package: setup.py and reorganize

.gitignore

@@ -1 +1,6 @@
-*.pyc
+*.pyc
+*.egg-info
+.mypy_cache
+__pycache__
+tests/*.txt
+tests/refin

Dockerfile

@@ -10,4 +10,5 @@ RUN yum install -y numpy scipy
 
 # Add everything to the container
 ADD . /ICA-AROMA
+RUN pip install -e /ICA-AROMA
 

MANIFEST.in

@@ -0,0 +1 @@
+include ica_aroma/data/*.nii.gz

Makefile

@@ -0,0 +1,9 @@
+MAKEFLAGS += --no-builtin-rules
+.SUFFIXES:
+.PHONY: test
+
+test: tests/output.txt
+tests/refin/mask.nii.gz:
+	cd tests && curl -L https://github.com/rtrhd/test-data/raw/master/icaaroma/0.4.0/refin.tar.bz2 | bunzip2 | tar x
+tests/output.txt: tests/refin/mask.nii.gz $(wildcard tests/*.py) $(wildcard ica_aroma/*py)
+	python -m pytest -s tests/ | tee $@

ica-aroma-via-docker.py

@@ -16,7 +16,7 @@
 mod_args[targ_ind] = os.path.abspath(mod_args[targ_ind])
 
 # Call the ICA-AROMA process
-cmd = "python /ICA-AROMA/ICA_AROMA.py " + " ".join(mod_args)
+cmd = "ica_aroma " + " ".join(mod_args)
 print("Running: " + cmd + "\n")
 process = Popen( cmd.split() ) 
 sys.exit( process.wait() )

ica_aroma/__init__.py

@@ -0,0 +1,20 @@
+import os
+import ica_aroma
+
+__version__ = "0.3-beta"
+
+
+def get_data_path():
+    """find directory location of
+     mask_csf.nii.gz, mask_edge.nii.gz, and mask_out.nii.gz.
+
+    will allow env var AROMADIR to overwrite package location
+    @return path to data/ (string)
+    """
+    datadir = os.environ.get("AROMADIR", None) or \
+        os.path.join(os.path.dirname(ica_aroma.__loader__.path), "data")
+
+    assert os.path.isdir(datadir)
+    assert os.path.isfile(os.path.join(datadir, 'mask_csf.nii.gz'))
+
+    return datadir

classification_plots.py → ica_aroma/classification_plots.py

@@ -38,7 +38,7 @@ def classification_plot(myinput, outDir):
             df = pd.DataFrame.from_records(res)
         else:
             df2 = pd.DataFrame.from_records(res)
-            df = df.append(df2, ignore_index=True)
+            df = pd.concat([df, df2], ignore_index=True)
 
         count += 1
 
@@ -53,13 +53,13 @@ def classification_plot(myinput, outDir):
         df3 = pd.DataFrame.from_records([["True", 1., 1., 0., 0.],
                                         ["True", 1., 1., 0., 0.],
                                         ["True", 1., 1., 0., 0.]])
-        df = df.append(df3, ignore_index=True)
+        df = pd.concat([df, df3], ignore_index=True)
     tmp = df.loc[df[0] == "False"]
     if len(tmp) < 3:
         df3 = pd.DataFrame.from_records([["False", 0., 0., 0., 0.],
                                         ["False", 0., 0., 0., 0.],
                                         ["False", 0., 0., 0., 0.]])
-        df = df.append(df3, ignore_index=True)
+        df = pd.concat([df, df3], ignore_index=True)
 
     # rename columns
     df = df.rename(index=str, columns={0: 'Motion',