Merge pull request datajoint#939 from rly/fix/np_deprecations

Replace use of numpy aliases of built-in types with built-in type

Author: guzman-raphael

CHANGELOG.md

@@ -1,7 +1,8 @@
 ## Release notes
 
-### 0.13.3 -- May 28, 2021
+### 0.13.3 -- TBD
 * 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
 
 ### 0.13.2 -- May 7, 2021
 * Update `setuptools_certificate` dependency to new name `otumat`
@@ -44,13 +45,13 @@
 * Fix display of part tables in `schema.save`. (#821) PR #833
 * Add `schema.list_tables`. (#838) PR #844
 * Fix minio new version regression.  PR #847
-* Add more S3 logging for debugging. (#831) PR #832 
+* Add more S3 logging for debugging. (#831) PR #832
 * Convert testing framework from TravisCI to GitHub Actions (#841) PR #840
- 
+
 ### 0.12.7 -- Oct 27, 2020
 * Fix case sensitivity issues to adapt to MySQL 8+.  PR #819
 * Fix pymysql regression bug (#814) PR #816
-* Adapted attribute types now have dtype=object in all recarray results. PR #811 
+* Adapted attribute types now have dtype=object in all recarray results. PR #811
 
 ### 0.12.6 -- May 15, 2020
 * Add `order_by` to `dj.kill` (#668, #779) PR #775, #783
@@ -142,9 +143,9 @@
 * Bugfix in restriction of the form (A & B) * B (#463)
 * Improved error messages (#466)
 
-### 0.10.0 -- Jan 10, 2018 
+### 0.10.0 -- Jan 10, 2018
 * Deletes are more efficient (#424)
-* ERD shows table definition on tooltip hover in Jupyter (#422) 
+* ERD shows table definition on tooltip hover in Jupyter (#422)
 * S3 external storage
 * Garbage collection for external sorage
 * Most operators and methods of tables can be invoked as class methods rather than instance methods (#407)
@@ -158,7 +159,7 @@
 * Implement union operator +
 * Implement file-based external storage
 
-### 0.8.0 -- Jul 26, 2017 
+### 0.8.0 -- Jul 26, 2017
 Documentation and tutorials available at https://docs.datajoint.io and https://tutorials.datajoint.io
 * improved the ERD graphics and features using the graphviz libraries (#207, #333)
 * improved password handling logic (#322, #321)
@@ -177,11 +178,11 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 * Added `dj.create_virtual_module`
 
 ### 0.4.10 (#286) -- Feb 6, 2017
-* Removed Vagrant and Readthedocs support 
+* Removed Vagrant and Readthedocs support
 * Explicit saving of configuration (issue #284)
 
 ### 0.4.9 (#285) -- Feb 2, 2017
-* Fixed setup.py for pip install 
+* Fixed setup.py for pip install
 
 ### 0.4.7 (#281) -- Jan 24, 2017
 * Fixed issues related to order of attributes in projection.
@@ -210,10 +211,10 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 
 ### 0.3.8  -- Aug 2, 2016
 * added the `_update` method in `base_relation`. It allows updating values in existing tuples.
-* bugfix in reading values of type double.  Previously it was cast as float32. 
+* bugfix in reading values of type double.  Previously it was cast as float32.
 
 ### 0.3.7  -- Jul 31, 2016
-* added parameter `ignore_extra_fields` in `insert` 
+* added parameter `ignore_extra_fields` in `insert`
 * `insert(..., skip_duplicates=True)` now relies on `SELECT IGNORE`.  Previously it explicitly checked if tuple already exists.
 * table previews now include blob attributes displaying the string <BLOB>
 

LNX-docker-compose.yml

@@ -32,7 +32,7 @@ services:
       interval: 1s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.0.16
+    image: datajoint/nginx:v0.0.17
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306

datajoint/blob.py

@@ -164,7 +164,7 @@ def pack_blob(self, obj):
             return self.pack_recarray(np.array(obj))
         if isinstance(obj, np.number):
             return self.pack_array(np.array(obj))
-        if isinstance(obj, (np.bool, np.bool_)):
+        if isinstance(obj, (bool, np.bool_)):
             return self.pack_array(np.array(obj))
         if isinstance(obj, (datetime.datetime, datetime.date, datetime.time)):
             return self.pack_datetime(obj)
@@ -365,7 +365,7 @@ def read_struct(self):
         raw_data = [
             tuple(self.read_blob(n_bytes=int(self.read_value('uint64'))) for _ in range(n_fields))
             for __ in range(n_elem)]
-        data = np.array(raw_data, dtype=list(zip(field_names, repeat(np.object))))
+        data = np.array(raw_data, dtype=list(zip(field_names, repeat(object))))
         return self.squeeze(data.reshape(shape, order="F"), convert_to_scalar=False).view(MatStruct)
 
     def pack_struct(self, array):

datajoint/table.py

@@ -586,7 +586,7 @@ def _update(self, attrname, value=None):
             value = blob.pack(value)
             placeholder = '%s'
         elif attr.numeric:
-            if value is None or np.isnan(np.float(value)):  # nans are turned into NULLs
+            if value is None or np.isnan(float(value)):  # nans are turned into NULLs
                 placeholder = 'NULL'
                 value = None
             else:
@@ -615,7 +615,7 @@ def __make_placeholder(self, name, value, ignore_extra_fields=False):
         attr = self.heading[name]
         if attr.adapter:
             value = attr.adapter.put(value)
-        if value is None or (attr.numeric and (value == '' or np.isnan(np.float(value)))):
+        if value is None or (attr.numeric and (value == '' or np.isnan(float(value)))):
             # set default value
             placeholder, value = 'DEFAULT', None
         else:  # not NULL

docs-parts/intro/Releases_lang1.rst

@@ -1,6 +1,7 @@
-0.13.3 -- May 28, 2021
+0.13.3 -- TBD
 ----------------------
 * 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
 
 0.13.2 -- May 7, 2021
 ----------------------
@@ -48,14 +49,14 @@
 * Fix display of part tables in `schema.save`. (#821) PR #833
 * Add `schema.list_tables`. (#838) PR #844
 * Fix minio new version regression.  PR #847
-* Add more S3 logging for debugging. (#831) PR #832 
+* Add more S3 logging for debugging. (#831) PR #832
 * Convert testing framework from TravisCI to GitHub Actions (#841) PR #840
 
 0.12.7 -- Oct 27, 2020
 ----------------------
 * Fix case sensitivity issues to adapt to MySQL 8+.  PR #819
 * Fix pymysql regression bug (#814) PR #816
-* Adapted attribute types now have `dtype=object` in all recarray results. PR #811 
+* Adapted attribute types now have `dtype=object` in all recarray results. PR #811
 
 0.12.6 -- May 15, 2020
 ----------------------
@@ -151,10 +152,10 @@
 * Bugfix in restriction of the form (A & B) * B (#463)
 * Improved error messages (#466)
 
-0.10.0 -- Jan 10, 2018 
+0.10.0 -- Jan 10, 2018
 ----------------------
 * Deletes are more efficient (#424)
-* ERD shows table definition on tooltip hover in Jupyter (#422) 
+* ERD shows table definition on tooltip hover in Jupyter (#422)
 * S3 external storage
 * Garbage collection for external sorage
 * Most operators and methods of tables can be invoked as class methods rather than instance methods (#407)
@@ -169,7 +170,7 @@
 * Implement union operator +
 * Implement file-based external storage
 
-0.8.0 -- Jul 26, 2017 
+0.8.0 -- Jul 26, 2017
 ---------------------
 Documentation and tutorials available at https://docs.datajoint.io and https://tutorials.datajoint.io
 * improved the ERD graphics and features using the graphviz libraries (#207, #333)
@@ -191,12 +192,12 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 
 0.4.10 (#286) -- Feb 6, 2017
 ----------------------------
-* Removed Vagrant and Readthedocs support 
+* Removed Vagrant and Readthedocs support
 * Explicit saving of configuration (issue #284)
 
 0.4.9 (#285) -- Feb 2, 2017
 ---------------------------
-* Fixed setup.py for pip install 
+* Fixed setup.py for pip install
 
 0.4.7 (#281) -- Jan 24, 2017
 ----------------------------
@@ -233,11 +234,11 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 0.3.8  -- Aug 2, 2016
 ---------------------
 * added the ``_update`` method in ``base_relation``. It allows updating values in existing tuples.
-* bugfix in reading values of type double.  Previously it was cast as float32. 
+* bugfix in reading values of type double.  Previously it was cast as float32.
 
 0.3.7  -- Jul 31, 2016
 ----------------------
-* added parameter ``ignore_extra_fields`` in ``insert`` 
+* added parameter ``ignore_extra_fields`` in ``insert``
 * ``insert(..., skip_duplicates=True)`` now relies on ``SELECT IGNORE``.  Previously it explicitly checked if tuple already exists.
 * table previews now include blob attributes displaying the string <BLOB>
 
@@ -263,7 +264,7 @@ Documentation and tutorials available at https://docs.datajoint.io and https://t
 * ERD() no longer text the context argument.
 * ERD.draw() now takes an optional context argument.  By default uses the caller's locals.
 
-0.3.2   
+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).

local-docker-compose.yml

@@ -34,7 +34,7 @@ services:
       interval: 1s
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.0.16
+    image: datajoint/nginx:v0.0.17
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306