Merge master into pre/v2.1

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: dimitri-yatsenko

.github/pr_labeler.yaml

@@ -1,7 +1,6 @@
 name: Post Draft Release Published
 
 on:
-  # Once draft release is released, trigger the docs release
   release:
     types:
       ## pre-release and stable release
@@ -11,8 +10,6 @@ on:
 run-name: Post ${{ github.event.release.name }}
 
 jobs:
-  call-publish-docs:
-    uses: ./.github/workflows/docs.yaml
   pypi-release:
     permissions:
       # write permission is required to update version.py
@@ -60,7 +57,8 @@ jobs:
           # Update src in the <img> tag
           sed -i 's|\(<img id="commit-since-release-img"[^>]*src="\)[^"]*\(".*\)|\1'"$NEW_SRC"'\2|' README.md
           git add README.md
-          git commit -m "Update README.md badge to ${{ github.event.release.tag_name }}"
+          # Only commit if there are changes (handles re-runs gracefully)
+          git diff --cached --quiet README.md || git commit -m "Update README.md badge to ${{ github.event.release.tag_name }}"
       - name: Set up Python ${{matrix.py_ver}}
         uses: actions/setup-python@v5
         with:

.github/workflows/docs.yaml

@@ -10,7 +10,7 @@ RUN ${CONDA_BIN} install --no-pin -qq -y -n base -c conda-forge \
     ${CONDA_BIN} clean -qq -afy
 ENV PATH="$PATH:/home/mambauser/.local/bin"
 
-COPY --chown=${HOST_UID:-1000}:mambauser ./pyproject.toml ./README.md ./LICENSE.txt /main/
+COPY --chown=${HOST_UID:-1000}:mambauser ./pyproject.toml ./README.md ./LICENSE /main/
 COPY --chown=${HOST_UID:-1000}:mambauser ./src/datajoint /main/src/datajoint
 
 VOLUME /src

.github/workflows/label_issues.yaml

@@ -10,7 +10,6 @@ dependencies = [
   "pymysql>=0.7.2",
   "deepdiff",
   "pyparsing",
-  "ipython",
   "pandas",
   "tqdm",
   "networkx",
@@ -86,6 +85,9 @@ test = [
   "pytest",
   "pytest-cov",
   "requests",
+  "faker",
+  "matplotlib",
+  "ipython",
   "graphviz",
   "testcontainers[mysql,minio,postgres]>=4.0",
   "polars>=0.20.0",
@@ -99,10 +101,14 @@ azure = ["adlfs>=2023.1.0"]
 postgres = ["psycopg2-binary>=2.9.0"]
 polars = ["polars>=0.20.0"]
 arrow = ["pyarrow>=14.0.0"]
+viz = ["matplotlib", "ipython"]
 test = [
   "pytest",
   "pytest-cov",
   "requests",
+  "faker",
+  "matplotlib",
+  "ipython",
   "s3fs>=2023.1.0",
   "testcontainers[mysql,minio,postgres]>=4.0",
   "psycopg2-binary>=2.9.0",

.github/workflows/label_prs.yaml

@@ -643,11 +643,12 @@ def fetch(
 
         # Handle specific attributes requested
         if attrs:
-            if as_dict or as_dict is None:
-                # fetch('col1', 'col2', as_dict=True) or fetch('col1', 'col2')
+            if as_dict is True:
+                # fetch('col1', 'col2', as_dict=True) -> list of dicts
                 return self.proj(*attrs).to_dicts(order_by=order_by, limit=limit, offset=offset, squeeze=squeeze)
             else:
-                # fetch('col1', 'col2', as_dict=False) -> tuple of arrays
+                # fetch('col1', 'col2') or fetch('col1', 'col2', as_dict=False) -> tuple of arrays
+                # This matches DJ 1.x behavior where fetch('col') returns array(['alpha', 'beta'])
                 return self.to_arrays(*attrs, order_by=order_by, limit=limit, offset=offset, squeeze=squeeze)
 
         # Handle as_dict=True -> to_dicts()

.github/workflows/post_draft_release_published.yaml

@@ -5,6 +5,11 @@
 Codec system, particularly for upgrading blob columns to use
 explicit `<blob>` type declarations.
 
+.. note::
+    This module is provided temporarily to assist with migration from pre-2.0.
+    It will be deprecated in DataJoint 2.1 and removed in 2.2.
+    Complete your migrations while on DataJoint 2.0.
+
 Note on Terminology
 -------------------
 This module uses "external storage" because that was the term in DataJoint 0.14.6.
@@ -16,9 +21,22 @@
 
 import logging
 import re
+import warnings
 from typing import TYPE_CHECKING
 
+from packaging.version import Version
+
 from .errors import DataJointError
+from .version import __version__
+
+# Show deprecation warning starting in 2.1
+if Version(__version__) >= Version("2.1"):
+    warnings.warn(
+        "datajoint.migrate is deprecated and will be removed in DataJoint 2.2. "
+        "Complete your schema migrations before upgrading.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
 
 if TYPE_CHECKING:
     from .schemas import Schema

Dockerfile

@@ -53,12 +53,23 @@ def test_fetch_as_dict_true(self, mock_expression):
 
         mock_expression.to_dicts.assert_called_once_with(order_by=None, limit=None, offset=None, squeeze=False)
 
-    def test_fetch_with_attrs_returns_dicts(self, mock_expression):
-        """fetch('col1', 'col2') should call proj().to_dicts()."""
+    def test_fetch_with_attrs_returns_arrays(self, mock_expression):
+        """fetch('col1', 'col2') should call to_arrays() - matches DJ 1.x behavior."""
         with warnings.catch_warnings():
             warnings.simplefilter("ignore", DeprecationWarning)
             mock_expression.fetch("col1", "col2")
 
+        # DJ 1.x: fetch('col') returns array(['alpha', 'beta']), not list of dicts
+        mock_expression.to_arrays.assert_called_once_with(
+            "col1", "col2", order_by=None, limit=None, offset=None, squeeze=False
+        )
+
+    def test_fetch_with_attrs_as_dict_true(self, mock_expression):
+        """fetch('col1', 'col2', as_dict=True) should call proj().to_dicts()."""
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", DeprecationWarning)
+            mock_expression.fetch("col1", "col2", as_dict=True)
+
         mock_expression.proj.assert_called_once_with("col1", "col2")
         mock_expression.to_dicts.assert_called_once()