It appears that calling readline() on a codecs.EncodedFile stream breaks seeking and causes subsequent attempts to iterate over the lines or call readline() to backtrack and return already consumed lines.

A minimal example:

from __future__ import print_function

import codecs
import io


def run(stream):
    offset = stream.tell()
    try:
        stream.seek(0)
        header_row = stream.readline()
    finally:
        stream.seek(offset)

    print('Got header: %r' % header_row)

    if stream.tell() == 0:
        print('Skipping the header: %r' % stream.readline())

    for index, line in enumerate(stream, start=2):
        print('Line %d: %r' % (index, line))


b = io.BytesIO(u'a,b\r\n"asdf","jkl;"\r\n'.encode('utf-16-le'))
s = codecs.EncodedFile(b, 'utf-8', 'utf-16-le')

run(s)

Output:

Got header: 'a,b\r\n'
Skipping the header: '"asdf","jkl;"\r\n'    <-- this is line 2
Line 2: 'a,b\r\n'                           <-- this is line 1
Line 3: '"asdf","jkl;"\r\n'                 <-- now we're back to line 2

As you can see, the line being skipped is actually the second line, and when we try reading from the stream again, the iterator starts from the beginning of the file.

Even weirder, adding a second call to readline() to skip the second line shows it's going **backwards**:

Got header: 'a,b\r\n'
Skipping the header: '"asdf","jkl;"\r\n'    <-- this is actually line 2
Skipping the second line: 'a,b\r\n'         <-- this is line 1
Line 2: '"asdf","jkl;"\r\n'                 <-- this is now correct

The expected output shows that we got a header, skipped it, and then read one data line.

Got header: 'a,b'
Skipping the header: 'a,b\r\n'
Line 2: '"asdf","jkl;"\r\n'

I'm sure this is related to the implementation of readline() because if we change this:

header_row = stream.readline()

to this:

header_row = stream.read().splitlines()[0]

then we get the expected output. If on the other hand we comment out the seek() in the finally clause, we also get the expected output (minus the "skipping the header") code.

I cannot replicate this when the stream is:

In: stream_ex = io.BytesIO(u"abc\ndef\nghi\n".encode("utf-8"))
In: f = codecs.EncodedFile(stream_ex, 'utf-8')

In: run(f)

Out: Got header: b'abc\n'
Skipping the header: b'abc\n'
Line 2: b'def\n'
Line 3: b'ghi\n'

That's because the stream isn't transcoding, since UTF-8 is ASCII-compatible. Try using something not ASCII-compatible as the codec e.g. 'ibm500' and it'll give incorrect results.

b = io.BytesIO(u'a,b\r\n"asdf","jkl;"\r\n'.encode('ibm500'))
s = codecs.EncodedFile(b, 'ibm500')

Got header: '\x81k\x82\r%'
Skipping the header. '\x7f\x81\xa2\x84\x86\x7fk\x7f\x91\x92\x93^\x7f\r%'
Line 2: '\x81k\x82\r%'
Line 3: '\x7f\x81\xa2\x84\x86\x7fk\x7f\x91\x92\x93^\x7f\r%'

Update: If I run your exact code it still breaks for me:

Got header: 'abc\n'
Skipping the header. 'def\n'
Line 2: 'ghi\n'
Line 3: 'abc\n'
Line 4: 'def\n'
Line 5: 'ghi\n'

I'm running Python 2.7.14 and 3.6.5 on OSX 10.13.4. Startup banners:

Python 2.7.14 (default, Feb 7 2018, 14:15:12)
[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.39.2)] on darwin

Python 3.6.5 (default, Apr 2 2018, 14:03:12)
[GCC 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.1)] on darwin

I've tried this with Python 3.6.0 on OSX 10.13.4

For you specific example I get also a weird result. Tried this in Python 2.7.10 and Python 3.6.0.

I've modified a little your example and it's clearly that the readline moves the cursor.

from __future__ import print_function

import codecs
import io


def run(stream):
    offset = stream.tell()
    try:
        stream.seek(0)
        header_row = stream.readline()
    finally:
        stream.seek(offset)
    print(offset)
    print(stream.tell())
    print('Got header: %r' % header_row)

    if stream.tell() == 0:
        print(stream.tell())
        print(stream.readline())
        print('Skipping the header: %r' % stream.readline())

    for index, line in enumerate(stream, start=2):
        print('Line %d: %r' % (index, line))


b = io.BytesIO(u'ab\r\ncd\ndef\n'.encode('utf-16-le'))
s = codecs.EncodedFile(b, 'utf-8', 'utf-16-le')
run(s)

The first call to readline returns cd instead of ab.

Update: Tested this on Python 3.5.4, 3.4.8, and 3.7.0b3 on OSX 10.13.4. They also exhibit the bug. Updating the ticket accordingly.

Bug still present in 3.7.0, now seeing it in 3.8.0a0 as well.

Possibly related to bpo-8260 ("When I use codecs.open(...) and f.readline() follow up by f.read() return bad result"), which was never fully fixed in that issue, though bpo-32110 ("Make codecs.StreamReader.read() more compatible with read() of other files") may have fixed more (all?) of it.

though bpo-32110 ("Make codecs.StreamReader.read() more compatible with read() of other files") may have fixed more (all?) of it.

Still seeing this in 3.7.3 so I don't think so?

New changeset a6ec1ce by Berker Peksag (Ammar Askar) in branch 'master':
bpo-33361: Fix bug with seeking in StreamRecoders (GH-8278)
a6ec1ce

New changeset a6dc5d4 by Berker Peksag (Miss Islington (bot)) in branch '3.7':
bpo-33361: Fix bug with seeking in StreamRecoders (GH-8278)
a6dc5d4

Thank you for the report, Diego and thank you for the patch, Ammar!