From ed804f2efd2bffecbfcd56f591b4c2f8082b1d3b Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 14:06:38 +0300
Subject: [PATCH 01/44] Fixing errors with python 3.12 on macos

---
 dev-dependencies.txt      | 3 +--
 spare_scores/mlp.py       | 6 +++---
 spare_scores/mlp_torch.py | 6 +++---
 spare_scores/svm.py       | 5 +++--
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index d12df9f..356c58a 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -3,7 +3,6 @@ attrs==23.1.0
 certifi==2023.5.7
 charset-normalizer==3.1.0
 click==8.1.3
-# contourpy==1.2.1
 cycler==0.11.0
 exceptiongroup==1.1.1
 filelock==3.12.2
@@ -33,7 +32,7 @@ pytz==2023.3
 PyYAML==6.0.2
 ray==2.34.0
 requests==2.31.0
-scikit-learn==1.0.1
+scikit-learn==1.3.2
 scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
diff --git a/spare_scores/mlp.py b/spare_scores/mlp.py
index afb233a..27a6b0a 100644
--- a/spare_scores/mlp.py
+++ b/spare_scores/mlp.py
@@ -100,7 +100,7 @@ def __init__(
                 "mlp__alpha": [0.001, 0.01, 0.05, 0.1],
                 "mlp__learning_rate": ["constant", "adaptive"],
                 "mlp__early_stopping": [True],
-                "mlp__max_iter": [500],
+                "mlp__max_iter": [1000],
             }
 
     def set_parameters(self, **parameters: Any) -> None:
@@ -113,11 +113,11 @@ def _fit(self, df: pd.DataFrame) -> None:
         y = df[self.to_predict].astype("float64")
 
         if self.task == "Regression":
-            mlp = MLPRegressor(early_stopping=True, max_iter=500)
+            mlp = MLPRegressor(early_stopping=True, max_iter=1000)
             scoring = "neg_mean_absolute_error"
             metrics = ["MAE", "RMSE", "R2"]
         else:
-            mlp = MLPClassifier(early_stopping=True, max_iter=500)
+            mlp = MLPClassifier(early_stopping=True, max_iter=1000)
             scoring = "balanced_accuracy"
             metrics = [
                 "AUC",
diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index b37a0ab..7d49afd 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -1,7 +1,7 @@
 import logging
 import os
 import time
-from typing import Any, Tuple
+from typing import Any, Tuple, List
 
 import numpy as np
 import optuna
@@ -220,7 +220,7 @@ def __init__(
         self.train_dl: Any
         self.val_dl: Any
 
-    def find_best_threshold(self, y_hat: list, y: list) -> Any:
+    def find_best_threshold(self, y_hat: list, y: list) -> List:
         """
         Returns best threshold value using the roc_curve
 
@@ -230,7 +230,7 @@ def find_best_threshold(self, y_hat: list, y: list) -> Any:
         :type y: list
 
         :return: the best threshold value
-        :rtype: Any
+        :rtype: List
 
         """
 
diff --git a/spare_scores/svm.py b/spare_scores/svm.py
index a3a7b30..3cf1031 100644
--- a/spare_scores/svm.py
+++ b/spare_scores/svm.py
@@ -249,7 +249,7 @@ def train_initialize(self, df: pd.DataFrame, to_predict: str) -> None:
             )
             self.to_predict, self.classify = to_predict, list(df[to_predict].unique())
             self.mdl = (
-                [LinearSVC(max_iter=100000, dual="auto")]
+                [LinearSVC(max_iter=100000, dual=False)]
                 if self.kernel == "linear"
                 else [SVC(max_iter=100000, kernel=self.kernel)]
             ) * len(self.folds)
@@ -260,7 +260,7 @@ def train_initialize(self, df: pd.DataFrame, to_predict: str) -> None:
                 ["MAE", "RMSE", "R2"],
             )
             self.to_predict, self.classify = to_predict, None
-            self.mdl = [LinearSVR(max_iter=100000, dual="auto")] * len(self.folds)
+            self.mdl = [LinearSVR(max_iter=100000, loss='squared_epsilon_insensitive', dual=False)] * len(self.folds)
             self.bias_correct = {
                 "slope": np.zeros((len(self.folds),)),
                 "int": np.zeros((len(self.folds),)),
@@ -320,6 +320,7 @@ def param_search(
             scoring=scoring,
             cv=self.k,
             return_train_score=True,
+            error_score=0.0,
             verbose=0,
         )
         gs.fit(X_train, y_train)

From 9fa0211860e07c6fd473014eb3723abcb8102e7f Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 14:37:53 +0300
Subject: [PATCH 02/44] Change variables to None from Any to stop the return
 error

---
 spare_scores/mlp_torch.py | 18 +++++++++---------
 spare_scores/svm.py       |  6 +++++-
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index 7d49afd..eca9174 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -1,7 +1,7 @@
 import logging
 import os
 import time
-from typing import Any, Tuple, List
+from typing import Any, Tuple
 
 import numpy as np
 import optuna
@@ -213,14 +213,14 @@ def __init__(
 
         # Model settings
         self.classification = True if self.task == "Classification" else False
-        self.mdl: Any
-        self.scaler: Any
-        self.stats: Any
-        self.param: Any
-        self.train_dl: Any
-        self.val_dl: Any
-
-    def find_best_threshold(self, y_hat: list, y: list) -> List:
+        self.mdl: None
+        self.scaler: None
+        self.stats: None
+        self.param: None
+        self.train_dl: None
+        self.val_dl: None
+
+    def find_best_threshold(self, y_hat: list, y: list) -> Any:
         """
         Returns best threshold value using the roc_curve
 
diff --git a/spare_scores/svm.py b/spare_scores/svm.py
index 3cf1031..2dd3dac 100644
--- a/spare_scores/svm.py
+++ b/spare_scores/svm.py
@@ -260,7 +260,11 @@ def train_initialize(self, df: pd.DataFrame, to_predict: str) -> None:
                 ["MAE", "RMSE", "R2"],
             )
             self.to_predict, self.classify = to_predict, None
-            self.mdl = [LinearSVR(max_iter=100000, loss='squared_epsilon_insensitive', dual=False)] * len(self.folds)
+            self.mdl = [
+                LinearSVR(
+                    max_iter=100000, loss="squared_epsilon_insensitive", dual=False
+                )
+            ] * len(self.folds)
             self.bias_correct = {
                 "slope": np.zeros((len(self.folds),)),
                 "int": np.zeros((len(self.folds),)),

From ea666fb14e1d4b03ff7197651c72645679ef8cb9 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 15:43:57 +0300
Subject: [PATCH 03/44] Change variable names with optional and Any | Fix test
 cases

---
 dev-dependencies.txt      |  4 ++--
 setup.cfg                 |  2 +-
 spare_scores/mlp_torch.py | 14 +++++++-------
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 356c58a..baf6b4c 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -37,8 +37,8 @@ scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.2.0
-torchvision==0.17.1
+torch==2.3.1
+torchvision==0.18.1
 typing_extensions==4.8.0
 tzdata==2023.3
 urllib3==2.0.3
diff --git a/setup.cfg b/setup.cfg
index aae17b1..d7ecc64 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -17,7 +17,7 @@ per-file-ignores =
     __init__.py: F401, F403
 
 [mypy]
-exclude= tests
+exclude = tests
 # Import discovery
 namespace_packages = False
 ignore_missing_imports = True
diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index eca9174..805caf8 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -1,7 +1,7 @@
 import logging
 import os
 import time
-from typing import Any, Tuple
+from typing import Any, Optional, Tuple
 
 import numpy as np
 import optuna
@@ -213,12 +213,12 @@ def __init__(
 
         # Model settings
         self.classification = True if self.task == "Classification" else False
-        self.mdl: None
-        self.scaler: None
-        self.stats: None
-        self.param: None
-        self.train_dl: None
-        self.val_dl: None
+        self.mdl: SimpleMLP
+        self.scaler: StandardScaler
+        self.stats: dict
+        self.param: Optional[Any] = None
+        self.train_dl: Optional[Any] = None
+        self.val_dl: Optional[Any] = None
 
     def find_best_threshold(self, y_hat: list, y: list) -> Any:
         """

From ab4c61b2beb686b67a00ac8450ece3b04c0fe439 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 16:17:20 +0300
Subject: [PATCH 04/44] Fixed issues with python 3.12 locally

---
 spare_scores/mlp_torch.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index 805caf8..17e5a1f 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -1,7 +1,7 @@
 import logging
 import os
 import time
-from typing import Any, Optional, Tuple
+from typing import Any, Tuple
 
 import numpy as np
 import optuna
@@ -216,9 +216,9 @@ def __init__(
         self.mdl: SimpleMLP
         self.scaler: StandardScaler
         self.stats: dict
-        self.param: Optional[Any] = None
-        self.train_dl: Optional[Any] = None
-        self.val_dl: Optional[Any] = None
+        self.param: dict
+        self.train_dl: DataLoader
+        self.val_dl: DataLoader
 
     def find_best_threshold(self, y_hat: list, y: list) -> Any:
         """

From 5b0f67e4f007b3205cfe52701fa54824bc2ea0bc Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 16:40:05 +0300
Subject: [PATCH 05/44] Added badges for building

---
 .github/workflows/macos_test_cases_p3-12.yml | 4 ++--
 README.md                                    | 6 +++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
index b9c42d4..cb70cc5 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -11,12 +11,12 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.12.4"
       - name: Set-up miniconda for macos and ubuntu
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.12
+          python-version: 3.12.4
           miniconda-version: "latest"
       - name: Create conda env
         run: conda create -n spare python=3.12
diff --git a/README.md b/README.md
index 1f5dd37..2284e45 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,8 @@
 [![codecov](https://codecov.io/gh/CBICA/spare_score/graph/badge.svg?token=7yk7pkydHE)](https://codecov.io/gh/CBICA/spare_score)
+![macos python=3.12 build](https://github.com/github/docs/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
+![macos python=3.8 build](https://github.com/github/docs/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
+![ubuntu python=3.12 build](https://github.com/github/docs/actions/workflows/ubuntu_test_cases_p3-12.yml/badge.svg)
+![ubuntu python=3.8 build](https://github.com/github/docs/actions/workflows/ubuntu_test_cases_p3-8.yml/badge.svg)
 
 # Compute SPARE Scores for Your Case
 
@@ -38,7 +42,7 @@ Please open an issue if you find any bugs for the newer versions of spare_score
     # for python 3.12
     git clone https://github.com/CBICA/spare_score.git
     cd spare_score
-    python -m pip install . 
+    python -m pip install .
 
     # for python 3.8...
     python setup.py bdist_wheel

From 23470d8b110c57c2b81d86e870631687f2d9ec0d Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 16:40:48 +0300
Subject: [PATCH 06/44] Remove conda env from workflow

---
 .github/workflows/macos_test_cases_p3-12.yml | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
index cb70cc5..2a0bec1 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -5,23 +5,13 @@ on: [push, pull_request, workflow_dispatch]
 
 jobs:
   build:
-    runs-on: ["macos-13"]
+    runs-on: ["macos-latest"]
 
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: "3.12.4"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.12.4
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.12
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           pip install setuptools twine wheel

From 0b5f677f0eb9e567d4a29af85da8be12dc25b214 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 16:48:33 +0300
Subject: [PATCH 07/44] Change macos version on workflow

---
 .github/workflows/macos_test_cases_p3-12.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
index 2a0bec1..86e5e6a 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -5,7 +5,7 @@ on: [push, pull_request, workflow_dispatch]
 
 jobs:
   build:
-    runs-on: ["macos-latest"]
+    runs-on: ["macos-13"]
 
     steps:
       - uses: actions/checkout@v4

From d2afb643d7137c57435d34c2b3325f33f7b8ff68 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 17:06:53 +0300
Subject: [PATCH 08/44] Try with pytest

---
 .github/workflows/macos_test_cases_p3-12.yml  | 4 ++--
 .github/workflows/macos_test_cases_p3-8.yml   | 2 +-
 .github/workflows/ubuntu_test_cases_p3-12.yml | 2 +-
 .github/workflows/ubuntu_test_cases_p3-8.yml  | 2 +-
 README.md                                     | 8 ++++----
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
index 86e5e6a..25c04e9 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -1,4 +1,4 @@
-name: spare_scores test cases on macos for python 3.12
+name: MacOS python=3.12
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -18,4 +18,4 @@ jobs:
           python -m pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/macos_test_cases_p3-8.yml b/.github/workflows/macos_test_cases_p3-8.yml
index 7c91627..a82fb4d 100644
--- a/.github/workflows/macos_test_cases_p3-8.yml
+++ b/.github/workflows/macos_test_cases_p3-8.yml
@@ -1,4 +1,4 @@
-name: spare_scores test cases on macos for python 3.8
+name: MacOS python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/ubuntu_test_cases_p3-12.yml b/.github/workflows/ubuntu_test_cases_p3-12.yml
index 8d71e56..766b588 100644
--- a/.github/workflows/ubuntu_test_cases_p3-12.yml
+++ b/.github/workflows/ubuntu_test_cases_p3-12.yml
@@ -1,4 +1,4 @@
-name: spare_scores test cases on ubuntu for python 3.12
+name: Ubuntu python=3.12
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/ubuntu_test_cases_p3-8.yml b/.github/workflows/ubuntu_test_cases_p3-8.yml
index 552323c..9a176d7 100644
--- a/.github/workflows/ubuntu_test_cases_p3-8.yml
+++ b/.github/workflows/ubuntu_test_cases_p3-8.yml
@@ -1,4 +1,4 @@
-name: spare_scores test cases on ubuntu for python 3.8
+name: Ubuntu python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/README.md b/README.md
index 2284e45..042ee73 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
 [![codecov](https://codecov.io/gh/CBICA/spare_score/graph/badge.svg?token=7yk7pkydHE)](https://codecov.io/gh/CBICA/spare_score)
-![macos python=3.12 build](https://github.com/github/docs/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
-![macos python=3.8 build](https://github.com/github/docs/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
-![ubuntu python=3.12 build](https://github.com/github/docs/actions/workflows/ubuntu_test_cases_p3-12.yml/badge.svg)
-![ubuntu python=3.8 build](https://github.com/github/docs/actions/workflows/ubuntu_test_cases_p3-8.yml/badge.svg)
+![macos python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
+![macos python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
+![ubuntu python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-12.yml/badge.svg)
+![ubuntu python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-8.yml/badge.svg)
 
 # Compute SPARE Scores for Your Case
 

From 1a22bf8b7d2e89bd43f7e5796ce4ce5d1b00905f Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 17:10:13 +0300
Subject: [PATCH 09/44] Add pytest-cov to workflow

---
 .github/workflows/macos_test_cases_p3-12.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
index 25c04e9..ce966bf 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -14,7 +14,7 @@ jobs:
           python-version: "3.12.4"
       - name: Install spare scores
         run: |
-          pip install setuptools twine wheel
+          pip install setuptools twine wheel pytest pytest-cov
           python -m pip install .
       - name: Run unit tests
         run: |

From 17032140f6d78ba38152b4ff9fe147a87e01b2f0 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 17:34:09 +0300
Subject: [PATCH 10/44] Change numpy version to 2.0.0

---
 dev-dependencies.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index baf6b4c..0b61fa4 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -17,7 +17,7 @@ jsonschema==4.17.3
 kiwisolver==1.4.4
 matplotlib==3.9.0
 msgpack==1.0.5
-numpy==1.22.0
+numpy==2.0.0
 packaging==23.1
 pandas==2.2.0
 Pillow==9.5.0

From 57981e4dd45a13ea11e6069c868d4576d9375455 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 18:01:40 +0300
Subject: [PATCH 11/44] Changed numpy version again

---
 dev-dependencies.txt | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 0b61fa4..278ace4 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -15,15 +15,14 @@ iniconfig==2.0.0
 joblib==1.3.1
 jsonschema==4.17.3
 kiwisolver==1.4.4
-matplotlib==3.9.0
+matplotlib==3.9.2
 msgpack==1.0.5
-numpy==2.0.0
+numpy==1.26.4
 packaging==23.1
-pandas==2.2.0
+pandas==2.2.2
 Pillow==9.5.0
 pkgutil_resolve_name==1.3.10
 pluggy==1.5.0
-protobuf==4.23.3
 pyparsing==3.1.0
 pyrsistent==0.19.3
 pytest==8.2.2

From aff177b66cabbbbeb7e36f1c4f6cd164ea7bac5c Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 18:38:02 +0300
Subject: [PATCH 12/44] Changed torch version

---
 dev-dependencies.txt | 4 ++--
 test_data_prep.py    | 0
 2 files changed, 2 insertions(+), 2 deletions(-)
 delete mode 100644 test_data_prep.py

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 278ace4..64baeb7 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -36,8 +36,8 @@ scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.3.1
-torchvision==0.18.1
+torch==2.2.2
+torchvision==0.17.2
 typing_extensions==4.8.0
 tzdata==2023.3
 urllib3==2.0.3
diff --git a/test_data_prep.py b/test_data_prep.py
deleted file mode 100644
index e69de29..0000000

From 9c102de4d5ecc6b75159d27891a07d22251eb996 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 19:00:09 +0300
Subject: [PATCH 13/44] Changed scikit learn and numpy versions

---
 dev-dependencies.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 64baeb7..9354ed5 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -17,7 +17,7 @@ jsonschema==4.17.3
 kiwisolver==1.4.4
 matplotlib==3.9.2
 msgpack==1.0.5
-numpy==1.26.4
+numpy==2.1.0
 packaging==23.1
 pandas==2.2.2
 Pillow==9.5.0
@@ -31,7 +31,7 @@ pytz==2023.3
 PyYAML==6.0.2
 ray==2.34.0
 requests==2.31.0
-scikit-learn==1.3.2
+scikit-learn==1.5.0
 scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0

From 05275b10effe12c2e31e8b3eb076b531adca5b99 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 19:03:36 +0300
Subject: [PATCH 14/44] Change MLPDataset to return torch.Tensor tuples instead
 of np.float32

---
 spare_scores/mlp_torch.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index 17e5a1f..9769050 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -59,13 +59,13 @@ def __len__(self) -> int:
         """
         return len(self.y)
 
-    def __getitem__(self, idx: int) -> Tuple[np.float32, np.float32]:
+    def __getitem__(self, idx: int) -> Tuple[torch.Tensor, torch.Tensor]:
         """
         (getter)returns the index of both X and y at index: idx(X[idx], y[idx])
         :param idx: the index
         :type idx: int
         """
-        return self.X[idx], self.y[idx]
+        return torch.tensor(self.X[idx]), torch.tensor(self.y[idx])
 
 
 class SimpleMLP(nn.Module):

From 8d51e794b6779663c4a990e44097197640e2f031 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 19:25:36 +0300
Subject: [PATCH 15/44] Changed all np.float32 to torch.Tensors

---
 spare_scores/mlp_torch.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index 9769050..5b8b596 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -50,8 +50,8 @@ class MLPDataset(Dataset):
     """
 
     def __init__(self, X: list, y: list):
-        self.X = np.array(X, dtype=np.float32)
-        self.y = np.array(y, dtype=np.float32)
+        self.X = np.array(X, dtype=torch.Tensor)
+        self.y = np.array(y, dtype=torch.Tensor)
 
     def __len__(self) -> int:
         """
@@ -65,7 +65,7 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, torch.Tensor]:
         :param idx: the index
         :type idx: int
         """
-        return torch.tensor(self.X[idx]), torch.tensor(self.y[idx])
+        return self.X[idx], self.y[idx]
 
 
 class SimpleMLP(nn.Module):
@@ -434,7 +434,7 @@ def fit(self, df: pd.DataFrame, verbose: int = 1, **kwargs: Any) -> dict:
         self.mdl.load_state_dict(best_model_state_dict)
         self.mdl.to(device)
         self.mdl.eval()
-        X_total = self.scaler.transform(np.array(X, dtype=np.float32))
+        X_total = self.scaler.transform(np.array(X, dtype=torch.Tensor))
         X_total = torch.tensor(X_total).to(device)
 
         self.y_pred = self.mdl(X_total).cpu().data.numpy()
@@ -475,7 +475,7 @@ def fit(self, df: pd.DataFrame, verbose: int = 1, **kwargs: Any) -> dict:
 
     def predict(self, df: pd.DataFrame) -> np.ndarray:
         X = df[self.predictors]
-        X = self.scaler.transform(np.array(X, dtype=np.float32))
+        X = self.scaler.transform(np.array(X, dtype=torch.Tensor))
         X = torch.tensor(X).to(device)
 
         checkpoint_dict = self.param

From 0962a6058d5cc8ac487d5d74a3f6c711e6fed53c Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 19:47:02 +0300
Subject: [PATCH 16/44] Changed part of the floats to tensors only

---
 spare_scores/mlp_torch.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index 5b8b596..afdd750 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -49,9 +49,9 @@ class MLPDataset(Dataset):
 
     """
 
-    def __init__(self, X: list, y: list):
-        self.X = np.array(X, dtype=torch.Tensor)
-        self.y = np.array(y, dtype=torch.Tensor)
+    def __init__(self, X: list, y: list) -> None:
+        self.X = np.array(X, dtype=np.float32)
+        self.y = np.array(y, dtype=np.float32)
 
     def __len__(self) -> int:
         """
@@ -65,7 +65,7 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, torch.Tensor]:
         :param idx: the index
         :type idx: int
         """
-        return self.X[idx], self.y[idx]
+        return torch.tensor(self.X[idx], dtype=torch.float32), torch.tensor(self.y[idx], dtype=torch.float32)
 
 
 class SimpleMLP(nn.Module):
@@ -434,7 +434,7 @@ def fit(self, df: pd.DataFrame, verbose: int = 1, **kwargs: Any) -> dict:
         self.mdl.load_state_dict(best_model_state_dict)
         self.mdl.to(device)
         self.mdl.eval()
-        X_total = self.scaler.transform(np.array(X, dtype=torch.Tensor))
+        X_total = self.scaler.transform(np.array(X, dtype=np.float32))
         X_total = torch.tensor(X_total).to(device)
 
         self.y_pred = self.mdl(X_total).cpu().data.numpy()
@@ -475,7 +475,7 @@ def fit(self, df: pd.DataFrame, verbose: int = 1, **kwargs: Any) -> dict:
 
     def predict(self, df: pd.DataFrame) -> np.ndarray:
         X = df[self.predictors]
-        X = self.scaler.transform(np.array(X, dtype=torch.Tensor))
+        X = self.scaler.transform(np.array(X, dtype=np.float32))
         X = torch.tensor(X).to(device)
 
         checkpoint_dict = self.param

From 78dd2e53833285e3e3c5a28d772742b2b376e489 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 20:14:19 +0300
Subject: [PATCH 17/44] Changed numpy version to 1.26.4 again as it wasnt the
 problem

---
 .github/workflows/macos_test_cases_p3-12.yml | 1 +
 dev-dependencies.txt                         | 6 +++---
 spare_scores/mlp_torch.py                    | 4 +++-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
index ce966bf..07b06cd 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -14,6 +14,7 @@ jobs:
           python-version: "3.12.4"
       - name: Install spare scores
         run: |
+          pip install -r dev-dependencies.txt
           pip install setuptools twine wheel pytest pytest-cov
           python -m pip install .
       - name: Run unit tests
diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 9354ed5..4b4bd6f 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -17,7 +17,7 @@ jsonschema==4.17.3
 kiwisolver==1.4.4
 matplotlib==3.9.2
 msgpack==1.0.5
-numpy==2.1.0
+numpy==1.26.4
 packaging==23.1
 pandas==2.2.2
 Pillow==9.5.0
@@ -36,8 +36,8 @@ scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.2.2
-torchvision==0.17.2
+torch==2.3.1
+torchvision==0.18.1
 typing_extensions==4.8.0
 tzdata==2023.3
 urllib3==2.0.3
diff --git a/spare_scores/mlp_torch.py b/spare_scores/mlp_torch.py
index afdd750..138ed33 100644
--- a/spare_scores/mlp_torch.py
+++ b/spare_scores/mlp_torch.py
@@ -65,7 +65,9 @@ def __getitem__(self, idx: int) -> Tuple[torch.Tensor, torch.Tensor]:
         :param idx: the index
         :type idx: int
         """
-        return torch.tensor(self.X[idx], dtype=torch.float32), torch.tensor(self.y[idx], dtype=torch.float32)
+        return torch.tensor(self.X[idx], dtype=torch.float32), torch.tensor(
+            self.y[idx], dtype=torch.float32
+        )
 
 
 class SimpleMLP(nn.Module):

From 349e5c6814aff7c017f3e9b44dc9b186e9f52b05 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 20:23:20 +0300
Subject: [PATCH 18/44] Required torch 2.2.2 version

---
 dev-dependencies.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 4b4bd6f..abfb848 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -36,8 +36,8 @@ scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.3.1
-torchvision==0.18.1
+torch==2.2.2
+torchvision==0.17.1
 typing_extensions==4.8.0
 tzdata==2023.3
 urllib3==2.0.3

From 33f86f4ed813958733d9717b1bec23fcd0728c8e Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 20:25:59 +0300
Subject: [PATCH 19/44] wrong torchvision version by mistake

---
 dev-dependencies.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index abfb848..e1752b5 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -36,7 +36,7 @@ scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.2.2
+torch==2.2.1
 torchvision==0.17.1
 typing_extensions==4.8.0
 tzdata==2023.3

From 01bc4e25cf30b555e2cde9ce65089dd8e65b9f5a Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Sun, 1 Sep 2024 20:54:50 +0300
Subject: [PATCH 20/44] Fixed small typo on readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 042ee73..2cbd8fc 100644
--- a/README.md
+++ b/README.md
@@ -44,7 +44,7 @@ Please open an issue if you find any bugs for the newer versions of spare_score
     cd spare_score
     python -m pip install .
 
-    # for python 3.8...
+    # for python 3.8
     python setup.py bdist_wheel
     cd dist && pip install ...
 

From 6460a124ae9aa7905930d32d4e652c682495f729 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 16:50:14 +0300
Subject: [PATCH 21/44] better workflows to run with all the python versions

---
 .github/workflows/codecov.yml                 | 46 +++++++++++++++----
 ...s_test_cases_p3-12.yml => macos-tests.yml} |  9 ++--
 .github/workflows/macos_test_cases_p3-8.yml   | 42 -----------------
 .github/workflows/ubuntu-tests.yml            | 25 ++++++++++
 .github/workflows/ubuntu_test_cases_p3-12.yml | 33 -------------
 .github/workflows/ubuntu_test_cases_p3-8.yml  | 36 ---------------
 README.md                                     |  7 +--
 7 files changed, 70 insertions(+), 128 deletions(-)
 rename .github/workflows/{macos_test_cases_p3-12.yml => macos-tests.yml} (70%)
 delete mode 100644 .github/workflows/macos_test_cases_p3-8.yml
 create mode 100644 .github/workflows/ubuntu-tests.yml
 delete mode 100644 .github/workflows/ubuntu_test_cases_p3-12.yml
 delete mode 100644 .github/workflows/ubuntu_test_cases_p3-8.yml

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
index 75aeba6..775bf83 100644
--- a/.github/workflows/codecov.yml
+++ b/.github/workflows/codecov.yml
@@ -1,14 +1,42 @@
-name: Test Coverage and Report to Codecov
-on: 
-  pull_request:
-    branches: ["main"]
+name: codecov report
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
 
-    
 jobs:
-  codecov:
-    runs-on: ubuntu-latest
+  build:
+    runs-on: ["macos-13"]
+
     steps:
-      - name: Upload coverage reports
-        uses: codecov/codecov-action@v4.5.0
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.8
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Generate Coverage Report
+        run: |
+          pip install pytest-cov
+          cd tests/unit && pytest --cov=../../ --cov-report=xml
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          slug: CBICA/spare_score
diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos-tests.yml
similarity index 70%
rename from .github/workflows/macos_test_cases_p3-12.yml
rename to .github/workflows/macos-tests.yml
index 07b06cd..23c5303 100644
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ b/.github/workflows/macos-tests.yml
@@ -1,4 +1,4 @@
-name: MacOS python=3.12
+name: macos tests
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -6,12 +6,15 @@ on: [push, pull_request, workflow_dispatch]
 jobs:
   build:
     runs-on: ["macos-13"]
-
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    name: Python ${{ matrix.python-version }} sample
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.12.4"
+          python-version: ${{ matrix.python-version }}
       - name: Install spare scores
         run: |
           pip install -r dev-dependencies.txt
diff --git a/.github/workflows/macos_test_cases_p3-8.yml b/.github/workflows/macos_test_cases_p3-8.yml
deleted file mode 100644
index a82fb4d..0000000
--- a/.github/workflows/macos_test_cases_p3-8.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-name: MacOS python=3.8
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["macos-13"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.8"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.8
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.8
-      - name: Install pip
-        run: conda run -n spare conda install pip
-      - name: Install spare scores
-        run: |
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Generate Coverage Report
-        run: |
-          pip install pytest-cov
-          cd tests/unit && pytest --cov=../../ --cov-report=xml
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: CBICA/spare_score
diff --git a/.github/workflows/ubuntu-tests.yml b/.github/workflows/ubuntu-tests.yml
new file mode 100644
index 0000000..bc8315b
--- /dev/null
+++ b/.github/workflows/ubuntu-tests.yml
@@ -0,0 +1,25 @@
+name: ubuntu tests
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    name: Python ${{ matrix.python-version }} sample
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel pytest pytest-cov
+          pip install -r dev-dependencies.txt
+          python -m pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu_test_cases_p3-12.yml b/.github/workflows/ubuntu_test_cases_p3-12.yml
deleted file mode 100644
index 766b588..0000000
--- a/.github/workflows/ubuntu_test_cases_p3-12.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: Ubuntu python=3.12
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["ubuntu-latest"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.12
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.12
-      - name: Install pip
-        run: conda run -n spare conda install pip
-      - name: Install spare scores
-        run: |
-          pip install setuptools twine wheel
-          python -m pip install .
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Run unit tests
-        run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu_test_cases_p3-8.yml b/.github/workflows/ubuntu_test_cases_p3-8.yml
deleted file mode 100644
index 9a176d7..0000000
--- a/.github/workflows/ubuntu_test_cases_p3-8.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-name: Ubuntu python=3.8
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["ubuntu-latest"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.8"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.8
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.8
-      - name: Install pip
-        run: conda run -n spare conda install pip
-      - name: Install spare scores
-        run: |
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Run unit tests
-        run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/README.md b/README.md
index 2cbd8fc..ee537d2 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,6 @@
 [![codecov](https://codecov.io/gh/CBICA/spare_score/graph/badge.svg?token=7yk7pkydHE)](https://codecov.io/gh/CBICA/spare_score)
-![macos python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
-![macos python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
-![ubuntu python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-12.yml/badge.svg)
-![ubuntu python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-8.yml/badge.svg)
-
+![macos build](https://github.com/CBICA/spare_score/actions/workflows/macos-tests.yml/badge.svg)
+![ubuntu build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests.yml/badge.svg)
 # Compute SPARE Scores for Your Case
 
 "SPARE" is short for "Spatial Pattern of Abnormalities for Recognition of ..." If you have brain images of a case population, such as the Alzheimer's disease (AD), the SPARE model will try to find characteristic brain patterns of AD with respect to a control population, such as cognitively normal. This would be an example of a classification-based SPARE model (currently powered by support vector machine or SVM). This model (that we named SPARE-AD) then computes SPARE-AD scores on an individual-basis that indicates how much the individual carries the learned brain patterns of AD.

From 7867e7f2fe25d4f5158f868a86e5d596d6e1eb3f Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 16:58:14 +0300
Subject: [PATCH 22/44] add conda envoronment and manual pip installation

---
 .github/workflows/macos-tests.yml  | 21 +++++++++++++++++----
 .github/workflows/ubuntu-tests.yml | 21 +++++++++++++++++----
 2 files changed, 34 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/macos-tests.yml b/.github/workflows/macos-tests.yml
index 23c5303..9f55a4c 100644
--- a/.github/workflows/macos-tests.yml
+++ b/.github/workflows/macos-tests.yml
@@ -9,17 +9,30 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-    name: Python ${{ matrix.python-version }} sample
+    name: Python ${{ matrix.python-version }} tests
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python= ${{ matrix.python-version }}
+      - name: Install pip
+        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
-          pip install -r dev-dependencies.txt
-          pip install setuptools twine wheel pytest pytest-cov
-          python -m pip install .
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+          pip install setuptools && pip install .
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests.yml b/.github/workflows/ubuntu-tests.yml
index bc8315b..8d9a1d5 100644
--- a/.github/workflows/ubuntu-tests.yml
+++ b/.github/workflows/ubuntu-tests.yml
@@ -9,17 +9,30 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-    name: Python ${{ matrix.python-version }} sample
+    name: Python ${{ matrix.python-version }} tests
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python= ${{ matrix.python-version }}
+      - name: Install pip
+        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
-          pip install setuptools twine wheel pytest pytest-cov
-          pip install -r dev-dependencies.txt
-          python -m pip install .
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+          pip install setuptools && pip install .
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../

From e0a26f65d3cf5e399c81e1c71a502d49212c2c83 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:16:13 +0300
Subject: [PATCH 23/44] Revert "add conda envoronment and manual pip
 installation"

This reverts commit 7867e7f2fe25d4f5158f868a86e5d596d6e1eb3f.
---
 .github/workflows/macos-tests.yml  | 21 ++++-----------------
 .github/workflows/ubuntu-tests.yml | 21 ++++-----------------
 2 files changed, 8 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/macos-tests.yml b/.github/workflows/macos-tests.yml
index 9f55a4c..23c5303 100644
--- a/.github/workflows/macos-tests.yml
+++ b/.github/workflows/macos-tests.yml
@@ -9,30 +9,17 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-    name: Python ${{ matrix.python-version }} tests
+    name: Python ${{ matrix.python-version }} sample
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python= ${{ matrix.python-version }}
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-          pip install setuptools && pip install .
+          pip install -r dev-dependencies.txt
+          pip install setuptools twine wheel pytest pytest-cov
+          python -m pip install .
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests.yml b/.github/workflows/ubuntu-tests.yml
index 8d9a1d5..bc8315b 100644
--- a/.github/workflows/ubuntu-tests.yml
+++ b/.github/workflows/ubuntu-tests.yml
@@ -9,30 +9,17 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-    name: Python ${{ matrix.python-version }} tests
+    name: Python ${{ matrix.python-version }} sample
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python= ${{ matrix.python-version }}
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-          pip install setuptools && pip install .
+          pip install setuptools twine wheel pytest pytest-cov
+          pip install -r dev-dependencies.txt
+          python -m pip install .
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../

From 068fe9a4be1139b945789690bdd74d98d08f2f1a Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:18:44 +0300
Subject: [PATCH 24/44] Revert "better workflows to run with all the python
 versions"

This reverts commit 6460a124ae9aa7905930d32d4e652c682495f729.
---
 .github/workflows/codecov.yml                 | 46 ++++---------------
 ...s-tests.yml => macos_test_cases_p3-12.yml} |  9 ++--
 .github/workflows/macos_test_cases_p3-8.yml   | 42 +++++++++++++++++
 .github/workflows/ubuntu-tests.yml            | 25 ----------
 .github/workflows/ubuntu_test_cases_p3-12.yml | 33 +++++++++++++
 .github/workflows/ubuntu_test_cases_p3-8.yml  | 36 +++++++++++++++
 README.md                                     |  7 ++-
 7 files changed, 128 insertions(+), 70 deletions(-)
 rename .github/workflows/{macos-tests.yml => macos_test_cases_p3-12.yml} (70%)
 create mode 100644 .github/workflows/macos_test_cases_p3-8.yml
 delete mode 100644 .github/workflows/ubuntu-tests.yml
 create mode 100644 .github/workflows/ubuntu_test_cases_p3-12.yml
 create mode 100644 .github/workflows/ubuntu_test_cases_p3-8.yml

diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
index 775bf83..75aeba6 100644
--- a/.github/workflows/codecov.yml
+++ b/.github/workflows/codecov.yml
@@ -1,42 +1,14 @@
-name: codecov report
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
+name: Test Coverage and Report to Codecov
+on: 
+  pull_request:
+    branches: ["main"]
 
+    
 jobs:
-  build:
-    runs-on: ["macos-13"]
-
+  codecov:
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.8"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.8
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.8
-      - name: Install pip
-        run: conda run -n spare conda install pip
-      - name: Install spare scores
-        run: |
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Generate Coverage Report
-        run: |
-          pip install pytest-cov
-          cd tests/unit && pytest --cov=../../ --cov-report=xml
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4.0.1
+      - name: Upload coverage reports
+        uses: codecov/codecov-action@v4.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          slug: CBICA/spare_score
diff --git a/.github/workflows/macos-tests.yml b/.github/workflows/macos_test_cases_p3-12.yml
similarity index 70%
rename from .github/workflows/macos-tests.yml
rename to .github/workflows/macos_test_cases_p3-12.yml
index 23c5303..07b06cd 100644
--- a/.github/workflows/macos-tests.yml
+++ b/.github/workflows/macos_test_cases_p3-12.yml
@@ -1,4 +1,4 @@
-name: macos tests
+name: MacOS python=3.12
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -6,15 +6,12 @@ on: [push, pull_request, workflow_dispatch]
 jobs:
   build:
     runs-on: ["macos-13"]
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-    name: Python ${{ matrix.python-version }} sample
+
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.12.4"
       - name: Install spare scores
         run: |
           pip install -r dev-dependencies.txt
diff --git a/.github/workflows/macos_test_cases_p3-8.yml b/.github/workflows/macos_test_cases_p3-8.yml
new file mode 100644
index 0000000..a82fb4d
--- /dev/null
+++ b/.github/workflows/macos_test_cases_p3-8.yml
@@ -0,0 +1,42 @@
+name: MacOS python=3.8
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["macos-13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.8
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Generate Coverage Report
+        run: |
+          pip install pytest-cov
+          cd tests/unit && pytest --cov=../../ --cov-report=xml
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: CBICA/spare_score
diff --git a/.github/workflows/ubuntu-tests.yml b/.github/workflows/ubuntu-tests.yml
deleted file mode 100644
index bc8315b..0000000
--- a/.github/workflows/ubuntu-tests.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-name: ubuntu tests
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["ubuntu-latest"]
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-    name: Python ${{ matrix.python-version }} sample
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install spare scores
-        run: |
-          pip install setuptools twine wheel pytest pytest-cov
-          pip install -r dev-dependencies.txt
-          python -m pip install .
-      - name: Run unit tests
-        run: |
-          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu_test_cases_p3-12.yml b/.github/workflows/ubuntu_test_cases_p3-12.yml
new file mode 100644
index 0000000..766b588
--- /dev/null
+++ b/.github/workflows/ubuntu_test_cases_p3-12.yml
@@ -0,0 +1,33 @@
+name: Ubuntu python=3.12
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.12
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.12
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python -m pip install .
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu_test_cases_p3-8.yml b/.github/workflows/ubuntu_test_cases_p3-8.yml
new file mode 100644
index 0000000..9a176d7
--- /dev/null
+++ b/.github/workflows/ubuntu_test_cases_p3-8.yml
@@ -0,0 +1,36 @@
+name: Ubuntu python=3.8
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.8
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/README.md b/README.md
index ee537d2..2cbd8fc 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,9 @@
 [![codecov](https://codecov.io/gh/CBICA/spare_score/graph/badge.svg?token=7yk7pkydHE)](https://codecov.io/gh/CBICA/spare_score)
-![macos build](https://github.com/CBICA/spare_score/actions/workflows/macos-tests.yml/badge.svg)
-![ubuntu build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests.yml/badge.svg)
+![macos python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
+![macos python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
+![ubuntu python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-12.yml/badge.svg)
+![ubuntu python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-8.yml/badge.svg)
+
 # Compute SPARE Scores for Your Case
 
 "SPARE" is short for "Spatial Pattern of Abnormalities for Recognition of ..." If you have brain images of a case population, such as the Alzheimer's disease (AD), the SPARE model will try to find characteristic brain patterns of AD with respect to a control population, such as cognitively normal. This would be an example of a classification-based SPARE model (currently powered by support vector machine or SVM). This model (that we named SPARE-AD) then computes SPARE-AD scores on an individual-basis that indicates how much the individual carries the learned brain patterns of AD.

From bf6c14293f7223a707eaf2ae9c7493a53532b719 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:19:07 +0300
Subject: [PATCH 25/44] revert the workflow changes

---
 .github/workflows/macos-tests-3.12.yml        | 33 +++++++++++++++++++
 ...est_cases_p3-8.yml => macos-tests-3.8.yml} |  0
 .github/workflows/macos_test_cases_p3-12.yml  | 22 -------------
 ...t_cases_p3-8.yml => ubuntu-tersts-3.8.yml} |  0
 ..._cases_p3-12.yml => ubuntu-tests-3.12.yml} |  0
 5 files changed, 33 insertions(+), 22 deletions(-)
 create mode 100644 .github/workflows/macos-tests-3.12.yml
 rename .github/workflows/{macos_test_cases_p3-8.yml => macos-tests-3.8.yml} (100%)
 delete mode 100644 .github/workflows/macos_test_cases_p3-12.yml
 rename .github/workflows/{ubuntu_test_cases_p3-8.yml => ubuntu-tersts-3.8.yml} (100%)
 rename .github/workflows/{ubuntu_test_cases_p3-12.yml => ubuntu-tests-3.12.yml} (100%)

diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
new file mode 100644
index 0000000..9717236
--- /dev/null
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -0,0 +1,33 @@
+name: macos python=3.12
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["macos-13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.12
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.12
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python -m pip install .
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/macos_test_cases_p3-8.yml b/.github/workflows/macos-tests-3.8.yml
similarity index 100%
rename from .github/workflows/macos_test_cases_p3-8.yml
rename to .github/workflows/macos-tests-3.8.yml
diff --git a/.github/workflows/macos_test_cases_p3-12.yml b/.github/workflows/macos_test_cases_p3-12.yml
deleted file mode 100644
index 07b06cd..0000000
--- a/.github/workflows/macos_test_cases_p3-12.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-name: MacOS python=3.12
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["macos-13"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.12.4"
-      - name: Install spare scores
-        run: |
-          pip install -r dev-dependencies.txt
-          pip install setuptools twine wheel pytest pytest-cov
-          python -m pip install .
-      - name: Run unit tests
-        run: |
-          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu_test_cases_p3-8.yml b/.github/workflows/ubuntu-tersts-3.8.yml
similarity index 100%
rename from .github/workflows/ubuntu_test_cases_p3-8.yml
rename to .github/workflows/ubuntu-tersts-3.8.yml
diff --git a/.github/workflows/ubuntu_test_cases_p3-12.yml b/.github/workflows/ubuntu-tests-3.12.yml
similarity index 100%
rename from .github/workflows/ubuntu_test_cases_p3-12.yml
rename to .github/workflows/ubuntu-tests-3.12.yml

From 644ad23f29b975210090c2e782eb58c6d77946a8 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:27:49 +0300
Subject: [PATCH 26/44] Manually added more workflows for the other versions

---
 .github/workflows/macos-tests-3.10.yml        | 42 +++++++++++++++++++
 .github/workflows/macos-tests-3.11.yml        | 42 +++++++++++++++++++
 .github/workflows/macos-tests-3.8.yml         |  2 +-
 .github/workflows/macos-tests-3.9.yml         | 42 +++++++++++++++++++
 .github/workflows/ubuntu-tests-3.10.yml       | 36 ++++++++++++++++
 .github/workflows/ubuntu-tests-3.11.yml       | 36 ++++++++++++++++
 .github/workflows/ubuntu-tests-3.12.yml       |  2 +-
 ...tu-tersts-3.8.yml => ubuntu-tests-3.8.yml} |  2 +-
 .github/workflows/ubuntu-tests-3.9.yml        | 36 ++++++++++++++++
 README.md                                     | 14 +++++--
 dev-dependencies.txt                          |  1 +
 11 files changed, 248 insertions(+), 7 deletions(-)
 create mode 100644 .github/workflows/macos-tests-3.10.yml
 create mode 100644 .github/workflows/macos-tests-3.11.yml
 create mode 100644 .github/workflows/macos-tests-3.9.yml
 create mode 100644 .github/workflows/ubuntu-tests-3.10.yml
 create mode 100644 .github/workflows/ubuntu-tests-3.11.yml
 rename .github/workflows/{ubuntu-tersts-3.8.yml => ubuntu-tests-3.8.yml} (97%)
 create mode 100644 .github/workflows/ubuntu-tests-3.9.yml

diff --git a/.github/workflows/macos-tests-3.10.yml b/.github/workflows/macos-tests-3.10.yml
new file mode 100644
index 0000000..490f8fd
--- /dev/null
+++ b/.github/workflows/macos-tests-3.10.yml
@@ -0,0 +1,42 @@
+name: macos python=3.10
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["macos-13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.10
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.10
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Generate Coverage Report
+        run: |
+          pip install pytest-cov
+          cd tests/unit && pytest --cov=../../ --cov-report=xml
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: CBICA/spare_score
diff --git a/.github/workflows/macos-tests-3.11.yml b/.github/workflows/macos-tests-3.11.yml
new file mode 100644
index 0000000..36f3619
--- /dev/null
+++ b/.github/workflows/macos-tests-3.11.yml
@@ -0,0 +1,42 @@
+name: macos python=3.11
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["macos-13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.11
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.11
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Generate Coverage Report
+        run: |
+          pip install pytest-cov
+          cd tests/unit && pytest --cov=../../ --cov-report=xml
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: CBICA/spare_score
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index a82fb4d..df3f903 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -1,4 +1,4 @@
-name: MacOS python=3.8
+name: macos python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/macos-tests-3.9.yml b/.github/workflows/macos-tests-3.9.yml
new file mode 100644
index 0000000..9022725
--- /dev/null
+++ b/.github/workflows/macos-tests-3.9.yml
@@ -0,0 +1,42 @@
+name: macos python=3.9
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["macos-13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.9
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.9
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Generate Coverage Report
+        run: |
+          pip install pytest-cov
+          cd tests/unit && pytest --cov=../../ --cov-report=xml
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: CBICA/spare_score
diff --git a/.github/workflows/ubuntu-tests-3.10.yml b/.github/workflows/ubuntu-tests-3.10.yml
new file mode 100644
index 0000000..46dcbeb
--- /dev/null
+++ b/.github/workflows/ubuntu-tests-3.10.yml
@@ -0,0 +1,36 @@
+name: ubuntu python=3.10
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.10
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.10
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.11.yml b/.github/workflows/ubuntu-tests-3.11.yml
new file mode 100644
index 0000000..f36b53b
--- /dev/null
+++ b/.github/workflows/ubuntu-tests-3.11.yml
@@ -0,0 +1,36 @@
+name: ubuntu python=3.11
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.11
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.11
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index 766b588..c6d2cb4 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -1,4 +1,4 @@
-name: Ubuntu python=3.12
+name: ubuntu python=3.12
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/ubuntu-tersts-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
similarity index 97%
rename from .github/workflows/ubuntu-tersts-3.8.yml
rename to .github/workflows/ubuntu-tests-3.8.yml
index 9a176d7..f4e30cd 100644
--- a/.github/workflows/ubuntu-tersts-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -1,4 +1,4 @@
-name: Ubuntu python=3.8
+name: ubuntu python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/ubuntu-tests-3.9.yml b/.github/workflows/ubuntu-tests-3.9.yml
new file mode 100644
index 0000000..d7fabfc
--- /dev/null
+++ b/.github/workflows/ubuntu-tests-3.9.yml
@@ -0,0 +1,36 @@
+name: ubuntu python=3.9
+
+# workflow dispatch has been added for testing purposes
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ["ubuntu-latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.9
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.9
+      - name: Install pip
+        run: conda run -n spare conda install pip
+      - name: Install spare scores
+        run: |
+          pip install setuptools twine wheel
+          python setup.py bdist_wheel
+          cd dist
+          WHEEL_FILE=$(ls spare_scores*)
+          pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
+      - name: Run unit tests
+        run: |
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/README.md b/README.md
index 2cbd8fc..b1ff1e9 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,14 @@
 [![codecov](https://codecov.io/gh/CBICA/spare_score/graph/badge.svg?token=7yk7pkydHE)](https://codecov.io/gh/CBICA/spare_score)
-![macos python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
-![macos python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/macos_test_cases_p3-12.yml/badge.svg)
-![ubuntu python=3.12 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-12.yml/badge.svg)
-![ubuntu python=3.8 build](https://github.com/CBICA/spare_score/actions/workflows/ubuntu_test_cases_p3-8.yml/badge.svg)
+![macos python=3.12](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.12.yml/badge.svg)
+![macos python=3.11](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.11.yml/badge.svg)
+![macos python=3.10](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.10.yml/badge.svg)
+![macos python=3.9](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.9.yml/badge.svg)
+![macos python=3.8](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.8.yml/badge.svg)
+![ubuntu python=3.12](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.12.yml/badge.svg)
+![ubuntu python=3.11](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.11.yml/badge.svg)
+![ubuntu python=3.10](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.10.yml/badge.svg)
+![ubuntu python=3.9](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.9.yml/badge.svg)
+![ubuntu python=3.8](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.8.yml/badge.svg)
 
 # Compute SPARE Scores for Your Case
 
diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index e1752b5..33a3c16 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -26,6 +26,7 @@ pluggy==1.5.0
 pyparsing==3.1.0
 pyrsistent==0.19.3
 pytest==8.2.2
+pytest-cov==5.0.0
 python-dateutil==2.8.2
 pytz==2023.3
 PyYAML==6.0.2

From fc446d151128d279ec2c533716e1ea2f1c0159ef Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:31:36 +0300
Subject: [PATCH 27/44] Added cache purge for pip install

---
 .github/workflows/macos-tests-3.10.yml  | 1 +
 .github/workflows/macos-tests-3.11.yml  | 1 +
 .github/workflows/macos-tests-3.12.yml  | 1 +
 .github/workflows/macos-tests-3.8.yml   | 1 +
 .github/workflows/macos-tests-3.9.yml   | 1 +
 .github/workflows/ubuntu-tests-3.10.yml | 1 +
 .github/workflows/ubuntu-tests-3.11.yml | 1 +
 .github/workflows/ubuntu-tests-3.12.yml | 1 +
 .github/workflows/ubuntu-tests-3.8.yml  | 1 +
 .github/workflows/ubuntu-tests-3.9.yml  | 1 +
 10 files changed, 10 insertions(+)

diff --git a/.github/workflows/macos-tests-3.10.yml b/.github/workflows/macos-tests-3.10.yml
index 490f8fd..70d2557 100644
--- a/.github/workflows/macos-tests-3.10.yml
+++ b/.github/workflows/macos-tests-3.10.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/macos-tests-3.11.yml b/.github/workflows/macos-tests-3.11.yml
index 36f3619..e897239 100644
--- a/.github/workflows/macos-tests-3.11.yml
+++ b/.github/workflows/macos-tests-3.11.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index 9717236..5fa18b8 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python -m pip install .
       - name: Download dependencies
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index df3f903..6c2eb7c 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/macos-tests-3.9.yml b/.github/workflows/macos-tests-3.9.yml
index 9022725..efa5a65 100644
--- a/.github/workflows/macos-tests-3.9.yml
+++ b/.github/workflows/macos-tests-3.9.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/ubuntu-tests-3.10.yml b/.github/workflows/ubuntu-tests-3.10.yml
index 46dcbeb..9e313a3 100644
--- a/.github/workflows/ubuntu-tests-3.10.yml
+++ b/.github/workflows/ubuntu-tests-3.10.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/ubuntu-tests-3.11.yml b/.github/workflows/ubuntu-tests-3.11.yml
index f36b53b..2daf4f2 100644
--- a/.github/workflows/ubuntu-tests-3.11.yml
+++ b/.github/workflows/ubuntu-tests-3.11.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index c6d2cb4..9c90ced 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python -m pip install .
       - name: Download dependencies
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index f4e30cd..58fa623 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/ubuntu-tests-3.9.yml b/.github/workflows/ubuntu-tests-3.9.yml
index d7fabfc..f774981 100644
--- a/.github/workflows/ubuntu-tests-3.9.yml
+++ b/.github/workflows/ubuntu-tests-3.9.yml
@@ -24,6 +24,7 @@ jobs:
         run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
+          python -m pip cache purge
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist

From 6ca8db1391ae9190a3f572f9ae4e71d32485ec2b Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:36:07 +0300
Subject: [PATCH 28/44] Remove conda environments and add only pytest

---
 .github/workflows/macos-tests-3.10.yml  | 10 ----------
 .github/workflows/macos-tests-3.11.yml  | 10 ----------
 .github/workflows/macos-tests-3.12.yml  | 10 ----------
 .github/workflows/macos-tests-3.8.yml   | 10 ----------
 .github/workflows/macos-tests-3.9.yml   | 10 ----------
 .github/workflows/ubuntu-tests-3.10.yml | 12 +-----------
 .github/workflows/ubuntu-tests-3.11.yml | 12 +-----------
 .github/workflows/ubuntu-tests-3.12.yml | 12 +-----------
 .github/workflows/ubuntu-tests-3.8.yml  | 12 +-----------
 .github/workflows/ubuntu-tests-3.9.yml  | 12 +-----------
 10 files changed, 5 insertions(+), 105 deletions(-)

diff --git a/.github/workflows/macos-tests-3.10.yml b/.github/workflows/macos-tests-3.10.yml
index 70d2557..f2b362b 100644
--- a/.github/workflows/macos-tests-3.10.yml
+++ b/.github/workflows/macos-tests-3.10.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.10
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.10
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
diff --git a/.github/workflows/macos-tests-3.11.yml b/.github/workflows/macos-tests-3.11.yml
index e897239..6e263f6 100644
--- a/.github/workflows/macos-tests-3.11.yml
+++ b/.github/workflows/macos-tests-3.11.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.11
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.11
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index 5fa18b8..5c5db75 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.12
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.12
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index 6c2eb7c..b90ad11 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.8"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.8
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.8
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
diff --git a/.github/workflows/macos-tests-3.9.yml b/.github/workflows/macos-tests-3.9.yml
index efa5a65..9e392d8 100644
--- a/.github/workflows/macos-tests-3.9.yml
+++ b/.github/workflows/macos-tests-3.9.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.9"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.9
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.9
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
diff --git a/.github/workflows/ubuntu-tests-3.10.yml b/.github/workflows/ubuntu-tests-3.10.yml
index 9e313a3..e633a42 100644
--- a/.github/workflows/ubuntu-tests-3.10.yml
+++ b/.github/workflows/ubuntu-tests-3.10.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.10
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.10
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
@@ -34,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.11.yml b/.github/workflows/ubuntu-tests-3.11.yml
index 2daf4f2..8156691 100644
--- a/.github/workflows/ubuntu-tests-3.11.yml
+++ b/.github/workflows/ubuntu-tests-3.11.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.11
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.11
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
@@ -34,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index 9c90ced..038f30d 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.12
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.12
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
@@ -31,4 +21,4 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index 58fa623..94d8070 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.8"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.8
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.8
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
@@ -34,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
+          cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.9.yml b/.github/workflows/ubuntu-tests-3.9.yml
index f774981..72f475e 100644
--- a/.github/workflows/ubuntu-tests-3.9.yml
+++ b/.github/workflows/ubuntu-tests-3.9.yml
@@ -12,16 +12,6 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.9"
-      - name: Set-up miniconda for macos and ubuntu
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.9
-          miniconda-version: "latest"
-      - name: Create conda env
-        run: conda create -n spare python=3.9
-      - name: Install pip
-        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
           python -m pip cache purge
@@ -34,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
+          cd tests/unit && pytest --cov=../../

From 0cf864ea43fc062a1af8948a5ad080d85ded3656 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:42:06 +0300
Subject: [PATCH 29/44] Add pytest installation to ubuntu workflows

---
 .github/workflows/ubuntu-tests-3.10.yml | 2 +-
 .github/workflows/ubuntu-tests-3.11.yml | 2 +-
 .github/workflows/ubuntu-tests-3.12.yml | 2 +-
 .github/workflows/ubuntu-tests-3.8.yml  | 2 +-
 .github/workflows/ubuntu-tests-3.9.yml  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ubuntu-tests-3.10.yml b/.github/workflows/ubuntu-tests-3.10.yml
index e633a42..a021079 100644
--- a/.github/workflows/ubuntu-tests-3.10.yml
+++ b/.github/workflows/ubuntu-tests-3.10.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.11.yml b/.github/workflows/ubuntu-tests-3.11.yml
index 8156691..529ece0 100644
--- a/.github/workflows/ubuntu-tests-3.11.yml
+++ b/.github/workflows/ubuntu-tests-3.11.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index 038f30d..da790fb 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -18,7 +18,7 @@ jobs:
           pip install setuptools twine wheel
           python -m pip install .
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index 94d8070..1b6ad6a 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/.github/workflows/ubuntu-tests-3.9.yml b/.github/workflows/ubuntu-tests-3.9.yml
index 72f475e..f7b3d98 100644
--- a/.github/workflows/ubuntu-tests-3.9.yml
+++ b/.github/workflows/ubuntu-tests-3.9.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../

From d53ff0225239f3cdd81a7e713895fdeb13fd718a Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:48:17 +0300
Subject: [PATCH 30/44] Change matplotlib version

---
 .github/workflows/ubuntu-tests-3.8.yml | 2 +-
 dev-dependencies.txt                   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index 1b6ad6a..94d8070 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
+        run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
           cd tests/unit && pytest --cov=../../
diff --git a/dev-dependencies.txt b/dev-dependencies.txt
index 33a3c16..2a90574 100644
--- a/dev-dependencies.txt
+++ b/dev-dependencies.txt
@@ -15,7 +15,7 @@ iniconfig==2.0.0
 joblib==1.3.1
 jsonschema==4.17.3
 kiwisolver==1.4.4
-matplotlib==3.9.2
+matplotlib==3.8.0
 msgpack==1.0.5
 numpy==1.26.4
 packaging==23.1

From 70eb8d8f03a3322bc79f57d8e0397d05afed16fa Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:51:03 +0300
Subject: [PATCH 31/44] Change pytest for ubuntu

---
 .github/workflows/ubuntu-tests-3.10.yml | 2 +-
 .github/workflows/ubuntu-tests-3.11.yml | 2 +-
 .github/workflows/ubuntu-tests-3.12.yml | 2 +-
 .github/workflows/ubuntu-tests-3.8.yml  | 2 +-
 .github/workflows/ubuntu-tests-3.9.yml  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ubuntu-tests-3.10.yml b/.github/workflows/ubuntu-tests-3.10.yml
index a021079..5b63c9e 100644
--- a/.github/workflows/ubuntu-tests-3.10.yml
+++ b/.github/workflows/ubuntu-tests-3.10.yml
@@ -24,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
-          cd tests/unit && pytest --cov=../../
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.11.yml b/.github/workflows/ubuntu-tests-3.11.yml
index 529ece0..3b00512 100644
--- a/.github/workflows/ubuntu-tests-3.11.yml
+++ b/.github/workflows/ubuntu-tests-3.11.yml
@@ -24,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
-          cd tests/unit && pytest --cov=../../
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index da790fb..64d7712 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -21,4 +21,4 @@ jobs:
         run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
-          cd tests/unit && pytest --cov=../../
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index 94d8070..e6b6959 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -24,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && pytest --cov=../../
+          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.9.yml b/.github/workflows/ubuntu-tests-3.9.yml
index f7b3d98..d9d6089 100644
--- a/.github/workflows/ubuntu-tests-3.9.yml
+++ b/.github/workflows/ubuntu-tests-3.9.yml
@@ -24,4 +24,4 @@ jobs:
         run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
-          cd tests/unit && pytest --cov=../../
+          cd tests/unit && python -m unittest discover -s . -p "*.py"

From 2a6c853b8532eaf7ede8a3862dca1848268fda0f Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:56:25 +0300
Subject: [PATCH 32/44] Fix readme builds and remove some workflows

---
 .github/workflows/macos-tests-3.10.yml  | 33 -------------------------
 .github/workflows/macos-tests-3.11.yml  | 33 -------------------------
 .github/workflows/macos-tests-3.9.yml   | 33 -------------------------
 .github/workflows/ubuntu-tests-3.10.yml | 27 --------------------
 .github/workflows/ubuntu-tests-3.11.yml | 27 --------------------
 .github/workflows/ubuntu-tests-3.9.yml  | 27 --------------------
 README.md                               | 12 ++-------
 7 files changed, 2 insertions(+), 190 deletions(-)
 delete mode 100644 .github/workflows/macos-tests-3.10.yml
 delete mode 100644 .github/workflows/macos-tests-3.11.yml
 delete mode 100644 .github/workflows/macos-tests-3.9.yml
 delete mode 100644 .github/workflows/ubuntu-tests-3.10.yml
 delete mode 100644 .github/workflows/ubuntu-tests-3.11.yml
 delete mode 100644 .github/workflows/ubuntu-tests-3.9.yml

diff --git a/.github/workflows/macos-tests-3.10.yml b/.github/workflows/macos-tests-3.10.yml
deleted file mode 100644
index f2b362b..0000000
--- a/.github/workflows/macos-tests-3.10.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: macos python=3.10
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["macos-13"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Generate Coverage Report
-        run: |
-          pip install pytest-cov
-          cd tests/unit && pytest --cov=../../ --cov-report=xml
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: CBICA/spare_score
diff --git a/.github/workflows/macos-tests-3.11.yml b/.github/workflows/macos-tests-3.11.yml
deleted file mode 100644
index 6e263f6..0000000
--- a/.github/workflows/macos-tests-3.11.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: macos python=3.11
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["macos-13"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Generate Coverage Report
-        run: |
-          pip install pytest-cov
-          cd tests/unit && pytest --cov=../../ --cov-report=xml
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: CBICA/spare_score
diff --git a/.github/workflows/macos-tests-3.9.yml b/.github/workflows/macos-tests-3.9.yml
deleted file mode 100644
index 9e392d8..0000000
--- a/.github/workflows/macos-tests-3.9.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-name: macos python=3.9
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["macos-13"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.9"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install .
-      - name: Generate Coverage Report
-        run: |
-          pip install pytest-cov
-          cd tests/unit && pytest --cov=../../ --cov-report=xml
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: CBICA/spare_score
diff --git a/.github/workflows/ubuntu-tests-3.10.yml b/.github/workflows/ubuntu-tests-3.10.yml
deleted file mode 100644
index 5b63c9e..0000000
--- a/.github/workflows/ubuntu-tests-3.10.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: ubuntu python=3.10
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["ubuntu-latest"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
-      - name: Run unit tests
-        run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.11.yml b/.github/workflows/ubuntu-tests-3.11.yml
deleted file mode 100644
index 3b00512..0000000
--- a/.github/workflows/ubuntu-tests-3.11.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: ubuntu python=3.11
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["ubuntu-latest"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
-      - name: Run unit tests
-        run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.9.yml b/.github/workflows/ubuntu-tests-3.9.yml
deleted file mode 100644
index d9d6089..0000000
--- a/.github/workflows/ubuntu-tests-3.9.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: ubuntu python=3.9
-
-# workflow dispatch has been added for testing purposes
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  build:
-    runs-on: ["ubuntu-latest"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.9"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install setuptools twine wheel
-          python setup.py bdist_wheel
-          cd dist
-          WHEEL_FILE=$(ls spare_scores*)
-          pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
-      - name: Run unit tests
-        run: |
-          cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/README.md b/README.md
index b1ff1e9..1111a3a 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,6 @@
 [![codecov](https://codecov.io/gh/CBICA/spare_score/graph/badge.svg?token=7yk7pkydHE)](https://codecov.io/gh/CBICA/spare_score)
-![macos python=3.12](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.12.yml/badge.svg)
-![macos python=3.11](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.11.yml/badge.svg)
-![macos python=3.10](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.10.yml/badge.svg)
-![macos python=3.9](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.9.yml/badge.svg)
-![macos python=3.8](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.8.yml/badge.svg)
-![ubuntu python=3.12](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.12.yml/badge.svg)
-![ubuntu python=3.11](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.11.yml/badge.svg)
-![ubuntu python=3.10](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.10.yml/badge.svg)
-![ubuntu python=3.9](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.9.yml/badge.svg)
-![ubuntu python=3.8](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.8.yml/badge.svg)
+![macos tests](https://github.com/CBICA/spare_score/actions/workflows/macos-tests-3.12.yml/badge.svg)
+![ubuntu tests](https://github.com/CBICA/spare_score/actions/workflows/ubuntu-tests-3.12.yml/badge.svg)
 
 # Compute SPARE Scores for Your Case
 

From ea16411f5767f2b068e8b5ebdb3878ecd446ccf4 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 17:57:28 +0300
Subject: [PATCH 33/44] Fix actions titles

---
 .github/workflows/macos-tests-3.12.yml  | 2 +-
 .github/workflows/macos-tests-3.8.yml   | 2 +-
 .github/workflows/ubuntu-tests-3.12.yml | 2 +-
 .github/workflows/ubuntu-tests-3.8.yml  | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index 5c5db75..aeaf295 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -1,4 +1,4 @@
-name: macos python=3.12
+name: macos build
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index b90ad11..793f4cd 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -1,4 +1,4 @@
-name: macos python=3.8
+name: macos build python=3.12
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index 64d7712..b0f51cb 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -1,4 +1,4 @@
-name: ubuntu python=3.12
+name: ubuntu build
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index e6b6959..0978109 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -1,4 +1,4 @@
-name: ubuntu python=3.8
+name: ubuntu build python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]

From 6f198e5c1eb9b2812ea4d10730fb0bf5ce309066 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:11:05 +0300
Subject: [PATCH 34/44] Fix pytest not exist

---
 .github/workflows/macos-tests-3.8.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index 793f4cd..da2f1de 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -1,4 +1,4 @@
-name: macos build python=3.12
+name: macos build python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -24,7 +24,7 @@ jobs:
         run: pip install setuptools && pip install .
       - name: Generate Coverage Report
         run: |
-          pip install pytest-cov
+          pip install pytest pytest-cov
           cd tests/unit && pytest --cov=../../ --cov-report=xml
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v4.0.1

From c31c32b08ed21934aed1f31c23b8513e50d53067 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:15:00 +0300
Subject: [PATCH 35/44] Add python -m on pytest

---
 .github/workflows/macos-tests-3.12.yml | 4 ++--
 .github/workflows/macos-tests-3.8.yml  | 2 +-
 .github/workflows/ubuntu-tests-3.8.yml | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index aeaf295..ae65612 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -18,7 +18,7 @@ jobs:
           pip install setuptools twine wheel
           python -m pip install .
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
-          cd tests/unit && pytest --cov=../../
+          cd tests/unit && python -m pytest --cov=../../
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index da2f1de..9e3aa92 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Generate Coverage Report
         run: |
           pip install pytest pytest-cov
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index 0978109..6ad7ba2 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -21,7 +21,7 @@ jobs:
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
       - name: Download dependencies
-        run: pip install setuptools && pip install .
+        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && python -m unittest discover -s . -p "*.py"

From 0131e46384e741179502d91e82b691b2c8c9ef0e Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:18:40 +0300
Subject: [PATCH 36/44] Minor changes

---
 .github/workflows/macos-tests-3.12.yml  | 2 --
 .github/workflows/macos-tests-3.8.yml   | 2 --
 .github/workflows/ubuntu-tests-3.12.yml | 2 --
 .github/workflows/ubuntu-tests-3.8.yml  | 2 --
 4 files changed, 8 deletions(-)

diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index ae65612..6fa0c74 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -17,8 +17,6 @@ jobs:
           python -m pip cache purge
           pip install setuptools twine wheel
           python -m pip install .
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && python -m pytest --cov=../../
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index 9e3aa92..5658b86 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -20,8 +20,6 @@ jobs:
           cd dist
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Generate Coverage Report
         run: |
           pip install pytest pytest-cov
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index b0f51cb..4badd0d 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -17,8 +17,6 @@ jobs:
           python -m pip cache purge
           pip install setuptools twine wheel
           python -m pip install .
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && python -m unittest discover -s . -p "*.py"
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index 6ad7ba2..ab66c74 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -20,8 +20,6 @@ jobs:
           cd dist
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
-      - name: Download dependencies
-        run: pip install setuptools && pip install -r dev-dependencies.txt
       - name: Run unit tests
         run: |
           cd tests/unit && python -m unittest discover -s . -p "*.py"

From bba047c5bc7681f42350c2b48983b5db1a84c514 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:21:24 +0300
Subject: [PATCH 37/44] re-add pytest

---
 .github/workflows/macos-tests-3.12.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index 6fa0c74..c38e14f 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -19,4 +19,5 @@ jobs:
           python -m pip install .
       - name: Run unit tests
         run: |
-          cd tests/unit && python -m pytest --cov=../../
+          pip install pytest pytest-cov
+          cd tests/unit && pytest --cov=../../

From 9744926abf81a79da7690816073d495ac96023a4 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:47:13 +0300
Subject: [PATCH 38/44] Add requirements.txt to every action

---
 .github/workflows/macos-tests-3.12.yml   | 1 +
 .github/workflows/macos-tests-3.8.yml    | 1 +
 .github/workflows/ubuntu-tests-3.12.yml  | 1 +
 .github/workflows/ubuntu-tests-3.8.yml   | 1 +
 dev-dependencies.txt => requirements.txt | 0
 5 files changed, 4 insertions(+)
 rename dev-dependencies.txt => requirements.txt (100%)

diff --git a/.github/workflows/macos-tests-3.12.yml b/.github/workflows/macos-tests-3.12.yml
index c38e14f..aebcadf 100644
--- a/.github/workflows/macos-tests-3.12.yml
+++ b/.github/workflows/macos-tests-3.12.yml
@@ -15,6 +15,7 @@ jobs:
       - name: Install spare scores
         run: |
           python -m pip cache purge
+          pip install -r requirements.txt
           pip install setuptools twine wheel
           python -m pip install .
       - name: Run unit tests
diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index 5658b86..ca9808b 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -15,6 +15,7 @@ jobs:
       - name: Install spare scores
         run: |
           python -m pip cache purge
+          pip install -r requirements.txt
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/.github/workflows/ubuntu-tests-3.12.yml b/.github/workflows/ubuntu-tests-3.12.yml
index 4badd0d..04f78ea 100644
--- a/.github/workflows/ubuntu-tests-3.12.yml
+++ b/.github/workflows/ubuntu-tests-3.12.yml
@@ -15,6 +15,7 @@ jobs:
       - name: Install spare scores
         run: |
           python -m pip cache purge
+          pip install -r requirements.txt
           pip install setuptools twine wheel
           python -m pip install .
       - name: Run unit tests
diff --git a/.github/workflows/ubuntu-tests-3.8.yml b/.github/workflows/ubuntu-tests-3.8.yml
index ab66c74..0c6b9ba 100644
--- a/.github/workflows/ubuntu-tests-3.8.yml
+++ b/.github/workflows/ubuntu-tests-3.8.yml
@@ -15,6 +15,7 @@ jobs:
       - name: Install spare scores
         run: |
           python -m pip cache purge
+          pip install -r requirements.txt
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
diff --git a/dev-dependencies.txt b/requirements.txt
similarity index 100%
rename from dev-dependencies.txt
rename to requirements.txt

From 213ed2fa631ca4b3e6e0fd695b8787414e8a8cf3 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:49:54 +0300
Subject: [PATCH 39/44] Change matplotlib version to 3.7.5

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 2a90574..7676074 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,7 +15,7 @@ iniconfig==2.0.0
 joblib==1.3.1
 jsonschema==4.17.3
 kiwisolver==1.4.4
-matplotlib==3.8.0
+matplotlib==3.7.5
 msgpack==1.0.5
 numpy==1.26.4
 packaging==23.1

From 50c7ec8fa22ff0dbb44af10f3d17b845bea855e9 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:53:42 +0300
Subject: [PATCH 40/44] Change numpy version to 1.24.4

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 7676074..833afe4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -17,7 +17,7 @@ jsonschema==4.17.3
 kiwisolver==1.4.4
 matplotlib==3.7.5
 msgpack==1.0.5
-numpy==1.26.4
+numpy==1.24.4
 packaging==23.1
 pandas==2.2.2
 Pillow==9.5.0

From ee6783fb77f92c17ec39f87b5e24256cc39db1b7 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 19:55:16 +0300
Subject: [PATCH 41/44] Change requirements

---
 requirements.txt | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 833afe4..d12df9f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,6 +3,7 @@ attrs==23.1.0
 certifi==2023.5.7
 charset-normalizer==3.1.0
 click==8.1.3
+# contourpy==1.2.1
 cycler==0.11.0
 exceptiongroup==1.1.1
 filelock==3.12.2
@@ -15,29 +16,29 @@ iniconfig==2.0.0
 joblib==1.3.1
 jsonschema==4.17.3
 kiwisolver==1.4.4
-matplotlib==3.7.5
+matplotlib==3.9.0
 msgpack==1.0.5
-numpy==1.24.4
+numpy==1.22.0
 packaging==23.1
-pandas==2.2.2
+pandas==2.2.0
 Pillow==9.5.0
 pkgutil_resolve_name==1.3.10
 pluggy==1.5.0
+protobuf==4.23.3
 pyparsing==3.1.0
 pyrsistent==0.19.3
 pytest==8.2.2
-pytest-cov==5.0.0
 python-dateutil==2.8.2
 pytz==2023.3
 PyYAML==6.0.2
 ray==2.34.0
 requests==2.31.0
-scikit-learn==1.5.0
+scikit-learn==1.0.1
 scipy==1.14.0
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.2.1
+torch==2.2.0
 torchvision==0.17.1
 typing_extensions==4.8.0
 tzdata==2023.3

From 5b03445e14986d072c52ea2710417981dd49e0ff Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 20:08:58 +0300
Subject: [PATCH 42/44] Reevaluated requirements

---
 requirements.txt | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index d12df9f..229043e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -16,11 +16,11 @@ iniconfig==2.0.0
 joblib==1.3.1
 jsonschema==4.17.3
 kiwisolver==1.4.4
-matplotlib==3.9.0
+matplotlib==3.7.5
 msgpack==1.0.5
 numpy==1.22.0
 packaging==23.1
-pandas==2.2.0
+pandas==2.0.3
 Pillow==9.5.0
 pkgutil_resolve_name==1.3.10
 pluggy==1.5.0
@@ -31,14 +31,13 @@ pytest==8.2.2
 python-dateutil==2.8.2
 pytz==2023.3
 PyYAML==6.0.2
-ray==2.34.0
 requests==2.31.0
-scikit-learn==1.0.1
-scipy==1.14.0
+scikit-learn==1.3.2
+scipy==1.10.1
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1
-torch==2.2.0
+torch==2.2.1
 torchvision==0.17.1
 typing_extensions==4.8.0
 tzdata==2023.3

From d2e6378c5daf93117aa91757f5b00580fd927e18 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 20:27:17 +0300
Subject: [PATCH 43/44] Changed requirements for different python versions

---
 requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 229043e..6eaf6a5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,7 +18,7 @@ jsonschema==4.17.3
 kiwisolver==1.4.4
 matplotlib==3.7.5
 msgpack==1.0.5
-numpy==1.22.0
+numpy
 packaging==23.1
 pandas==2.0.3
 Pillow==9.5.0
@@ -33,7 +33,7 @@ pytz==2023.3
 PyYAML==6.0.2
 requests==2.31.0
 scikit-learn==1.3.2
-scipy==1.10.1
+scipy
 six==1.16.0
 threadpoolctl==3.1.0
 tomli==2.0.1

From bae560aab64f1e48e52f92de0bb82ac98a1117c9 Mon Sep 17 00:00:00 2001
From: Spiros Maggioros <spirosastro@gmail.com>
Date: Mon, 2 Sep 2024 21:43:38 +0300
Subject: [PATCH 44/44] minor change in codecov to upload correctly

---
 .github/workflows/macos-tests-3.8.yml | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/macos-tests-3.8.yml b/.github/workflows/macos-tests-3.8.yml
index ca9808b..08c3735 100644
--- a/.github/workflows/macos-tests-3.8.yml
+++ b/.github/workflows/macos-tests-3.8.yml
@@ -1,4 +1,4 @@
-name: macos build python=3.8
+name: macos tests python=3.8
 
 # workflow dispatch has been added for testing purposes
 on: [push, pull_request, workflow_dispatch]
@@ -12,18 +12,28 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.8"
+      - name: Set-up miniconda for macos and ubuntu
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.8
+          miniconda-version: "latest"
+      - name: Create conda env
+        run: conda create -n spare python=3.8
+      - name: Install pip
+        run: conda run -n spare conda install pip
       - name: Install spare scores
         run: |
-          python -m pip cache purge
-          pip install -r requirements.txt
           pip install setuptools twine wheel
           python setup.py bdist_wheel
           cd dist
           WHEEL_FILE=$(ls spare_scores*)
           pip install "$WHEEL_FILE"
+      - name: Download dependencies
+        run: pip install setuptools && pip install .
       - name: Generate Coverage Report
         run: |
-          pip install pytest pytest-cov
+          pip install pytest-cov
           cd tests/unit && pytest --cov=../../ --cov-report=xml
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v4.0.1