
+01,008,0.616,cohort_a
+01,009,0.618,cohort_a
+01,010,0.620,cohort_a
+02,001,0.615,cohort_a
+02,002,0.618,cohort_a
+02,003,0.620,cohort_a
+02,004,0.621,cohort_a
+02,005,0.622,cohort_a
+02,006,0.623,cohort_a
+02,007,0.624,cohort_a
+02,008,0.626,cohort_a
+02,009,0.628,cohort_a
+02,010,0.630,cohort_a

jarvisplot-2.1.11/Example/forest/data/summary-rows.csv

@@ -0,0 +1,3 @@
+row,label,N,stats,lower,q1,median,q3,upper
+01,$S_1$,3,"0.612 [0.610,0.614]",0.605,0.610,0.612,0.614,0.620
+02,$S_2$,4,"0.622 [0.620,0.624]",0.615,0.620,0.622,0.624,0.630

jarvisplot-2.1.11/Example/forest/interval.yaml

@@ -0,0 +1,21 @@
+version: '0.3'
+DataSet:
+- name: rows
+  path: ./data/interval.csv
+  type: csv
+Figures:
+- name: forest-interval
+  type: forest
+  data: rows
+  glyph: interval
+  title:
+    text: Generic interval comparison
+  x:
+    label: Supplied coordinates
+    reference: 0
+output:
+  dir: ../../Workshop/forest_native
+  formats:
+  - png
+  - svg
+  dpi: 220

jarvisplot-2.1.11/Example/forest/intervals-only.yaml

@@ -0,0 +1,52 @@
+# No primary glyph coordinates or points; every row displays three supplied intervals.
+DataSet:
+- {name: rows, path: ./data/summary-labels.csv, type: csv}
+- {name: intervals, path: ./data/summary-intervals.csv, type: csv}
+Figures:
+- name: forest-intervals-only
+  type: forest
+  data: rows
+  intervals: intervals
+  title: {text: Supplied intervals only, fontsize: 7}
+  header_note: {text: 'MC entries supplied by the caller', fontsize: 4.3}
+  columns:
+  - {field: label, label: Input set, role: row_name, math: true}
+  - {field: N, label: N inputs, role: left}
+  x:
+    label: Supplied coordinate
+    lim: [0.60, 0.66]
+    ticks: [0.60, 0.61, 0.62, 0.63, 0.64, 0.65, 0.66]
+  description:
+    text: |
+      Supplied summaries.
+      SD is not a CI.
+
+      Example cut:
+      $p_T > 25\,\mathrm{GeV}$
+    fontsize: 4.3
+    math: true
+  frame: {axlogo: false}
+  forest:
+    legend_math: true
+    typography: {family: DejaVu Sans}
+    geometry:
+      footer_mm: 32
+      point_band_mm: 7
+      row_band_mm: 10
+      row_pitch_mm: 10.3
+      plot_y_mm: 6
+      cell_y_mm: 1.2
+      value_column_mm: 0
+      legend_start_columns: [2, 6]
+      description_start_column: 9
+      description_columns: 4
+    axis: {tick_suffix: ''}
+    grid: {show: true, divisions: 4, alpha: 0.12}
+    overlays:
+      legend: {label: '$\mathrm{mean}\pm\mathrm{SD}$', color: '#000000'}
+      annotation: {field: stats, fontsize: 4.3, gap_mm: 0.5}
+      classes:
+        cohort_a: {label: A, color: '#0072B2', offset_mm: -1.6}
+        cohort_b: {label: B, color: '#D55E00', alpha: 0.6, linestyle: '--', offset_mm: 0}
+        repeat: {label: Repeat, color: '#009E73', marker: x, offset_mm: 1.6}
+output: {dir: /tmp/jarvisplot-forest-examples, formats: [png, pdf], dpi: 220}