From 64e4dbbe4aeae8e6a3f71ca8b2e50a798a6b7f78 Mon Sep 17 00:00:00 2001
From: Praneeth Bhatt <praneethsbhatt@gmail.com>
Date: Mon, 26 Aug 2024 18:20:43 -0400
Subject: [PATCH] added Cython to requirements to use pyximport

---
 requirements.txt      |  3 ++-
 src/icikt/__init__.py | 12 +++++++++---
 src/icikt/__main__.py | 13 +++++++------
 src/icikt/methods.py  |  7 ++++---
 4 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index c029b5b..a306f47 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
 numpy >= 1.24.1
 scipy >= 1.4.1
-docopt >= 0.6.2
\ No newline at end of file
+docopt >= 0.6.2
+Cython >= 3.0.0
\ No newline at end of file
diff --git a/src/icikt/__init__.py b/src/icikt/__init__.py
index f101e16..4de5e6c 100644
--- a/src/icikt/__init__.py
+++ b/src/icikt/__init__.py
@@ -9,9 +9,15 @@
     from os import path as _path
     __version__ = _gv(_path.join(_path.dirname(__file__), _path.pardir))
 
-
 from icikt.methods import icikt
 from icikt.methods import iciktArray
 from icikt.left_censorship import leftCensorTest
-from icikt.utility import setupMissingMatrix
-
+# from icikt.utility import setupMissingMatrix
+#
+#
+# # try:
+# #     from icikt import c_kendall_dis
+# # except ImportError:
+# #     # from icikt import kendall_dis as _kendall_dis
+# #     from icikt import kendall_dis as c_kendall_dis
+# from icikt import c_kendall_dis
\ No newline at end of file
diff --git a/src/icikt/__main__.py b/src/icikt/__main__.py
index fe97110..4c84f3b 100644
--- a/src/icikt/__main__.py
+++ b/src/icikt/__main__.py
@@ -24,9 +24,10 @@
 
 """
 
-from icikt.methods import iciktArray
-from icikt.left_censorship import leftCensorTest
-from icikt.__init__ import __version__ as ver
+# from icikt.methods import iciktArray
+# from icikt.left_censorship import leftCensorTest
+# from icikt import __version__ as ver
+import icikt
 import multiprocessing
 import docopt
 import numpy as np
@@ -38,7 +39,7 @@ def main():
     args = docopt.docopt(__doc__)
 
     if args["--version"]:
-        print(ver)
+        print(icikt.__version__)
 
     if args["leftCensor"]:
 
@@ -69,7 +70,7 @@ def main():
                 sys.exit(1)
 
         try:
-            results = leftCensorTest(args["<dataFilePath>"], globalNA=args["--replace"], sampleClasses=args["--samples"])
+            results = icikt.leftCensorTest(args["<dataFilePath>"], globalNA=args["--replace"], sampleClasses=args["--samples"])
             print(results)
         except Exception as e:
             print(e)
@@ -122,7 +123,7 @@ def main():
             sys.exit(1)
 
         try:
-            out, corr, pVal, tMax = iciktArray(dataArray=args["<dataFilePath>"], globalNA=args["--replace"], perspective=args["--mode"], scaleMax=args["--scale"], diagGood=args["--diag"], chunkSize=int(args["--chunk"]), includeOnly=args['--include'])
+            out, corr, pVal, tMax = icikt.iciktArray(dataArray=args["<dataFilePath>"], globalNA=args["--replace"], perspective=args["--mode"], scaleMax=args["--scale"], diagGood=args["--diag"], chunkSize=int(args["--chunk"]), includeOnly=args['--include'])
 
             if args["--output"] is not None:
                 np.savetxt(args["--output"]+'outArray.csv', out, delimiter=',')
diff --git a/src/icikt/methods.py b/src/icikt/methods.py
index 54004d8..236dd64 100644
--- a/src/icikt/methods.py
+++ b/src/icikt/methods.py
@@ -18,11 +18,12 @@
 from scipy.stats import distributions
 from icikt.utility import setupMissingMatrix
 
+import pyximport
+pyximport.install()
 try:
     from icikt import c_kendall_dis
 except ImportError:
-    # from icikt import kendall_dis as _kendall_dis
-    from icikt.kendall_dis import kendall_dis as c_kendall_dis
+    from icikt import kendall_dis as c_kendall_dis
 
 
 def initialize_global_data(data):
@@ -129,7 +130,7 @@ def normtestFinish(z: float) -> tuple:
     x, y = x[perm], y[perm]
     x = np.r_[True, x[1:] != x[:-1]].cumsum(dtype=np.intp)
 
-    dis = _kendall_dis.kendall_dis(x, y)  # discordant pairs
+    dis = c_kendall_dis.kendall_dis(x, y)  # discordant pairs
 
     obs = np.r_[True, (x[1:] != x[:-1]) | (y[1:] != y[:-1]), True]
     cnt = np.diff(np.nonzero(obs)[0]).astype('int64', copy=False)