Fix some bugs in test workflows (#10)

* Fix import order in python test files

* Fix working directories in test workflows

* Fix run command in python test workflows

* Add install of matplotlib to build workflow

* Add compilation of c++ binding in python workflow

* Add installation of pybind11 to workflow

* Change compilation command in workflow

* Looking for "pybind11.h"

* Install the library in test workflow

* Update to python 3.11 for conda workflow

* Update to python 3.10 in conda env

* Update to python 3.11 in conda env

* Trying to fix conda dependencies error

* Fix path in anaconda workflow

.env/test_env.yml

@@ -1,6 +1,6 @@
 name: test-with-conda
 dependencies:
-  - python==3.8
+  - python>=3.10
   - numpy
   - matplotlib
   - scikit-learn

.github/workflows/make.yml

@@ -23,7 +23,7 @@ jobs:
         sudo apt-get install -y doctest
     # Sets up Python on the machine with the right version
     - name: Compile and run the C++ tests
+      working-directory: ${{github.workspace}}/CLUEstering/include/test
       run: |
-        cd ./CLUEstering/include/test/ && make
-        ./run_tests.sh
+        make && ./run_tests.sh
 

.github/workflows/python-package-anaconda.yml

@@ -15,10 +15,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: "3.11"
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
@@ -33,7 +33,11 @@ jobs:
     #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
     #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
     #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+    - name: Install locally
+      working-directory: ${{github.workspace}}
       run: |
         pip install .
-        ./tests/run_test.sh
+    - name: Test with pytest
+      working-directory: ${{github.workspace}}/tests
+      run: |
+        python3 -m pytest ./*.py

.github/workflows/python-package.yml

@@ -31,12 +31,19 @@ jobs:
         python -m pip install flake8 pytest
         python -m pip install scikit-learn 
         python -m pip install pandas
+        python -m pip install matplotlib
+        python -m pip install pybind11
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install CLUEstering
+      working-directory: ${{github.workspace}}
+      run: |
+        pip install .
     - name: Run tests of the Python library
+      working-directory: ${{github.workspace}}/tests
       run: |
-        ./tests/run_test.sh 
+        python3 -m pytest ./*.py

tests/test_blob_dataset.py

@@ -4,13 +4,13 @@
 '''
 
 from filecmp import cmp
-import CLUEstering as clue
 import numpy as np
 import os
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_change_domains.py

@@ -3,11 +3,11 @@
 '''
 
 from math import pi
-import CLUEstering as clue
 import numpy as np
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_circles_dataset.py

@@ -4,13 +4,13 @@
 '''
 
 from filecmp import cmp
-import CLUEstering as clue
 import numpy as np
 import os
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_clusterer_equality.py

@@ -2,11 +2,11 @@
 Test that the equality operator for clusterer objects works correctly
 '''
 
-import CLUEstering as clue
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_domain_extremes.py

@@ -3,11 +3,11 @@
 '''
 
 from math import pi
-import CLUEstering as clue
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_input_datatypes.py

@@ -2,12 +2,12 @@
 Testing the algorithm with all the supported input data types
 '''
 
-import CLUEstering as clue
 import numpy as np
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 def test_read_array_except():

tests/test_kernels.py

@@ -2,10 +2,10 @@
 Test of the convolutional kernels
 '''
 
-import CLUEstering as clue
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 def test_flat_kernel_except():

tests/test_moons_dataset.py

@@ -4,12 +4,12 @@
 '''
 
 from filecmp import cmp
-import CLUEstering as clue
 import os
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_sissa_dataset.py

@@ -4,12 +4,12 @@
 '''
 
 from filecmp import cmp
-import CLUEstering as clue
 import os
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture

tests/test_test_blobs.py

@@ -2,10 +2,10 @@
 Test the test_blobs function, which produces a set of gaussianely distributed blobs
 '''
 
-import CLUEstering as clue
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 def test_except_1():

tests/test_toydetector_dataset.py

@@ -4,12 +4,12 @@
 '''
 
 from filecmp import cmp
-import CLUEstering as clue
 import os
 import pandas as pd
 import pytest
 import sys
 sys.path.insert(1, '../CLUEstering/')
+import CLUEstering as clue
 
 
 @pytest.fixture