[med-svn] [Git][med-team/community/helper-scripts][master] automatic update
Andreas Tille pushed to branch master at Debian Med / community / helper-scripts Commits: acac674b by Andreas Tille at 2023-01-30T01:42:28+00:00 automatic update - - - - - 4 changed files: - debian-med-tests.txt - debian-science-tests.txt - outdated_med-packages.txt - python-team-tests.txt Changes: = debian-med-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Sun, 29 Jan 2023 13:42:04 + +Last-Update: Mon, 30 Jan 2023 01:42:04 + Source| Vote | Tasks | Tags ---++-+-- = debian-science-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Sun, 29 Jan 2023 13:42:06 + +Last-Update: Mon, 30 Jan 2023 01:42:05 + Source | Vote | Tasks |Tags -+++ = outdated_med-packages.txt = The diff for this file was not included because it is too large. = python-team-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Sun, 29 Jan 2023 13:42:07 + +Last-Update: Mon, 30 Jan 2023 01:42:05 + Source | Vote | Tags --++ View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/acac674b3a188c6d1597999be3238e8f867704da -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/acac674b3a188c6d1597999be3238e8f867704da You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/phyx][bullseye] Remove unnecessary Build-Depend on libatlas-cpp
Olek Wojnar pushed to branch bullseye at Debian Med / phyx Commits: 8229f203 by Olek Wojnar at 2023-01-29T18:33:58-05:00 Remove unnecessary Build-Depend on libatlas-cpp The atlas-cpp package is in the process of being removed from Debian - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -1,3 +1,13 @@ +phyx (1.01+ds-2+deb11u1) bullseye; urgency=medium + + * Team upload + * Remove erroneous Build Dependency on libatlas-cpp +- libatlas-cpp is completely unrelated to phyx and phyx does not use it +- The BD was added accidentally and needs to be removed for proper + dependency resolution + + -- Olek Wojnar Sun, 29 Jan 2023 18:27:53 -0500 + phyx (1.01+ds-2) unstable; urgency=medium * Team upload = debian/control = @@ -8,7 +8,6 @@ Build-Depends: debhelper-compat (= 12), liblapack-dev, libnlopt-cxx-dev, libnlopt-dev, - libatlas-cpp-0.6-dev, libarmadillo-dev Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/phyx View it on GitLab: https://salsa.debian.org/med-team/phyx/-/commit/8229f2033087fb594567e483bc3650d426696548 -- View it on GitLab: https://salsa.debian.org/med-team/phyx/-/commit/8229f2033087fb594567e483bc3650d426696548 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-skbio][master] 3 commits: Fix some more numpy issues
Andreas Tille pushed to branch master at Debian Med / python-skbio
Commits:
27b8db6f by Andreas Tille at 2023-01-29T17:30:49+01:00
Fix some more numpy issues
- - - - -
b2462a75 by Andreas Tille at 2023-01-29T19:07:48+01:00
Temporary unavailable python-scipy-doc
- - - - -
ab3e3d2c by Andreas Tille at 2023-01-29T19:08:12+01:00
More numpy issues
- - - - -
2 changed files:
- debian/control
- debian/patches/numpy-1.24.patch
Changes:
=
debian/control
=
@@ -28,7 +28,7 @@ Build-Depends-Arch: python3-lockfile ,
Build-Depends-Indep: python3-sphinx ,
python3-sphinx-bootstrap-theme ,
python3-doc ,
- python-scipy-doc ,
+# python-scipy-doc ,
python-biom-format-doc ,
python-pandas-doc
Standards-Version: 4.6.2
=
debian/patches/numpy-1.24.patch
=
@@ -58,3 +58,72 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
except ValueError:
raise QUALFormatError(
"Could not convert quality scores to integers:\n%s"
+--- a/skbio/metadata/_testing.py
b/skbio/metadata/_testing.py
+@@ -457,7 +457,7 @@ class PositionalMetadataMixinTests:
+
+ def test_eq_from_different_source(self):
+ obj1 = self._positional_metadata_constructor_(
+-3, positional_metadata={'foo': np.array([1, 2, 3])})
++3, positional_metadata={'foo': np.array([1, 2, 3],
dtype=np.int64)})
+ obj2 = self._positional_metadata_constructor_(
+ 3, positional_metadata=pd.DataFrame({'foo': [1, 2, 3]},
+ index=['foo', 'bar', 'baz']))
+--- a/skbio/alignment/tests/test_tabular_msa.py
b/skbio/alignment/tests/test_tabular_msa.py
+@@ -1661,7 +1661,7 @@ class TestILoc(SharedPropertyIndexTests,
+ TabularMSA([a[0:0], b[0:0], c[0:0]],
+ metadata={3: 3},
+ positional_metadata={3: np.array(
+-[], dtype=int)}))
++[], dtype=np.int64)}))
+
+ def test_fancy_empty_both_axes(self):
+ a = DNA("ACGT", metadata={0: 0}, positional_metadata={0: [1, 2, 3,
4]})
+--- a/skbio/stats/_subsample.py
b/skbio/stats/_subsample.py
+@@ -226,7 +226,7 @@ def subsample_counts(counts, n, replace=
+ raise ValueError("n cannot be negative.")
+
+ counts = np.asarray(counts)
+-counts = counts.astype(int, casting='safe')
++counts = counts.astype(np.int64, casting='safe')
+
+ if counts.ndim != 1:
+ raise ValueError("Only 1-D vectors are supported.")
+--- a/skbio/diversity/tests/test_driver.py
b/skbio/diversity/tests/test_driver.py
+@@ -157,7 +157,7 @@ class AlphaDiversityTests(TestCase):
+
+ def test_empty(self):
+ # empty vector
+-actual = alpha_diversity('observed_otus', np.array([],
dtype=np.int64))
++actual = alpha_diversity('observed_otus', np.array([],
dtype=np.int32))
+ expected = pd.Series([0])
+ assert_series_almost_equal(actual, expected)
+
+@@ -194,11 +194,11 @@ class AlphaDiversityTests(TestCase):
+ assert_series_almost_equal(actual, expected)
+
+ def test_single_count_vector(self):
+-actual = alpha_diversity('observed_otus', np.array([1, 0, 2]))
++actual = alpha_diversity('observed_otus', np.array([1, 0, 2],
np.int32))
+ expected = pd.Series([2])
+ assert_series_almost_equal(actual, expected)
+
+-actual = alpha_diversity('faith_pd', np.array([1, 3, 0, 1, 0]),
++actual = alpha_diversity('faith_pd', np.array([1, 3, 0, 1, 0],
np.int32),
+ tree=self.tree1, otu_ids=self.oids1)
+ self.assertAlmostEqual(actual[0], 4.5)
+
+@@ -252,6 +252,10 @@ class AlphaDiversityTests(TestCase):
+ def test_no_ids(self):
+ # expected values hand-calculated
+ expected = pd.Series([3, 3, 3, 3])
++# All this does not help
++# expected = pd.Series(np.array([3, 3, 3, 3], int32))
++# actual = np.int64(alpha_diversity('observed_otus', self.table1))
++# actual = np.dtype('int64').type(alpha_diversity('observed_otus',
self.table1))
+ actual = alpha_diversity('observed_otus', self.table1)
+ assert_series_almost_equal(actual, expected)
+
View it on GitLab:
https://salsa.debian.org/med-team/python-skbio/-/compare/25c2f7dc92b4a683f456bceeb43f8c517a59595c...ab3e3d2cd2247f85503db43b49301d80472fa186
--
View it on GitLab:
https://salsa.debian.org/med-team/python-skbio/-/compare/25c2f7dc92b4a683f456bceeb43f8c517a59595c...ab3e3d2cd2247f85503db43b49301d80472fa186
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[med-svn] [Git][med-team/gdcm] Pushed new tag upstream/3.0.21
Mathieu Malaterre pushed new tag upstream/3.0.21 at Debian Med / gdcm -- View it on GitLab: https://salsa.debian.org/med-team/gdcm/-/tree/upstream/3.0.21 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gdcm] Pushed new tag debian/3.0.21-1
Mathieu Malaterre pushed new tag debian/3.0.21-1 at Debian Med / gdcm -- View it on GitLab: https://salsa.debian.org/med-team/gdcm/-/tree/debian/3.0.21-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gdcm][master] 5 commits: New upstream version 3.0.17
Mathieu Malaterre pushed to branch master at Debian Med / gdcm
Commits:
b736dc5f by Andreas Tille at 2022-10-25T11:35:00+02:00
New upstream version 3.0.17
- - - - -
e5299e8f by Mathieu Malaterre at 2023-01-05T08:08:27+01:00
New upstream version 3.0.20
- - - - -
a47b3374 by Mathieu Malaterre at 2023-01-29T13:04:17+01:00
New upstream version 3.0.21
- - - - -
03446e84 by Mathieu Malaterre at 2023-01-29T13:04:18+01:00
Update upstream source from tag 'upstream/3.0.21'
Update to upstream version '3.0.21'
with Debian dir d15e1cf00da90788ee76970040e33e56b0b0566c
- - - - -
8845a7fa by Mathieu Malaterre at 2023-01-29T15:21:50+01:00
d/changelog: Upload 3.0.21-1 to unstable
- - - - -
4 changed files:
- .github/workflows/c-cpp.yml
- CMakeLists.txt
- Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
- debian/changelog
Changes:
=
.github/workflows/c-cpp.yml
=
@@ -19,7 +19,7 @@ jobs:
submodules: true
fetch-depth: 2
- name: configure
- run: cmake -DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF
-DCMAKE_BUILD_TYPE:STRING=None -B build
+ run: cmake -DGDCM_BUILD_SHARED_LIBS=ON
-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=None -B build
- name: make
run: cmake --build build
- name: make check
=
CMakeLists.txt
=
@@ -17,7 +17,7 @@ endif()
#
project(GDCM
- VERSION 3.0.20
+ VERSION 3.0.21
LANGUAGES CXX C
)
## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0
=
Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
=
@@ -1174,7 +1174,7 @@ std::vector
ImageHelper::GetRescaleInterceptSlopeValue(File const & f)
interceptslope[1] = el_rs.GetValue();
if( interceptslope[1] == 0 )
interceptslope[1] = 1;
-gdcmWarningMacro( "PMS Modality LUT loaded for MR Image Storage: [" <<
interceptslope[0] << "," << interceptslope[1] << "]" );
+gdcmDebugMacro( "PMS Modality LUT loaded for MR Image Storage: [" <<
interceptslope[0] << "," << interceptslope[1] << "]" );
}
}
else
@@ -1182,8 +1182,13 @@ std::vector
ImageHelper::GetRescaleInterceptSlopeValue(File const & f)
std::vector dummy(2);
if( GetRescaleInterceptSlopeValueFromDataSet(ds, dummy) )
{
-// for everyone else, read your DCS, and set:
ForceRescaleInterceptSlope = true if needed
-gdcmDebugMacro( "Modality LUT unused for MR Image Storage: [" <<
dummy[0] << "," << dummy[1] << "]" );
+if(dummy[0] != 0 || dummy[1] != 1) {
+// SIEMENS is sending MFSPLIT with Modality LUT
+ // Case is: MAGNETOM Prisma / syngo MR XA30A with MFSPLIT
+interceptslope[0] = dummy[0];
+interceptslope[1] = dummy[1];
+gdcmWarningMacro( "Forcing Modality LUT used for MR Image Storage: ["
<< dummy[0] << "," << dummy[1] << "]" );
+}
}
}
#endif
@@ -2477,7 +2482,7 @@ bool ImageHelper::GetRealWorldValueMappingContent(File
const & f, RealWorldValue
ms.SetFromFile(f);
const DataSet& ds = f.GetDataSet();
- if( ms == MediaStorage::MRImageStorage )
+ if( ms == MediaStorage::MRImageStorage || ms ==
MediaStorage::NuclearMedicineImageStorage )
{
const Tag trwvms(0x0040,0x9096); // Real World Value Mapping Sequence
if( ds.FindDataElement( trwvms ) )
=
debian/changelog
=
@@ -1,3 +1,10 @@
+gdcm (3.0.21-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 3.0.21
+
+ -- Mathieu Malaterre Sun, 29 Jan 2023 15:21:24 +0100
+
gdcm (3.0.20-3) unstable; urgency=medium
* d/python3-vtkgdcm: Fix hard-coded install path
View it on GitLab:
https://salsa.debian.org/med-team/gdcm/-/compare/f3836363d5f1bdb09901df6bf9a242c7d7b3ebd6...8845a7fa2591e1aab4efda1fd86b58d21fa05849
--
View it on GitLab:
https://salsa.debian.org/med-team/gdcm/-/compare/f3836363d5f1bdb09901df6bf9a242c7d7b3ebd6...8845a7fa2591e1aab4efda1fd86b58d21fa05849
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[med-svn] [Git][med-team/gdcm][upstream] New upstream version 3.0.21
Mathieu Malaterre pushed to branch upstream at Debian Med / gdcm
Commits:
a47b3374 by Mathieu Malaterre at 2023-01-29T13:04:17+01:00
New upstream version 3.0.21
- - - - -
3 changed files:
- .github/workflows/c-cpp.yml
- CMakeLists.txt
- Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
Changes:
=
.github/workflows/c-cpp.yml
=
@@ -19,7 +19,7 @@ jobs:
submodules: true
fetch-depth: 2
- name: configure
- run: cmake -DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF
-DCMAKE_BUILD_TYPE:STRING=None -B build
+ run: cmake -DGDCM_BUILD_SHARED_LIBS=ON
-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=None -B build
- name: make
run: cmake --build build
- name: make check
=
CMakeLists.txt
=
@@ -17,7 +17,7 @@ endif()
#
project(GDCM
- VERSION 3.0.20
+ VERSION 3.0.21
LANGUAGES CXX C
)
## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0
=
Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
=
@@ -1174,7 +1174,7 @@ std::vector
ImageHelper::GetRescaleInterceptSlopeValue(File const & f)
interceptslope[1] = el_rs.GetValue();
if( interceptslope[1] == 0 )
interceptslope[1] = 1;
-gdcmWarningMacro( "PMS Modality LUT loaded for MR Image Storage: [" <<
interceptslope[0] << "," << interceptslope[1] << "]" );
+gdcmDebugMacro( "PMS Modality LUT loaded for MR Image Storage: [" <<
interceptslope[0] << "," << interceptslope[1] << "]" );
}
}
else
@@ -1182,8 +1182,13 @@ std::vector
ImageHelper::GetRescaleInterceptSlopeValue(File const & f)
std::vector dummy(2);
if( GetRescaleInterceptSlopeValueFromDataSet(ds, dummy) )
{
-// for everyone else, read your DCS, and set:
ForceRescaleInterceptSlope = true if needed
-gdcmDebugMacro( "Modality LUT unused for MR Image Storage: [" <<
dummy[0] << "," << dummy[1] << "]" );
+if(dummy[0] != 0 || dummy[1] != 1) {
+// SIEMENS is sending MFSPLIT with Modality LUT
+ // Case is: MAGNETOM Prisma / syngo MR XA30A with MFSPLIT
+interceptslope[0] = dummy[0];
+interceptslope[1] = dummy[1];
+gdcmWarningMacro( "Forcing Modality LUT used for MR Image Storage: ["
<< dummy[0] << "," << dummy[1] << "]" );
+}
}
}
#endif
@@ -2477,7 +2482,7 @@ bool ImageHelper::GetRealWorldValueMappingContent(File
const & f, RealWorldValue
ms.SetFromFile(f);
const DataSet& ds = f.GetDataSet();
- if( ms == MediaStorage::MRImageStorage )
+ if( ms == MediaStorage::MRImageStorage || ms ==
MediaStorage::NuclearMedicineImageStorage )
{
const Tag trwvms(0x0040,0x9096); // Real World Value Mapping Sequence
if( ds.FindDataElement( trwvms ) )
View it on GitLab:
https://salsa.debian.org/med-team/gdcm/-/commit/a47b33746368cf8beb19eca279532eac4cfc442b
--
View it on GitLab:
https://salsa.debian.org/med-team/gdcm/-/commit/a47b33746368cf8beb19eca279532eac4cfc442b
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[med-svn] [Git][med-team/python-skbio][master] Fix some more numpy issues
Andreas Tille pushed to branch master at Debian Med / python-skbio
Commits:
25c2f7dc by Andreas Tille at 2023-01-29T11:45:30+01:00
Fix some more numpy issues
- - - - -
1 changed file:
- debian/patches/numpy-1.24.patch
Changes:
=
debian/patches/numpy-1.24.patch
=
@@ -29,6 +29,15 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
# invalid input type (non-numpy.ndarray input)
with self.assertRaisesRegex(TypeError, r'tuple'):
+@@ -885,7 +885,7 @@ class TestSequence(TestSequenceBase, Rea
+ metadata={'id': 'id9', 'description': 'dsc9'},
+ positional_metadata={'quality': [0, 1, 2, 3, 15, 14,
+ 13, 9]})
+-self.assertEqual(seq[np.array([0, 1, 2, 3, 15, 14, 13, 9])], eseq)
++self.assertEqual(seq[np.array([0, 1, 2, 3, 15, 14, 13, 9],
dtype=np.int32)], eseq)
+
+ def test_getitem_with_numpy_index_no_positional_metadata(self):
+ s = "0123456789abcdef"
@@ -2212,7 +2212,7 @@ class TestSequence(TestSequenceBase, Rea
yield i
else:
@@ -45,7 +54,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
qual_str = ' '.join(chunks)
try:
-quality = np.asarray(qual_str.split(), dtype=int)
-+quality = np.asarray(qual_str.split(), dtype=int64)
++quality = np.asarray(qual_str.split(), dtype=np.int64)
except ValueError:
raise QUALFormatError(
"Could not convert quality scores to integers:\n%s"
View it on GitLab:
https://salsa.debian.org/med-team/python-skbio/-/commit/25c2f7dc92b4a683f456bceeb43f8c517a59595c
--
View it on GitLab:
https://salsa.debian.org/med-team/python-skbio/-/commit/25c2f7dc92b4a683f456bceeb43f8c517a59595c
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[med-svn] [Git][med-team/python-skbio][master] Try fixing some issue for 32bit architectures
Andreas Tille pushed to branch master at Debian Med / python-skbio Commits: 086d2b59 by Andreas Tille at 2023-01-29T11:26:08+01:00 Try fixing some issue for 32bit architectures - - - - - 3 changed files: - debian/changelog - debian/patches/numpy-1.24.patch - debian/salsa-ci.yml Changes: = debian/changelog = @@ -1,3 +1,9 @@ +python-skbio (0.5.8-2exp2) UNRELEASED; urgency=medium + + * Try fixing some issue for 32bit architectures + + -- Andreas Tille Sun, 29 Jan 2023 11:25:28 +0100 + python-skbio (0.5.8-2exp1) experimental; urgency=medium * Deactivate patch that builds against scipy 1.81. and building against = debian/patches/numpy-1.24.patch = @@ -6,7 +6,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839 --- a/skbio/alignment/_indexing.py +++ b/skbio/alignment/_indexing.py -@@ -113,7 +113,10 @@ +@@ -113,7 +113,10 @@ class _Indexing(metaclass=ABCMeta): if isinstance(indexable, np.ndarray): pass elif hasattr(indexable, '__iter__'): @@ -20,7 +20,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839 --- a/skbio/sequence/tests/test_sequence.py +++ b/skbio/sequence/tests/test_sequence.py -@@ -459,7 +459,7 @@ +@@ -459,7 +459,7 @@ class TestSequence(TestSequenceBase, Rea Sequence(np.array([1, "23", 3])) with self.assertRaises(TypeError): # object @@ -29,7 +29,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839 # invalid input type (non-numpy.ndarray input) with self.assertRaisesRegex(TypeError, r'tuple'): -@@ -2212,7 +2212,7 @@ +@@ -2212,7 +2212,7 @@ class TestSequence(TestSequenceBase, Rea yield i else: yield np.array([i], dtype=int) @@ -38,3 +38,14 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839 lambda x: pd.Series(tuple(x))): exp = np.arange(10, dtype=int) obs = s._munge_to_index_array(c(mixed())) +--- a/skbio/io/format/fasta.py b/skbio/io/format/fasta.py +@@ -880,7 +880,7 @@ def _parse_quality_scores(chunks): + + qual_str = ' '.join(chunks) + try: +-quality = np.asarray(qual_str.split(), dtype=int) ++quality = np.asarray(qual_str.split(), dtype=int64) + except ValueError: + raise QUALFormatError( + "Could not convert quality scores to integers:\n%s" = debian/salsa-ci.yml = @@ -4,7 +4,5 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml variables: - # i386 is explicitly excluded - SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1 # Build against scipy 1.10 in experimental RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/086d2b596a637c18c4d8ef9307ea941d24df5afc -- View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/086d2b596a637c18c4d8ef9307ea941d24df5afc You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kma] Pushed new tag upstream/1.4.11
Nilesh Patra pushed new tag upstream/1.4.11 at Debian Med / kma -- View it on GitLab: https://salsa.debian.org/med-team/kma/-/tree/upstream/1.4.11 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kma] Pushed new tag debian/1.4.11-1
Nilesh Patra pushed new tag debian/1.4.11-1 at Debian Med / kma -- View it on GitLab: https://salsa.debian.org/med-team/kma/-/tree/debian/1.4.11-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kma][pristine-tar] pristine-tar data for kma_1.4.11.orig.tar.xz
Nilesh Patra pushed to branch pristine-tar at Debian Med / kma Commits: 270fde49 by Nilesh Patra at 2023-01-29T15:05:20+05:30 pristine-tar data for kma_1.4.11.orig.tar.xz - - - - - 2 changed files: - + kma_1.4.11.orig.tar.xz.delta - + kma_1.4.11.orig.tar.xz.id Changes: = kma_1.4.11.orig.tar.xz.delta = Binary files /dev/null and b/kma_1.4.11.orig.tar.xz.delta differ = kma_1.4.11.orig.tar.xz.id = @@ -0,0 +1 @@ +633526b8b5c73d7675a74be662cc3ced54f58267 View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/270fde496e20ad0a49dc92cc30043318939accb7 -- View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/270fde496e20ad0a49dc92cc30043318939accb7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tiddit] Pushed new tag debian/3.5.1+dfsg-1
Nilesh Patra pushed new tag debian/3.5.1+dfsg-1 at Debian Med / tiddit -- View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/tree/debian/3.5.1+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tiddit][upstream] New upstream version 3.5.1+dfsg
Nilesh Patra pushed to branch upstream at Debian Med / tiddit
Commits:
228e8323 by Nilesh Patra at 2023-01-29T14:59:29+05:30
New upstream version 3.5.1+dfsg
- - - - -
4 changed files:
- README.md
- setup.py
- tiddit/__main__.py
- tiddit/tiddit_coverage_analysis.pyx
Changes:
=
README.md
=
@@ -42,23 +42,13 @@ TIDDIT may be installed using bioconda:
```
conda install tiddit
```
-
-Next, you may run TIDDIT like this:
-```
-tiddit --help
-tiddit --sv
-tiddit --cov
-```
-TIDDIT is also distributed with a Docker container
(http://singularity.lbl.gov/index.html). Type the following command to download
the container:
+or using the docker image on biocontainers
```
-singularity pull --name TIDDIT.simg
+docker pull quay.io/biocontainers/tiddit:
```
+visit https://quay.io/repository/biocontainers/tiddit?tab=tags for tags.
-Type the following to run tiddit:
-```
-singularity exec TIDDIT.simg tiddit
-```
The SV module
=
=
setup.py
=
@@ -20,7 +20,7 @@ else:
setup(
name = 'tiddit',
-version = '3.4.0',
+version = '3.5.1',
url = "https://github.com/SciLifeLab/TIDDIT";,
author = "Jesper Eisfeldt",
=
tiddit/__main__.py
=
@@ -17,7 +17,7 @@ import tiddit.tiddit_variant as tiddit_variant
import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
def main():
- version="3.4.0"
+ version="3.5.1"
parser =
argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
parser.add_argument("--sv" , help="call structural variation",
required=False, action="store_true")
parser.add_argument("--cov", help="generate a coverage bed
file", required=False, action="store_true")
@@ -115,11 +115,8 @@ def main():
i+=1
prefix=args.o
- try:
- os.mkdir( "{}_tiddit".format(prefix) )
- os.mkdir("{}_tiddit/clips".format(prefix) )
- except:
- print("Folder already exists")
+ os.mkdir(f"{prefix}_tiddit")
+ os.mkdir(f"{prefix}_tiddit/clips")
pysam.index("-c","-m","6","-@",str(args.threads),bam_file_name,"{}_tiddit/{}.csi".format(args.o,sample_id))
=
tiddit/tiddit_coverage_analysis.pyx
=
@@ -1,4 +1,5 @@
import numpy
+import re
cimport numpy
import pysam
import gzip
@@ -19,7 +20,9 @@ def get_gc(str reference_fasta,bam_header,bin_size):
with gzip.open(reference_fasta, 'r') as f:
sequence=f.read()
- split_reference=sequence.split(">")
+
+ #split_reference=sequence.split(">")
+ split_reference=re.split("\n>|^>", sequence)
del sequence
del split_reference[0]
View it on GitLab:
https://salsa.debian.org/med-team/tiddit/-/commit/228e83238ce14f577ef3a6e6bd35afa86d4d533e
--
View it on GitLab:
https://salsa.debian.org/med-team/tiddit/-/commit/228e83238ce14f577ef3a6e6bd35afa86d4d533e
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[med-svn] [Git][med-team/tiddit] Pushed new tag upstream/3.5.1+dfsg
Nilesh Patra pushed new tag upstream/3.5.1+dfsg at Debian Med / tiddit -- View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/tree/upstream/3.5.1+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tiddit][master] 3 commits: New upstream version 3.5.1+dfsg
Nilesh Patra pushed to branch master at Debian Med / tiddit
Commits:
228e8323 by Nilesh Patra at 2023-01-29T14:59:29+05:30
New upstream version 3.5.1+dfsg
- - - - -
675c87c5 by Nilesh Patra at 2023-01-29T14:59:29+05:30
Update upstream source from tag 'upstream/3.5.1+dfsg'
Update to upstream version '3.5.1+dfsg'
with Debian dir 02b5eb9f17b7051c9096364b0fa64125d8d39cad
- - - - -
c284581f by Nilesh Patra at 2023-01-29T15:00:02+05:30
Upload to unstable
- - - - -
5 changed files:
- README.md
- debian/changelog
- setup.py
- tiddit/__main__.py
- tiddit/tiddit_coverage_analysis.pyx
Changes:
=
README.md
=
@@ -42,23 +42,13 @@ TIDDIT may be installed using bioconda:
```
conda install tiddit
```
-
-Next, you may run TIDDIT like this:
-```
-tiddit --help
-tiddit --sv
-tiddit --cov
-```
-TIDDIT is also distributed with a Docker container
(http://singularity.lbl.gov/index.html). Type the following command to download
the container:
+or using the docker image on biocontainers
```
-singularity pull --name TIDDIT.simg
+docker pull quay.io/biocontainers/tiddit:
```
+visit https://quay.io/repository/biocontainers/tiddit?tab=tags for tags.
-Type the following to run tiddit:
-```
-singularity exec TIDDIT.simg tiddit
-```
The SV module
=
=
debian/changelog
=
@@ -1,3 +1,10 @@
+tiddit (3.5.1+dfsg-1) unstable; urgency=medium
+
+ * Team Upload.
+ * New upstream version 3.5.1+dfsg
+
+ -- Nilesh Patra Sun, 29 Jan 2023 14:59:51 +0530
+
tiddit (3.4.0+dfsg-1) unstable; urgency=medium
* Team Upload.
=
setup.py
=
@@ -20,7 +20,7 @@ else:
setup(
name = 'tiddit',
-version = '3.4.0',
+version = '3.5.1',
url = "https://github.com/SciLifeLab/TIDDIT";,
author = "Jesper Eisfeldt",
=
tiddit/__main__.py
=
@@ -17,7 +17,7 @@ import tiddit.tiddit_variant as tiddit_variant
import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
def main():
- version="3.4.0"
+ version="3.5.1"
parser =
argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
parser.add_argument("--sv" , help="call structural variation",
required=False, action="store_true")
parser.add_argument("--cov", help="generate a coverage bed
file", required=False, action="store_true")
@@ -115,11 +115,8 @@ def main():
i+=1
prefix=args.o
- try:
- os.mkdir( "{}_tiddit".format(prefix) )
- os.mkdir("{}_tiddit/clips".format(prefix) )
- except:
- print("Folder already exists")
+ os.mkdir(f"{prefix}_tiddit")
+ os.mkdir(f"{prefix}_tiddit/clips")
pysam.index("-c","-m","6","-@",str(args.threads),bam_file_name,"{}_tiddit/{}.csi".format(args.o,sample_id))
=
tiddit/tiddit_coverage_analysis.pyx
=
@@ -1,4 +1,5 @@
import numpy
+import re
cimport numpy
import pysam
import gzip
@@ -19,7 +20,9 @@ def get_gc(str reference_fasta,bam_header,bin_size):
with gzip.open(reference_fasta, 'r') as f:
sequence=f.read()
- split_reference=sequence.split(">")
+
+ #split_reference=sequence.split(">")
+ split_reference=re.split("\n>|^>", sequence)
del sequence
del split_reference[0]
View it on GitLab:
https://salsa.debian.org/med-team/tiddit/-/compare/09348e8503ffd89bff845e64ad81b7686beeb66e...c284581f3bc8fe877654e1be7eca6266d1ce2f90
--
View it on GitLab:
https://salsa.debian.org/med-team/tiddit/-/compare/09348e8503ffd89bff845e64ad81b7686beeb66e...c284581f3bc8fe877654e1be7eca6266d1ce2f90
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/tiddit][pristine-tar] pristine-tar data for tiddit_3.5.1+dfsg.orig.tar.xz
Nilesh Patra pushed to branch pristine-tar at Debian Med / tiddit Commits: 2a455be6 by Nilesh Patra at 2023-01-29T14:59:29+05:30 pristine-tar data for tiddit_3.5.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + tiddit_3.5.1+dfsg.orig.tar.xz.delta - + tiddit_3.5.1+dfsg.orig.tar.xz.id Changes: = tiddit_3.5.1+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/tiddit_3.5.1+dfsg.orig.tar.xz.delta differ = tiddit_3.5.1+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +ce22c0a42ebd11c6b6ad76de0442df1e4b608382 View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/2a455be6223667fe400a8cfb00e589844e36d37c -- View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/2a455be6223667fe400a8cfb00e589844e36d37c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
