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BUG: Don't over-optimize memory with jagged CSV
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With jagged CSV's, we risk being too quick
to dump memory that we need to allocate
because previous chunks would have
indicated much larger rows than we can
anticipate in subsequent chunks.

Closes gh-23509.
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gfyoung committed Nov 11, 2018
1 parent 2cea659 commit 015a193
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Showing 5 changed files with 33 additions and 2 deletions.
1 change: 1 addition & 0 deletions doc/source/whatsnew/v0.24.0.txt
Original file line number Diff line number Diff line change
Expand Up @@ -1290,6 +1290,7 @@ Notice how we now instead output ``np.nan`` itself instead of a stringified form
- :func:`read_excel()` will correctly show the deprecation warning for previously deprecated ``sheetname`` (:issue:`17994`)
- :func:`read_csv()` and func:`read_table()` will throw ``UnicodeError`` and not coredump on badly encoded strings (:issue:`22748`)
- :func:`read_csv()` will correctly parse timezone-aware datetimes (:issue:`22256`)
- Bug in :func:`read_csv()` in which memory management was prematurely optimized for the C engine when the data was being read in chunks (:issue:`23509`)
- :func:`read_sas()` will parse numbers in sas7bdat-files that have width less than 8 bytes correctly. (:issue:`21616`)
- :func:`read_sas()` will correctly parse sas7bdat files with many columns (:issue:`22628`)
- :func:`read_sas()` will correctly parse sas7bdat files with data page types having also bit 7 set (so page type is 128 + 256 = 384) (:issue:`16615`)
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1 change: 1 addition & 0 deletions pandas/_libs/parsers.pyx
Original file line number Diff line number Diff line change
Expand Up @@ -132,6 +132,7 @@ cdef extern from "parser/tokenizer.h":
int64_t *word_starts # where we are in the stream
int64_t words_len
int64_t words_cap
int64_t max_words_cap # maximum word cap encountered

char *pword_start # pointer to stream start of current field
int64_t word_start # position start of current field
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16 changes: 14 additions & 2 deletions pandas/_libs/src/parser/tokenizer.c
Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,7 @@ int parser_init(parser_t *self) {
sz = sz ? sz : 1;
self->words = (char **)malloc(sz * sizeof(char *));
self->word_starts = (int64_t *)malloc(sz * sizeof(int64_t));
self->max_words_cap = sz;
self->words_cap = sz;
self->words_len = 0;

Expand Down Expand Up @@ -247,7 +248,7 @@ void parser_del(parser_t *self) {
}

static int make_stream_space(parser_t *self, size_t nbytes) {
int64_t i, cap;
int64_t i, cap, length;
int status;
void *orig_ptr, *newptr;

Expand Down Expand Up @@ -287,8 +288,15 @@ static int make_stream_space(parser_t *self, size_t nbytes) {
*/

cap = self->words_cap;

if (self->words_len + nbytes < self->max_words_cap) {
length = self->max_words_cap - nbytes;
} else {
length = self->words_len;
}

self->words =
(char **)grow_buffer((void *)self->words, self->words_len,
(char **)grow_buffer((void *)self->words, length,
(int64_t*)&self->words_cap, nbytes,
sizeof(char *), &status);
TRACE(
Expand Down Expand Up @@ -1241,6 +1249,10 @@ int parser_trim_buffers(parser_t *self) {

int64_t i;

if (self->words_cap > self->max_words_cap) {
self->max_words_cap = self->words_cap;
}

/* trim words, word_starts */
new_cap = _next_pow2(self->words_len) + 1;
if (new_cap < self->words_cap) {
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1 change: 1 addition & 0 deletions pandas/_libs/src/parser/tokenizer.h
Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,7 @@ typedef struct parser_t {
int64_t *word_starts; // where we are in the stream
int64_t words_len;
int64_t words_cap;
int64_t max_words_cap; // maximum word cap encountered

char *pword_start; // pointer to stream start of current field
int64_t word_start; // position start of current field
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16 changes: 16 additions & 0 deletions pandas/tests/io/parser/common.py
Original file line number Diff line number Diff line change
Expand Up @@ -458,6 +458,22 @@ def test_read_chunksize_generated_index(self):

tm.assert_frame_equal(pd.concat(reader), df)

def test_read_chunksize_jagged_names(self):
# see gh-23509
data = "\n".join(["0"] * 7 + [",".join(["0"] * 10)])
reader = self.read_csv(StringIO(data), names=range(10), chunksize=4)

expected = DataFrame()

for i in range(10):
if i == 0:
expected[i] = [0] * 8
else:
expected[i] = [np.nan] * 7 + [0]

result = pd.concat(reader)
tm.assert_frame_equal(result, expected)

def test_read_text_list(self):
data = """A,B,C\nfoo,1,2,3\nbar,4,5,6"""
as_list = [['A', 'B', 'C'], ['foo', '1', '2', '3'], ['bar',
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