Remove deprecated features + small fixes

.gitignore

@@ -29,4 +29,5 @@ docs/site
 
 
 !.vscode/settings.json
+!.vscode/launch.json
 !.devcontainer/devcontainer.json

.vscode/launch.json

@@ -0,0 +1,16 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": false
+        }
+    ]
+}

.vscode/settings.json

@@ -7,5 +7,9 @@
     "python.formatting.provider": "black",
     "[python]": {
         "editor.defaultFormatter": null
-    }
+    },
+    "[markdown]": {
+        "editor.defaultFormatter": "disable"
+    },
+    "files.autoSave": "off"
 }

CHANGELOG.md

@@ -6,6 +6,12 @@
 - Added - Support for inserting data with CSV files - PR [#1067](https://github.com/datajoint/datajoint-python/pull/1067)
 - Changed - Switch testing image from `pydev` to `djtest` PR [#1012](https://github.com/datajoint/datajoint-python/pull/1012)
 - Added - DevContainer development environment compatible with GH Codespaces PR [1071](https://github.com/datajoint/datajoint-python/pull/1071)
+- Fixed - Convert lingering prints by replacing with logs PR [#1073](https://github.com/datajoint/datajoint-python/pull/1073)
+- Changed - `table.progress()` defaults to no stdout PR [#1073](https://github.com/datajoint/datajoint-python/pull/1073)
+- Changed - `table.describe()` defaults to no stdout PR [#1073](https://github.com/datajoint/datajoint-python/pull/1073)
+- Deprecated - `table._update()` PR [#1073](https://github.com/datajoint/datajoint-python/pull/1073)
+- Deprecated - old-style foreign key syntax PR [#1073](https://github.com/datajoint/datajoint-python/pull/1073)
+- Deprecated - `dj.migrate_dj011_external_blob_storage_to_dj012()` PR [#1073](https://github.com/datajoint/datajoint-python/pull/1073)
 
 ### 0.13.8 -- Sep 21, 2022
 - Added - New documentation structure based on markdown PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)

LNX-docker-compose.yml

@@ -1,6 +1,7 @@
 # PY_VER=3.8 MYSQL_VER=5.7 DISTRO=alpine MINIO_VER=RELEASE.2022-08-11T04-37-28Z HOST_UID=$(id -u) docker compose -f LNX-docker-compose.yml up --exit-code-from app --build
 version: "2.4"
-x-net: &net
+x-net:
+  &net
   networks:
     - main
 services:
@@ -13,6 +14,11 @@ services:
     #   - "3306:3306"
     # volumes:
     #   - ./mysql/data:/var/lib/mysql
+    healthcheck:
+      test: [ "CMD", "mysqladmin", "ping", "-h", "localhost" ]
+      timeout: 30s
+      retries: 5
+      interval: 15s
   minio:
     <<: *net
     image: minio/minio:${MINIO_VER}
@@ -26,10 +32,16 @@ services:
     #   - ./minio/data:/data
     command: server --address ":9000" /data
     healthcheck:
-      test: ["CMD", "curl", "--fail", "http://minio:9000/minio/health/live"]
-      timeout: 5s
-      retries: 60
-      interval: 1s
+      test:
+        [
+          "CMD",
+          "curl",
+          "--fail",
+          "http://minio:9000/minio/health/live"
+        ]
+      timeout: 30s
+      retries: 5
+      interval: 15s
   fakeservices.datajoint.io:
     <<: *net
     image: datajoint/nginx:v0.2.4

datajoint/__init__.py

@@ -51,7 +51,6 @@
     "key",
     "key_hash",
     "logger",
-    "migrate_dj011_external_blob_storage_to_dj012",
 ]
 
 from .logging import logger
@@ -71,7 +70,6 @@
 from .attribute_adapter import AttributeAdapter
 from . import errors
 from .errors import DataJointError
-from .migrate import migrate_dj011_external_blob_storage_to_dj012
 
 ERD = Di = Diagram  # Aliases for Diagram
 schema = Schema  # Aliases for Schema

datajoint/admin.py

@@ -3,6 +3,9 @@
 from .connection import conn
 from .settings import config
 from .utils import user_choice
+import logging
+
+logger = logging.getLogger(__name__.split(".")[0])
 
 
 def set_password(
@@ -13,10 +16,10 @@ def set_password(
         new_password = getpass("New password: ")
         confirm_password = getpass("Confirm password: ")
         if new_password != confirm_password:
-            print("Failed to confirm the password! Aborting password change.")
+            logger.warn("Failed to confirm the password! Aborting password change.")
             return
     connection.query("SET PASSWORD = PASSWORD('%s')" % new_password)
-    print("Password updated.")
+    logger.info("Password updated.")
 
     if update_config or (
         update_config is None and user_choice("Update local setting?") == "yes"
@@ -81,7 +84,7 @@ def kill(restriction=None, connection=None, order_by=None):  # pragma: no cover
                 try:
                     connection.query("kill %d" % pid)
                 except pymysql.err.InternalError:
-                    print("Process not found")
+                    logger.warn("Process not found")
 
 
 def kill_quick(restriction=None, connection=None):

datajoint/autopopulate.py

@@ -325,7 +325,7 @@ def _populate1(
                 finally:
                     self.__class__._allow_insert = False
 
-    def progress(self, *restrictions, display=True):
+    def progress(self, *restrictions, display=False):
         """
         Report the progress of populating the table.
         :return: (remaining, total) -- numbers of tuples to be populated
@@ -334,9 +334,9 @@ def progress(self, *restrictions, display=True):
         total = len(todo)
         remaining = len(todo - self.target)
         if display:
-            print(
-                "%-20s" % self.__class__.__name__,
-                "Completed %d of %d (%2.1f%%)   %s"
+            logger.info(
+                "%-20s" % self.__class__.__name__
+                + " Completed %d of %d (%2.1f%%)   %s"
                 % (
                     total - remaining,
                     total,
@@ -345,6 +345,5 @@ def progress(self, *restrictions, display=True):
                         datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
                     ),
                 ),
-                flush=True,
             )
         return remaining, total

datajoint/declare.py

@@ -177,19 +177,14 @@ def compile_foreign_key(
     from .table import Table
     from .expression import QueryExpression
 
-    obsolete = False  # See issue #436.  Old style to be deprecated in a future release
     try:
         result = foreign_key_parser.parseString(line)
-    except pp.ParseException:
-        try:
-            result = foreign_key_parser_old.parseString(line)
-        except pp.ParseBaseException as err:
-            raise DataJointError('Parsing error in line "%s". %s.' % (line, err))
-        else:
-            obsolete = True
+    except pp.ParseException as err:
+        raise DataJointError('Parsing error in line "%s". %s.' % (line, err))
+
     try:
         ref = eval(result.ref_table, context)
-    except NameError if obsolete else Exception:
+    except Exception:
         raise DataJointError(
             "Foreign key reference %s could not be resolved" % result.ref_table
         )
@@ -205,18 +200,6 @@ def compile_foreign_key(
             'Primary dependencies cannot be nullable in line "{line}"'.format(line=line)
         )
 
-    if obsolete:
-        logger.warning(
-            'Line "{line}" uses obsolete syntax that will no longer be supported in datajoint 0.14. '
-            "For details, see issue #780 https://github.com/datajoint/datajoint-python/issues/780".format(
-                line=line
-            )
-        )
-        if not isinstance(ref, type) or not issubclass(ref, Table):
-            raise DataJointError(
-                "Foreign key reference %r must be a valid query" % result.ref_table
-            )
-
     if isinstance(ref, type) and issubclass(ref, Table):
         ref = ref()
 
@@ -232,55 +215,6 @@ def compile_foreign_key(
             % result.ref_table
         )
 
-    if obsolete:
-        # for backward compatibility with old-style dependency declarations.  See issue #436
-        if not isinstance(ref, Table):
-            DataJointError(
-                'Dependency "%s" is not supported. Check documentation.'
-                % result.ref_table
-            )
-        if not all(r in ref.primary_key for r in result.ref_attrs):
-            raise DataJointError('Invalid foreign key attributes in "%s"' % line)
-        try:
-            raise DataJointError(
-                'Duplicate attributes "{attr}" in "{line}"'.format(
-                    attr=next(attr for attr in result.new_attrs if attr in attributes),
-                    line=line,
-                )
-            )
-        except StopIteration:
-            pass  # the normal outcome
-
-        # Match the primary attributes of the referenced table to local attributes
-        new_attrs = list(result.new_attrs)
-        ref_attrs = list(result.ref_attrs)
-
-        # special case, the renamed attribute is implicit
-        if new_attrs and not ref_attrs:
-            if len(new_attrs) != 1:
-                raise DataJointError(
-                    'Renamed foreign key must be mapped to the primary key in "%s"'
-                    % line
-                )
-            if len(ref.primary_key) == 1:
-                # if the primary key has one attribute, allow implicit renaming
-                ref_attrs = ref.primary_key
-            else:
-                # if only one primary key attribute remains, then allow implicit renaming
-                ref_attrs = [attr for attr in ref.primary_key if attr not in attributes]
-                if len(ref_attrs) != 1:
-                    raise DataJointError(
-                        'Could not resolve which primary key attribute should be referenced in "%s"'
-                        % line
-                    )
-
-        if len(new_attrs) != len(ref_attrs):
-            raise DataJointError('Mismatched attributes in foreign key "%s"' % line)
-
-        if ref_attrs:
-            # convert to projected dependency
-            ref = ref.proj(**dict(zip(new_attrs, ref_attrs)))
-
     # declare new foreign key attributes
     for attr in ref.primary_key:
         if attr not in attributes:

datajoint/diagram.py

@@ -383,9 +383,7 @@ def make_dot(self):
                 if name.split(".")[0] in self.context:
                     cls = eval(name, self.context)
                     assert issubclass(cls, Table)
-                    description = (
-                        cls().describe(context=self.context, printout=False).split("\n")
-                    )
+                    description = cls().describe(context=self.context).split("\n")
                     description = (
                         "-" * 30
                         if q.startswith("---")