Serve the 2026-09 release from Cameo and execute all docs notebooks against it

.github/workflows/docs.yaml

@@ -33,14 +33,17 @@ jobs:
           cache-downloads: true
           cache-environment: true
           post-cleanup: all
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        shell: bash -el {0}
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact --extra docs
       - name: Build docs
         shell: bash -el {0}
         id: build
-        run: |
-          which python
-          python -m pip install six
-          python -m pip install '.[docs,loader]'
-          sphinx-build docs build/docs
+        run: sphinx-build docs build/docs
       - name: Upload build artifact
         uses: actions/upload-pages-artifact@v3
         with:

.github/workflows/main.yaml

@@ -2,7 +2,6 @@ name: Package
 permissions:
   contents: write
   id-token: write
-  packages: write
 on:
   push:
     branches:
@@ -14,51 +13,48 @@ jobs:
     name: Package
     if: ${{ ! contains(toJSON(github.event.commits.*.message), '[skip ci]') }}
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Setup python
-        uses: actions/setup-python@v5
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: "3.12"
-      - name: Configure docker
-        run: echo ${{ secrets.GITHUB_TOKEN }} | docker login ghcr.io -u ${{ github.repository_owner }} --password-stdin
-      - name: Install build and tag requirements
-        run: python -m pip install build semver
+          environment-file: environment.yml
+          create-args: python=3.12
+          init-shell: bash
+          cache-downloads: true
+          cache-environment: true
+          post-cleanup: all
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
       - name: Get version bump
         id: get-tag
-        run: echo "bump=$(python flows/docker.py bump)" >> $GITHUB_OUTPUT
-      - name: Pull, build, tag, bump base image
-        if: steps.get-tag.outputs.bump != ''
-        run: python flows/docker.py pull --build --promote
-      - name: Build image
+        run: echo "bump=$(python version.py)" >> $GITHUB_OUTPUT
+      - name: Run tests
         if: steps.get-tag.outputs.bump != ''
-        run: python flows/docker.py build
-      - name: Run tests against new image and save images
+        env:
+          PLINDER_OFFLINE: "true"
+        run: python -m pytest -n auto -v
+      - name: Tag release
         if: steps.get-tag.outputs.bump != ''
-        run: |
-          python flows/docker.py test --push
-          if ! test -f reports/.coverage; then
-            echo "Missing test coverage reports (reports/.coverage). Not all tests have passed?"
-            exit 1
-          else
-            echo "Test coverage report found!"
-          fi
+        run: git tag ${{ steps.get-tag.outputs.bump }}
       - name: Build distribution
-        run: python -m build
+        run: uv build
       - name: Publish package distributions to PyPI
         if: steps.get-tag.outputs.bump != ''
         uses: pypa/gh-action-pypi-publish@release/v1
       - name: Save git tag
         if: steps.get-tag.outputs.bump != ''
         run: git push origin ${{ steps.get-tag.outputs.bump }}
-      - name: Copy and surgery coverage
-        if: steps.get-tag.outputs.bump != ''
-        run: |
-          cp reports/.coverage .
-          sqlite3 .coverage "update file set path='src/' || substr(path, 40);"
       - name: Post coverage comment
         if: steps.get-tag.outputs.bump != ''
         uses: py-cov-action/python-coverage-comment-action@v3

.github/workflows/pr.yaml

@@ -3,7 +3,6 @@ name: CI Workflow
 permissions:
   contents: write
   id-token: write
-  packages: read
   pull-requests: write
 
 concurrency:
@@ -37,53 +36,37 @@ jobs:
             tox-${{ runner.os }}-3.12-
 
   test:
-    name: Build and test docker image
+    name: Test
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
           fetch-depth: 0
-      - name: Configure docker
-        run: echo ${{ secrets.GITHUB_TOKEN }} | docker login ghcr.io -u ${{ github.repository_owner }} --password-stdin
-      - name: Get changed source files
-        id: changed-src
-        uses: tj-actions/changed-files@v41
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          files: src/**
-      - name: Get changed base image files
-        if: steps.changed-src.outputs.any_changed == 'true'
-        id: changed-base
-        uses: tj-actions/changed-files@v41
+          environment-file: environment.yml
+          create-args: python=3.12
+          init-shell: bash
+          cache-downloads: true
+          cache-environment: true
+          post-cleanup: all
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
         with:
-          files: dockerfiles/base/*
-      - name: Pull base image and build
-        if: steps.changed-src.outputs.any_changed == 'true' && steps.changed-base.outputs.any_changed == 'true'
-        run: python flows/docker.py pull --build
-      - name: Pull base image
-        if: steps.changed-src.outputs.any_changed == 'true' && steps.changed-base.outputs.any_changed != 'true'
-        run: python flows/docker.py pull
-      - name: Build image
-        if: steps.changed-base.outputs.any_changed == 'true' || steps.changed-src.outputs.any_changed == 'true'
-        run: python flows/docker.py build
-      - name: Run test image
-        if: steps.changed-base.outputs.any_changed == 'true' || steps.changed-src.outputs.any_changed == 'true'
-        run: |
-          python flows/docker.py test
-          if ! test -f reports/.coverage; then
-            echo "Missing test coverage reports (reports/.coverage). Not all tests have passed?"
-            exit 1
-          else
-            echo "Test coverage report found!"
-          fi
-      - name: Copy and surgery coverage
-        if: steps.changed-base.outputs.any_changed == 'true' || steps.changed-src.outputs.any_changed == 'true'
-        run: |
-          cp reports/.coverage .
-          sqlite3 .coverage "update file set path='src/' || substr(path, 40);"
+          enable-cache: true
+      - name: Install plinder
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact
+      - name: Run tests
+        env:
+          PLINDER_OFFLINE: "true"
+        run: python -m pytest -n auto -v
       - name: Post coverage comment
-        if: steps.changed-src.outputs.any_changed == 'true'
         uses: py-cov-action/python-coverage-comment-action@v3
         with:
           GITHUB_TOKEN: ${{ github.token }}
@@ -106,7 +89,14 @@ jobs:
           cache-downloads: true
           cache-environment: true
           post-cleanup: all
-      - name: Install Python requirements
-        run: pip install six ".[docs,loader]"
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: Install plinder
+        run: UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact --extra docs
       - name: Build the documentation
         run: sphinx-build --fail-on-warning docs build/docs
+      - name: Show notebook errors
+        if: failure()
+        run: cat build/docs/reports/examples/*.err.log 2>/dev/null || true

.gitignore

@@ -195,3 +195,6 @@ tmp_foldseek
 tmp_mmseqs
 artifacts
 logs/
+
+# uv lockfile: not committed; CI resolves the latest versions allowed by pyproject.toml
+uv.lock

.python-version

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

README.md

@@ -43,10 +43,9 @@ More details about the competition and other helpful practical tips can be found
 
 ## 🔢 Plinder versions
 
-We version the `plinder` dataset with two controls:
-
-- `PLINDER_RELEASE`: the month stamp of the last RCSB sync
-- `PLINDER_RELEASE_NUMBER`: numbered release within that ingest month
+We version the `plinder` dataset by the month stamp (`YYYY-MM`) of the RCSB
+sync it was built from, set with `PLINDER_RELEASE`. The current release,
+`2026-09`, is the default.
 
 We version the `plinder` application using an automated semantic
 versioning scheme based on the `git` commit history.
@@ -57,7 +56,7 @@ with the dataset.
 #### Changelog:
 
 - WIP (Current — unreleased):
-    - **Public downloads on Cloudflare R2**: `2024-06/v2` now downloads from `https://plinderdata.org` instead of GCS; `PLINDER_MIRROR_URL` selects another HTTP mirror. Downloads stream to disk and verify size and MD5 before atomic replacement, interrupted transfers retry from the start, and cached files with the expected size are reused (force a refresh to repair same-size local corruption). Google storage dependencies are now optional: install `plinder[data]` for the GCS data-generation utilities.
+    - **Public downloads from Cameo**: releases download directly from `https://cameo3d.org/plinder/PLINDER-<YYYY-MM>/` (currently `2026-09`); `PLINDER_MIRROR_URL` selects another HTTP file server with the same directory layout. Downloads stream to disk, validate HTTP Content-Length, and replace cached files atomically. Interrupted transfers retry from the start. Cached files are reused when their size and Last-Modified time match the server, so data hotfixes are fetched on the next access. Google storage dependencies are optional: install `plinder[data]` for the GCS data-generation utilities.
     - **Major backend refactor**: replaced OST, gemmi, plip, openbabel with biotite + peppr for data generation; removed 6 dependencies from ingest pipeline
     - **Nucleic acid support**: DNA/RNA chains now correctly included as receptor neighbors, mainchain/sidechain detection works for both protein and nucleic acids ([#61](https://github.com/plinder-org/plinder/issues/61))
     - **Custom CIF support**: new `Entry.from_custom_cif_file` for structure-prediction outputs (Boltz, AlphaFold3, Chai-1) that ship CIFs without `_chem_comp_bond` ([#117](https://github.com/plinder-org/plinder/issues/117)). Bond orders come from `ligand_smiles_dict` via positional atom-order match (the convention these tools follow); element/count mismatches raise with the offending position, `force_substructure_match=True` opts into substructure matching when atom order isn't preserved. User SMILES win over CCD for both `smiles` and `resolved_stereo_matches_template` — closes a silent gap where biotite's `LIG` placeholder would pass any 3D conformer. Input CIFs are never mutated; optional `save_fixed_cif` persists the enriched copy.
@@ -108,7 +107,7 @@ Moreover, as we enticipate this resource to be used for benchmarking a wide rang
 The *PLINDER* dataset is provided in two ways:
 
 - You can either use the files from the dataset directly using your preferred tooling
-  by downloading the data from `https://plinderdata.org` (Cloudflare R2),
+  by downloading the data from the [Cameo file server](https://cameo3d.org/plinder/PLINDER-2026-09/),
 - or you can utilize the dedicated `plinder` Python package for interfacing the data.
 
 
@@ -118,14 +117,15 @@ After installing the package, download the index tables and cluster assignments
 for a release with:
 
 ```console
-$ plinder_download --release 2024-06 --release-number v2
+$ plinder_download --release 2026-09
 ```
 
 The command offers the larger ligand, alignment, score, export, and search
 database groups separately, and dataset APIs also download required files
-lazily. No Google Cloud credentials or SDK are needed: `2024-06/v2` downloads
-from `https://plinderdata.org`; `PLINDER_MIRROR_URL` can select another HTTP
-mirror. Other release versions are unavailable through the public downloader.
+lazily. No Google Cloud credentials or SDK are needed: releases download
+from `https://cameo3d.org/plinder/PLINDER-2026-09/`; `PLINDER_MIRROR_URL`
+can select another HTTP file-server root containing `PLINDER-<YYYY-MM>/`
+directories. The legacy `2024-06/v2` layout requires an earlier `plinder` version.
 For details on the release paths, see [Documentation](https://plinder-org.github.io/plinder/tutorial/dataset.html).
 
 ## Installing the Python package