[Git][reproducible-builds/diffoscope][master] 3 commits: Use assert_diff in tests/comparators/test_rdata.py.
Chris Lamb (@lamby)
gitlab at salsa.debian.org
Tue Sep 14 14:38:35 UTC 2021
Chris Lamb pushed to branch master at Reproducible Builds / diffoscope
Commits:
d12af4cc by Chris Lamb at 2021-09-14T11:31:45+01:00
Use assert_diff in tests/comparators/test_rdata.py.
- - - - -
ac1bcb6a by Chris Lamb at 2021-09-14T15:37:02+01:00
Support a newer format version of R .rds files.
- - - - -
622d1cac by Chris Lamb at 2021-09-14T15:37:02+01:00
Fix (and test) the comparison of R's .rdb files after refactoring of temporary directory handling.
This was a regression introduced in 1ee33f4e72e6 -- what was happening was
that the two files to be compared were copied to a temporary directory,
overwriting each other. This commit ensures they do not collide.
Signed-off-by: Chris Lamb <lamby at debian.org>
- - - - -
10 changed files:
- diffoscope/comparators/rdata.py
- tests/comparators/test_rdata.py
- + tests/data/rdb_expected_diff
- tests/data/rds_expected_diff
- + tests/data/test1.rdb
- tests/data/test1.rdx
- + tests/data/test2.rdb
- tests/data/test2.rdx
- tests/test_source.py
- tests/utils/data.py
Changes:
=====================================
diffoscope/comparators/rdata.py
=====================================
@@ -33,6 +33,7 @@ import binascii
RDS_HEADERS = {
binascii.a2b_hex("580a000000020003"),
binascii.a2b_hex("580a000000030003"),
+ binascii.a2b_hex("580a000000030004"),
}
DUMP_RDB = rb"""
@@ -73,7 +74,7 @@ def check_rds_extension(f):
return f.name.endswith(".rds") or f.name.endswith(".rdx")
-def get_module_path_for_rdb(rdb, temp_dir):
+def get_module_path_for_rdb(rdb, temp_dir, module_name):
"""
R's lazyLoad method does not take a filename directly to an .rdb file (eg.
`/path/to/foo.rdb`) but rather the path without any extension (eg.
@@ -106,7 +107,7 @@ def get_module_path_for_rdb(rdb, temp_dir):
# Corresponding .rdx does not exist
return None
- prefix = os.path.join(temp_dir, "temp")
+ prefix = os.path.join(temp_dir, module_name)
logger.debug("Copying %s and %s to %s", rdx.path, rdb.path, temp_dir)
shutil.copy(rdb.path, f"{prefix}.rdb")
@@ -162,8 +163,8 @@ class RdbFile(File):
def compare_details(self, other, source=None):
with get_temporary_directory(suffix="rdb") as tmpdir:
- a = get_module_path_for_rdb(self, tmpdir)
- b = get_module_path_for_rdb(other, tmpdir)
+ a = get_module_path_for_rdb(self, tmpdir, "a")
+ b = get_module_path_for_rdb(other, tmpdir, "b")
if a is None or b is None:
return []
=====================================
tests/comparators/test_rdata.py
=====================================
@@ -2,7 +2,7 @@
# diffoscope: in-depth comparison of files, archives, and directories
#
# Copyright © 2017 Ximin Luo <infinity0 at debian.org>
-# Copyright © 2017, 2020 Chris Lamb <lamby at debian.org>
+# Copyright © 2017, 2020-2021 Chris Lamb <lamby at debian.org>
#
# diffoscope is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -20,37 +20,56 @@
import pytest
from diffoscope.comparators.gzip import GzipFile
+from diffoscope.comparators.rdata import RdbFile
-from ..utils.data import load_fixture, get_data
+from ..utils.data import load_fixture, get_data, assert_diff
from ..utils.tools import skip_unless_tools_exist
-file1 = load_fixture("test1.rdx")
-file2 = load_fixture("test2.rdx")
+rdb1 = load_fixture("test1.rdb")
+rdb2 = load_fixture("test2.rdb")
+rdx1 = load_fixture("test1.rdx")
+rdx2 = load_fixture("test2.rdx")
-def test_identification(file1):
- assert isinstance(file1, GzipFile)
+def test_identification(rdb1, rdx1):
+ assert isinstance(rdb1, RdbFile)
+ assert isinstance(rdx1, GzipFile)
-def test_no_differences(file1):
- difference = file1.compare(file1)
- assert difference is None
+def test_no_differences(rdb1, rdx1):
+ assert rdx1.compare(rdx1) is None
+ assert rdx1.compare(rdx1) is None
@pytest.fixture
-def differences(file1, file2):
- return file1.compare(file2).details
+def differences_rdb(rdb1, rdb2):
+ return rdb1.compare(rdb2).details
+
+
+ at pytest.fixture
+def differences_rdx(rdx1, rdx2):
+ return rdx1.compare(rdx2).details
+
+
+ at skip_unless_tools_exist("Rscript")
+def test_num_items_rdb(differences_rdb):
+ assert len(differences_rdb) == 1
+
+
+ at skip_unless_tools_exist("Rscript")
+def test_item_rdb(differences_rdb):
+ assert differences_rdb[0].source1.startswith("Rscript")
+ assert_diff(differences_rdb[0], "rdb_expected_diff")
@skip_unless_tools_exist("Rscript")
-def test_num_items(differences):
- assert len(differences) == 1
+def test_num_items_rdx(differences_rdx):
+ assert len(differences_rdx) == 1
@skip_unless_tools_exist("Rscript")
-def test_item_rds(differences):
- assert differences[0].source1 == "test1.rdx-content"
- assert differences[0].source2 == "test2.rdx-content"
- expected_diff = get_data("rds_expected_diff")
- assert differences[0].details[0].unified_diff == expected_diff
+def test_item_rdx(differences_rdx):
+ assert differences_rdx[0].source1 == "test1.rdx-content"
+ assert differences_rdx[0].source2 == "test2.rdx-content"
+ assert_diff(differences_rdx[0].details[0], "rds_expected_diff")
=====================================
tests/data/rdb_expected_diff
=====================================
The diff for this file was not included because it is too large.
=====================================
tests/data/rds_expected_diff
=====================================
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-@@ -1,40 +1,40 @@
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+-$variables$print.summary.netlm
+-[1] 491309 4083
++$variables$noiseq
++[1] 360209 4099
+
+-$variables$print.summary.netlogit
+-[1] 495392 4160
++$variables$noiseqbio
++[1] 364308 6161
+
+-$variables$print.summary.qaptest
+-[1] 499552 1154
++$variables$plot.y2
++[1] 370469 2410
+
+-$variables$pstar
+-[1] 500706 8639
++$variables$probdeg
++[1] 372879 1399
+
+-$variables$qaptest
+-[1] 509345 1304
++$variables$ranking
++[1] 374278 1038
+
+-$variables$reachability
+-[1] 510649 2096
++$variables$readData
++[1] 375316 2539
+
+-$variables$read.dot
+-[1] 512745 1508
++$variables$rpkm
++[1] 377855 1016
+
+-$variables$read.nos
+-[1] 514253 1427
++$variables$saturation.dat
++[1] 378871 6983
+
+-$variables$redist
+-[1] 515680 5254
++$variables$saturation.plot
++[1] 385854 6714
+
+-$variables$rewire.ud
+-[1] 520934 1289
++$variables$share.info
++[1] 392568 5438
+
+-$variables$rewire.ws
+-[1] 522223 1345
++$variables$sim.samples
++[1] 398006 1485
+
+-$variables$rgbn
+-[1] 523568 3630
++$variables$sinceros
++[1] 399491 761
+
+-$variables$rgnm
+-[1] 527198 2754
++$variables$tmm
++[1] 400252 1494
+
+-$variables$rgnmix
+-[1] 529952 3644
++$variables$uqua
++[1] 401746 1700
+
+-$variables$rgraph
+-[1] 533596 3332
+
+-$variables$rguman
+-[1] 536928 2836
++$references
++$references$`env::1`
++[1] 5706 6699
+
+-$variables$rgws
+-[1] 539764 1749
++$references$`env::10`
++[1] 20320 270
+
+-$variables$rmperm
+-[1] 541513 1394
++$references$`env::11`
++[1] 18100 1110
+
+-$variables$rperm
+-[1] 542907 710
++$references$`env::12`
++[1] 19210 1110
+
+-$variables$sdmat
+-[1] 543617 1626
++$references$`env::13`
++[1] 181233 4032
+
+-$variables$se.lnam
+-[1] 545243 906
++$references$`env::14`
++[1] 180761 472
+
+-$variables$sedist
+-[1] 546149 4970
++$references$`env::15`
++[1] 139943 20409
+
+-$variables$simmelian
+-[1] 551119 1029
++$references$`env::16`
++[1] 21762 183
+
+-$variables$sociomatrixplot
+-[1] 552148 3263
++$references$`env::17`
++[1] 21945 1535
+
+-$variables$sr2css
+-[1] 555411 826
++$references$`env::18`
++[1] 137619 2324
+
+-$variables$stackcount
+-[1] 556237 356
++$references$`env::19`
++[1] 123123 152
+
+-$variables$stresscent
+-[1] 556593 2275
++$references$`env::2`
++[1] 5398 140
+
+-$variables$structdist
+-[1] 558868 5365
++$references$`env::20`
++[1] 117923 5200
+
+-$variables$structure.statistics
+-[1] 564233 1325
++$references$`env::21`
++[1] 117182 741
+
+-$variables$summary.bayes.factor
+-[1] 565558 1076
++$references$`env::22`
++[1] 32250 152
+
+-$variables$summary.bbnam
+-[1] 566634 379
++$references$`env::23`
++[1] 23480 8770
+
+-$variables$summary.bbnam.actor
+-[1] 567013 385
++$references$`env::24`
++[1] 112363 4819
+
+-$variables$summary.bbnam.fixed
+-[1] 567398 386
++$references$`env::25`
++[1] 39689 49420
+
+-$variables$summary.bbnam.pooled
+-[1] 567784 386
++$references$`env::26`
++[1] 36359 347
+
+-$variables$summary.blockmodel
+-[1] 568170 334
++$references$`env::27`
++[1] 33177 3182
+
+-$variables$summary.bn
+-[1] 568504 376
++$references$`env::28`
++[1] 32402 775
+
+-$variables$summary.brokerage
+-[1] 568880 304
++$references$`env::29`
++[1] 36706 875
+
+-$variables$summary.cugtest
+-[1] 569184 381
++$references$`env::3`
++[1] 5538 168
+
+-$variables$summary.lnam
+-[1] 569565 349
++$references$`env::30`
++[1] 37581 1787
+
+-$variables$summary.netcancor
+-[1] 569914 383
++$references$`env::31`
++[1] 39368 321
+
+-$variables$summary.netlm
+-[1] 570297 379
++$references$`env::32`
++[1] 89109 23254
+
+-$variables$summary.netlogit
+-[1] 570676 382
++$references$`env::33`
++[1] 129040 2484
+
+-$variables$summary.qaptest
+-[1] 571058 381
++$references$`env::34`
++[1] 128873 167
+
+-$variables$symmetrize
+-[1] 571439 4336
++$references$`env::35`
++[1] 123275 5598
+
+-$variables$triad.census
+-[1] 575775 1992
++$references$`env::36`
++[1] 137467 152
+
+-$variables$triad.classify
+-[1] 577767 1663
++$references$`env::37`
++[1] 132265 5202
+
+-$variables$upper.tri.remove
+-[1] 579430 1036
++$references$`env::38`
++[1] 131524 741
+
+-$variables$write.dl
+-[1] 580466 2744
++$references$`env::39`
++[1] 160352 20409
+
+-$variables$write.nos
+-[1] 583210 1860
++$references$`env::4`
++[1] 12467 140
+
++$references$`env::5`
++[1] 16338 1700
+
+-$references
+-$references$`env::1`
+-[1] 866 6681
++$references$`env::6`
++[1] 16069 269
+
+-$references$`env::2`
+-[1] 561 140
++$references$`env::7`
++[1] 12669 1700
+
+-$references$`env::3`
+-[1] 701 165
++$references$`env::8`
++[1] 14369 1700
+
+-$references$`env::4`
+-[1] 7609 140
++$references$`env::9`
++[1] 20590 1110
$compressed
=====================================
tests/data/test1.rdb
=====================================
Binary files /dev/null and b/tests/data/test1.rdb differ
=====================================
tests/data/test1.rdx
=====================================
Binary files a/tests/data/test1.rdx and b/tests/data/test1.rdx differ
=====================================
tests/data/test2.rdb
=====================================
Binary files /dev/null and b/tests/data/test2.rdb differ
=====================================
tests/data/test2.rdx
=====================================
Binary files a/tests/data/test2.rdx and b/tests/data/test2.rdx differ
=====================================
tests/test_source.py
=====================================
@@ -130,6 +130,7 @@ ALLOWED_TEST_FILES = {
"test1.png",
"test1.ppu",
"test1.ps",
+ "test1.rdb",
"test1.rdx",
"test1.rlib",
"test1.rpm",
@@ -191,6 +192,7 @@ ALLOWED_TEST_FILES = {
"test2.png",
"test2.ppu",
"test2.ps",
+ "test2.rdb",
"test2.rdx",
"test2.rlib",
"test2.rpm",
=====================================
tests/utils/data.py
=====================================
@@ -24,6 +24,7 @@ import re
import pytest
from diffoscope.comparators.binary import FilesystemFile
+from diffoscope.comparators.directory import FilesystemDirectory
from diffoscope.comparators.utils.specialize import specialize
re_normalize_zeros = re.compile(
@@ -31,8 +32,17 @@ re_normalize_zeros = re.compile(
)
+def init_file(filename):
+ # Ensure that any (specialized) FilesystemFile in tests have a
+ # corresponding Container for any comparator that needs to know which
+ # directory the file came from (eg. rdata)
+ container = FilesystemDirectory(os.path.dirname(filename)).as_container
+
+ return specialize(FilesystemFile(filename, container))
+
+
def init_fixture(filename):
- return pytest.fixture(lambda: specialize(FilesystemFile(filename)))
+ return pytest.fixture(lambda: init_file(filename))
def data(filename):
View it on GitLab: https://salsa.debian.org/reproducible-builds/diffoscope/-/compare/2fae7e85506f3fdff8f2117dd7a4c3340b7c47ef...622d1cac0ab65edfd217149ae20ce16f807dd658
--
View it on GitLab: https://salsa.debian.org/reproducible-builds/diffoscope/-/compare/2fae7e85506f3fdff8f2117dd7a4c3340b7c47ef...622d1cac0ab65edfd217149ae20ce16f807dd658
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