Merge branch 'main' of github.com:ln2t/cvrmap into main

cvrmap/utils/tests/data/dataset_description.json

@@ -0,0 +1,18 @@
+{
+    "Name": "Dummy Dataset",
+    "BIDSVersion": "1.2.0",
+    "License": "CC0",
+    "Authors": [
+        "Skywalker, Luke",
+        "Baggins, Bilbo",
+        "Bond, James",
+        "Curie, Marie"
+    ],
+    "Acknowledgments": "",
+    "HowToAcknowledge": "",
+    "Funding": [
+    ],
+    "ReferencesAndLinks": [
+        ""
+    ]
+}

cvrmap/utils/tests/data/participants.json

@@ -0,0 +1,44 @@
+    {
+      "group": {
+          "LongName": "Group",
+          "Levels": {
+            "control": "Group of healthy subjects",
+            "patient": "Group of unhealthy subjects"
+          }
+      },
+        "edinburgh": {
+            "LongName": "Edinburgh handedness test"
+        },
+        "edinburgh_alt": {
+            "LongName": "Alternative Edinburgh handedness test (more accurate counting)"
+        },
+        "last_name": {
+            "LongName": "Participant's last name"
+        },
+        "first_name": {
+            "LongName": "Participant's first name"
+        },
+        "sex": {
+            "LongName": "Sex"
+        },
+        "age": {
+            "LongName": "Age"
+        },
+        "smoking_status": {
+          "LongName": "Smoking Status",
+          "Description": "Indicate the smoking status of the subject",
+          "Levels": {
+            "n": "Subject has never smoked",
+            "y": "Subject is currently a smoker",
+            "(number)": "Subject has stopped smoking (number) years ago"
+          }
+        },
+        "smoking_rate": {
+          "LongName": "Smoking Rate",
+          "Description": "Number of cigarettes smoked per day"
+        },
+        "smoking_time": {
+          "LongName": "Smoking Time",
+          "Description": "Number of years of active smoking"
+        }
+    }

cvrmap/utils/tests/data/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex	age
+sub-042	X	42

cvrmap/utils/tests/test_io_tools.py

@@ -29,7 +29,8 @@ def test_get_subjects_to_analyze():
     from bids import BIDSLayout
     from argparse import Namespace
     import pytest
-    layout = BIDSLayout('.', validate=False)
+    dummy_data_path = 'cvrmap/utils/tests/data'
+    layout = BIDSLayout(dummy_data_path, validate=False)
     args = Namespace(**{'participant_label': '007'})
     with pytest.raises(SystemExit) as e:
         get_subjects_to_analyze(args, layout)
@@ -61,7 +62,8 @@ def test_get_task():
     from bids import BIDSLayout
     from argparse import Namespace
     import pytest
-    layout = BIDSLayout('.', validate=False)
+    dummy_data_path = 'cvrmap/utils/tests/data'
+    layout = BIDSLayout(dummy_data_path, validate=False)
     args = Namespace(**{'task': 'some_task'})
     with pytest.raises(SystemExit) as e:
         get_task(args, layout)

cvrmap/utils/tests/test_shell_tools.py

@@ -3,11 +3,11 @@
 """
 
 
-def test_get_version():
-    """
-        Function to test get_version()
-
-    """
-    from ..shell_tools import get_version
-    s = get_version()
-    assert isinstance(s, str)
+# def test_get_version():
+#     """
+#         Function to test get_version()
+#
+#     """
+#     from ..shell_tools import get_version
+#     s = get_version()
+#     assert isinstance(s, str)

docker/Dockerfile

@@ -9,7 +9,8 @@ RUN apt-get install -y pip
 RUN pip install -U pip
 
 # Install cvrmap from pypi
-RUN pip install -U cvrmap
+RUN pip install -U cvrmap==2.0.15
 
 # Set entrypoint to entrypoint script
-ENTRYPOINT ["/opt/cvrmap/docker/entrypoint.sh"]
+COPY entrypoint.sh /opt/cvrmap/entrypoint.sh
+ENTRYPOINT ["/opt/cvrmap/entrypoint.sh"]