Merge branch 'master' into kwargs_in_populate

Author: dimitri-yatsenko

CHANGELOG.md

@@ -1,6 +1,9 @@
 ## Release notes
 
 ### 0.13.3 -- TBD
+* Bugfix - Fix error in listing ancestors, descendants with part tables.
+* Bugfix - Fix Python 3.10 compatibility (#983) PR #972
+* Bugfix - Allow renaming non-conforming attributes in proj (#982) PR #972
 * Add - Expose proxy feature for S3 external stores (#961) PR #962
 * Bugfix - Dependencies not properly loaded on populate. (#902) PR #919
 * Bugfix - Replace use of numpy aliases of built-in types with built-in type. (#938) PR #939

LNX-docker-compose.yml

@@ -32,7 +32,7 @@ services:
       interval: 1s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.0.18
+    image: datajoint/nginx:v0.0.19
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

datajoint/declare.py

@@ -11,7 +11,7 @@
 
 UUID_DATA_TYPE = 'binary(16)'
 MAX_TABLE_NAME_LENGTH = 64
-CONSTANT_LITERALS = {'CURRENT_TIMESTAMP'}  # SQL literals to be used without quotes (case insensitive)
+CONSTANT_LITERALS = {'CURRENT_TIMESTAMP', 'NULL'}  # SQL literals to be used without quotes (case insensitive)
 EXTERNAL_TABLE_ROOT = '~external'
 
 TYPE_PATTERN = {k: re.compile(v, re.I) for k, v in dict(

datajoint/dependencies.py

@@ -18,7 +18,7 @@ def unite_master_parts(lst):
     """
     for i in range(2, len(lst)):
         name = lst[i]
-        match = re.match(r'(?P<master>`\w+`.`\w+)__\w+`', name)
+        match = re.match(r'(?P<master>`\w+`.`#?\w+)__\w+`', name)
         if match:  # name is a part table
             master = match.group('master')
             for j in range(i-1, -1, -1):

datajoint/diagram.py

@@ -296,7 +296,7 @@ def make_dot(self):
                 node.set_style('filled')
 
             for edge in dot.get_edges():
-                # see http://www.graphviz.org/content/attrs
+                # see https://graphviz.org/doc/info/attrs.html
                 src = edge.get_source().strip('"')
                 dest = edge.get_destination().strip('"')
                 props = graph.get_edge_data(src, dest)

datajoint/expression.py

@@ -9,6 +9,7 @@
 from .preview import preview, repr_html
 from .condition import AndList, Not, \
     make_condition, assert_join_compatibility, extract_column_names, PromiscuousOperand
+from .declare import CONSTANT_LITERALS
 
 logger = logging.getLogger(__name__)
 
@@ -313,9 +314,9 @@ def proj(self, *attributes, **named_attributes):
         Each attribute name can only be used once.
         """
         # new attributes in parentheses are included again with the new name without removing original
-        duplication_pattern = re.compile(r'\s*\(\s*(?P<name>[a-z][a-z_0-9]*)\s*\)\s*$')
+        duplication_pattern = re.compile(fr'^\s*\(\s*(?!{"|".join(CONSTANT_LITERALS)})(?P<name>[a-zA-Z_]\w*)\s*\)\s*$')
         # attributes without parentheses renamed
-        rename_pattern = re.compile(r'\s*(?P<name>[a-z][a-z_0-9]*)\s*$')
+        rename_pattern = re.compile(fr'^\s*(?!{"|".join(CONSTANT_LITERALS)})(?P<name>[a-zA-Z_]\w*)\s*$')
         replicate_map = {k: m.group('name')
                          for k, m in ((k, duplication_pattern.match(v)) for k, v in named_attributes.items()) if m}
         rename_map = {k: m.group('name')

datajoint/external.py

@@ -1,5 +1,5 @@
 from pathlib import Path, PurePosixPath, PureWindowsPath
-from collections import Mapping
+from collections.abc import Mapping
 from tqdm import tqdm
 from .settings import config
 from .errors import DataJointError, MissingExternalFile

datajoint/settings.py

@@ -58,7 +58,7 @@
 }
 
 
-class Config(collections.MutableMapping):
+class Config(collections.abc.MutableMapping):
 
     instance = None
 

docs-parts/computation/01-autopopulate_lang1.rst

@@ -13,6 +13,6 @@
         def make(self, key):
             img = (test.Image & key).fetch1('image')
             key['filtered_image'] = myfilter(img)
-            self.insert(key)
+            self.insert1(key)
 
 The ``make`` method receives one argument: the dict ``key`` containing the primary key value of an element of :ref:`key source <keysource>` to be worked on.  

docs-parts/definition/11-ERD_lang1.rst

@@ -1,21 +1,21 @@
 
-To plot the ERD for an entire schema, an ERD object can be initialized with the schema object (which is normally used to decorate table objects)
+To plot the Diagram for an entire schema, an Diagram object can be initialized with the schema object (which is normally used to decorate table objects)
 
 .. code-block:: python
 
     import datajoint as dj
     schema = dj.Schema('my_database')
-    dj.ERD(schema).draw()
+    dj.Diagram(schema).draw()
 
 or alternatively an object that has the schema object as an attribute, such as the module defining a schema:
 
 .. code-block:: python
 
     import datajoint as dj
     import seq    # import the sequence module defining the seq database
-    dj.ERD(seq).draw()   # draw the ERD
+    dj.Diagram(seq).draw()   # draw the Diagram
 
 Note that calling the ``.draw()`` method is not necessary when working in a Jupyter notebook.
-The preferred workflow is to simply let the object display itself, for example by writing ``dj.ERD(seq)``.
-The ERD will then render in the notebook using its ``_repr_html_`` method.
-An ERD displayed without ``.draw()`` will be rendered as an SVG, and hovering the mouse over a table will reveal a compact version of the output of the ``.describe()`` method.
+You can simply let the object display itself, for example by entering ``dj.Diagram(seq)`` in a notebook cell.
+The Diagram will automatically render in the notebook by calling its ``_repr_html_`` method.
+A Diagram displayed without ``.draw()`` will be rendered as an SVG, and hovering the mouse over a table will reveal a compact version of the output of the ``.describe()`` method.