💯 🧼 Finalize PyKEEN 1.5.0 (pykeen#449)

* Fix entrypoints * Update translational_toy_example.rst * Update moves.py * Bump version: 1.4.1-dev → 1.5.0-dev * Update README * Update README.md * Add funding section * Add details box * Update header * Revert * Add pygments to doctests environment This is used by doctests for nice colored output * Update funding * Update author information in setup * Update README.md * Update setup.cfg * Update README.md * Improve grammar * Update conf.py * Update setup.cfg * Create .mailmap * Update CHANGELOG.rst * Final update Trigger CI * Update MANIFEST.in Trigger CI Co-authored-by: Laurent Vermue <lvermue@users.noreply.github.com> Co-authored-by: Max Berrendorf <berrendorf@dbs.ifi.lmu.de>
gaybro8777 · Jun 13, 2021 · df53e4c · df53e4c
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1-dev
+current_version = 1.5.0-dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?

diff --git a/.mailmap b/.mailmap
@@ -0,0 +1,8 @@
+Laurent Vermue <lauve@dtu.dk> Laurent Vermue <l.vermue@me.com>
+Laurent Vermue <lauve@dtu.dk> Laurent Vermue <lvermue@users.noreply.github.com>
+Daniel Domingo-Fernández <danieldomingofernandez@hotmail.com> ddomingof <danieldomingofernandez@hotmail.com>
+Daniel Domingo-Fernández <danieldomingofernandez@hotmail.com> daniel.domingo.fernandez <danieldomingofernandez@hotmail.com>
+Mehdi Ali <ali-mehdi@live.de> mali <ali-mehdi@live.de>
+Mehdi Ali <ali-mehdi@live.de> Mehdi Ali <33023925+mali-git@users.noreply.github.com>
+Anna Breit <anna@breit-mail.at> anna <anna@breit-mail.at>
+Sahand Sharifzadeh <sahand.sharifzadeh@gmail.com>
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -5,8 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
 and this project adheres to `Semantic Versioning <http://semver.org/>`_
 
-`Unreleased <https://github.com/pykeen/pykeen/compare/v1.4.0...HEAD>`_
+`Unreleased <https://github.com/pykeen/pykeen/compare/v1.5.0...HEAD>`_
 -----------------------------------------------------------------------
+
+`1.5.0 <https://github.com/pykeen/pykeen/compare/v1.4.0...v1.5.0>`_ - 2021-06-13
+--------------------------------------------------------------------------------
 New Metrics
 ~~~~~~~~~~~
 - Adjusted Arithmetic Mean Rank Index (https://github.com/pykeen/pykeen/pull/378)
@@ -22,32 +25,60 @@ New Models
 - QuatE (https://github.com/pykeen/pykeen/pull/367)
 - CompGCN (https://github.com/pykeen/pykeen/pull/382)
 - CrossE (https://github.com/pykeen/pykeen/pull/467)
+- Reimplementation of LiteralE with arbitrary combination (g) function (https://github.com/pykeen/pykeen/pull/245)
+
+New Negative Samplers
+~~~~~~~~~~~~~~~~~~~~~
+- Pseudo-typed Negative Sampler (https://github.com/pykeen/pykeen/pull/412)
 
 Datasets
 ~~~~~~~~
-- Removed invalid datasets (OpenBioLink filtered sets; https://github.com/pykeen/pykeen/pull/#439)
+- Removed invalid datasets (OpenBioLink filtered sets; https://github.com/pykeen/pykeen/pull/https://github.com/pykeen/pykeen/pull/439)
+- Added WK3k-15K (https://github.com/pykeen/pykeen/pull/403)
+- Added WK3l-120K (https://github.com/pykeen/pykeen/pull/403)
+- Added CN3l (https://github.com/pykeen/pykeen/pull/403)
 
 Added
 ~~~~~
 - Documentation on using PyKEEN in Google Colab and Kaggle (https://github.com/pykeen/pykeen/pull/379,
   thanks `@jerryIsHere <https://github.com/jerryIsHere>`_)
-- Documentation on
 - Pass custom training loops to pipeline (https://github.com/pykeen/pykeen/pull/334)
 - Compatibility later for the fft module (https://github.com/pykeen/pykeen/pull/288)
 - Official Python 3.9 support, now that PyTorch has it (https://github.com/pykeen/pykeen/pull/223)
 - Utilities for dataset analysis (https://github.com/pykeen/pykeen/pull/16, https://github.com/pykeen/pykeen/pull/392)
+- Filtering of negative sampling now uses a bloom filter by default (https://github.com/pykeen/pykeen/pull/401)
+- Optional embedding dropout (https://github.com/pykeen/pykeen/pull/422)
+- Added more HPO suggestion methods and docs (https://github.com/pykeen/pykeen/pull/446)
+- Training callbacks (https://github.com/pykeen/pykeen/pull/429)
+- Class resolver for datasets (https://github.com/pykeen/pykeen/pull/473)
+
 Updated
 ~~~~~~~
 - R-GCN implementation now uses new-style models and is super idiomatic (https://github.com/pykeen/pykeen/pull/110)
-
-Changed
-~~~~~~~
+- Enable passing of interaction function by string in base model class (https://github.com/pykeen/pykeen/pull/384,
+  https://github.com/pykeen/pykeen/pull/387)
+- Bump scipy requirement to 1.5.0+
 - Updated interfaces of models and negative samplers to enforce kwargs (https://github.com/pykeen/pykeen/pull/445)
+- Reorganize filtering, negative sampling, and remove triples factory from most objects (
+  https://github.com/pykeen/pykeen/pull/400, https://github.com/pykeen/pykeen/pull/405,
+  https://github.com/pykeen/pykeen/pull/406, https://github.com/pykeen/pykeen/pull/409,
+  https://github.com/pykeen/pykeen/pull/420)
+- Update automatic memory optimization (https://github.com/pykeen/pykeen/pull/404)
+- Flexibly define positive triples for filtering (https://github.com/pykeen/pykeen/pull/398)
+- Completely reimplemented negative sampling interface in training loops (https://github.com/pykeen/pykeen/pull/427)
+- Completely reimplemented loss function in training loops (https://github.com/pykeen/pykeen/pull/448)
+- Forward-compatibility of embeddings in old-style models and updated docs on
+  how to use embeddings (https://github.com/pykeen/pykeen/pull/474)
 
 Fixed
 ~~~~~
 - Regularizer passing in the pipeline and HPO (https://github.com/pykeen/pykeen/pull/345)
 - Saving results when using multimodal models (https://github.com/pykeen/pykeen/pull/349)
+- Add missing diagonal constraint on MuRE Model (https://github.com/pykeen/pykeen/pull/353)
+- Fix early stopper handling (https://github.com/pykeen/pykeen/pull/419)
+- Fixed saving results from pipeline (https://github.com/pykeen/pykeen/pull/428, thanks @kantholtz)
+- Fix OOM issues with early stopper and AMO (https://github.com/pykeen/pykeen/pull/433)
+- Fix ER-MLP functional form (https://github.com/pykeen/pykeen/pull/444)
 
 `1.4.0 <https://github.com/pykeen/pykeen/compare/v1.3.0...v1.4.0>`_ - 2021-03-04
 --------------------------------------------------------------------------------

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -15,5 +15,5 @@ include config/config.ini
 
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 
-exclude .bumpversion.cfg .coveragerc .flake8 .travis.yml .readthedocs.yml tox.ini .pre-commit-config.yaml
+exclude .bumpversion.cfg .coveragerc .flake8 .travis.yml .readthedocs.yml tox.ini .pre-commit-config.yaml .mailmap
 include LICENSE *.md *.rst
diff --git a/README.md b/README.md
@@ -340,10 +340,12 @@ This project has been supported by several organizations (in alphabetical order)
 
 The development of PyKEEN has been funded by the following grants:
 
-| Funding Body                                             | Program                                                                                                                       | Grant         |
-|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|---------------|
-| DARPA                                                    | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |
-| German Federal Ministry of Education and Research (BMBF) | [Maschinelles Lernen mit Wissensgraphen (MLWin)](https://mlwin.de)                                                            | 01IS18050D    |
+| Funding Body                                             | Program                                                                                                                       | Grant           |
+|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------|
+| DARPA                                                    | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009   |
+| German Federal Ministry of Education and Research (BMBF) | [Maschinelles Lernen mit Wissensgraphen (MLWin)](https://mlwin.de)                                                            | 01IS18050D      |
+| German Federal Ministry of Education and Research (BMBF) | [Munich Center for Machine Learning (MCML)](https://mcml.ai)                                                            | 01IS18036A      |
+| Innovation Fund Denmark (Innovationsfonden)              | [Danish Center for Big Data Analytics driven Innovation (DABAI)](https://dabai.dk)                                            | Grand Solutions |
 
 ### Logo
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -52,7 +52,7 @@
 author = 'PyKEEN Project Team'
 
 # The full version, including alpha/beta/rc tags.
-release = '1.4.1-dev'
+release = '1.5.0-dev'
 
 # The short X.Y version.
 parsed_version = re.match(
@@ -263,3 +263,6 @@
 }
 
 autoclass_content = 'both'
+# autodoc_member_order = 'bysource'
+# autodoc_typehints = 'both' # TODO turn on after 4.1 release
+# autodoc_preserve_defaults = True
diff --git a/setup.cfg b/setup.cfg
@@ -16,10 +16,10 @@ project_urls =
     Bug Tracker = https://github.com/pykeen/pykeen/issues
 
 # Author information
-author = Mehdi Ali
-author_email = mehdi.ali@cs.uni-bonn.de
-maintainer = Mehdi Ali
-maintainer_email = mehdi.ali@cs.uni-bonn.de
+author = "Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue"
+author_email = "<mehdi.ali@cs.uni-bonn.de>, <max.berrendorf@gmail.com>, <cthoyt@gmail.com>, <lauve@dtu.dk>"
+maintainer = "Mehdi Ali, Max Berrendorf, Charles Tapley Hoyt, Laurent Vermue"
+maintainer_email = "<mehdi.ali@cs.uni-bonn.de>, <max.berrendorf@gmail.com>, <cthoyt@gmail.com>, <lauve@dtu.dk>"
 
 # License information
 license = MIT

diff --git a/src/pykeen/losses.py b/src/pykeen/losses.py
@@ -586,7 +586,7 @@ def __init__(self, margin: float = 9.0, adversarial_temperature: float = 1.0, re
             The name of the reduction operation to aggregate the individual loss values from a batch to a scalar loss
             value. From {'mean', 'sum'}.
 
-        .. note:: The default hyperparameters are based the experiments for FB15k-237 in [sun2019]_.
+        .. note:: The default hyperparameters are based on the experiments for FB15k-237 in [sun2019]_.
         """
         super().__init__(reduction=reduction)
         self.inverse_softmax_temperature = adversarial_temperature

diff --git a/src/pykeen/models/cli/builders.py b/src/pykeen/models/cli/builders.py
@@ -9,12 +9,14 @@
 from typing import Any, Mapping, Optional, Type, Union
 
 import click
+from class_resolver import HintOrType
 from torch import nn
 
 from . import options
 from .options import CLI_OPTIONS
 from ..base import Model
 from ...nn.message_passing import Decomposition
+from ...regularizers import Regularizer
 from ...triples import TriplesFactory
 from ...typing import Constrainer, Hint, Initializer, Normalizer
 
@@ -44,6 +46,14 @@
     Optional[Mapping[str, Any]],
     Union[None, str, nn.Module],
     Union[None, str, Decomposition],
+
+}
+_SKIP_HINTS = {
+    Hint[Initializer],
+    Hint[Constrainer],
+    Hint[Normalizer],
+    Hint[Regularizer],
+    HintOrType[nn.Module],
 }
 
 
@@ -68,7 +78,7 @@ def _decorate_model_kwargs(command: click.Command) -> click.Command:
 
             else:
                 parameter = signature.parameters[name]
-                if annotation in {Hint[Initializer], Hint[Constrainer], Hint[Normalizer]}:  # type: ignore
+                if annotation in _SKIP_HINTS:
                     logger.debug('Unhandled hint: %s', annotation)
                     continue
                 if parameter.default is None:

diff --git a/src/pykeen/models/cli/options.py b/src/pykeen/models/cli/options.py
@@ -84,6 +84,10 @@ def _callback(_, __, value):
         '--clamp-score',
         type=float,
     ),
+    'combination_dropout': click.option(
+        '--combination-dropout',
+        type=float,
+    ),
 }
 
 device_option = click.option(

diff --git a/src/pykeen/templates/README.md b/src/pykeen/templates/README.md
@@ -224,10 +224,12 @@ This project has been supported by several organizations (in alphabetical order)
 
 The development of PyKEEN has been funded by the following grants:
 
-| Funding Body                                             | Program                                                                                                                       | Grant         |
-|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|---------------|
-| DARPA                                                    | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |
-| German Federal Ministry of Education and Research (BMBF) | [Maschinelles Lernen mit Wissensgraphen (MLWin)](https://mlwin.de)                                                            | 01IS18050D    |
+| Funding Body                                             | Program                                                                                                                       | Grant           |
+|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------|
+| DARPA                                                    | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009   |
+| German Federal Ministry of Education and Research (BMBF) | [Maschinelles Lernen mit Wissensgraphen (MLWin)](https://mlwin.de)                                                            | 01IS18050D      |
+| German Federal Ministry of Education and Research (BMBF) | [Munich Center for Machine Learning (MCML)](https://mcml.ai)                                                            | 01IS18036A      |
+| Innovation Fund Denmark (Innovationsfonden)              | [Danish Center for Big Data Analytics driven Innovation (DABAI)](https://dabai.dk)                                            | Grand Solutions |
 
 ### Logo
 

diff --git a/src/pykeen/version.py b/src/pykeen/version.py
@@ -16,7 +16,7 @@
     'env',
 ]
 
-VERSION = '1.4.1-dev'
+VERSION = '1.5.0-dev'
 
 
 @lru_cache(maxsize=2)
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,7 +16,7 @@ @@
         'env',
     ]
-    VERSION = '1.4.1-dev'
+    VERSION = '1.5.0-dev'
     @lru_cache(maxsize=2)
@@ Expand Down @@