Merge branch 'master' into populate_success_count

Author: Thinh Nguyen

.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

@@ -1,5 +1,16 @@
 ## Release notes
 
+### 0.14.1 -- Jun 02, 2023
+- Fixed - Fix altering a part table that uses the "master" keyword - PR [#991](https://github.com/datajoint/datajoint-python/pull/991)
+- Fixed - `.ipynb` output in tutorials is not visible in dark mode ([#1078](https://github.com/datajoint/datajoint-python/issues/1078)) PR [#1080](https://github.com/datajoint/datajoint-python/pull/1080)
+- Fixed - preview table font for darkmode PR [#1089](https://github.com/datajoint/datajoint-python/pull/1089)
+- Changed - Readme to update links and include example pipeline image
+- 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)
 - Fixed - Activating a schema requires all tables to exist even if `create_tables=False` PR [#1058](https://github.com/datajoint/datajoint-python/pull/1058)
@@ -13,7 +24,7 @@
 - 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)
-* Added - Method to set job keys to "ignore" status - PR [#1068](https://github.com/datajoint/datajoint-python/pull/1068)
+- Added - Method to set job keys to "ignore" status - PR [#1068](https://github.com/datajoint/datajoint-python/pull/1068)
 
 ### 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

@@ -44,7 +44,7 @@ services:
       interval: 15s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.2.4
+    image: datajoint/nginx:v0.2.5
     environment:
       - ADD_db_TYPE=DATABASE
       - ADD_db_ENDPOINT=db:3306
@@ -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

README.md

@@ -1,8 +1,6 @@
 [![DOI](https://zenodo.org/badge/16774/datajoint/datajoint-python.svg)](https://zenodo.org/badge/latestdoi/16774/datajoint/datajoint-python)
-[![Build Status](https://travis-ci.org/datajoint/datajoint-python.svg?branch=master)](https://travis-ci.org/datajoint/datajoint-python)
 [![Coverage Status](https://coveralls.io/repos/datajoint/datajoint-python/badge.svg?branch=master&service=github)](https://coveralls.io/github/datajoint/datajoint-python?branch=master)
 [![PyPI version](https://badge.fury.io/py/datajoint.svg)](http://badge.fury.io/py/datajoint)
-[![Requirements Status](https://requires.io/github/datajoint/datajoint-python/requirements.svg?branch=master)](https://requires.io/github/datajoint/datajoint-python/requirements/?branch=master)
 [![Slack](https://img.shields.io/badge/slack-chat-green.svg)](https://datajoint.slack.com/)
 
 # Welcome to DataJoint for Python!
@@ -12,22 +10,32 @@ DataJoint for Python is a framework for scientific workflow management based on
 DataJoint was initially developed in 2009 by Dimitri Yatsenko in Andreas Tolias' Lab at Baylor College of Medicine for the distributed processing and management of large volumes of data streaming from regular experiments. Starting in 2011, DataJoint has been available as an open-source project adopted by other labs and improved through contributions from several developers.
 Presently, the primary developer of DataJoint open-source software is the company DataJoint (https://datajoint.com).
 
-- [Getting Started](https://datajoint.com/docs/core/datajoint-python/latest/getting-started/)
-- [DataJoint Elements](https://datajoint.com/docs/elements/) - Catalog of example pipelines
-- [DataJoint CodeBook](https://codebook.datajoint.io) - Interactive online tutorials
-- Contribute
+## Data Pipeline Example
+
+![pipeline](https://raw.githubusercontent.com/datajoint/datajoint-python/master/images/pipeline.png)
+
+[Yatsenko et al., bioRxiv 2021](https://doi.org/10.1101/2021.03.30.437358)
+
+## Getting Started
+
+- Install from PyPI
+
+     ```bash
+     pip install datajoint
+     ```
+
+- [Documentation & Tutorials](https://datajoint.com/docs/core/datajoint-python/)
+
+- [Interactive Tutorials](https://github.com/datajoint/datajoint-tutorials) on GitHub Codespaces
 
+- [DataJoint Elements](https://datajoint.com/docs/elements/) - Catalog of example pipelines for neuroscience experiments
+
+- Contribute
   - [Development Environment](https://datajoint.com/docs/core/datajoint-python/latest/develop/)
+
   - [Guidelines](https://datajoint.com/docs/community/contribute/)
 
 - Legacy Resources (To be replaced by above)
   - [Documentation](https://docs.datajoint.org)
-  - [Tutorials](https://tutorials.datajoint.org)
 
-## Citation
-
-- If your work uses DataJoint for Python, please cite the following Research Resource Identifier (RRID) and manuscript.
-
-- DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for Python (version `<Enter version number>`)
-
-- Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
+  - [Tutorials](https://tutorials.datajoint.org)

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