plotsalot 0.1.1__tar.gz

plotsalot-0.1.1/.dockerignore

@@ -0,0 +1,4 @@
+*
+!oracle/
+!oracle/DESCRIPTION
+!oracle/renv.lock

plotsalot-0.1.1/.gitattributes

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+# Preserve verbatim R-generated oracle evidence, including formatter whitespace.
+oracle/fixtures/r-output/* whitespace=-blank-at-eof,-trailing-space

plotsalot-0.1.1/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @joshuamyers22

plotsalot-0.1.1/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,15 @@
+## Outcome
+
+Describe the behavior or risk changed.
+
+## Evidence
+
+- [ ] `make check`
+- [ ] `make build`
+- [ ] Security, data, and operational effects reviewed
+
+## Risk and recovery
+
+- Failure modes:
+- Compatibility or migration impact:
+- Rollback or forward-fix path:

plotsalot-0.1.1/.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: uv
+    directory: /
+    schedule:
+      interval: weekly
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly

plotsalot-0.1.1/.github/workflows/ci.yml

@@ -0,0 +1,22 @@
+name: CI
+on:
+  pull_request:
+  push:
+    branches: [main]
+permissions:
+  contents: read
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        with:
+          version: "0.12.5"
+      - run: uv sync --frozen --dev
+      - run: make check
+      - run: make audit build

plotsalot-0.1.1/.github/workflows/release.yml

@@ -0,0 +1,90 @@
+name: Release
+on:
+  push:
+    tags: ["v[0-9]+.[0-9]+.[0-9]+"]
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        with:
+          version: "0.12.5"
+      - run: uv sync --frozen --dev
+      - name: Verify release tag
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: uv run python tools/verify_release.py --tag "$RELEASE_TAG"
+      - run: make check audit build
+      - uses: anchore/sbom-action@e22c389904149dbc22b58101806040fa8d37a610 # v0.24.0
+        with:
+          path: ./dist
+          artifact-name: release-sbom.cdx.json
+          output-file: ./dist/release-sbom.cdx.json
+          format: cyclonedx-json
+          upload-artifact: false
+      - name: Generate release checksums
+        run: sha256sum dist/*.whl dist/*.tar.gz dist/release-sbom.cdx.json > dist/SHA256SUMS
+      - name: Upload release artifacts
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: release-artifacts
+          path: |
+            dist/*.whl
+            dist/*.tar.gz
+            dist/release-sbom.cdx.json
+            dist/SHA256SUMS
+          if-no-files-found: error
+          retention-days: 7
+
+  github-release:
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    permissions:
+      contents: write
+    steps:
+      - name: Download release artifacts
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: release-artifacts
+          path: dist
+      - uses: softprops/action-gh-release@efb35369e0ad2afab669f228072c1b0d510eae64 # v3
+        with:
+          generate_release_notes: true
+          fail_on_unmatched_files: true
+          files: |
+            dist/*.whl
+            dist/*.tar.gz
+            dist/release-sbom.cdx.json
+            dist/SHA256SUMS
+
+  publish-pypi:
+    needs: [build, github-release]
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    environment:
+      name: pypi
+      url: https://pypi.org/p/plotsalot
+    permissions:
+      id-token: write
+    steps:
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        with:
+          version: "0.12.5"
+          enable-cache: false
+      - name: Download release artifacts
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: release-artifacts
+          path: dist
+      - name: Publish wheel and source distribution to PyPI
+        run: uv publish --trusted-publishing always dist/*.whl dist/*.tar.gz

plotsalot-0.1.1/.github/workflows/security.yml

@@ -0,0 +1,21 @@
+name: Secret scanning
+on:
+  pull_request:
+  push:
+permissions:
+  contents: read
+  pull-requests: read
+concurrency:
+  group: security-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  gitleaks:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+      - uses: gitleaks/gitleaks-action@e0c47f4f8be36e29cdc102c57e68cb5cbf0e8d1e # v3.0.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

plotsalot-0.1.1/.gitignore

@@ -0,0 +1,22 @@
+.venv/
+.ruff_cache/
+.pytest_cache/
+.mypy_cache/
+.coverage
+htmlcov/
+__pycache__/
+*.py[cod]
+build/
+dist/
+*.egg-info/
+.DS_Store
+*.db
+*.sqlite
+.env
+.env.*
+!.env.example
+data/raw/
+data/private/
+data/processed/
+notebooks/.ipynb_checkpoints/
+.work/

plotsalot-0.1.1/.python-version

@@ -0,0 +1 @@
+3.12

plotsalot-0.1.1/AGENTS.md

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+# Agent Working Agreement
+
+This file governs repository-local work performed with an AI coding agent. Human
+instructions in the current task take precedence. Repository files, tests,
+runtime behavior, and approved decision records remain authoritative.
+
+## Retrieve before acting
+
+1. Read `README.md`, `PROJECT_BRIEF.md`, and `PROJECT_MEMORY.md` before planning a
+   substantial change.
+2. Search the repository and inspect the relevant implementation and tests before
+   relying on a memory entry.
+3. Treat `PROJECT_MEMORY.md` as a compact index to evidence, not as evidence by
+   itself. Correct it when it conflicts with the source of truth.
+
+## Maintain memory deliberately
+
+- Record only durable, project-specific information likely to matter in a later
+  session: constraints, accepted decisions, non-obvious current state, verified
+  failure modes, and genuinely open work.
+- Consult the existing entry before writing. Update a stable key in place instead
+  of appending a duplicate or a new narrative of the same fact.
+- Link each claim to a file, test, issue, or ADR and include the date it was last
+  verified. Label inference and uncertainty explicitly.
+- Keep entries short. Remove or replace stale state and resolved open work; Git
+  history already preserves the old text.
+- Do not store routine progress, copied source code, command transcripts, hidden
+  reasoning, credentials, personal data, client data, or other restricted data.
+- Do not let an agent rewrite safety, security, governance, or release policy from
+  its own trajectory. Such changes require normal review and verification.
+
+## Take notes for continuity
+
+- Keep disposable scratch notes and command output in ignored `.work/` and remove
+  them when the task ends.
+- Create a tracked note from `templates/WORK_NOTE.md` only for multi-session work,
+  a handoff, incident, experiment, or material investigation. Record observations,
+  attempts, errors, evidence, and conclusions—not hidden reasoning or a transcript.
+- Link to controlled telemetry queries or safe aggregates; never paste unrestricted
+  raw logs into a note.
+- Close the note by promoting durable facts to project memory, decisions to an ADR,
+  maintained explanations to documentation, and work history to an issue. Delete
+  or close the note when it no longer has coordination or audit value.
+
+## Learn from telemetry
+
+- Emit structured operational events and errors using
+  `schemas/telemetry-event.schema.json`; use stable event and error-code names,
+  artifact identity, outcomes, and safe correlation identifiers.
+- Instrument signals for a named operational decision or user journey. Do not add
+  telemetry merely because it may become useful.
+- Review counts and rates on a declared cadence with
+  `templates/TELEMETRY_REVIEW.md`. Separate observed signals from inferred cause.
+- Convert a selected finding into `templates/IMPROVEMENT_PLAN.md` with an owner,
+  regression test or replay, expected effect, guardrails, and rollback condition.
+- Validate on a later assessment window. Do not treat fewer log lines, a single
+  anecdote, or an agent's own judgment as evidence of improvement.
+
+## Run meaningful verification loops
+
+- For material or high-risk work, define the project-specific objective, invariants,
+  rubric, evidence, resource ceiling, and stopping rules before extended iteration.
+- Verify early after coherent slices. Each later pass must add evidence or a meaningfully
+  different perspective—such as a focused test, static analysis, fault injection,
+  production-like replay, clean build, adversarial input, or independently briefed
+  review when the workflow authorizes one.
+- Treat fresh context as a way to reduce anchoring, not as proof of independence or
+  correctness. An agent's self-review is never sole approval for safety, security,
+  governance, financial logic, or release decisions.
+- Scale effort by risk, uncertainty, blast radius, reversibility, dependency reach, and
+  test strength. Token, iteration, and elapsed-time budgets are ceilings rather than
+  quality targets; lines of code alone do not determine them.
+- Stop on the declared pass threshold, diminishing-return rule, resource ceiling, or
+  need for domain authority. Report unresolved findings instead of repeating the same
+  review against unchanged evidence.
+- Use `templates/AGENTIC_VERIFICATION_LOOP.md` for auditable multi-pass work. Record
+  finding evidence and dispositions, never hidden reasoning or prompt transcripts.
+
+## Close the loop
+
+After a material change, update `PROJECT_MEMORY.md` only if durable project
+knowledge changed. Review the diff, run the applicable quality gate, and ensure
+the memory entry points to the evidence that passed.

plotsalot-0.1.1/CHANGELOG.md

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+# Changelog
+
+Notable user-visible changes are recorded here. Plotsalot follows semantic
+versioning for published package releases.
+
+## 0.1.1 - 2026-09-15
+
+- Reorganized the package documentation around installation, getting started,
+  task-oriented workflows, interpretation boundaries, and maintained evidence.
+- Aligned repository setup, package metadata, documentation checks, and release
+  artifact handling with the production-project-template baseline.
+
+## 0.1.0 - 2026-09-15
+
+### Added
+
+- Polars-first one-sample histograms, labeled dot plots, scatter plots,
+  correlation matrices, independent and repeated comparisons, categorical bar
+  and pie analyses, coefficient plots, and aggregate meta-analysis workflows.
+- Atomic grouped analysis, result-preserving plot composition, local Matplotlib
+  themes, and separate analysis/rendering APIs.
+- Immutable, JSON-safe structured results with versioned schemas, sample and
+  method provenance, correction metadata, resource limits, and owned numerical
+  boundaries.
+- Approved classical, fixed-20%-trim robust, and proper-prior Bayesian modes for
+  their documented workflow families, including deterministic bounded bootstrap,
+  quadrature, and randomized quasi-Monte Carlo computation.
+- Strict caller-reported robust and posterior coefficient profiles plus
+  fixed-Student-t robust and proper-prior Bayesian aggregate meta-analysis.
+- Pinned R-oracle fixtures, independent analytic checks, retained performance
+  baselines, installed-wheel smoke tests, vulnerability/license gates, and
+  milestone-specific verification and sign-off records.
+
+### Compatibility
+
+- Established plotsalot as an independent, adapted Python implementation of
+  selected `ggstatsplot` behavior rather than a line-by-line or pixel-identical
+  port.
+- Adopted explicit subject identity for repeated designs, strict non-finite and
+  degenerate-sample rejection, owned Matplotlib rendering, and no silent method
+  fallback or partial grouped success.
+
+### Known limitations
+
+- M7 compatibility closure and 1.0 API hardening remain.
+- The accepted M6C zero-heterogeneity calibration disposition is provisional and
+  must be revisited before 1.0.
+- Nonparametric families, general fitted-model dispatch, arbitrary ggplot layer
+  compatibility, and unsupported upstream arguments remain deferred.

plotsalot-0.1.1/CONTRIBUTING.md

@@ -0,0 +1,59 @@
+# Contributing
+
+Plotsalot is a pre-1.0 scientific Python project. Keep changes bounded, preserve
+the declared statistical and ownership contracts, and add evidence for changed
+behavior.
+
+## Set up a checkout
+
+Use Python 3.11 or newer and the locked development environment:
+
+```sh
+make setup
+```
+
+For a new clone or maintainer machine, complete
+[`checklists/REPOSITORY_SETUP.md`](checklists/REPOSITORY_SETUP.md) before the
+first commit or push.
+
+## Make a change
+
+- Work on a focused branch rather than directly on `main`.
+- Keep Polars as the public tabular boundary and make numerical ownership
+  explicit.
+- Do not change an approved statistical method, compatibility classification,
+  license, security policy, or release policy without the corresponding review.
+- Add a regression test for corrected defects and deterministic seeds for random
+  procedures.
+- Update user documentation, method specifications, schemas, and changelog
+  entries in the same change when public behavior changes.
+- Keep credentials, private data, generated distributions, and raw telemetry out
+  of Git.
+
+## Verify the change
+
+Run the local quality and packaging gates:
+
+```sh
+make check
+make audit
+make build
+```
+
+`make oracle` regenerates the pinned R compatibility evidence and requires
+Docker. `make benchmark` refreshes retained performance evidence. Run either only
+when the change affects its declared boundary, then review the resulting diff.
+
+## Submit a pull request
+
+Pull requests must state:
+
+- the user-visible or risk-reducing outcome;
+- compatibility, statistical, security, and data-boundary effects;
+- verification evidence and any deliberately unrun gate; and
+- a rollback or forward-fix path.
+
+The accountable owner must review release, security, governance, license, and
+statistical-method changes. Automated checks and agent review do not replace
+that approval. Maintainers should follow the [release procedure](docs/RELEASING.md)
+and complete the release-readiness checklist before creating a version tag.

plotsalot-0.1.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Joshua Myers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

plotsalot-0.1.1/Makefile

@@ -0,0 +1,41 @@
+.PHONY: setup format lint typecheck test docs check audit build oracle verify-oracle benchmark verify-benchmark
+setup:
+	uv sync --frozen --dev
+format:
+	uv run ruff format .
+lint:
+	uv run ruff check .
+	uv run ruff format --check .
+typecheck:
+	uv run pyright
+test:
+	uv run coverage run -m unittest discover -s tests
+	uv run coverage report
+docs:
+	uv run python tools/check_docs.py
+check: lint typecheck test docs
+audit:
+	uv audit --preview-features audit-command --locked --no-dev
+	uv run python tools/check_licenses.py
+build:
+	uv build --no-sources
+oracle:
+	docker build --platform linux/arm64 --build-arg GGSTATSPLOT_REVISION=7a724cd0ab55668b9d0b2e84b12c711c5be68ac8 -t plotsalot-r-oracle:m0 -f oracle/Dockerfile .
+	docker run --rm --platform linux/arm64 -v "$(CURDIR):/work" plotsalot-r-oracle:m0
+	uv run python tools/verify_oracle.py --write-manifest
+	uv run python tools/verify_oracle.py
+verify-oracle:
+	uv run python tools/verify_oracle.py
+benchmark:
+	uv run python benchmarks/benchmark_m0.py
+	uv run python benchmarks/benchmark_m2.py
+	uv run python benchmarks/benchmark_m3.py
+	uv run python benchmarks/benchmark_m4.py
+	uv run python benchmarks/benchmark_m5a.py
+	uv run python benchmarks/benchmark_m5b.py
+	uv run python benchmarks/benchmark_m6a.py
+	uv run python benchmarks/benchmark_m6b.py
+	uv run python benchmarks/benchmark_m6c.py
+	uv run python tools/verify_benchmark.py
+verify-benchmark:
+	uv run python tools/verify_benchmark.py

plotsalot-0.1.1/PKG-INFO

@@ -0,0 +1,149 @@
+Metadata-Version: 2.5
+Name: plotsalot
+Version: 0.1.1
+Summary: Statistical visualizations and distribution diagnostics for Python
+Project-URL: Homepage, https://github.com/joshuamyers22/plotsalot
+Project-URL: Documentation, https://github.com/joshuamyers22/plotsalot/tree/main/docs
+Project-URL: Repository, https://github.com/joshuamyers22/plotsalot
+Project-URL: Issues, https://github.com/joshuamyers22/plotsalot/issues
+Project-URL: Changelog, https://github.com/joshuamyers22/plotsalot/blob/main/CHANGELOG.md
+Author: Joshua Myers
+License-Expression: MIT
+License-File: LICENSE
+Keywords: ggstatsplot,matplotlib,polars,statistics,visualization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: matplotlib<4,>=3.10
+Requires-Dist: numpy<3,>=2
+Requires-Dist: polars<2,>=1.44.1
+Requires-Dist: scipy<2,>=1.16
+Requires-Dist: statsmodels<0.16,>=0.15
+Description-Content-Type: text/markdown
+
+# plotsalot
+
+`plotsalot` is an independent Python library for statistical visualizations with
+structured, extractable results. It provides Polars-first analysis workflows and
+Matplotlib figures inspired by the public behavior of
+[`ggstatsplot`](https://github.com/IndrajeetPatil/ggstatsplot).
+
+The project is pre-1.0 alpha software. Its classical, robust, Bayesian,
+categorical, coefficient, and meta-analysis families have passed their recorded
+M0–M6 technical and statistical gates, but M7 compatibility closure and 1.0
+hardening remain. Do not treat a successful computation or plot as automatic
+validation of a statistical model or a substantive conclusion.
+
+## Install
+
+Plotsalot supports Python 3.11 and newer on Linux and macOS. After the first PyPI
+release:
+
+```sh
+python -m pip install plotsalot
+```
+
+For development from a checkout:
+
+```sh
+make setup
+```
+
+R and Docker are development-only oracle tools. They are not package runtime
+dependencies.
+
+## Quick start
+
+```python
+import polars as pl
+
+from plotsalot import gghistostats
+
+data = pl.DataFrame({"value": [1.0, 2.0, 3.0, 4.0, 5.0]})
+plot = gghistostats(data, "value", test_value=0.0)
+
+print(plot.result.to_dict())
+plot.figure.savefig("histogram.svg")
+```
+
+Each plotting function returns a typed container with a Matplotlib figure, named
+axes, annotations, and a structured result. Analysis and rendering can also be
+separated so visual changes do not recompute statistics:
+
+```python
+from plotsalot import analyze_gghistostats, render_gghistostats
+
+analysis = analyze_gghistostats(data, "value", test_value=0.0)
+plot = render_gghistostats(analysis, title="Observed values")
+plot.axes["main"].grid(axis="y", alpha=0.2)
+```
+
+## Find the right documentation
+
+| Need | Go to |
+|---|---|
+| Complete a first analysis | [Getting started](docs/GETTING_STARTED.md) |
+| Choose a plot or analysis family | [User guide](docs/USER_GUIDE.md) |
+| Interpret results and failure boundaries | [Interpretation and limitations](docs/INTERPRETATION_AND_LIMITATIONS.md) |
+| Understand result and rendering contracts | [Contracts](docs/CONTRACTS.md) |
+| Compare behavior with `ggstatsplot` | [Compatibility matrix](docs/compatibility.md) |
+| Review statistical definitions | [Statistical methods index](docs/README.md#statistical-methods) |
+| Reproduce tests, oracles, and benchmarks | [Reproducibility](REPRODUCIBILITY.md) |
+| Contribute a change | [Contributing](CONTRIBUTING.md) |
+
+## Supported workflow families
+
+- one-sample histograms and labeled dot plots;
+- scatter plots and correlation matrices;
+- independent- and repeated-group comparisons;
+- categorical bar and pie analyses;
+- coefficient and aggregate meta-analysis plots;
+- atomic grouped variants, plot composition, and local themes; and
+- explicit classical, fixed-trim robust, and approved Bayesian modes where
+  listed in the [compatibility matrix](docs/compatibility.md).
+
+The implementation is adapted rather than a drop-in port. It uses explicit
+column names, typed Python results, owned NumPy boundaries, and Matplotlib
+rendering. Unsupported modes fail explicitly; grouped operations do not return
+partial results.
+
+## Development
+
+```sh
+make setup
+make check
+make audit
+make build
+```
+
+The default quality gate runs formatting, linting, strict type checking, the test
+suite, coverage enforcement, and documentation-link checks. Frozen R-oracle and
+benchmark evidence are verified by the normal tests; regenerating them is an
+explicit operation:
+
+```sh
+make oracle
+make benchmark
+```
+
+See [the documentation index](docs/README.md) for project plans, decisions,
+method specifications, and retained verification evidence.
+
+## Project identity and license
+
+Plotsalot is an independent project and is not endorsed by or affiliated with
+the `ggstatsplot` maintainers. The upstream project is used as a pinned behavioral
+reference under the adaptation rules recorded in the repository.
+
+Plotsalot is MIT licensed. See [LICENSE](LICENSE) and
+[ADR-010](docs/adr/ADR-010-license-posture.md) for the accepted distribution and
+upstream-notice rules. Report security concerns according to
+[SECURITY.md](SECURITY.md).