Merge branch 'master' of https://github.com/datajoint/datajoint-python into top-restrcition

Author: A-Baji

.devcontainer/Dockerfile

@@ -4,7 +4,7 @@ FROM mcr.microsoft.com/devcontainers/python:3.7-bullseye
 RUN \
     apt update && \
     apt-get install bash-completion graphviz default-mysql-client -y && \
-    pip install flake8 black faker ipykernel nose nose-cov datajoint && \
+    pip install flake8 black faker ipykernel pytest pytest-cov nose nose-cov datajoint && \
     pip uninstall datajoint -y
 
 ENV DJ_HOST fakeservices.datajoint.io

.devcontainer/devcontainer.json

@@ -16,7 +16,7 @@
 		"ghcr.io/guiyomh/features/vim:0": {}
 	},
 	"onCreateCommand": "pip install -e .",
-	"postStartCommand": "MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml down && MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml up --build --wait",
+	"postStartCommand": "MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml down && docker volume prune -f && MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml up --build --wait",
 	"forwardPorts": [
 		80,
 		443,

.github/workflows/development.yaml

@@ -92,6 +92,7 @@ jobs:
                  --count --max-complexity=62 --max-line-length=127 --statistics
           black datajoint --check -v
           black tests --check -v
+          black tests_old --check -v
   publish-docs:
     if: |
       github.event_name == 'push' &&

.vscode/settings.json

@@ -11,5 +11,11 @@
     "[markdown]": {
         "editor.defaultFormatter": "disable"
     },
+    "[yaml]": {
+        "editor.defaultFormatter": "disable"
+    },
+    "[dockercompose]": {
+        "editor.defaultFormatter": "disable"
+    },
     "files.autoSave": "off"
 }

CHANGELOG.md

@@ -8,6 +8,8 @@
 - Changed - Docs to add landing page and update navigation
 - Changed - `.data` method to `.stream` in the `get()` method for S3 (external) objects PR [#1085](https://github.com/datajoint/datajoint-python/pull/1085)
 - Fixed - Docs to rename `create_virtual_module` to `VirtualModule`
+- Added - Skeleton from `datajoint-company/datajoint-docs` repository for docs migration
+- Added - Initial `pytest` for `test_connection`
 
 ### 0.14.0 -- Feb 13, 2023
 - Added - `json` data type ([#245](https://github.com/datajoint/datajoint-python/issues/245)) PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)

LNX-docker-compose.yml

@@ -89,7 +89,8 @@ services:
         pip install --user nose nose-cov
         pip install -e .
         pip list --format=freeze | grep datajoint
-        nosetests -vsw tests --with-coverage --cover-package=datajoint
+        pytest -sv --cov-report term-missing --cov=datajoint tests
+        nosetests -vsw tests_old --with-coverage --cover-package=datajoint
     # ports:
     #   - "8888:8888"
     user: ${HOST_UID}:anaconda

datajoint/admin.py

@@ -8,9 +8,7 @@
 logger = logging.getLogger(__name__.split(".")[0])
 
 
-def set_password(
-    new_password=None, connection=None, update_config=None
-):  # pragma: no cover
+def set_password(new_password=None, connection=None, update_config=None):
     connection = conn() if connection is None else connection
     if new_password is None:
         new_password = getpass("New password: ")
@@ -28,7 +26,7 @@ def set_password(
         config.save_local(verbose=True)
 
 
-def kill(restriction=None, connection=None, order_by=None):  # pragma: no cover
+def kill(restriction=None, connection=None, order_by=None):
     """
     view and kill database connections.
 

datajoint/connection.py

@@ -120,9 +120,9 @@ def conn(
         host = host if host is not None else config["database.host"]
         user = user if user is not None else config["database.user"]
         password = password if password is not None else config["database.password"]
-        if user is None:  # pragma: no cover
+        if user is None:
             user = input("Please enter DataJoint username: ")
-        if password is None:  # pragma: no cover
+        if password is None:
             password = getpass(prompt="Please enter DataJoint password: ")
         init_fun = (
             init_fun if init_fun is not None else config["connection.init_function"]

datajoint/dependencies.py

@@ -127,7 +127,7 @@ def load(self, force=True):
                 self.add_edge(fk["referenced_table"], alias_node, **props)
                 self.add_edge(alias_node, fk["referencing_table"], **props)
 
-        if not nx.is_directed_acyclic_graph(self):  # pragma: no cover
+        if not nx.is_directed_acyclic_graph(self):
             raise DataJointError("DataJoint can only work with acyclic dependencies")
         self._loaded = True
 

docs/mkdocs.yaml

@@ -6,20 +6,72 @@ repo_name: datajoint/datajoint-python
 nav:
   - DataJoint Python: index.md
   - Getting Started: getting-started/index.md
-  - Existing Pipelines: concepts/existing-pipelines.md
-  - Query Language:
-      - Common Commands: query-lang/common-commands.md
-      - Operators: query-lang/operators.md
-      - Iteration: query-lang/iteration.md
-      - Query Caching: query-lang/query-caching.md
+  - Concepts: 
+    - Principles: concepts/principles.md
+    - Glossary: concepts/glossary.md
+  - System Administration: 
+    - Database Administration: sysadmin/dba.md
+    - File Storage: sysadmin/filestore.md
+  - Client Configuration: 
+    - Install: client/install.md
+    - Credentials: client/creds.md
+    - Settings: client/settings.md
+    - File Stores: client/stores.md
+  - Schema Design:
+    - Schema Creation: design/schema.md
+    - Table Definition:
+      - Table Tiers: design/tables/tiers.md
+      - Declaration Syntax: design/tables/declare.md
+      - Primary Key: design/tables/primary.md
+      - Attributes: design/tables/attributes.md
+      - Lookup Tables: design/tables/lookup.md
+      - Blobs: design/tables/blobs.md
+      - Attachments: design/tables/attach.md
+      - Filepaths: design/tables/filepath.md
+      - Custom Datatypes: design/tables/customtype.md
+      - Dependencies: design/tables/dependencies.md
+      - Indexes: design/tables/indexes.md
+      - Master-Part Relationships: design/tables/master-part.md
+    - Schema Diagrams: design/diagrams.md
+    - Entity Normalization: design/normalization.md 
+    - Data Integrity: design/integrity.md
+    - Schema Recall: design/recall.md
+    - Schema Drop: design/drop.md
+    - Schema Modification: design/alter.md
+  - Data Manipulations:
+    - Insert: manipulation/insert.md
+    - Delete: manipulation/delete.md
+    - Update: manipulation/update.md
+    - Transactions: manipulation/transactions.md
+  - Data Queries:
+    - Common Commands: query/common-commands.md
+    - Fetch: query/fetch.md
+    - Iteration: query/iteration.md
+    - Operators: query/operators.md
+    - Restrict: query/restrict.md
+    - Projection: query/project.md
+    - Join: query/join.md
+    - Aggregation: query/aggregation.md
+    - Union: query/union.md
+    - Universal Sets: query/universals.md
+    - Query Caching: query/query-caching.md
+  - Computations:
+    - Make Method: compute/make.md
+    - Populate: compute/populate.md
+    - Key Source: compute/key-source.md
+    - Distributed Computing: compute/distributed.md
+  - Internals:
+    - SQL Transpilation: internal/transpilation.md
   - Reproducibility:
       - Table Tiers: reproduce/table-tiers.md
       - Make Method: reproduce/make-method.md
+  - Existing Pipelines: existing-pipelines.md
   - Tutorials:
       - tutorials/json.ipynb
+  - FAQ: faq.md
   - Develop: develop.md
   - Citation: citation.md
-  - Changelog: about/changelog.md
+  - Changelog: changelog.md
   - API: api/ # defer to gen-files + literate-nav
 
 # ---------------------------- STANDARD -----------------------------