Merge pull request #47 from VirtualFlyBrain/testing-changes

Changes to cache usage on PRs and versioning mechanism

Author: Clare72

.github/workflows/docker.yml

@@ -25,22 +25,22 @@ jobs:
         echo "tag=$TAG" >> $GITHUB_OUTPUT
 
     # Mirror what publish_to_pypi.yaml does so the docker image and the
-    # PyPI wheel never disagree about their own version.
-    - name: Sync setup.py / __init__.py version to tag
+    # PyPI wheel never disagree about their own version. The version lives in a
+    # single source file (src/vfbquery/_version.py); setup.py reads it at build
+    # time and __init__.py imports it, so only _version.py is bumped here.
+    - name: Sync version to tag
       id: version
       run: |
         if [[ "$GITHUB_REF" == refs/tags/v* ]]; then
           VERSION=${GITHUB_REF#refs/tags/v}
           echo "Tag build detected: syncing __version__ to $VERSION"
-          sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" setup.py
-          sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" src/vfbquery/__init__.py
+          sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" src/vfbquery/_version.py
         else
-          VERSION=$(grep '^__version__' setup.py | sed 's/.*"\(.*\)".*/\1/')
+          VERSION=$(grep '^__version__' src/vfbquery/_version.py | sed 's/.*"\(.*\)".*/\1/')
           echo "Branch / dev build: using committed version $VERSION"
         fi
         echo "version=$VERSION" >> $GITHUB_OUTPUT
-        echo "  setup.py:    $(grep ^__version__ setup.py)"
-        echo "  __init__.py: $(grep ^__version__ src/vfbquery/__init__.py)"
+        echo "  _version.py: $(grep ^__version__ src/vfbquery/_version.py)"
 
     - name: Build test Docker image
       run: docker build --no-cache . --file Dockerfile --tag test-image

.github/workflows/performance-test.yml

@@ -60,6 +60,12 @@ jobs:
         # IMPORTANT: the retry OVERWRITES performance_test_output.log so the
         # downstream "Fail job on test failures" step grades on the second
         # attempt's output only.
+        env:
+          # Read-only on PRs so a PR check never writes/purges the shared prod
+          # cache; writable on push-to-main and scheduled runs so those refresh
+          # and warm it (e.g. after a minor/major release). See
+          # solr_caching_readonly().
+          VFBQUERY_CACHE_READONLY: ${{ github.event_name == 'pull_request' && 'true' || 'false' }}
         run: |
           set +e
           echo "=== Performance test attempt 1/2 (parallel) ==="
@@ -80,6 +86,9 @@ jobs:
         if: always()
         env:
           VFBQUERY_CACHE_ENABLED: 'true'
+          # Read-only on PRs (never write/purge the shared prod cache); writable
+          # on push-to-main and scheduled runs so those refresh/warm it.
+          VFBQUERY_CACHE_READONLY: ${{ github.event_name == 'pull_request' && 'true' || 'false' }}
           MPLBACKEND: 'Agg'
           VISPY_GL_LIB: 'osmesa'
           VISPY_USE_EGL: '0'
@@ -107,7 +116,11 @@ jobs:
       - name: Run Connectivity Tests
         if: always()
         env:
-          VFBQUERY_CACHE_ENABLED: 'true'
+          # Disable the result cache so the connectivity integration tests
+          # validate the LIVE query against the database, rather than reading
+          # (possibly stale) entries from the shared production cache or writing
+          # this run's results back into it. See solr_caching_disabled().
+          VFBQUERY_CACHE_ENABLED: 'false'
           MPLBACKEND: 'Agg'
           VISPY_GL_LIB: 'osmesa'
           VISPY_USE_EGL: '0'

.github/workflows/publish_to_pypi.yaml

@@ -10,6 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      contents: write  # allows the post-publish step to commit the version bump back to main
     steps:
     - uses: actions/checkout@v4
       with:
@@ -43,22 +44,18 @@ jobs:
           # Set environment variables for the build
           echo "VERSION=$VERSION" >> $GITHUB_ENV
           
-          # Update version in setup.py
-          echo "Updating version in setup.py to $VERSION"
-          sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" setup.py
-          
-          # Update version in package __init__.py
-          echo "Updating version in src/vfbquery/__init__.py to $VERSION"
-          sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" src/vfbquery/__init__.py
-          
-          echo "Updated setup.py version:"
-          grep "__version__" setup.py
-          echo "Updated package version:"
-          grep "__version__" src/vfbquery/__init__.py
+          # Single source of truth: bump only _version.py. setup.py reads it at
+          # build time and vfbquery.__init__ imports it at runtime, so the wheel
+          # metadata, vfbquery.__version__ and the cache version stamp all follow.
+          echo "Updating version in src/vfbquery/_version.py to $VERSION"
+          sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" src/vfbquery/_version.py
+
+          echo "Updated version:"
+          grep "__version__" src/vfbquery/_version.py
         else
           # Not running from a tag, show current version
-          echo "Not running from a tag, using existing version from setup.py"
-          grep "__version__" setup.py
+          echo "Not running from a tag, using existing version from _version.py"
+          grep "__version__" src/vfbquery/_version.py
         fi
     
     - name: Build distributions
@@ -110,6 +107,33 @@ jobs:
     
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@v1.12.2
+
+    - name: Commit version bump back to main
+      # Runs only after a successful publish from a release tag. The build above
+      # runs from a detached tag checkout, so here we switch to the live main
+      # branch, re-apply the released version to the single source file
+      # (_version.py) and push. [skip ci] keeps this housekeeping commit from
+      # retriggering the test/perf workflows.
+      if: success() && startsWith(github.ref, 'refs/tags/v')
+      run: |
+        set -e
+        if [[ -z "$VERSION" ]]; then
+          echo "VERSION not set; nothing to commit."
+          exit 0
+        fi
+        git config user.email "action@github.com"
+        git config user.name "GitHub Action"
+        git fetch origin main
+        git reset --hard origin/main
+        sed -i "s/__version__ = \"[^\"]*\"/__version__ = \"$VERSION\"/" src/vfbquery/_version.py
+        git add src/vfbquery/_version.py
+        if git diff --staged --quiet; then
+          echo "main already at version $VERSION; nothing to commit."
+        else
+          git commit -m "Bump version to $VERSION [skip ci]"
+          git push origin HEAD:main
+        fi
+
 #    - name: Publish package to TestPyPI
 #      uses: pypa/gh-action-pypi-publish@release/v1
 #      with:

CACHING.md

@@ -111,6 +111,35 @@ Note: data reads in `vfb_queries.py` (term_info, painted domains, ontology
 label lookups, etc.) still go to `solr.virtualflybrain.org` — only the result
 *cache* moved. The two are independent.
 
+## Cache versioning and invalidation
+
+Every cache entry is stamped with the VFBquery package version (major.minor) that
+wrote it, so results from an old code version aren't served after an upgrade.
+
+The **running** version is resolved (in `solr_result_cache.py`) as:
+
+1. the `VFBQUERY_VERSION` environment variable if set, otherwise
+2. the installed package version (`importlib.metadata.version('vfbquery')`),
+
+normalized to **major.minor**. That value comes from the single source of truth,
+`src/vfbquery/_version.py` (see [RELEASING.md](RELEASING.md)).
+
+On read, if an entry's stamp differs from the running version, invalidation is
+**monotonic** — it only discards entries written by an *older* version:
+
+- **Older (or unversioned) entry** → invalidated, deleted, and recomputed by the
+  current code.
+- **Newer entry** (seen by a stale/older install, or by an older deploy running
+  alongside a newer one) → treated as a miss but **not deleted**. An older client
+  must never purge a fresher entry; the previous `!=` check did, which let
+  downgrades wipe live entries and made concurrent versions thrash each other.
+
+Consequences for the major.minor namespace:
+
+- **Patch bumps** (`1.20.0 → 1.20.3`) share the cache — no invalidation.
+- **Minor/major bumps** (`1.20 → 1.21`) invalidate older entries on read, so a
+  release that changes query output naturally refreshes the cache.
+
 ## Runtime Configuration
 
 Control caching behavior:
@@ -133,6 +162,54 @@ Disable caching globally if needed:
 export VFBQUERY_CACHE_ENABLED=false
 ```
 
+When disabled, the cache layer is **fully bypassed** — every query runs live
+against Neo4j/Owlery/Solr with **no read, no write, no version-invalidation, and
+no contact with the cache server** (`solr_caching_disabled()` in
+`solr_result_cache.py`; mirrored in `vfb_connectivity.query_connectivity`).
+
+This is how the **integration tests** run in CI. The test steps that assert on
+query *results* (`test_neuron_neuron_connectivity`, `test_neuron_region_connectivity`,
+`test_vfb_connectivity`, the unit tests in `python-test.yml`, and `examples.yml`)
+set `VFBQUERY_CACHE_ENABLED=false` so they:
+
+- validate the **live** query for the branch under test, not a (possibly stale)
+  cached result, and
+- never write a PR/branch's output back into the **shared production cache**.
+
+The performance workflow's perf-timing steps keep caching enabled on purpose
+(they measure warm-cache latency); only the result-asserting steps disable it.
+
+#### Read-only mode
+
+```bash
+export VFBQUERY_CACHE_READONLY=true
+```
+
+Read-only mode still **reads** the cache (warm results are served), but
+suppresses every **mutation** — no writes, no force-refresh clears, and no
+version/expiry purges (`solr_caching_readonly()`, gating `cache_result`,
+`clear_cache_entry` and `_clear_expired_cache_document`).
+
+This is used by the **performance-test workflow's perf-timing steps**, but only
+on **pull requests** — `VFBQUERY_CACHE_READONLY` is set from
+`github.event_name == 'pull_request'`. So:
+
+- **On PRs** the perf steps read warm entries for representative timings but
+  never write or purge. Combined with `VFBQUERY_CACHE_ENABLED=false` on the
+  result-asserting steps, **no PR run can modify the production cache**.
+- **On push-to-`main` and scheduled runs** those perf steps are *writable*, so
+  they refresh/warm the cache under the current `main` version.
+
+That post-merge + daily-scheduled warming (plus lazy refresh by production
+traffic) is what keeps the cache populated for the version on `main`, including
+after a release bumps it. There's no dedicated release-triggered warm.
+
+Caveat: a PR that bumps the **minor/major** version reads cold in read-only mode
+(its version's entries don't exist yet — see version invalidation below);
+same-version PRs read the already-warm production entries. If you'd rather PR
+checks read *and* write a cache without touching production, point them at a
+separate collection with `VFBQUERY_SOLR_URL` instead.
+
 ## Performance Benefits
 
 VFBquery SOLR caching provides significant performance improvements:

README.md

@@ -28,6 +28,11 @@ result2 = vfb.get_term_info('FBbt_00003748')  # 54,000x faster!
 similar = vfb.get_similar_neurons('VFB_jrchk00s')  # Fast after first run
 ```
 
+📚 See [CACHING.md](CACHING.md) for cache configuration, the `VFBQUERY_CACHE_ENABLED`
+bypass (used by the tests), and version-based invalidation; and
+[RELEASING.md](RELEASING.md) for how the single-source version (`_version.py`) is
+bumped from the release tag.
+
 To get term info for a term:
 get_term_info(ID)
 

RELEASING.md

@@ -0,0 +1,76 @@
+# Releasing VFBquery
+
+## Version: single source of truth
+
+The package version lives in exactly one place:
+
+```
+src/vfbquery/_version.py   ->   __version__ = "X.Y.Z"
+```
+
+Everything else derives from it, so the fields can never drift apart:
+
+- **`setup.py`** reads `_version.py` at build time (via `exec`, without importing
+  the package), so the wheel/sdist metadata matches.
+- **`vfbquery/__init__.py`** does `from ._version import __version__`, so
+  `vfbquery.__version__` (and `ha_api.py`'s version reporting) matches.
+- **The SOLR result cache** stamps entries with this version (major.minor) and
+  uses it for invalidation — see [CACHING.md](CACHING.md#cache-versioning-and-invalidation).
+
+Do **not** hard-code the version anywhere else.
+
+## Cutting a release
+
+1. Create a **GitHub Release** with a tag of the form `vX.Y.Z` (e.g. `v1.21.0`).
+
+That's it — the `Publish 🐍 📦 to PyPI` workflow
+(`.github/workflows/publish_to_pypi.yaml`) does the rest:
+
+1. Checks out the tag, extracts `X.Y.Z` from `refs/tags/vX.Y.Z`, and writes it
+   into `_version.py` (`sed`).
+2. Builds the sdist/wheel (version comes from `_version.py`) and verifies the
+   metadata matches the tag.
+3. **Publishes to PyPI** via trusted publishing.
+4. **Commits the bump back to `main`** — switches from the detached tag checkout
+   to live `main`, re-applies `X.Y.Z` to `_version.py`, and pushes
+   `Bump version to X.Y.Z [skip ci]`.
+
+So after a release, **`main` reflects the released version** too — you don't have
+to bump it by hand.
+
+## Cache warming after a release
+
+A minor/major bump invalidates the previous version's cache entries
+(see [CACHING.md](CACHING.md#cache-versioning-and-invalidation)), so they're
+refilled with the new version's output. That happens two ways, with no dedicated
+release-triggered step:
+
+- **Lazily**, by the deployed production service as it serves traffic (the
+  primary path — each query refreshes on first read).
+- **By the `performance-test` workflow on `main`** — its perf steps are writable
+  on push-to-`main` and scheduled (daily) runs (read-only only on PRs), so they
+  recompute and re-cache the perf-test query set under the current `main`
+  version. The daily schedule guarantees the new version's entries are warmed
+  within a day of a release, so later PR runs read a warm cache.
+
+### Notes & guarantees
+
+- The commit-back step runs **only after a successful publish** and only for
+  `refs/tags/v*` (`if: success() && startsWith(github.ref, 'refs/tags/v')`).
+- It's a **no-op if `main` is already at that version** (guarded by
+  `git diff --staged --quiet`), so you can also bump `_version.py` in a PR before
+  tagging and the workflow won't create an empty commit.
+- The push needs `contents: write`, which is declared in the workflow's job
+  `permissions` alongside the `id-token: write` used for PyPI.
+- `[skip ci]` keeps the housekeeping commit from retriggering the test/perf
+  workflows.
+
+### Choosing the version bump
+
+Because the cache namespace is keyed on **major.minor**
+(see [CACHING.md](CACHING.md#cache-versioning-and-invalidation)):
+
+- Bump the **patch** for changes that don't alter query *output* — cached results
+  stay valid (no invalidation).
+- Bump **minor/major** when query output changes — older cache entries are then
+  invalidated on read, so users get refreshed results.

setup.py

@@ -3,7 +3,12 @@
 
 here = path.abspath(path.dirname(__file__))
 
-__version__ = "1.20.0"
+# Single source of truth: read __version__ from src/vfbquery/_version.py without
+# importing the package (which would pull in runtime dependencies at build time).
+_version_ns = {}
+with open(path.join(here, "src", "vfbquery", "_version.py")) as _vf:
+    exec(_vf.read(), _version_ns)
+__version__ = _version_ns["__version__"]
 
 # Get the long description from the README file
 with open(path.join(here, 'README.md')) as f:

src/vfbquery/__init__.py

@@ -98,5 +98,5 @@ def clear_solr_cache(query_type: str, term_id: str) -> bool:
 except ImportError:
     __solr_caching_available__ = False
 
-# Version information
-__version__ = "1.12.1"
+# Version information (single source of truth — see _version.py)
+from ._version import __version__

src/vfbquery/_version.py

@@ -0,0 +1,9 @@
+"""Single source of truth for the VFBquery package version.
+
+Both ``setup.py`` (read at build time) and ``vfbquery.__init__`` (imported at
+runtime) take ``__version__`` from here, and the release workflow bumps only
+this file, so the packaging metadata, ``vfbquery.__version__`` and the SOLR
+cache's version stamp can never drift apart.
+"""
+
+__version__ = "1.20.0"