From daadf177bbd61511e36392bed4cebe0eeb650096 Mon Sep 17 00:00:00 2001
From: Nezar Abdennur <nabdennur@gmail.com>
Date: Fri, 25 Sep 2020 10:28:39 -0400
Subject: [PATCH 1/2] Fix get_header to work with different peek
 implementations

---
 cooler/cli/cload.py          |  21 ++++++++++++++++-----
 tests/data/toy_hash.pairs.gz | Bin 0 -> 625 bytes
 tests/test_create_ingest.py  |   5 +++++
 3 files changed, 21 insertions(+), 5 deletions(-)
 create mode 100644 tests/data/toy_hash.pairs.gz

diff --git a/cooler/cli/cload.py b/cooler/cli/cload.py
index 605dae31..4fb245cd 100644
--- a/cooler/cli/cload.py
+++ b/cooler/cli/cload.py
@@ -49,17 +49,28 @@ def get_header(instream, comment_char='#'):
         raise ValueError('Please, provide a comment char!')
     comment_byte = comment_char.encode()
     # get peekable buffer for the instream
-    inbuffer = instream.buffer
-    current_peek = inbuffer.peek()
+    read_f, peek_f = None, None
+    if hasattr(instream, 'buffer'):
+        peek_f = instream.buffer.peek
+        readline_f = instream.buffer.readline
+    elif hasattr(instream, 'peek'):
+        peek_f = instream.peek
+        readline_f = instream.readline
+    else:
+        raise ValueError('Cannot find the peek() function of the provided stream!')
+
+    current_peek = peek_f(1)
     while current_peek.startswith(comment_byte):
         # consuming a line from buffer guarantees
         # that the remainder of the buffer starts
         # with the beginning of the line.
-        line = inbuffer.readline()
+        line = readline_f()
+        if isinstance(line, bytes):
+            line = line.decode()
         # append line to header, since it does start with header
-        header.append(line.decode().strip())
+        header.append(line.strip())
         # peek into the remainder of the instream
-        current_peek = inbuffer.peek()
+        current_peek = peek_f(1)
     # apparently, next line does not start with the comment
     # return header and the instream, advanced to the beginning of the data
     return header, instream
diff --git a/tests/data/toy_hash.pairs.gz b/tests/data/toy_hash.pairs.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e4675cf737dfd10a75a1f1674eb64f5df6352433
GIT binary patch
literal 625
zcmV-%0*?J3iwFpm8OB}!19WeBUua=-XfAMJX>xM_ZI(gK)-Vi2*X0^45vaD)B)!Ie
z0|ZE{x&Hz|{gT+tYNU?7#rK>U`{UR5pP%LU@%xV)NISkBUyk#eeERt3>hsw}dUWmi
z>>_t`%k$Yq&*)yyXBU;|*5|W}YINK4*+nh7{rT*oCA#<X*+sAD%IW{bRcrF$<f@66
zKnie)n83<a6EksIs3mIRyiiNr#EGGn$jN_ZdJIi=_s_2R*SFiQ3A~>EE7wF`#ckJw
zUe#^aL|)Bp*Zfe6+pdYbUT(W4>{{J+m4sa#7b=OH!V7*0oH{U65;=2Xs3dge$WTe_
z%$cE*;F&S*?W-{0?H`q0jC=bgtupTIleWgVw~4UMxVM3_n{jXRSWd>hjdKykz3qac
zW8B*&DK^Hv?V(b}xVJ4<t}*Uy2bMa<y>HMq#=Y&|(#N>B?Ok|oZL~t{V4hnatrC5n
z+dWz-`b3u2O#Ch~OKT>67w?YNO#CiVOKavGLTn4A9&J*4u@Rz8Xe;X^+GMt|i{gf&
z>^h4q+LYbR7K}E5Jz1gAwl(jPd$^W0?vh))@?5qZUrE}w;%i%W`m5n<Uv~Pd;Oo8Y
z^jE*PbJ^*ydT+Aq^jEt#U3U7b+?y>s{nhP_aPipFBWlnBSK`$O7iE!;5yC}TBxa3p
zQ5K0>BV3e4;?@ZlWs%7BdAbqy=+EPgut$HMZ-hPi^ME7l(Vr(AVUPYi;s|^6=NU)X
zqdyNh!XEv3%8~YX@Xb?>xJQ4Ua^yYw^OPg-(VwRriI4s~<%oRr=P5_#qd!kMLXZC!
L`#Pu<!3zKYVmny~

literal 0
HcmV?d00001

diff --git a/tests/test_create_ingest.py b/tests/test_create_ingest.py
index 089ac6aa..fcc140e4 100644
--- a/tests/test_create_ingest.py
+++ b/tests/test_create_ingest.py
@@ -256,6 +256,11 @@ def test_cload_pairix(bins_path, pairs_path, ref_path):
             op.join(testdir, "data", "toy.bins.var.bed"),
             op.join(testdir, "data", "toy_hash.pairs"),
             op.join(testdir, "data", "toy.symm.upper.var.cool"),
+        ),
+        (
+            op.join(testdir, "data", "toy.bins.var.bed"),
+            op.join(testdir, "data", "toy_hash.pairs.gz"),
+            op.join(testdir, "data", "toy.symm.upper.var.cool"),
         )
     ],
 )

From 10b414a73c4ee0adc2c4be89fa5cc386558f80e5 Mon Sep 17 00:00:00 2001
From: Nezar Abdennur <nabdennur@gmail.com>
Date: Fri, 25 Sep 2020 10:28:52 -0400
Subject: [PATCH 2/2] Stop testing 2.7 in ci

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 27ab68b8..f1cfff76 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,7 +1,6 @@
 language: python
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
-  - "2.7"
   - "3.6"
   - "3.7"
   - "3.8"