Merge branch 'main' into add-estimate-dual-cone-spherical-volume

Author: ValerianRey

.github/dependabot.yml

@@ -0,0 +1,19 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: ""
+    labels:
+      - "cc: chore"
+
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: ""
+    labels:
+      - "cc: chore"

.github/workflows/build-deploy-docs.yml

@@ -6,6 +6,10 @@ on:
     tags:
       - 'v[0-9]*.[0-9]*.[0-9]*'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
 env:
   UV_NO_SYNC: 1
 

.github/workflows/checks.yml

@@ -6,6 +6,10 @@ on:
   schedule:
     - cron: '41 16 * * *'  # Every day at 16:41 UTC (to avoid high load at exact hour values).
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   UV_NO_SYNC: 1
 
@@ -56,7 +60,7 @@ jobs:
           PYTEST_TORCH_DTYPE: ${{ matrix.dtype || 'float32' }}
 
       - name: Upload results to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -85,7 +89,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       # This will restore the cache for the current commit if it exists, or the most recent lychee
       # cache otherwise (including those saved for the main branch). It will also save the cache for
@@ -94,7 +98,7 @@ jobs:
       # temporary (rate limiting, network issue, etc.), and we always want to retry those links
       # everytime this action is run.
       - name: Restore lychee cache
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
@@ -110,7 +114,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   code-quality:
-    name: Code quality (ty and ruff)
+    name: Code quality (ty and pre-commit hooks)
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
@@ -125,8 +129,8 @@ jobs:
         with:
           groups: check test plot
 
+      - name: Run pre-commit hooks
+        run: uv run pre-commit run --all-files
+
       - name: Run ty
         run: uv run ty check --output-format=github
-
-      - name: Run ruff
-        run: uv run ruff check --output-format=github

.github/workflows/opencode.yml

@@ -0,0 +1,68 @@
+name: opencode
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  opencode:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '/opencode:')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '/opencode:')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '/opencode:')) ||
+      (github.event_name == 'issues' && contains(github.event.issue.body, '/opencode:'))
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: write
+      pull-requests: write
+      issues: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
+          persist-credentials: false
+
+      - name: Extract agent name
+        id: agent
+        env:
+          COMMENT_BODY: ${{ github.event.comment.body || github.event.review.body || github.event.issue.body }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          AGENT=$(echo "$COMMENT_BODY" | grep -oP '/opencode:\K[A-Za-z]+' | head -1)
+          if [[ ! "$AGENT" =~ ^(Build|Plan)$ ]]; then
+            ERROR_MSG="Error: Invalid agent '$AGENT'. Must be Build or Plan"
+            echo "$ERROR_MSG"
+
+            # Post comment with error
+            if [ "${{ github.event_name }}" = "issues" ]; then
+              NUMBER=${{ github.event.issue.number }}
+            else
+              NUMBER=${{ github.event.issue.number || github.event.pull_request.number }}
+            fi
+
+            curl -s -X POST \
+              -H "Authorization: token $GITHUB_TOKEN" \
+              -H "Accept: application/vnd.github.v3+json" \
+              "https://api.github.com/repos/${{ github.repository }}/issues/$NUMBER/comments" \
+              -d "{\"body\": \"❌ $ERROR_MSG\"}"
+
+            exit 1
+          fi
+          echo "agent=$AGENT" >> $GITHUB_OUTPUT
+
+      - name: Run opencode
+        uses: anomalyco/opencode/github@latest
+        env:
+          OPENCODE_API_KEY: ${{ secrets.OPENCODE_API_KEY }}
+          OPENCODE_PERMISSION: '{"bash": "deny"}'
+        with:
+          model: opencode-go/kimi-k2.5
+          agent: ${{ steps.agent.outputs.agent }}

.github/workflows/title-formatter.yml

@@ -0,0 +1,75 @@
+name: PR Title Formatter
+
+on:
+  pull_request_target:
+    types: [opened, edited, reopened, labeled, unlabeled, synchronize]
+
+jobs:
+  format-title:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Format PR Title from Labels
+        uses: actions/github-script@v8
+        with:
+          script: |
+            const { owner, repo } = context.repo;
+            const pr_number = context.payload.pull_request.number;
+            const rawTitle = context.payload.pull_request.title;
+
+            const ccRegex = /^[a-z-]+(?:\([^)]+\))?!?: (.+)$/;
+            const ccMatch = rawTitle.match(ccRegex);
+            let description = ccMatch ? ccMatch[1] : rawTitle;
+
+            description = description.charAt(0).toUpperCase() + description.slice(1);
+
+            const prLabels = await github.rest.issues.listLabelsOnIssue({
+              owner,
+              repo,
+              issue_number: pr_number,
+              per_page: 100,
+            });
+            const labelNames = prLabels.data.map(l => l.name);
+
+            const ccLabels = labelNames.filter(n => n.startsWith('cc: '));
+            if (ccLabels.length === 0) {
+              core.setFailed('No "cc: <type>" label found on this PR. Please add exactly one.');
+              return;
+            }
+            if (ccLabels.length > 1) {
+              core.setFailed(`Multiple "cc: <type>" labels found: ${ccLabels.join(', ')}. Please keep exactly one.`);
+              return;
+            }
+            const type = ccLabels[0].slice(4);
+
+            const packageLabels = labelNames.filter(n => n.startsWith('package: '));
+            const scope = packageLabels.length === 1 ? packageLabels[0].slice(9) : null;
+
+            const isBreaking = labelNames.includes('breaking-change');
+
+            let newTitle = type;
+            if (scope) newTitle += `(${scope})`;
+            if (isBreaking) newTitle += '!';
+            newTitle += `: ${description}`;
+
+            if (rawTitle === newTitle) {
+              console.log("Title is already correctly formatted. Skipping update.");
+              return;
+            }
+
+            const displayTitle = `${newTitle} (#${pr_number})`;
+            if (displayTitle.length > 72) {
+              core.setFailed(
+                `Formatted title is too long by ${displayTitle.length - 72} characters: "${displayTitle}"`
+              );
+              return;
+            }
+
+            await github.rest.pulls.update({
+              owner,
+              repo,
+              pull_number: pr_number,
+              title: newTitle,
+            });
+            console.log(`PR title updated to: "${newTitle}"`);

.gitignore

@@ -1,3 +1,6 @@
+# Claude (see https://github.com/anthropics/claude-code/issues/6235)
+CLAUDE.md
+
 # Profiling results
 traces/
 

.pre-commit-config.yaml

@@ -10,12 +10,8 @@ repos:
     -   id: check-merge-conflict  # Check for files that contain merge conflict strings.
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.1
+    rev: v0.15.5
     hooks:
       - id: ruff-check
         args: [ --fix, --ignore, FIX ]  # Allow committing with TODOs. Only CI checks should prevent merging with TODOs.
       - id: ruff-format
-
-ci:
-    autoupdate_commit_msg: 'chore: Update pre-commit hooks'
-    autoupdate_schedule: quarterly

CHANGELOG.md

@@ -8,11 +8,21 @@ changelog does not include internal changes that do not affect the user.
 
 ## [Unreleased]
 
+## [0.9.0] - 2026-02-24
+
 ### Added
 
 - Added the function `torchjd.autojac.jac`. It's the same as `torchjd.autojac.backward` except that
   it returns the Jacobians as a tuple instead of storing them in the `.jac` fields of the inputs.
   Its interface is analog to that of `torch.autograd.grad`.
+- Added a `jac_tensors` parameter to `backward`, allowing to pre-multiply the Jacobian computation
+  by initial Jacobians. This enables multi-step chain rule computations and is analogous to the
+  `grad_tensors` parameter in `torch.autograd.backward`.
+- Added a `grad_tensors` parameter to `mtl_backward`, allowing to use non-scalar `losses` (now
+  renamed to `tensors`). This is analogous to the `grad_tensors` parameter of
+  `torch.autograd.backward`. When using `scalar` losses, the usage does not change.
+- Added a `jac_outputs` parameter to `jac`, allowing to pre-multiply the Jacobian computation by
+  initial Jacobians. This is analogous to the `grad_outputs` parameter in `torch.autograd.grad`.
 - Added a `scale_mode` parameter to `AlignedMTL` and `AlignedMTLWeighting`, allowing to choose
   between `"min"`, `"median"`, and `"rmse"` scaling.
 - Added an attribute `gramian_weighting` to all aggregators that use a gramian-based `Weighting`.
@@ -45,11 +55,23 @@ changelog does not include internal changes that do not affect the user.
   mtl_backward(losses, features)
   jac_to_grad(shared_module.parameters(), aggregator)
   ```
-
-- Removed an unnecessary memory duplication. This should significantly improve the memory efficiency
-  of `autojac`.
-- Removed an unnecessary internal cloning of gradient. This should slightly improve the memory
-  efficiency of `autojac`.
+- **BREAKING**: Made some parameters of the public interface of `torchjd` positional-only or
+  keyword-only:
+  - `backward`: The `tensors` parameter is now positional-only. Suggested change:
+    `backward(tensors=losses)` => `backward(losses)`. All other parameters are now keyword-only.
+  - `mtl_backward`: The `tensors` parameter (previously named `losses`) is now positional-only.
+    Suggested change: `mtl_backward(losses=losses, features=features)` =>
+    `mtl_backward(losses, features=features)`. The `features` parameter remains usable as positional
+    or keyword. All other parameters are now keyword-only.
+  - `Aggregator.__call__`: The `matrix` parameter is now positonal-only. Suggested change:
+    `aggregator(matrix=matrix)` => `aggregator(matrix)`.
+  - `Weighting.__call__`: The `stat` parameter is now positional-only. Suggested change:
+    `weighting(stat=gramian)` => `weighting(gramian)`.
+  - `GeneralizedWeighting.__call__`: The `generalized_gramian` parameter is now positional-only.
+    Suggested change: `generalized_weighting(generalized_gramian=generalized_gramian)` =>
+    `generalized_weighting(generalized_gramian)`.
+- Removed several unnecessary memory duplications. This should significantly improve the memory
+  efficiency and speed of `autojac`.
 - Increased the lower bounds of the torch (from 2.0.0 to 2.3.0) and numpy (from 1.21.0
   to 1.21.2) dependencies to reflect what really works with torchjd. We now also run torchjd's tests
   with the dependency lower-bounds specified in `pyproject.toml`, so we should now always accurately