From a425602391b4e1d7e1b6953be7cf1135ebb789f4 Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Wed, 3 Apr 2024 07:50:14 +0100
Subject: [PATCH] Fix doctests

---
 python/Makefile                |  2 +-
 python/src/conftest.py         |  6 ++++++
 python/src/moocore/_moocore.py | 33 +++++++++++++--------------------
 python/tests/conftest.py       |  2 --
 python/tests/test_moocore.py   | 18 +++++++++---------
 python/tox.ini                 | 12 +++++++++---
 6 files changed, 38 insertions(+), 35 deletions(-)
 create mode 100644 python/src/conftest.py

diff --git a/python/Makefile b/python/Makefile
index 86f7a97d..e0cb3cea 100644
--- a/python/Makefile
+++ b/python/Makefile
@@ -1,7 +1,7 @@
 .PHONY : install build test doc clean
 
 install: build
-	python3 -m pip install -e .
+	python3 -m pip install -e . --disable-pip-version-check
 
 build:
 	python3 -m build
diff --git a/python/src/conftest.py b/python/src/conftest.py
new file mode 100644
index 00000000..4aeb7261
--- /dev/null
+++ b/python/src/conftest.py
@@ -0,0 +1,6 @@
+import pytest
+import moocore
+
+@pytest.fixture(autouse=True)
+def add_doctest_imports(doctest_namespace) -> None:
+    doctest_namespace["moocore"] = moocore
diff --git a/python/src/moocore/_moocore.py b/python/src/moocore/_moocore.py
index 5512a608..f2f5b0e3 100644
--- a/python/src/moocore/_moocore.py
+++ b/python/src/moocore/_moocore.py
@@ -405,20 +405,17 @@ def filter_dominated_within_sets(data, maximise=False, keep_weakly=False):
     >>> x = moocore.read_datasets("./doc/examples/input1.dat")
     >>> pf_per_set = moocore.filter_dominated_within_sets(x)
     >>> len(pf_per_set)
+    42
     >>> pf = moocore.filter_dominated(x[:, :-1])
     >>> len(pf)
-    >>> pf                                          # doctest: +ELLIPSIS
-    array([[2.60764118, 6.31309852, 3.        ],
-           [3.22509709, 6.1522834 , 3.        ],
-           [0.37731545, 9.02211752, 3.        ],
-           [4.61023932, 2.29231998, 3.        ],
-           [0.2901393 , 8.32259412, 4.        ],
-           [1.54506255, 0.38303122, 4.        ],
-           [4.43498452, 4.13150648, 5.        ],
-           [9.78758589, 1.41238277, 5.        ],
-           [7.85344142, 3.02219054, 5.        ],
-           [0.9017068 , 7.49376946, 5.        ],
-           [0.17470556, 8.89066343, 5.        ]])
+    6
+    >>> pf
+    array([[0.20816431, 4.62275469],
+           [0.22997367, 1.11772205],
+           [0.58799475, 0.73891181],
+           [1.54506255, 0.38303122],
+           [0.17470556, 8.89066343],
+           [8.57911868, 0.35169752]])
 
     See Also
     --------
@@ -432,15 +429,11 @@ def filter_dominated_within_sets(data, maximise=False, keep_weakly=False):
         )
     nobjs = ncols - 1
     uniq_sets, uniq_index = np.unique(data[:, -1], return_index=True)
+    # FIXME: Is there a more efficient way to do this that just creates views and not copies?
     x_split = np.vsplit(data[:, :-1], uniq_index[1:])
-    is_nondom = np.fromiter(
-        (
-            is_nondominated(g, maximise=maximise, keep_weakly=keep_weakly)
-            for g in x_split
-        ),
-        dtype=float,
-        count=data.shape[0],
-    )
+    is_nondom = np.concatenate(
+        [ is_nondominated(g, maximise=maximise, keep_weakly=keep_weakly) for g in x_split ],
+        dtype=bool, casting = 'no')
     return data[is_nondom, :]
 
 
diff --git a/python/tests/conftest.py b/python/tests/conftest.py
index 6433ab18..dc1ad1f8 100644
--- a/python/tests/conftest.py
+++ b/python/tests/conftest.py
@@ -5,8 +5,6 @@
 @pytest.fixture(autouse=True, scope="module")
 def test_datapath(request):
     """Return the directory of the currently running test script"""
-
     def _(file_path: str):
         return request.path.parent.joinpath("test_data/" + file_path)
-
     return _
diff --git a/python/tests/test_moocore.py b/python/tests/test_moocore.py
index 6734745f..27f4d711 100644
--- a/python/tests/test_moocore.py
+++ b/python/tests/test_moocore.py
@@ -4,15 +4,15 @@
 
 import moocore
 
-
-def test_docstrings():
-    import doctest
-
-    doctest.FLOAT_EPSILON = 1e-9
-    # Run doctests for "moocore" module and fail if one of the docstring tests is incorrect.
-    # Pass in the "moocore" module so that the docstrings don't have to import every time
-    doctest.testmod(moocore, raise_on_error=True, extraglobs={"moocore": moocore})
-
+# FIXME: For some reason this stopped working!!!
+# def test_docstrings():
+#     import doctest
+#     doctest.FLOAT_EPSILON = 1e-9
+#     # Run doctests for "moocore" module and fail if one of the docstring tests is incorrect.
+#     failed, total = doctest.testmod(moocore, raise_on_error=True)
+#     assert failed == 0
+#     assert total > 0
+    
 
 def test_read_datasets_data(test_datapath):
     """
diff --git a/python/tox.ini b/python/tox.ini
index c8974838..4ae60462 100644
--- a/python/tox.ini
+++ b/python/tox.ini
@@ -1,16 +1,22 @@
 [tox]
 min_version = 4.0
-env_list = py{38,39,310,311}
+env_list =
+   py{38,39,310,311}
+   
 
 [testenv]
+description = run unit tests
 package = wheel
 wheel_build_env = .pkg
-description = run unit tests
 deps =
     pytest>=7
 commands =
-    pytest --doctest-modules --ignore-glob="*generate-expected-output.py"
+    pytest --doctest-modules --pyargs moocore
+    pytest {posargs:{env:_PYTEST_TOX_DEFAULT_POSARGS:}}
     
+[pytest]
+addopts = --ignore-glob="*generate-expected-output.py"
+
 [testenv:coverage]
 description = run coverage
 deps =