tree-annotated-plot 0.0.1__tar.gz → 0.1.0__tar.gz

{tree_annotated_plot-0.0.1 → tree_annotated_plot-0.1.0}/.github/workflows/release.yml

@@ -1,4 +1,6 @@
-# Build wheel + sdist and publish to PyPI when a `v*` tag is pushed.
+# When a `v*` tag is pushed: build wheel + sdist, publish to PyPI,
+# then create a GitHub Release with auto-generated notes and the
+# wheel + sdist attached as downloadable assets.
 #
 # Uses PyPI trusted publishing (OIDC) — no API token / password is
 # stored in the repo. The trusted-publisher relationship must be
@@ -80,3 +82,31 @@ jobs:
           path: dist/
 
       - uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    # Runs only after PyPI publish succeeds, so a transient PyPI failure
+    # doesn't leave a GitHub Release pointing at a version that isn't on
+    # PyPI. The Release page links to the tag, the wheel + sdist, and an
+    # auto-generated changelog (PR titles + commit list since the
+    # previous tag).
+    needs: publish
+    runs-on: ubuntu-latest
+    permissions:
+      # `softprops/action-gh-release` needs write access to create a
+      # Release on the tag and upload the dist files as assets.
+      contents: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+
+      - uses: softprops/action-gh-release@v3
+        with:
+          # Attach the same wheel + sdist that went to PyPI so the
+          # Release page is a complete record of what was published.
+          files: dist/*
+          # Auto-generate notes from PR titles + commits since the
+          # previous tag. Maintainer can edit them after the fact in
+          # the Releases UI without re-running the workflow.
+          generate_release_notes: true

tree_annotated_plot-0.0.1/.github/workflows/ci.yml → tree_annotated_plot-0.1.0/.github/workflows/tests.yml

@@ -1,10 +1,16 @@
 # Run lint, format-check, and tests on every push to main and on every PR.
 #
+# The workflow `name` is "tests" because that's what the README badge
+# displays — readers (especially the biology audience) parse "tests
+# passing" more readily than "CI passing". Behaviorally, this workflow
+# also runs ruff and black (i.e. it's the project's full CI gate, not
+# only tests); the slight label overload is intentional.
+#
 # Local equivalent: `scripts/check.sh` (which expects a local .venv;
 # this workflow uses the runner's python directly so it doesn't depend
 # on that layout).
 
-name: ci
+name: tests
 
 on:
   push:

{tree_annotated_plot-0.0.1 → tree_annotated_plot-0.1.0}/CLAUDE.md

@@ -57,7 +57,7 @@
   scripts/check.sh
   ```
   The same three checks run in CI via
-  [`.github/workflows/ci.yml`](.github/workflows/ci.yml) on push to
+  [`.github/workflows/tests.yml`](.github/workflows/tests.yml) on push to
   `main` and on PRs (CI also fetches the upstream Kikawa Auspice JSONs
   so real-data tests run rather than skip). Local green ≈ CI green.
 - **Build docs alongside checks** when changing public API surface:
@@ -95,11 +95,13 @@
 - **Releases are tag-driven**. Push a `vX.Y.Z` tag (after bumping
   `pyproject.toml`'s `version`) and
   [`.github/workflows/release.yml`](.github/workflows/release.yml)
-  builds wheel + sdist and publishes to PyPI via trusted publishing
-  (OIDC — no token in the repo). The build job verifies the tag and
-  `pyproject.toml` version match before publishing. Per-release recipe
-  and one-time PyPI configuration steps are in `README.md` under
-  "Releasing a new version".
+  builds wheel + sdist, publishes to PyPI via trusted publishing
+  (OIDC — no token in the repo), and creates a matching GitHub
+  Release with auto-generated notes + the wheel/sdist attached as
+  assets. The build job verifies the tag and `pyproject.toml` version
+  match before publishing. Per-release recipe and one-time PyPI
+  configuration steps are in `README.md` under "Releasing a new
+  version".
 - **Adding a new example** (full recipe in `README.md`):
   1. Self-contained module under `examples/` with module-level
      helpers (callable from outside).

{tree_annotated_plot-0.0.1 → tree_annotated_plot-0.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tree-annotated-plot
-Version: 0.0.1
+Version: 0.1.0
 Summary: Annotate the axis of an Altair / Vega-Lite plot with a phylogenetic tree.
 Project-URL: Documentation, https://jbloomlab.github.io/tree-annotated-plot/
 Project-URL: Homepage, https://github.com/jbloomlab/tree-annotated-plot
@@ -51,6 +51,10 @@ Description-Content-Type: text/markdown
 
 # `tree-annotated-plot`: annotate the axis of an Altair / Vega-Lite plot with a phylogenetic tree
 
+[![PyPI version](https://img.shields.io/pypi/v/tree-annotated-plot.svg)](https://pypi.org/project/tree-annotated-plot/)
+[![Python versions](https://img.shields.io/pypi/pyversions/tree-annotated-plot.svg)](https://pypi.org/project/tree-annotated-plot/)
+[![tests](https://github.com/jbloomlab/tree-annotated-plot/actions/workflows/tests.yml/badge.svg)](https://github.com/jbloomlab/tree-annotated-plot/actions/workflows/tests.yml)
+[![Docs](https://img.shields.io/github/deployments/jbloomlab/tree-annotated-plot/github-pages?label=docs)](https://jbloomlab.github.io/tree-annotated-plot/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
@@ -60,6 +64,22 @@ See [https://jbloomlab.github.io/tree-annotated-plot/](https://jbloomlab.github.
 
 > **Note:** charts must be saved from altair 6+ (Vega-Lite v6). Older specs raise by default; pass `--no-strict-version` (CLI) or `strict_version=False` (Python) to override at your own risk. See the [docs](https://jbloomlab.github.io/tree-annotated-plot/) for details.
 
+## Installation
+
+Released on [PyPI](https://pypi.org/project/tree-annotated-plot/). Requires Python 3.13+.
+
+```bash
+pip install tree-annotated-plot
+```
+
+To install the bleeding edge directly from this repository:
+
+```bash
+pip install git+https://github.com/jbloomlab/tree-annotated-plot.git
+```
+
+For a development checkout, see [Installation (development)](#installation-development) below.
+
 ## Notes for developing the package
 
 ### Installation (development)
@@ -110,9 +130,9 @@ Then open `site/examples.html` in a browser and, for each example:
 If something visibly regresses, fix it before pushing — there's no
 CI gate that will catch a visual regression for you.
 
-### Continuous integration
+### Continuous integration tests
 
-[`.github/workflows/ci.yml`](.github/workflows/ci.yml) runs on every
+[`.github/workflows/tests.yml`](.github/workflows/tests.yml) runs on every
 push to `main` and every pull request: it installs the package, fetches
 the upstream Kikawa Auspice JSONs (so the real-data tests actually
 exercise rather than skip), builds the Kikawa titer chart specs, and
@@ -129,8 +149,11 @@ merge), and additionally deploys `site/` to GitHub Pages on push to
 
 A third workflow,
 [`.github/workflows/release.yml`](.github/workflows/release.yml),
-builds the sdist + wheel and publishes them to PyPI when a `v*` tag
-is pushed (see "Releasing a new version" below).
+builds the sdist + wheel when a `v*` tag is pushed, publishes them
+to PyPI, and creates a matching
+[GitHub Release](https://github.com/jbloomlab/tree-annotated-plot/releases)
+with auto-generated notes and the wheel/sdist attached (see
+"Releasing a new version" below).
 
 ### Releasing a new version
 

{tree_annotated_plot-0.0.1 → tree_annotated_plot-0.1.0}/README.md

@@ -1,5 +1,9 @@
 # `tree-annotated-plot`: annotate the axis of an Altair / Vega-Lite plot with a phylogenetic tree
 
+[![PyPI version](https://img.shields.io/pypi/v/tree-annotated-plot.svg)](https://pypi.org/project/tree-annotated-plot/)
+[![Python versions](https://img.shields.io/pypi/pyversions/tree-annotated-plot.svg)](https://pypi.org/project/tree-annotated-plot/)
+[![tests](https://github.com/jbloomlab/tree-annotated-plot/actions/workflows/tests.yml/badge.svg)](https://github.com/jbloomlab/tree-annotated-plot/actions/workflows/tests.yml)
+[![Docs](https://img.shields.io/github/deployments/jbloomlab/tree-annotated-plot/github-pages?label=docs)](https://jbloomlab.github.io/tree-annotated-plot/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
@@ -9,6 +13,22 @@ See [https://jbloomlab.github.io/tree-annotated-plot/](https://jbloomlab.github.
 
 > **Note:** charts must be saved from altair 6+ (Vega-Lite v6). Older specs raise by default; pass `--no-strict-version` (CLI) or `strict_version=False` (Python) to override at your own risk. See the [docs](https://jbloomlab.github.io/tree-annotated-plot/) for details.
 
+## Installation
+
+Released on [PyPI](https://pypi.org/project/tree-annotated-plot/). Requires Python 3.13+.
+
+```bash
+pip install tree-annotated-plot
+```
+
+To install the bleeding edge directly from this repository:
+
+```bash
+pip install git+https://github.com/jbloomlab/tree-annotated-plot.git
+```
+
+For a development checkout, see [Installation (development)](#installation-development) below.
+
 ## Notes for developing the package
 
 ### Installation (development)
@@ -59,9 +79,9 @@ Then open `site/examples.html` in a browser and, for each example:
 If something visibly regresses, fix it before pushing — there's no
 CI gate that will catch a visual regression for you.
 
-### Continuous integration
+### Continuous integration tests
 
-[`.github/workflows/ci.yml`](.github/workflows/ci.yml) runs on every
+[`.github/workflows/tests.yml`](.github/workflows/tests.yml) runs on every
 push to `main` and every pull request: it installs the package, fetches
 the upstream Kikawa Auspice JSONs (so the real-data tests actually
 exercise rather than skip), builds the Kikawa titer chart specs, and
@@ -78,8 +98,11 @@ merge), and additionally deploys `site/` to GitHub Pages on push to
 
 A third workflow,
 [`.github/workflows/release.yml`](.github/workflows/release.yml),
-builds the sdist + wheel and publishes them to PyPI when a `v*` tag
-is pushed (see "Releasing a new version" below).
+builds the sdist + wheel when a `v*` tag is pushed, publishes them
+to PyPI, and creates a matching
+[GitHub Release](https://github.com/jbloomlab/tree-annotated-plot/releases)
+with auto-generated notes and the wheel/sdist attached (see
+"Releasing a new version" below).
 
 ### Releasing a new version
 

{tree_annotated_plot-0.0.1 → tree_annotated_plot-0.1.0}/docs/index.md

@@ -24,6 +24,31 @@ with `Chart` / `LayerChart` / `FacetChart` / `HConcatChart` /
 axis. The tree drops to whichever side of the chart the strain labels
 sit on by default (left for y-axis, bottom for x-axis).
 
+## Installation
+
+Released on [PyPI](https://pypi.org/project/tree-annotated-plot/).
+Requires Python 3.13+.
+
+```bash
+pip install tree-annotated-plot
+```
+
+To pin a specific version:
+
+```bash
+pip install tree-annotated-plot==0.0.1
+```
+
+To install the bleeding edge directly from the
+[GitHub source](https://github.com/jbloomlab/tree-annotated-plot):
+
+```bash
+pip install git+https://github.com/jbloomlab/tree-annotated-plot.git
+```
+
+For a development checkout (contributors), see the README's
+[development install](https://github.com/jbloomlab/tree-annotated-plot#installation-development).
+
 ## 30-second example
 
 Given an Auspice tree at `h3n2.auspice.json` and a Vega-Lite chart spec

{tree_annotated_plot-0.0.1 → tree_annotated_plot-0.1.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "tree-annotated-plot"
-version = "0.0.1"
+version = "0.1.0"
 description = "Annotate the axis of an Altair / Vega-Lite plot with a phylogenetic tree."
 readme = "README.md"
 requires-python = ">=3.13"

tree_annotated_plot-0.0.1/NEXT_STEPS.md

@@ -1,94 +0,0 @@
-# Next steps
-
-Phase 2 is complete. This file is the to-do list for resuming —
-either by Jesse picking up later or by a future Claude session.
-Lifecycle: shrink as items get done; delete the file when only
-hypothetical Phase 3 work is left.
-
-## Immediate actions (not yet done)
-
-1. **Push to GitHub.** Local commits haven't been pushed yet.
-   ```bash
-   git push -u origin main
-   ```
-2. **Enable Pages.** GitHub repo → Settings → Pages → Source:
-   "GitHub Actions". This activates the dormant
-   `.github/workflows/docs.yml` so the next push to `main` builds
-   and deploys the docs site to
-   https://jbloomlab.github.io/tree-annotated-plot/.
-3. **Verify the deployed site.** Click through Home / Python API /
-   Command line / Examples. On the Examples page, each "Open the
-   interactive chart →" link should open a working interactive
-   Altair chart with tooltips and selection bindings. If any link
-   404s or any image is missing, the `Generate chart assets` step
-   in the workflow probably failed — check the Actions tab.
-4. **Bump the version + cut a tag** when you're ready for v0.1.0.
-   `pyproject.toml`'s `version = "0.0.1"` is an alpha placeholder.
-   ```bash
-   # edit pyproject.toml: version = "0.1.0"
-   git commit -am "release v0.1.0" && git tag v0.1.0
-   git push && git push --tags
-   ```
-5. **Add a GitHub action to run the tests**: this should include running any tests, examples, linting, and code formatting
-6. **Add installation instructions to the docs and README**: assume it can be installed from PyPI but have documentation also link to GitHub source
-
-## Phase 3 candidate features (deferred from Phase 2)
-
-The Phase 2 plan's "Out of scope" section listed these explicitly
-and the user signed off on deferring them. Pick from this list when
-adding the next round of features:
-
-- **Clade coloring / tree decoration.** API shape undecided. Two
-  options on the table:
-  - Declarative: `clades=[{"node_attr": "subclade", "values_to_colors": {...}}]` and the package paints branches.
-  - Lower-level: expose `tree_chart()` returning the tree panel as
-    an editable `alt.Chart` so users layer their own decoration.
-- **Image-snapshot regression tests.** Render via
-  `vl-convert-python` (already a dep) to PNG and compare with a
-  structural diff or perceptual-similarity metric. Tool choice
-  undecided (`pytest-mpl` is matplotlib-only; would need to find or
-  build something for Vega-Lite output).
-- **Newick / Nexus tree input.** Auspice JSON v2 is the only tree
-  format today.
-- **Static (matplotlib) backend.** Only altair-via-Vega-Lite today.
-- **HTML chart-spec extraction beyond the default altair template.**
-  Today we parse `var spec = {...}` out of altair's standard
-  `to_html()` output via stdlib `html.parser` +
-  `json.JSONDecoder.raw_decode()`. Custom `chart.save(template=...)`
-  outputs would need a real JS-AST parser (e.g. `esprima`).
-- **Per-clade collapsing of subtrees** (different from the
-  topology-pruning we already do for `prune_tree_to_chart`).
-- **Vega-Lite v5 → v6 auto-upgrade** of stale specs. We currently
-  detect-and-report; we don't translate.
-
-## Smaller polish items
-
-- **Add `CHANGELOG.md`.** None today; `git log --oneline` is the
-  de-facto record. Worth one if multiple releases pile up.
-- **Add a PyPI publish workflow.**
-  `.github/workflows/release.yml` triggered on tag, building wheel +
-  sdist, uploading via trusted publishing. None today; would
-  complement the existing docs-deploy workflow.
-- **Compress the H1N1 docs PNG** (currently ~1 MB). Options:
-  - Pass `optimize=True` to the PIL save (might need post-processing
-    after `chart.save()`).
-  - Lower PPI in `scripts/generate_docs_assets.py` from 96 to 72.
-  - Crop or resize after rendering.
-- **Investigate the "Automatically deduplicated selection parameter"
-  altair warning** that appears when the Kikawa chart-builder runs.
-  Pre-existing and cosmetic, but it'd be cleaner to silence
-  (probably needs explicit `name=` on the selection params).
-- **Add badges to README** Add badges for GitHub Actions test and PyPI version to the README.
-  Is there also a badge I can add for the docs, or other badges to consider?
-
-## State at session close
-
-- 21 commits on `main`, none pushed.
-- All 102 tests pass via `scripts/check.sh`.
-- `scripts/build_docs.sh` produces a viewable `site/` from a clean
-  checkout.
-- `plan.md` is gone (disassembled per its own Lifecycle section in
-  commit `b9beb66`).
-- `docs_plan.md` is gone (transient design note for the docs
-  deployment + asset strategy; written, reviewed, and removed in
-  commit `f1f551d`).