Fix merge conflicts.

Author: guzman-raphael

.github/ISSUE_TEMPLATE/bug_report.md

@@ -2,7 +2,7 @@
 name: Bug report
 about: Create a report to help us improve
 title: ''
-labels: 'bug, awaiting-triage'
+labels: 'bug'
 assignees: ''
 
 ---

CHANGELOG.md

@@ -1,10 +1,13 @@
 ## Release notes
 
-### 0.14.0 -- TBA
-* Add `json` data type ([#245](https://github.com/datajoint/datajoint-python/issues/245)) PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
-- Fix lingering prints by replacing with logs PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
-- `table.progress()` defaults to no stdout PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
-- `table.describe()` defaults to no stdout PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
+### 0.14.0 -- Feb 08, 2023
+* Add - `json` data type ([#245](https://github.com/datajoint/datajoint-python/issues/245)) PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
+* Bugfix - Convert lingering prints by replacing with logs PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
+* Update - `table.progress()` defaults to no stdout PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
+* Update - `table.describe()` defaults to no stdout PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
+* Bugfix - Activating a schema requires all tables to exist even if `create_tables=False` PR [#1058](https://github.com/datajoint/datajoint-python/pull/1058)
+* Update - Populate call with `reserve_jobs=True` to exclude `error` and `ignore` keys PR [#1062](https://github.com/datajoint/datajoint-python/pull/1062)
+* Add - Support for inserting data with CSV files PR [#1067](https://github.com/datajoint/datajoint-python/pull/1067)
 
 ### 0.13.8 -- Sep 21, 2022
 * Add - New documentation structure based on markdown PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)
@@ -276,7 +279,7 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 
 ### 0.3.4
 * Added method the `ERD.add_parts` method, which adds the part tables of all tables currently in the ERD.
-* `ERD() + arg` and `ERD() - arg` can now accept relation classes as arg.
+* `ERD() + arg` and `ERD() - arg` can now accept table classes as arg.
 
 ### 0.3.3
 * Suppressed warnings (redirected them to logging).  Previoiusly, scipy would throw warnings in ERD, for example.
@@ -286,5 +289,5 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 
 ### 0.3.2.
 * Fixed issue #223:  `insert` can insert relations without fetching.
-* ERD() now takes the `context` argument, which specifies in which context to look for classes. The default is taken from the argument (schema or relation).
+* ERD() now takes the `context` argument, which specifies in which context to look for classes. The default is taken from the argument (schema or table).
 * ERD.draw() no longer has the `prefix` argument: class names are shown as found in the context.

LNX-docker-compose.yml

@@ -37,7 +37,7 @@ services:
       interval: 15s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.2.3
+    image: datajoint/nginx:v0.2.4
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

README.md

@@ -112,15 +112,15 @@ important DataJoint schema or records.
 
 ### API docs
 
-The API documentation can be built using sphinx by running
+The API documentation can be built with mkdocs using the docker compose file in
+`docs/` with the following command:
 
 ``` bash
-pip install sphinx sphinx_rtd_theme 
-(cd docs-api/sphinx && make html)
+MODE="LIVE" PACKAGE=datajoint UPSTREAM_REPO=https://github.com/datajoint/datajoint-python.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
 ```
 
-Generated docs are written to `docs-api/docs/html/index.html`.
-More details in [docs-api/README.md](docs-api/README.md).
+The site will then be available at `http://localhost/`. When finished, be sure to run
+the same command as above, but replace `up --build` with `down`.
 
 ## Running Tests Locally
 <details>
@@ -141,11 +141,11 @@ HOST_GID=1000
 * Add entry in `/etc/hosts` for `127.0.0.1 fakeservices.datajoint.io`
 * Run desired tests. Some examples are as follows:
 
-| Use Case                     | Shell Code                                                                    |
-| ---------------------------- | ------------------------------------------------------------------------------ |
-| Run all tests                | `nosetests -vsw tests --with-coverage --cover-package=datajoint`                                                              |
-| Run one specific class test       | `nosetests -vs --tests=tests.test_fetch:TestFetch.test_getattribute_for_fetch1`                                                           |
-| Run one specific basic test        | `nosetests -vs --tests=tests.test_external_class:test_insert_and_fetch`                                   |
+| Use Case                     | Shell Code                                                                      |
+| ---------------------------- | ------------------------------------------------------------------------------  |
+| Run all tests                | `nosetests -vsw tests --with-coverage --cover-package=datajoint`                |
+| Run one specific class test  | `nosetests -vs --tests=tests.test_fetch:TestFetch.test_getattribute_for_fetch1` |
+| Run one specific basic test  | `nosetests -vs --tests=tests.test_external_class:test_insert_and_fetch`         |
 
 
 ### Launch Docker Terminal

datajoint/autopopulate.py

@@ -5,6 +5,7 @@
 import random
 import inspect
 from tqdm import tqdm
+from .hash import key_hash
 from .expression import QueryExpression, AndList
 from .errors import DataJointError, LostConnectionError
 import signal
@@ -43,8 +44,8 @@ def _call_populate1(key):
 
 class AutoPopulate:
     """
-    AutoPopulate is a mixin class that adds the method populate() to a Relation class.
-    Auto-populated relations must inherit from both Relation and AutoPopulate,
+    AutoPopulate is a mixin class that adds the method populate() to a Table class.
+    Auto-populated tables must inherit from both Table and AutoPopulate,
     must define the property `key_source`, and must define the callback method `make`.
     """
 
@@ -117,7 +118,7 @@ def _job_key(self, key):
 
     def _jobs_to_do(self, restrictions):
         """
-        :return: the relation containing the keys to be computed (derived from self.key_source)
+        :return: the query yeilding the keys to be computed (derived from self.key_source)
         """
         if self.restriction:
             raise DataJointError(
@@ -202,6 +203,16 @@ def handler(signum, frame):
             old_handler = signal.signal(signal.SIGTERM, handler)
 
         keys = (self._jobs_to_do(restrictions) - self.target).fetch("KEY", limit=limit)
+
+        # exclude "error" or "ignore" jobs
+        if reserve_jobs:
+            exclude_key_hashes = (
+                jobs
+                & {"table_name": self.target.table_name}
+                & 'status in ("error", "ignore")'
+            ).fetch("key_hash")
+            keys = [key for key in keys if key_hash(key) not in exclude_key_hashes]
+
         if order == "reverse":
             keys.reverse()
         elif order == "random":

datajoint/diagram.py

@@ -78,7 +78,7 @@ class Diagram(nx.DiGraph):
 
         >>>  diag = Diagram(source)
 
-        source can be a base relation object, a base relation class, a schema, or a module that has a schema.
+        source can be a base table object, a base table class, a schema, or a module that has a schema.
 
         >>> diag.draw()
 

datajoint/fetch.py

@@ -160,7 +160,7 @@ def __call__(
         unpacks blob attributes.
 
         :param attrs: zero or more attributes to fetch. If not provided, the call will return all attributes of this
-                        relation. If provided, returns tuples with an entry for each attribute.
+                        table. If provided, returns tuples with an entry for each attribute.
         :param offset: the number of tuples to skip in the returned result
         :param limit: the maximum number of tuples to return
         :param order_by: a single attribute or the list of attributes to order the results. No ordering should be assumed
@@ -172,7 +172,7 @@ def __call__(
                         True for .fetch('KEY')
         :param squeeze:  if True, remove extra dimensions from arrays
         :param download_path: for fetches that download data, e.g. attachments
-        :return: the contents of the relation in the form of a structured numpy.array or a dict list
+        :return: the contents of the table in the form of a structured numpy.array or a dict list
         """
         if order_by is not None:
             # if 'order_by' passed in a string, make into list
@@ -319,7 +319,7 @@ def __call__(self, *attrs, squeeze=False, download_path="."):
                  If attrs is empty, the return result is a dict
         :param squeeze:  When true, remove extra dimensions from arrays in attributes
         :param download_path: for fetches that download data, e.g. attachments
-        :return: the one tuple in the relation in the form of a dict
+        :return: the one tuple in the table in the form of a dict
         """
         heading = self._expression.heading
 

datajoint/heading.py

@@ -85,7 +85,7 @@ def original_name(self):
 
 class Heading:
     """
-    Local class for relations' headings.
+    Local class for table headings.
     Heading contains the property attributes, which is an dict in which the keys are
     the attribute names and the values are Attributes.
     """

datajoint/jobs.py

@@ -12,7 +12,7 @@
 
 class JobTable(Table):
     """
-    A base relation with no definition. Allows reserving jobs
+    A base table with no definition. Allows reserving jobs
     """
 
     def __init__(self, conn, database):

datajoint/preview.py

@@ -56,20 +56,20 @@ def repr_html(query_expression):
 
     css = """
     <style type="text/css">
-        .Relation{
+        .Table{
             border-collapse:collapse;
         }
-        .Relation th{
+        .Table th{
             background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;
             font-weight: normal; font-family: monospace; font-size: 100%;
         }
-        .Relation td{
+        .Table td{
             padding:4px; border:#f0e0e0 1px solid; font-size:100%;
         }
-        .Relation tr:nth-child(odd){
+        .Table tr:nth-child(odd){
             background: #ffffff;
         }
-        .Relation tr:nth-child(even){
+        .Table tr:nth-child(even){
             background: #f3f1ff;
         }
         /* Tooltip container */
@@ -111,7 +111,7 @@ def repr_html(query_expression):
     {css}
     {title}
         <div style="max-height:1000px;max-width:1500px;overflow:auto;">
-        <table border="1" class="Relation">
+        <table border="1" class="Table">
             <thead> <tr style="text-align: right;"> <th> {head} </th> </tr> </thead>
             <tbody> <tr> {body} </tr> </tbody>
         </table>