Merge branch 'datajoint:master' into multi-processing-bug-fix

Author: Ernaldis

.github/workflows/development.yaml

@@ -9,6 +9,23 @@ on:
       - '**' # every branch
       - '!stage*' # exclude branches beginning with stage
 jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_CLIENT_TIMEOUT: "120"
+      COMPOSE_HTTP_TIMEOUT: "120"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Compile docs static artifacts
+        run: |
+          export HOST_UID=$(id -u)
+          docker-compose -f ./docs-api/docker-compose.yaml up --exit-code-from docs-builder --build 
+      - name: Add docs static artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: docs-api-static
+          path: docs-api/build/html
+          retention-days: 1
   test:
     if: github.event_name == 'push' || github.event_name == 'pull_request'
     runs-on: ubuntu-latest
@@ -51,3 +68,42 @@ jobs:
                  --count --max-complexity=62 --max-line-length=127 --statistics
           black datajoint --check -v
           black tests --check -v
+  publish-docs:
+    if: |
+      github.event_name == 'push' &&
+      (
+        github.repository_owner == 'datajoint' ||
+        github.repository_owner == 'datajoint-company' ||
+        github.repository_owner == 'dj-sciops'
+      )
+    needs: build-docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Fetch docs static artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: docs-api-static
+          path: docs-api/build/html
+      - name: Commit documentation changes
+        run: |
+          git clone https://github.com/${GITHUB_REPOSITORY}.git \
+              --branch gh-pages --single-branch gh-pages
+          rm -R gh-pages/*
+          cp -r docs-api/build/html/* gh-pages/
+          cp .gitignore gh-pages/
+          touch gh-pages/.nojekyll
+          echo "docs-api.datajoint.org" > gh-pages/CNAME
+          cd gh-pages
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add . --all
+          git commit -m "Update documentation" -a || true
+          # The above command will fail if no changes were present, so we ignore
+          # the return code.
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: gh-pages
+          github_token: ${{secrets.GITHUB_TOKEN}}

.nojekyll

@@ -1,5 +1,8 @@
 ## Release notes
 
+### 0.13.5 -- May 13, 2022
+* Update - Import ABC from collections.abc for Python 3.10 compatibility
+
 ### 0.13.4 -- March, 28 2022
 * Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995
 * Bugfix - Add missing `jobs` argument for multiprocessing PR #997

CHANGELOG.md

@@ -10,8 +10,9 @@
 that any use of DataJoint leading to a publication be acknowledged in the publication.
 
 Please cite:
-    http://biorxiv.org/content/early/2015/11/14/031658
-    http://dx.doi.org/10.1101/031658
+
+  - http://biorxiv.org/content/early/2015/11/14/031658
+  - http://dx.doi.org/10.1101/031658
 """
 
 __author__ = "DataJoint Contributors"

datajoint/__init__.py

@@ -28,6 +28,7 @@ def set_password(
 def kill(restriction=None, connection=None, order_by=None):  # pragma: no cover
     """
     view and kill database connections.
+
     :param restriction: restriction to be applied to processlist
     :param connection: a datajoint.Connection object. Default calls datajoint.conn()
     :param order_by: order by a single attribute or the list of attributes. defaults to 'id'.
@@ -86,6 +87,7 @@ def kill(restriction=None, connection=None, order_by=None):  # pragma: no cover
 def kill_quick(restriction=None, connection=None):
     """
     Kill database connections without prompting. Returns number of terminated connections.
+
     :param restriction: restriction to be applied to processlist
     :param connection: a datajoint.Connection object. Default calls datajoint.conn()
 

datajoint/admin.py

@@ -18,14 +18,17 @@ def attribute_type(self):
     def get(self, value):
         """
         convert value retrieved from the the attribute in a table into the adapted type
+
         :param value: value from the database
+
         :return: object of the adapted type
         """
         raise NotImplementedError("Undefined attribute adapter")
 
     def put(self, obj):
         """
         convert an object of the adapted type into a value that DataJoint can store in a table attribute
+
         :param obj: an object of the adapted type
         :return: value to store in the database
         """

datajoint/attribute_adapter.py

@@ -188,17 +188,17 @@ def pack_blob(self, obj):
             return self.pack_decimal(obj)
         if isinstance(obj, uuid.UUID):
             return self.pack_uuid(obj)
-        if isinstance(obj, collections.Mapping):
+        if isinstance(obj, collections.abc.Mapping):
             return self.pack_dict(obj)
         if isinstance(obj, str):
             return self.pack_string(obj)
-        if isinstance(obj, collections.ByteString):
+        if isinstance(obj, collections.abc.ByteString):
             return self.pack_bytes(obj)
-        if isinstance(obj, collections.MutableSequence):
+        if isinstance(obj, collections.abc.MutableSequence):
             return self.pack_list(obj)
-        if isinstance(obj, collections.Sequence):
+        if isinstance(obj, collections.abc.Sequence):
             return self.pack_tuple(obj)
-        if isinstance(obj, collections.Set):
+        if isinstance(obj, collections.abc.Set):
             return self.pack_set(obj)
         if obj is None:
             return self.pack_none()

datajoint/blob.py

@@ -1,6 +1,6 @@
 """
-This module contains the Connection class that manages the connection to the database,
- and the `conn` function that provides access to a persistent connection in datajoint.
+This module contains the Connection class that manages the connection to the database, and
+the ``conn`` function that provides access to a persistent connection in datajoint.
 """
 import warnings
 from contextlib import contextmanager
@@ -52,6 +52,7 @@ def connect_host_hook(connection_obj):
 def translate_query_error(client_error, query):
     """
     Take client error and original query and return the corresponding DataJoint exception.
+
     :param client_error: the exception raised by the client interface
     :param query: sql query with placeholders
     :return: an instance of the corresponding subclass of datajoint.errors.DataJointError
@@ -108,11 +109,9 @@ def conn(
     :param password: mysql password
     :param init_fun: initialization function
     :param reset: whether the connection should be reset or not
-    :param use_tls: TLS encryption option. Valid options are: True (required),
-                    False (required no TLS), None (TLS prefered, default),
-                    dict (Manually specify values per
-                    https://dev.mysql.com/doc/refman/5.7/en/connection-options.html
-                        #encrypted-connection-options).
+    :param use_tls: TLS encryption option. Valid options are: True (required), False
+        (required no TLS), None (TLS prefered, default), dict (Manually specify values per
+        https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options).
     """
     if not hasattr(conn, "connection") or reset:
         host = host if host is not None else config["database.host"]
@@ -247,6 +246,7 @@ def set_query_cache(self, query_cache=None):
         1. Only SELECT queries are allowed.
         2. The results of queries are cached under the path indicated by dj.config['query_cache']
         3. query_cache is a string that differentiates different cache states.
+
         :param query_cache: a string to initialize the hash for query results
         """
         self._query_cache = query_cache
@@ -298,6 +298,7 @@ def query(
     ):
         """
         Execute the specified query and return the tuple generator (cursor).
+
         :param query: SQL query
         :param args: additional arguments for the client.cursor
         :param as_dict: If as_dict is set to True, the returned cursor objects returns

datajoint/connection.py

@@ -153,6 +153,7 @@ def build_index_parser():
 
 def is_foreign_key(line):
     """
+
     :param line: a line from the table definition
     :return: true if the line appears to be a foreign key definition
     """
@@ -366,6 +367,7 @@ def prepare_declare(definition, context):
 def declare(full_table_name, definition, context):
     """
     Parse declaration and generate the SQL CREATE TABLE code
+
     :param full_table_name: full name of the table
     :param definition: DataJoint table definition
     :param context: dictionary of objects that might be referred to in the table
@@ -566,6 +568,7 @@ def substitute_special_type(match, category, foreign_key_sql, context):
 def compile_attribute(line, in_key, foreign_key_sql, context):
     """
     Convert attribute definition from DataJoint format to SQL
+
     :param line: attribution line
     :param in_key: set to True if attribute is in primary key set
     :param foreign_key_sql: the list of foreign key declarations to add to

datajoint/declare.py

@@ -146,6 +146,7 @@ def __init__(self, source, context=None):
         def from_sequence(cls, sequence):
             """
             The join Diagram for all objects in sequence
+
             :param sequence: a sequence (e.g. list, tuple)
             :return: Diagram(arg1) + ... + Diagram(argn)
             """