Merge pull request #48 from bio-ontology-research-group/inductive

Inductive

Author: ferzcam

.github/workflows/python-package_3_8.yml

@@ -37,7 +37,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest coverage
+        python -m pip install flake8 nose pinocchio nose-exclude coverage
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
       run: |
@@ -47,4 +47,4 @@ jobs:
         flake8 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
     - name: Test with nose
       run: |
-        pytest tests
+        nosetests tests

.github/workflows/python-package_3_9.yml

@@ -37,7 +37,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest coverage
+        python -m pip install flake8 nose pinocchio nose-exclude coverage
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
       run: |
@@ -47,4 +47,4 @@ jobs:
         flake8 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics
     - name: Test with nose
       run: |
-        pytest tests
+        nosetests tests

CHANGELOG.md

@@ -8,8 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 ### Added
 - [BoxSquaredEL](https://arxiv.org/abs/2301.11118) module added to `mowl.nn`
+- Implemented `model.from_pretrained` method. Related to issue #43
 - Implemented `model.add_axioms` method. Related to issue #43
-- Added models `RandomWalkPlusW2VModel`, `GraphPlusPyKEENModel`, `SyntacticPlusW2VModel`
+- Added models `RandomWalkPlusW2VModel`, `GraphPlusPyKEENModel`, `SyntacticPlusW2VModel`, 
 
 ### Changed
 - Bug fixed in corpus generation methods. Issue #36.

envs/environment_dev_3_8.yml

@@ -14,7 +14,6 @@ dependencies:
   - JPype1
   - pandas
   - protobuf
-  - pytest
   - pyyaml
   - requests
   - scipy
@@ -29,8 +28,10 @@ dependencies:
     - build
     - pykeen>=1.9.*
     - sphinx-rtd-theme
-    - pytest
+    - nose
+    - nose-exclude
     - coverage
+    - pinocchio
     - flake8
     - autopep8
     - memory-profiler

envs/environment_dev_3_9.yml

@@ -14,7 +14,6 @@ dependencies:
   - JPype1
   - pandas
   - protobuf
-  - pytest
   - pyyaml
   - requests
   - scipy
@@ -29,8 +28,10 @@ dependencies:
     - build
     - pykeen>=1.9.*
     - sphinx-rtd-theme
-    - pytest
+    - nose
+    - nose-exclude
     - coverage
+    - pinocchio
     - flake8
     - autopep8
     - memory-profiler

test.sh

@@ -0,0 +1 @@
+coverage run -m pytest tests && coverage report -m

tests/__init__.py

@@ -7,11 +7,10 @@
 from mowl.datasets.builtin import FamilyDataset, GDAHumanELDataset, GDAMouseELDataset, \
     PPIYeastSlimDataset
 
-
 logger = logging.getLogger("Downloader")
 
-
-def setUpPackage():
+def setUpModule():
+    print("Downloading datasets")
     logger.info("Downloading family dataset")
     FamilyDataset()
     logger.info("Downloading gda_el_human dataset")
@@ -22,12 +21,16 @@ def setUpPackage():
     PPIYeastSlimDataset()
 
 
-# def tearDownPackage():
-    # os.remove('ppi_yeast_slim.tar.gz')
-    # os.remove('gda_human_el.tar.gz')
-    # os.remove('gda_mouse_el.tar.gz')
-    # os.remove('family.tar.gz')
-    # shutil.rmtree('ppi_yeast_slim')
-    # shutil.rmtree('gda_human_el')
-    # shutil.rmtree('gda_mouse_el')
-    # shutil.rmtree('family')
+def tearDownModule():
+    os.remove('ppi_yeast_slim.tar.gz')
+    os.remove('gda_human_el.tar.gz')
+    os.remove('gda_mouse_el.tar.gz')
+    os.remove('family.tar.gz')
+    shutil.rmtree('ppi_yeast_slim')
+    shutil.rmtree('gda_human_el')
+    shutil.rmtree('gda_mouse_el')
+    shutil.rmtree('family')
+
+
+
+

tests/base_models/test_elmodel.py

@@ -2,7 +2,7 @@
 from mowl.base_models.elmodel import EmbeddingELModel
 from mowl.base_models.model import EmbeddingModel
 from mowl.datasets import Dataset
-from mowl.datasets.builtin import FamilyDataset, PPIYeastSlimDataset
+from tests.datasetFactory import FamilyDataset, PPIYeastSlimDataset
 from mowl.datasets.el import ELDataset
 from mowl.models import ELEmbeddings
 import random

tests/models/test_elboxembeddings_gda.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from mowl.datasets.builtin import GDAHumanELDataset
+from tests.datasetFactory import GDAHumanELDataset
 from mowl.models.elboxembeddings.examples.model_gda import ELBoxGDA
 
 

tests/models/test_elboxembeddings_ppi.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from mowl.datasets.builtin import PPIYeastSlimDataset
+from tests.datasetFactory import PPIYeastSlimDataset
 from mowl.models.elboxembeddings.examples.model_ppi import ELBoxPPI
 
 

tests/models/test_elembeddings_gda.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from mowl.datasets.builtin import GDAHumanELDataset
+from tests.datasetFactory import GDAHumanELDataset
 from mowl.models.elembeddings.examples.model_gda import ELEmGDA
 
 

tests/models/test_elembeddings_ppi.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from mowl.datasets.builtin import PPIYeastSlimDataset
+from tests.datasetFactory import PPIYeastSlimDataset
 from mowl.models.elembeddings.examples.model_ppi import ELEmPPI
 
 

tests/models/test_falcon_ppi.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-from mowl.datasets.builtin import PPIYeastSlimDataset
+from tests.datasetFactory import PPIYeastSlimDataset
 from mowl.models.falcon.examples.model_ppi import FALCON
 from mowl.datasets import Dataset
 from mowl.owlapi import OWLAPIAdapter

tests/ontology/test_normalize.py

@@ -1,7 +1,7 @@
 from unittest import TestCase
 from mowl.ontology.normalize import ELNormalizer, GCI, GCI0, GCI1, GCI2, GCI3, GCI0_BOT, \
     GCI1_BOT, GCI3_BOT, process_axiom
-from mowl.datasets.builtin import FamilyDataset
+from tests.datasetFactory import FamilyDataset
 from mowl.owlapi import OWLAPIAdapter
 from mowl.owlapi.defaults import BOT
 

tests/projection/test_owl2vec.py

@@ -3,7 +3,7 @@
 from unittest import TestCase
 from mowl.owlapi.defaults import TOP
 from mowl.owlapi import OWLAPIAdapter
-from mowl.datasets.builtin import FamilyDataset
+from tests.datasetFactory import FamilyDataset
 from org.semanticweb.owlapi.model import IRI
 
 import jpype.imports