bindsight 0.3.5__tar.gz → 0.3.6__tar.gz

{bindsight-0.3.5 → bindsight-0.3.6}/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -41,7 +41,7 @@ body:
     attributes:
       label: Version
       description: "Output of `bindsight --version`."
-      placeholder: "0.3.5"
+      placeholder: "0.3.6"
     validations:
       required: true
 
@@ -59,6 +59,7 @@ body:
     attributes:
       label: How you installed it
       options:
+        - "pip install bindsight (PyPI)"
         - "git clone + pip install -e"
         - "conda/mamba from envs/discover.yaml"
         - "Docker"

{bindsight-0.3.5 → bindsight-0.3.6}/.github/workflows/docs.yml

@@ -1,7 +1,8 @@
 name: Docs
 
-# Build the mkdocs-material site and publish it to GitHub Pages.
-# Enable once in repo Settings → Pages → Source: "GitHub Actions".
+# Build the mkdocs-material site and publish it to GitHub Pages. Pages is
+# served from GitHub Actions (Settings → Pages → Source: "GitHub Actions"),
+# which is what lets this deploy without a gh-pages branch.
 
 on:
   push:

{bindsight-0.3.5 → bindsight-0.3.6}/.github/workflows/release-artifacts.yml

@@ -1,17 +1,17 @@
 name: Release artifacts
 
 # Attach a wheel, an sdist and their SHA-256 checksums to every published
-# release, and — once PyPI trusted publishing is configured — upload the same
-# artifacts to PyPI.
+# release, and upload the same two files to PyPI.
 #
 # The attach job always runs, so a release is installable without PyPI:
 #     pip install https://github.com/mikhaeelatefrizk/bindsight/releases/download/<tag>/bindsight-<version>-py3-none-any.whl
 #
-# The PyPI job is dormant until the project is registered as a trusted publisher
-# (pypi.org → project → Publishing → add GitHub as a publisher with this
-# repository, workflow `release-artifacts.yml` and environment `pypi`). It uses
-# OIDC, so no API token is ever stored in this repository. Until the
-# `pypi` environment exists the job is skipped rather than failing.
+# The PyPI job runs when the `PYPI_TRUSTED_PUBLISHING` repository variable is
+# `true` and the `pypi` environment exists -- both since 0.3.5, the first
+# release published there. The project is registered on PyPI as a trusted
+# publisher of this repository, workflow `release-artifacts.yml`, environment
+# `pypi`, so the upload is authorised by OIDC and no API token is ever stored
+# in this repository. Without the variable the job is skipped, not failed.
 
 on:
   release:
@@ -31,6 +31,11 @@ jobs:
         with:
           python-version: "3.12"
       - run: python -m pip install --quiet build twine
+      - name: Point the README's relative links at this tag for PyPI
+        # PyPI renders the long description with no base URL, so every
+        # relative link in README.md is dead there. The checkout is rewritten
+        # (never committed) so the sdist and wheel carry absolute links.
+        run: python scripts/pypi_readme.py --write --ref "${{ github.event.release.tag_name || github.ref_name }}"
       - run: python -m build
       - name: Check metadata
         run: python -m twine check dist/*
@@ -82,7 +87,7 @@ jobs:
       # a statement of intent; a branch is not.
       #
       # This SHA is what `release/v1` points at today and what the `v1.14.2`
-      # tag dereferences to, so pinning changes nothing now. The job is dormant
-      # until `vars.PYPI_TRUSTED_PUBLISHING` is set, which makes now the
-      # cheapest possible moment.
+      # tag dereferences to, so pinning changed nothing at the time. The job
+      # was dormant until `vars.PYPI_TRUSTED_PUBLISHING` was set for 0.3.5,
+      # which made that the cheapest possible moment.
       - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33  # v1.14.2

{bindsight-0.3.5 → bindsight-0.3.6}/CHANGELOG.md

@@ -6,6 +6,84 @@ The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and
 
 ---
 
+## [0.3.6] - 2026-09-20
+
+0.3.5 published this project to PyPI for the first time, and PyPI renders a
+package's long description with no base URL. Every relative link in
+`README.md` is therefore dead on that project page, and PyPI does not let a
+description be edited after upload. The rewrite that fixes it landed on `main`
+an hour after the tag, so only a release can carry it to the page a reader
+actually lands on. That is what this one is for.
+
+### Fixed — the local GPU runner pulled an image nothing publishes
+
+`LocalDockerRunner` defaulted to `ghcr.io/mikhaeelatefrizk/bindsight:dev`.
+No workflow has ever pushed a `:dev` tag: `docker.yml` publishes `latest`,
+one tag per commit SHA, and one per release. `docs/how-to-use.md` lists
+`local_docker` beside `modal` and `kaggle` as a backend a reader can pick,
+so following the documentation into Docker mode ended at a pull that could
+not succeed — and had never been able to.
+
+It defaults to `:latest` now, which is the only tag always published. A
+moving tag is safe here in a way it is not for a CI action: the image carries
+its own bindsight and runs it, and `pipelines.full_run._container_ref`
+records the resolved *digest* in the manifest rather than the tag, for exactly
+this reason — "a manifest must not claim an image identity it could not
+verify, and a tag is not one". The published tags are now read out of the
+workflow by a test rather than repeated in one, so renaming one fails loudly.
+
+### Fixed — two headings that closed a tag they did not open
+
+`try.html.j2` and `your_data.html.j2` opened `<h2 class="card__title">` and
+closed `</h3>`. The `h2` was itself a fix: both pages had gone from `<h1>`
+straight to `<h3>`, which tells a screen reader a section was skipped, and the
+level had been chosen by what the class made it look like rather than by where
+it sat. The repair changed the opening tag and left the closing one, which
+every browser silently puts right -- so the rendered document was correct, the
+markup was not, and nothing failed either way.
+
+Several modules already parse these templates: for inline scripts, for
+colours, for chart specifications. None looked at heading structure, which is
+why the skip got in and why the mismatch that replaced it got in too. Two
+rules now do, over every `.j2` under `bindsight/report/` found by globbing
+rather than by a list: a heading closes the tag it opened, and no page jumps a
+level. Shown red three ways -- the closing tag drifted back, the title demoted
+to recreate the original skip, and the glob pointed at an empty directory to
+prove the sweep is reading anything at all.
+
+### Changed — installed from PyPI
+
+0.3.5 is the first release published to PyPI. `release-artifacts.yml`'s `pypi`
+job ran on the `release: published` event under trusted publishing, and the
+two files it uploaded are the wheel and sdist attached to the release: PyPI's
+SHA-256 digests equal the release's `SHA256SUMS`. The install instructions
+say `pip install` now, with the checkout form kept for development. The
+runners that install bindsight into a remote image or a generated notebook
+keep installing from this repository, so a remote runs the caller's checkout
+rather than the last published release; their comments say that instead of
+"not on PyPI".
+
+### Fixed — what a thirteen-way visitor sweep found
+
+Thirteen readers went through the tree, the release page, PyPI, the container
+registry and the documentation site as a visiting department head would, with
+two skeptics refuting each finding. Four stood. PyPI renders a package's long
+description with no base URL, so all 65 relative links in `README.md` are
+dead on the 0.3.5 project page; `scripts/pypi_readme.py` now points them at
+the release tag on GitHub before `release-artifacts.yml` builds the wheel and
+sdist, the tree's README keeps its relative links so GitHub renders them, and
+`tests/test_pypi_readme.py` holds both halves and the step order. The 0.3.5
+page itself cannot be re-rendered: PyPI does not let a description be edited
+after upload. `docs.yml` said Pages had yet to be enabled, three months after
+it was. `paper.md` names Modal and now cites it; the 0.3.5 entry said the
+`Modal` bibliography entry stayed uncited on purpose, and this reverses that.
+And that entry omitted one change the release carried: `bindsight/io/gdc.py`'s
+docstring pointed at a TCGA publication-guidelines page that no longer
+exists, and 14d2bf1 replaced it with the current one. A PyPI badge joins the
+README's badge row.
+
+---
+
 ## [0.3.5] - 2026-09-20
 
 0.3.4 is the current release, and its web interface renders every page with

{bindsight-0.3.5 → bindsight-0.3.6}/CITATION.cff

@@ -38,5 +38,5 @@ keywords:
   - RO-Crate
   - target-discovery
   - cancer-immunotherapy
-version: 0.3.5
+version: 0.3.6
 date-released: "2026-09-20"

{bindsight-0.3.5 → bindsight-0.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: bindsight
-Version: 0.3.5
+Version: 0.3.6
 Summary: A reproducible bridge from RNA-seq to de novo protein binder design, with end-to-end provenance.
 Project-URL: Homepage, https://mikhaeelatefrizk.github.io/bindsight/
 Project-URL: Documentation, https://mikhaeelatefrizk.github.io/bindsight/
@@ -94,7 +94,8 @@ Description-Content-Type: text/markdown
 > it came from.
 
 [![CI](https://github.com/mikhaeelatefrizk/bindsight/actions/workflows/ci.yml/badge.svg)](https://github.com/mikhaeelatefrizk/bindsight/actions/workflows/ci.yml)
-[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/bindsight.svg)](https://pypi.org/project/bindsight/)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSE)
 [![Python: 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
 [![Workflow: Snakemake](https://img.shields.io/badge/workflow-Snakemake-brightgreen.svg)](https://snakemake.github.io/)
 
@@ -115,15 +116,15 @@ an account, or a GPU to read.
 | **Run it in five minutes** | [Install](#install), then `bindsight demo` |
 | **See what it has and has not shown** | [What the evidence says](#what-the-evidence-says) |
 | **Reproduce a published number** | [Reproducing the results](#reproducing-the-results) |
-| **Understand how it works** | [ARCHITECTURE.md](ARCHITECTURE.md) |
-| **Read the study** | [`benchmarks/study/`](benchmarks/study/) · [write-up](paper/validation/manuscript.md) |
-| **Read the control that withdrew a headline** | [`benchmarks/calibration/`](benchmarks/calibration/) |
-| **See the provenance chain, run end to end** | [`benchmarks/provenance_join/`](benchmarks/provenance_join/) |
+| **Understand how it works** | [ARCHITECTURE.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/ARCHITECTURE.md) |
+| **Read the study** | [`benchmarks/study/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/study) · [write-up](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/paper/validation/manuscript.md) |
+| **Read the control that withdrew a headline** | [`benchmarks/calibration/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/calibration) |
+| **See the provenance chain, run end to end** | [`benchmarks/provenance_join/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/provenance_join) |
 | **Find your way around the code** | [Repository map](#repository-map) |
 | **Use your own data** | [Scope — what it accepts](#scope--what-it-accepts) |
-| **Design binders on a free GPU** | [`RUN_FREE_GPU.md`](benchmarks/designer_benchmark/RUN_FREE_GPU.md) |
-| **Look up a term** (PROV-O, RO-Crate, ipTM, PAE-int…) | [Glossary](docs/glossary.md) |
-| **Contribute** | [CONTRIBUTING.md](CONTRIBUTING.md) |
+| **Design binders on a free GPU** | [`RUN_FREE_GPU.md`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/benchmarks/designer_benchmark/RUN_FREE_GPU.md) |
+| **Look up a term** (PROV-O, RO-Crate, ipTM, PAE-int…) | [Glossary](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/docs/glossary.md) |
+| **Contribute** | [CONTRIBUTING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CONTRIBUTING.md) |
 | **Cite it** | [Citation](#citation) |
 
 ---
@@ -133,12 +134,11 @@ an account, or a GPU to read.
 One command, one way. Python 3.11+, Windows / macOS / Linux, CPU only.
 
 ```bash
-git clone https://github.com/mikhaeelatefrizk/bindsight.git
-cd bindsight
-pip install -e ".[discover,report]"
+pip install "bindsight[discover,report]"
 ```
 
-Add `dev` if you intend to run the tests (`pip install -e ".[dev,discover,report]"`),
+From a checkout, `pip install -e ".[discover,report]"` instead. Add `dev` if you
+intend to run the tests (`pip install -e ".[dev,discover,report]"`),
 and `runners` if you intend to send work to a GPU backend. Conda users can build the
 same dependency set first with `mamba env create -f envs/discover.yaml`.
 
@@ -208,7 +208,7 @@ stated as such: at rank 20 it is 1 of 17 on approved-agent antigens (95% CI
 0.01–0.27). Most clinically validated antigens are simply not significantly
 over-expressed in an unstratified bulk contrast.
 
-→ [`benchmarks/study/RESULTS.md`](benchmarks/study/RESULTS.md) · [write-up](paper/validation/manuscript.md)
+→ [`benchmarks/study/RESULTS.md`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/benchmarks/study/RESULTS.md) · [write-up](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/paper/validation/manuscript.md)
 
 ### The design half
 
@@ -227,7 +227,7 @@ page does not quote it as one. The ipTM values are real Boltz-2 outputs; what do
 not follow is that the rate measures the designs. The control's predictions were
 written down before its data arrived.
 
-→ [`benchmarks/calibration/`](benchmarks/calibration/) · [`benchmarks/designer_benchmark/`](benchmarks/designer_benchmark/)
+→ [`benchmarks/calibration/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/calibration) · [`benchmarks/designer_benchmark/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/designer_benchmark)
 
 ### The join
 
@@ -238,7 +238,7 @@ carried through to 40 designs and a walkable PROV-O graph. The committed manifes
 lets you verify the first three steps of that walk from this clone; the rest needs
 the crate rebuilt, and that directory says so precisely.
 
-→ [`benchmarks/provenance_join/`](benchmarks/provenance_join/)
+→ [`benchmarks/provenance_join/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/provenance_join)
 
 ### What has not been done
 
@@ -256,7 +256,7 @@ the crate rebuilt, and that directory says so precisely.
 The pipeline takes a **counts matrix** and a **sample design table** naming a
 two-level factor, and contrasts those two levels. Nothing on that path knows about
 cancer. `tumor` and `normal` are values you supply, not values the code expects:
-[`tests/test_non_cancer_cohort.py`](tests/test_non_cancer_cohort.py) drives the whole
+[`tests/test_non_cancer_cohort.py`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/tests/test_non_cancer_cohort.py) drives the whole
 documented path on a drug-versus-vehicle experiment paired within donor, with no
 oncology vocabulary anywhere, and asserts that none leaks into the provenance
 manifest.
@@ -372,7 +372,7 @@ python benchmarks/run_study.py --score-only     # re-scores what is already on d
 
 `score_run.py` is a scorer, not a runner: it consumes the archive a GPU run
 produces. The full chain is in
-[`RUN_FREE_GPU.md`](benchmarks/designer_benchmark/RUN_FREE_GPU.md), which runs on a
+[`RUN_FREE_GPU.md`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/benchmarks/designer_benchmark/RUN_FREE_GPU.md), which runs on a
 free Kaggle T4.
 
 ```bash
@@ -390,32 +390,32 @@ python benchmarks/designer_benchmark/score_run.py <out_dir>/<id>.tar.gz \
 ## Repository map
 
 Each top-level area carries its own `README.md` explaining what is in it and
-why — [`bindsight/`](bindsight/), [`tests/`](tests/), [`scripts/`](scripts/),
-[`benchmarks/`](benchmarks/) and each benchmark under it, [`docs/`](docs/),
-[`examples/`](examples/), [`envs/`](envs/) and [`paper/`](paper/). Package
+why — [`bindsight/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight), [`tests/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/tests), [`scripts/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/scripts),
+[`benchmarks/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks) and each benchmark under it, [`docs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/docs),
+[`examples/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/examples), [`envs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/envs) and [`paper/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/paper). Package
 subdirectories are documented in the table below rather than individually.
 
 | Path | What it holds |
 |---|---|
-| [`bindsight/`](bindsight/) | The Python package — [`io`](bindsight/io/), [`deg`](bindsight/deg/), [`targets`](bindsight/targets/), [`surfaceome`](bindsight/surfaceome/), [`structures`](bindsight/structures/), [`epitopes`](bindsight/epitopes/), [`design`](bindsight/design/), [`runners`](bindsight/runners/), [`validate`](bindsight/validate/), [`rank`](bindsight/rank/), [`benchmark`](bindsight/benchmark/), [`pipelines`](bindsight/pipelines/), [`provenance`](bindsight/provenance/), [`export`](bindsight/export/), [`report`](bindsight/report/) |
-| [`benchmarks/`](benchmarks/) | All the evidence — the [study](benchmarks/study/), the [calibration control](benchmarks/calibration/), the [designer benchmark](benchmarks/designer_benchmark/), the [provenance join](benchmarks/provenance_join/), and the held-out antigen set |
-| [`tests/`](tests/) | 2,000+ tests. Many are guards on published claims, not on code |
-| [`paper/`](paper/) | JOSS and bioRxiv manuscripts, and the validation write-up |
-| [`docs/`](docs/) | Long-form documentation (mkdocs-material source) |
-| [`examples/`](examples/) | Runnable pipeline configs |
-| [`envs/`](envs/) | Conda environment for the discovery half, with pinned constraints |
-| [`scripts/`](scripts/) | Generators for vendored data and published pages |
-| [`.github/workflows/`](.github/workflows/) | CI, docs, docker, release artifacts, and the two paper PDFs |
+| [`bindsight/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight) | The Python package — [`io`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/io), [`deg`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/deg), [`targets`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/targets), [`surfaceome`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/surfaceome), [`structures`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/structures), [`epitopes`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/epitopes), [`design`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/design), [`runners`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/runners), [`validate`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/validate), [`rank`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/rank), [`benchmark`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/benchmark), [`pipelines`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/pipelines), [`provenance`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/provenance), [`export`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/export), [`report`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/report) |
+| [`benchmarks/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks) | All the evidence — the [study](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/study), the [calibration control](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/calibration), the [designer benchmark](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/designer_benchmark), the [provenance join](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/provenance_join), and the held-out antigen set |
+| [`tests/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/tests) | 2,000+ tests. Many are guards on published claims, not on code |
+| [`paper/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/paper) | JOSS and bioRxiv manuscripts, and the validation write-up |
+| [`docs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/docs) | Long-form documentation (mkdocs-material source) |
+| [`examples/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/examples) | Runnable pipeline configs |
+| [`envs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/envs) | Conda environment for the discovery half, with pinned constraints |
+| [`scripts/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/scripts) | Generators for vendored data and published pages |
+| [`.github/workflows/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/.github/workflows) | CI, docs, docker, release artifacts, and the two paper PDFs |
 
 | File | What it is |
 |---|---|
-| [ARCHITECTURE.md](ARCHITECTURE.md) | The architectural source of truth |
-| [CHANGELOG.md](CHANGELOG.md) | Per-version changes |
-| [CONTRIBUTING.md](CONTRIBUTING.md) | Dev setup, testing, commit conventions |
-| [LICENSING.md](LICENSING.md) | Per-dependency licence inventory and commercial-use guidance |
-| [SECURITY.md](SECURITY.md) | How to report a vulnerability |
-| [CITATION.cff](CITATION.cff) | Citation metadata |
-| [Snakefile](Snakefile) | The Snakemake DAG front-end |
+| [ARCHITECTURE.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/ARCHITECTURE.md) | The architectural source of truth |
+| [CHANGELOG.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CHANGELOG.md) | Per-version changes |
+| [CONTRIBUTING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CONTRIBUTING.md) | Dev setup, testing, commit conventions |
+| [LICENSING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSING.md) | Per-dependency licence inventory and commercial-use guidance |
+| [SECURITY.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/SECURITY.md) | How to report a vulnerability |
+| [CITATION.cff](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CITATION.cff) | Citation metadata |
+| [Snakefile](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/Snakefile) | The Snakemake DAG front-end |
 
 ---
 
@@ -441,14 +441,14 @@ subdirectories are documented in the table below rather than individually.
 | Citability | Code dump | Tagged releases with SHA-256 checksums, JSON-Schema-validated outputs |
 
 For the full landscape comparison, see
-[ARCHITECTURE.md § 8](ARCHITECTURE.md#8-comparison-vs-existing-tools).
+[ARCHITECTURE.md § 8](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/ARCHITECTURE.md#8-comparison-vs-existing-tools).
 
 ---
 
 ## Acknowledgments
 
 bindsight is an opinionated wrapper. Real intellectual credit belongs to the upstream
-tool authors. See [LICENSING.md](LICENSING.md) for the full inventory; the work this
+tool authors. See [LICENSING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSING.md) for the full inventory; the work this
 builds on most directly:
 
 - [SURFACE-Bind](https://github.com/hamedkhakzad/SURFACE-Bind) (Balbi et al., PNAS 2026) — the targetable-sites catalog that makes the bridge tractable
@@ -468,7 +468,7 @@ and the checksums attached to the release, plus the author:
 > novo protein binder design* (version X.Y.Z).
 > <https://github.com/mikhaeelatefrizk/bindsight>
 
-Citation metadata also lives in [CITATION.cff](CITATION.cff); GitHub's "Cite this
+Citation metadata also lives in [CITATION.cff](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CITATION.cff); GitHub's "Cite this
 repository" button generates BibTeX and APA from it. Every release attaches a
 wheel, an sdist and a `SHA256SUMS` file, and every image is digest-pinned, so
 the artifacts behind a version are checkable even though the version has no
@@ -487,9 +487,9 @@ independent researcher in Cairo, Egypt.
 
 ## License
 
-- **Code:** [GNU AGPL-3.0-or-later](LICENSE) — copyright notice in [COPYRIGHT](COPYRIGHT). You may use, study, modify, and
+- **Code:** [GNU AGPL-3.0-or-later](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSE) — copyright notice in [COPYRIGHT](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/COPYRIGHT). You may use, study, modify, and
   redistribute bindsight freely; if you distribute a modified version **or run it as
   a network service**, you must make your source available under the same licence,
-  with attribution preserved. See [LICENSING.md](LICENSING.md) for component-level
+  with attribution preserved. See [LICENSING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSING.md) for component-level
   details — bindsight orchestrates external tools that keep their own licences, and
   some carry non-commercial terms.

{bindsight-0.3.5 → bindsight-0.3.6}/README.md

@@ -6,7 +6,8 @@
 > it came from.
 
 [![CI](https://github.com/mikhaeelatefrizk/bindsight/actions/workflows/ci.yml/badge.svg)](https://github.com/mikhaeelatefrizk/bindsight/actions/workflows/ci.yml)
-[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/bindsight.svg)](https://pypi.org/project/bindsight/)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSE)
 [![Python: 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
 [![Workflow: Snakemake](https://img.shields.io/badge/workflow-Snakemake-brightgreen.svg)](https://snakemake.github.io/)
 
@@ -27,15 +28,15 @@ an account, or a GPU to read.
 | **Run it in five minutes** | [Install](#install), then `bindsight demo` |
 | **See what it has and has not shown** | [What the evidence says](#what-the-evidence-says) |
 | **Reproduce a published number** | [Reproducing the results](#reproducing-the-results) |
-| **Understand how it works** | [ARCHITECTURE.md](ARCHITECTURE.md) |
-| **Read the study** | [`benchmarks/study/`](benchmarks/study/) · [write-up](paper/validation/manuscript.md) |
-| **Read the control that withdrew a headline** | [`benchmarks/calibration/`](benchmarks/calibration/) |
-| **See the provenance chain, run end to end** | [`benchmarks/provenance_join/`](benchmarks/provenance_join/) |
+| **Understand how it works** | [ARCHITECTURE.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/ARCHITECTURE.md) |
+| **Read the study** | [`benchmarks/study/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/study) · [write-up](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/paper/validation/manuscript.md) |
+| **Read the control that withdrew a headline** | [`benchmarks/calibration/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/calibration) |
+| **See the provenance chain, run end to end** | [`benchmarks/provenance_join/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/provenance_join) |
 | **Find your way around the code** | [Repository map](#repository-map) |
 | **Use your own data** | [Scope — what it accepts](#scope--what-it-accepts) |
-| **Design binders on a free GPU** | [`RUN_FREE_GPU.md`](benchmarks/designer_benchmark/RUN_FREE_GPU.md) |
-| **Look up a term** (PROV-O, RO-Crate, ipTM, PAE-int…) | [Glossary](docs/glossary.md) |
-| **Contribute** | [CONTRIBUTING.md](CONTRIBUTING.md) |
+| **Design binders on a free GPU** | [`RUN_FREE_GPU.md`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/benchmarks/designer_benchmark/RUN_FREE_GPU.md) |
+| **Look up a term** (PROV-O, RO-Crate, ipTM, PAE-int…) | [Glossary](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/docs/glossary.md) |
+| **Contribute** | [CONTRIBUTING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CONTRIBUTING.md) |
 | **Cite it** | [Citation](#citation) |
 
 ---
@@ -45,12 +46,11 @@ an account, or a GPU to read.
 One command, one way. Python 3.11+, Windows / macOS / Linux, CPU only.
 
 ```bash
-git clone https://github.com/mikhaeelatefrizk/bindsight.git
-cd bindsight
-pip install -e ".[discover,report]"
+pip install "bindsight[discover,report]"
 ```
 
-Add `dev` if you intend to run the tests (`pip install -e ".[dev,discover,report]"`),
+From a checkout, `pip install -e ".[discover,report]"` instead. Add `dev` if you
+intend to run the tests (`pip install -e ".[dev,discover,report]"`),
 and `runners` if you intend to send work to a GPU backend. Conda users can build the
 same dependency set first with `mamba env create -f envs/discover.yaml`.
 
@@ -120,7 +120,7 @@ stated as such: at rank 20 it is 1 of 17 on approved-agent antigens (95% CI
 0.01–0.27). Most clinically validated antigens are simply not significantly
 over-expressed in an unstratified bulk contrast.
 
-→ [`benchmarks/study/RESULTS.md`](benchmarks/study/RESULTS.md) · [write-up](paper/validation/manuscript.md)
+→ [`benchmarks/study/RESULTS.md`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/benchmarks/study/RESULTS.md) · [write-up](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/paper/validation/manuscript.md)
 
 ### The design half
 
@@ -139,7 +139,7 @@ page does not quote it as one. The ipTM values are real Boltz-2 outputs; what do
 not follow is that the rate measures the designs. The control's predictions were
 written down before its data arrived.
 
-→ [`benchmarks/calibration/`](benchmarks/calibration/) · [`benchmarks/designer_benchmark/`](benchmarks/designer_benchmark/)
+→ [`benchmarks/calibration/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/calibration) · [`benchmarks/designer_benchmark/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/designer_benchmark)
 
 ### The join
 
@@ -150,7 +150,7 @@ carried through to 40 designs and a walkable PROV-O graph. The committed manifes
 lets you verify the first three steps of that walk from this clone; the rest needs
 the crate rebuilt, and that directory says so precisely.
 
-→ [`benchmarks/provenance_join/`](benchmarks/provenance_join/)
+→ [`benchmarks/provenance_join/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/provenance_join)
 
 ### What has not been done
 
@@ -168,7 +168,7 @@ the crate rebuilt, and that directory says so precisely.
 The pipeline takes a **counts matrix** and a **sample design table** naming a
 two-level factor, and contrasts those two levels. Nothing on that path knows about
 cancer. `tumor` and `normal` are values you supply, not values the code expects:
-[`tests/test_non_cancer_cohort.py`](tests/test_non_cancer_cohort.py) drives the whole
+[`tests/test_non_cancer_cohort.py`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/tests/test_non_cancer_cohort.py) drives the whole
 documented path on a drug-versus-vehicle experiment paired within donor, with no
 oncology vocabulary anywhere, and asserts that none leaks into the provenance
 manifest.
@@ -284,7 +284,7 @@ python benchmarks/run_study.py --score-only     # re-scores what is already on d
 
 `score_run.py` is a scorer, not a runner: it consumes the archive a GPU run
 produces. The full chain is in
-[`RUN_FREE_GPU.md`](benchmarks/designer_benchmark/RUN_FREE_GPU.md), which runs on a
+[`RUN_FREE_GPU.md`](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/benchmarks/designer_benchmark/RUN_FREE_GPU.md), which runs on a
 free Kaggle T4.
 
 ```bash
@@ -302,32 +302,32 @@ python benchmarks/designer_benchmark/score_run.py <out_dir>/<id>.tar.gz \
 ## Repository map
 
 Each top-level area carries its own `README.md` explaining what is in it and
-why — [`bindsight/`](bindsight/), [`tests/`](tests/), [`scripts/`](scripts/),
-[`benchmarks/`](benchmarks/) and each benchmark under it, [`docs/`](docs/),
-[`examples/`](examples/), [`envs/`](envs/) and [`paper/`](paper/). Package
+why — [`bindsight/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight), [`tests/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/tests), [`scripts/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/scripts),
+[`benchmarks/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks) and each benchmark under it, [`docs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/docs),
+[`examples/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/examples), [`envs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/envs) and [`paper/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/paper). Package
 subdirectories are documented in the table below rather than individually.
 
 | Path | What it holds |
 |---|---|
-| [`bindsight/`](bindsight/) | The Python package — [`io`](bindsight/io/), [`deg`](bindsight/deg/), [`targets`](bindsight/targets/), [`surfaceome`](bindsight/surfaceome/), [`structures`](bindsight/structures/), [`epitopes`](bindsight/epitopes/), [`design`](bindsight/design/), [`runners`](bindsight/runners/), [`validate`](bindsight/validate/), [`rank`](bindsight/rank/), [`benchmark`](bindsight/benchmark/), [`pipelines`](bindsight/pipelines/), [`provenance`](bindsight/provenance/), [`export`](bindsight/export/), [`report`](bindsight/report/) |
-| [`benchmarks/`](benchmarks/) | All the evidence — the [study](benchmarks/study/), the [calibration control](benchmarks/calibration/), the [designer benchmark](benchmarks/designer_benchmark/), the [provenance join](benchmarks/provenance_join/), and the held-out antigen set |
-| [`tests/`](tests/) | 2,000+ tests. Many are guards on published claims, not on code |
-| [`paper/`](paper/) | JOSS and bioRxiv manuscripts, and the validation write-up |
-| [`docs/`](docs/) | Long-form documentation (mkdocs-material source) |
-| [`examples/`](examples/) | Runnable pipeline configs |
-| [`envs/`](envs/) | Conda environment for the discovery half, with pinned constraints |
-| [`scripts/`](scripts/) | Generators for vendored data and published pages |
-| [`.github/workflows/`](.github/workflows/) | CI, docs, docker, release artifacts, and the two paper PDFs |
+| [`bindsight/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight) | The Python package — [`io`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/io), [`deg`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/deg), [`targets`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/targets), [`surfaceome`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/surfaceome), [`structures`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/structures), [`epitopes`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/epitopes), [`design`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/design), [`runners`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/runners), [`validate`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/validate), [`rank`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/rank), [`benchmark`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/benchmark), [`pipelines`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/pipelines), [`provenance`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/provenance), [`export`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/export), [`report`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/bindsight/report) |
+| [`benchmarks/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks) | All the evidence — the [study](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/study), the [calibration control](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/calibration), the [designer benchmark](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/designer_benchmark), the [provenance join](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/benchmarks/provenance_join), and the held-out antigen set |
+| [`tests/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/tests) | 2,000+ tests. Many are guards on published claims, not on code |
+| [`paper/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/paper) | JOSS and bioRxiv manuscripts, and the validation write-up |
+| [`docs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/docs) | Long-form documentation (mkdocs-material source) |
+| [`examples/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/examples) | Runnable pipeline configs |
+| [`envs/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/envs) | Conda environment for the discovery half, with pinned constraints |
+| [`scripts/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/scripts) | Generators for vendored data and published pages |
+| [`.github/workflows/`](https://github.com/mikhaeelatefrizk/bindsight/tree/v0.3.6/.github/workflows) | CI, docs, docker, release artifacts, and the two paper PDFs |
 
 | File | What it is |
 |---|---|
-| [ARCHITECTURE.md](ARCHITECTURE.md) | The architectural source of truth |
-| [CHANGELOG.md](CHANGELOG.md) | Per-version changes |
-| [CONTRIBUTING.md](CONTRIBUTING.md) | Dev setup, testing, commit conventions |
-| [LICENSING.md](LICENSING.md) | Per-dependency licence inventory and commercial-use guidance |
-| [SECURITY.md](SECURITY.md) | How to report a vulnerability |
-| [CITATION.cff](CITATION.cff) | Citation metadata |
-| [Snakefile](Snakefile) | The Snakemake DAG front-end |
+| [ARCHITECTURE.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/ARCHITECTURE.md) | The architectural source of truth |
+| [CHANGELOG.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CHANGELOG.md) | Per-version changes |
+| [CONTRIBUTING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CONTRIBUTING.md) | Dev setup, testing, commit conventions |
+| [LICENSING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSING.md) | Per-dependency licence inventory and commercial-use guidance |
+| [SECURITY.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/SECURITY.md) | How to report a vulnerability |
+| [CITATION.cff](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CITATION.cff) | Citation metadata |
+| [Snakefile](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/Snakefile) | The Snakemake DAG front-end |
 
 ---
 
@@ -353,14 +353,14 @@ subdirectories are documented in the table below rather than individually.
 | Citability | Code dump | Tagged releases with SHA-256 checksums, JSON-Schema-validated outputs |
 
 For the full landscape comparison, see
-[ARCHITECTURE.md § 8](ARCHITECTURE.md#8-comparison-vs-existing-tools).
+[ARCHITECTURE.md § 8](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/ARCHITECTURE.md#8-comparison-vs-existing-tools).
 
 ---
 
 ## Acknowledgments
 
 bindsight is an opinionated wrapper. Real intellectual credit belongs to the upstream
-tool authors. See [LICENSING.md](LICENSING.md) for the full inventory; the work this
+tool authors. See [LICENSING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSING.md) for the full inventory; the work this
 builds on most directly:
 
 - [SURFACE-Bind](https://github.com/hamedkhakzad/SURFACE-Bind) (Balbi et al., PNAS 2026) — the targetable-sites catalog that makes the bridge tractable
@@ -380,7 +380,7 @@ and the checksums attached to the release, plus the author:
 > novo protein binder design* (version X.Y.Z).
 > <https://github.com/mikhaeelatefrizk/bindsight>
 
-Citation metadata also lives in [CITATION.cff](CITATION.cff); GitHub's "Cite this
+Citation metadata also lives in [CITATION.cff](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/CITATION.cff); GitHub's "Cite this
 repository" button generates BibTeX and APA from it. Every release attaches a
 wheel, an sdist and a `SHA256SUMS` file, and every image is digest-pinned, so
 the artifacts behind a version are checkable even though the version has no
@@ -399,9 +399,9 @@ independent researcher in Cairo, Egypt.
 
 ## License
 
-- **Code:** [GNU AGPL-3.0-or-later](LICENSE) — copyright notice in [COPYRIGHT](COPYRIGHT). You may use, study, modify, and
+- **Code:** [GNU AGPL-3.0-or-later](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSE) — copyright notice in [COPYRIGHT](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/COPYRIGHT). You may use, study, modify, and
   redistribute bindsight freely; if you distribute a modified version **or run it as
   a network service**, you must make your source available under the same licence,
-  with attribution preserved. See [LICENSING.md](LICENSING.md) for component-level
+  with attribution preserved. See [LICENSING.md](https://github.com/mikhaeelatefrizk/bindsight/blob/v0.3.6/LICENSING.md) for component-level
   details — bindsight orchestrates external tools that keep their own licences, and
   some carry non-commercial terms.

{bindsight-0.3.5 → bindsight-0.3.6}/bindsight/report/web/templates/try.html.j2

@@ -9,7 +9,7 @@
 </p>
 
 <div class="card">
-  <h2 class="card__title">What this runs</h3>
+  <h2 class="card__title">What this runs</h2>
   <div class="grid grid--2">
     {#- `.fact`, not `.stat`. A `.stat` is a measurement and must carry its
         denominator or interval; these are descriptions, and borrowing the

{bindsight-0.3.5 → bindsight-0.3.6}/bindsight/report/web/templates/your_data.html.j2

@@ -10,7 +10,7 @@
 </p>
 
 <div class="card">
-  <h2 class="card__title">Files</h3>
+  <h2 class="card__title">Files</h2>
   <div class="field">
     <label for="counts">Counts matrix <span class="muted">(.tsv, .txt, .gz)</span></label>
     <input type="file" id="counts" accept=".tsv,.txt,.gz">

{bindsight-0.3.5 → bindsight-0.3.6}/bindsight/runners/local_docker.py

@@ -48,7 +48,13 @@ class LocalDockerRunner:
         designer: str = "rfdiff_mpnn",
         n_units_per_target: int = 50,
         gpu_type: str = "A100-40GB",
-        image: str = "ghcr.io/mikhaeelatefrizk/bindsight:dev",
+        # `:latest` because it is the only tag `docker.yml` always publishes:
+        # the others are the commit SHA and, on a tag push, the release. There
+        # has never been a `:dev`. A moving tag is safe here in a way it is not
+        # for a CI action -- the image carries its own bindsight and runs it, and
+        # `pipelines.full_run._container_ref` records the resolved *digest* in the
+        # manifest, never the tag, for exactly this reason.
+        image: str = "ghcr.io/mikhaeelatefrizk/bindsight:latest",
         native: bool | None = None,
     ) -> None:
         self.designer = designer