Merge origin/main: accept deletion of archived publications.md

The file was archived on origin in commit 9ac20a1. Resolving
modify/delete conflict by accepting the deletion.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: dimitri-yatsenko

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = .git,*.pdf,*.svg
+skip = .git,*.pdf,*.svg,*.ipynb,llms-full.txt,*/data/*
 #
-ignore-words-list = shepard,nevers,nin
+ignore-words-list = shepard,nevers,nin,rever

.github/DISCUSSION_TEMPLATE/rfc.yml

@@ -0,0 +1,107 @@
+title: "[RFC] "
+labels:
+  - rfc
+  - "status: proposed"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## DataJoint Enhancement Proposal
+
+        Use this template to propose changes to DataJoint specifications, APIs, or documentation structure.
+
+        **Before submitting:**
+        - Search existing discussions to avoid duplicates
+        - Consider starting with an informal discussion in the Ideas category first
+
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: A brief, one-paragraph explanation of the proposal.
+      placeholder: This proposal adds/changes/removes...
+    validations:
+      required: true
+
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Motivation
+      description: |
+        Why is this change needed? What problem does it solve?
+        Include concrete use cases and examples where possible.
+      placeholder: |
+        Currently, users need to...
+        This causes problems when...
+        With this change, users could...
+    validations:
+      required: true
+
+  - type: textarea
+    id: design
+    attributes:
+      label: Proposed Design
+      description: |
+        Detailed explanation of the proposed solution.
+        Include code examples, API signatures, or schema definitions as appropriate.
+      placeholder: |
+        ## API Changes
+        ```python
+        # Example usage
+        ```
+
+        ## Behavior
+        - When X happens, Y should occur
+        - Error handling: ...
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: What other approaches were considered and why were they not chosen?
+      placeholder: |
+        1. Alternative A: ...
+           Rejected because: ...
+
+        2. Alternative B: ...
+           Rejected because: ...
+
+  - type: textarea
+    id: compatibility
+    attributes:
+      label: Backwards Compatibility
+      description: |
+        How does this affect existing users?
+        - Breaking changes?
+        - Migration path?
+        - Deprecation timeline?
+      placeholder: |
+        This change is/is not backwards compatible.
+
+        Migration path:
+        1. ...
+
+  - type: textarea
+    id: implementation
+    attributes:
+      label: Implementation Notes
+      description: |
+        Optional: Technical details, affected files, estimated scope.
+        Prototyping in parallel with RFC discussion is encouraged.
+      placeholder: |
+        Affected components:
+        - datajoint-python/src/datajoint/...
+
+        Estimated scope: small/medium/large
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: I have searched existing discussions and issues for duplicates
+          required: true
+        - label: I have considered backwards compatibility
+          required: true

.github/workflows/development.yml

@@ -3,6 +3,7 @@ on:
   push:
     branches:
       - main
+  workflow_dispatch:
 jobs:
   deploy-docs:
     runs-on: ubuntu-latest
@@ -12,9 +13,15 @@ jobs:
       DJBOT_GH_TOKEN: ${{secrets.djbot_gh_token}}
     steps:
       - uses: actions/checkout@v2
+      - name: Checkout datajoint-python
+        uses: actions/checkout@v2
+        with:
+          repository: datajoint/datajoint-python
+          ref: pre/v2.2
+          path: datajoint-python
       - name: Compile docs static artifacts
         run: |
-          BOT_PAT=$DJBOT_GH_TOKEN MODE=BUILD HOST_UID=$(id -u) docker compose up --exit-code-from docs --build
+          BOT_PAT=$DJBOT_GH_TOKEN MODE=BUILD DJ_PYTHON_PATH=./datajoint-python HOST_UID=$(id -u) docker compose up --exit-code-from docs --build
       - name: Commit documentation changes
         run: |
           git clone https://github.com/${GITHUB_REPOSITORY}.git \

.github/workflows/linkcheck.yml

@@ -0,0 +1,28 @@
+name: Link Check
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  linkcheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Check internal links in source files
+        uses: lycheeverse/lychee-action@v2
+        with:
+          args: >-
+            --offline
+            --no-progress
+            --exclude-path src/api
+            --exclude-path src/elements
+            --exclude '^https?://'
+            --exclude 'api/datajoint'
+            --exclude 'elements/element-'
+            'src/**/*.md'
+            'src/**/*.ipynb'
+          fail: true

.gitignore

@@ -1,4 +1,13 @@
 site
 .env
 .DS_Store
-temp*
+temp*
+
+# DataJoint secrets (credentials)
+.secrets/
+
+# Generated documentation files
+src/llms-full.txt
+site/llms-full.txt
+dj_local_conf.json
+__pycache__/

Dockerfile

@@ -1,10 +1,10 @@
-FROM python:3-alpine
+FROM python:3.12-alpine
 
 WORKDIR /main
 COPY mkdocs.yaml mkdocs.yaml
 COPY src/ src/
 COPY pip_requirements.txt pip_requirements.txt
 
 RUN \
-    apk add --no-cache git && \
+    apk add --no-cache git gcc g++ musl-dev linux-headers freetype-dev libpng-dev graphviz && \
     pip install --no-cache-dir -r /main/pip_requirements.txt

LICENSE

@@ -1,21 +1,27 @@
-MIT License
-
-Copyright (c) 2022 DataJoint
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+Creative Commons Attribution 4.0 International License (CC BY 4.0)
+
+Copyright 2014-2026 DataJoint Inc. and contributors
+
+You are free to:
+
+  Share — copy and redistribute the material in any medium or format
+  Adapt — remix, transform, and build upon the material for any purpose,
+          even commercially
+
+Under the following terms:
+
+  Attribution — You must give appropriate credit, provide a link to the
+                license, and indicate if changes were made. You may do so
+                in any reasonable manner, but not in any way that suggests
+                the licensor endorses you or your use.
+
+  No additional restrictions — You may not apply legal terms or
+                               technological measures that legally restrict
+                               others from doing anything the license permits.
+
+Full license text: https://creativecommons.org/licenses/by/4.0/legalcode
+
+---
+
+Note: The DataJoint software library is licensed separately under the
+Apache License 2.0. See https://github.com/datajoint/datajoint-python/blob/master/LICENSE