[med-svn] [Git][med-team/libmmap-allocator][master] Minor fix to hardening patch

2024-05-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / libmmap-allocator


Commits:
af74417f by Nilesh Patra at 2024-05-26T16:09:47+05:30
Minor fix to hardening patch

- - - - -


1 changed file:

- debian/patches/hardening.patch


Changes:

=
debian/patches/hardening.patch
=
@@ -20,3 +20,12 @@
  
  libmmap_allocator.a: mmap_file_pool.o
$(AR) r libmmap_allocator.a mmap_file_pool.o
+@@ -44,7 +44,7 @@
+   bash -c 'export LD_LIBRARY_PATH=. ; ./test_allocator'
+ 
+ test_allocator: mmap_allocator.h mmap_file_pool.o test_allocator.o 
$(LIBRARIES)
+-  $(CXX) test_allocator.o -L. -lmmap_allocator -o test_allocator
++  $(CXX) test_allocator.o -L. -lmmap_allocator -o test_allocator 
$(LDFLAGS)
+ 
+ test_mmap_fixed: test_mmap_fixed.c
+   $(CC) $(CFLAGS) test_mmap_fixed.c -o test_mmap_fixed



View it on GitLab: 
https://salsa.debian.org/med-team/libmmap-allocator/-/commit/af74417f1154bc6de9ad30066205748d58cd830b

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[med-svn] [Git][med-team/libmmap-allocator] Pushed new tag debian/0.4.0+git20200122.adbfbe1-2

2024-05-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/0.4.0+git20200122.adbfbe1-2 at Debian Med / 
libmmap-allocator

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[med-svn] [Git][med-team/libmmap-allocator][master] 5 commits: Add patch to get package cross-building

2024-05-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / libmmap-allocator


Commits:
df9fcfaa by Nilesh Patra at 2024-05-26T15:26:12+05:30
Add patch to get package cross-building

- - - - -
f5a37322 by Nilesh Patra at 2024-05-26T15:27:13+05:30
d/rules: Use dh_auto_build instead of hardcoding MAKE

- - - - -
4b774a89 by Nilesh Patra at 2024-05-26T15:27:19+05:30
Revert "Install shared lib as well"

This reverts commit f5227650a16a6340a8bccf2b3a9ea169e375cbff.

- - - - -
f3ce162f by Nilesh Patra at 2024-05-26T15:31:20+05:30
Add patch for hardening opts

- - - - -
bd89e519 by Nilesh Patra at 2024-05-26T15:35:05+05:30
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/install
- + debian/patches/cross.patch
- + debian/patches/hardening.patch
- debian/patches/series
- debian/rules


Changes:

=
debian/changelog
=
@@ -1,3 +1,14 @@
+libmmap-allocator (0.4.0+git20200122.adbfbe1-2) unstable; urgency=medium
+
+  * Team Upload.
+  * Install shared lib as well
+  * Bump Standards-Version to 4.7.0 (no changes needed)
+  * Add patch to get package cross-building
+  * d/rules: Use dh_auto_build instead of hardcoding MAKE
+  * Add patch for hardening opts
+
+ -- Nilesh Patra   Sun, 26 May 2024 15:34:47 +0530
+
 libmmap-allocator (0.4.0+git20200122.adbfbe1-1) unstable; urgency=medium
 
   * For iitii package the latest commit is needed


=
debian/install
=
@@ -1,4 +1,4 @@
 #!/usr/bin/dh-exec
 *.husr/include
-libmmap_allocator.so   usr/lib/${DEB_HOST_MULTIARCH}
+#libmmap_allocator.so  usr/lib/${DEB_HOST_MULTIARCH}
 libmmap_allocator.ausr/lib/${DEB_HOST_MULTIARCH}


=
debian/patches/cross.patch
=
@@ -0,0 +1,35 @@
+--- a/Makefile
 b/Makefile
+@@ -1,3 +1,6 @@
++CC ?= gcc
++CXX ?= g++
++AR ?= ar
+ CPPFLAGS=-g -Wall -fPIC
+ CFLAGS=-g -Wall -fPIC
+ 
+@@ -20,10 +23,10 @@
+ debug: clean all
+ 
+ libmmap_allocator.so: mmap_file_pool.o
+-  g++ -shared -o libmmap_allocator.so mmap_file_pool.o
++  $(CXX) -shared -o libmmap_allocator.so mmap_file_pool.o
+ 
+ libmmap_allocator.a: mmap_file_pool.o
+-  ar r libmmap_allocator.a mmap_file_pool.o
++  $(AR) r libmmap_allocator.a mmap_file_pool.o
+ 
+ install_sources: $(SOURCES)
+   cp $(SOURCES) $(SRC_INSTALL_TARGET_DIR)
+@@ -41,10 +44,10 @@
+   bash -c 'export LD_LIBRARY_PATH=. ; ./test_allocator'
+ 
+ test_allocator: mmap_allocator.h mmap_file_pool.o test_allocator.o 
$(LIBRARIES)
+-  g++ test_allocator.o -L. -lmmap_allocator -o test_allocator
++  $(CXX) test_allocator.o -L. -lmmap_allocator -o test_allocator
+ 
+ test_mmap_fixed: test_mmap_fixed.c
+-  gcc $(CFLAGS) test_mmap_fixed.c -o test_mmap_fixed
++  $(CC) $(CFLAGS) test_mmap_fixed.c -o test_mmap_fixed
+ 
+ clean:
+   rm -f test_allocator test_mmap_fixed testfile testfile2 *.o $(LIBRARIES)


=
debian/patches/hardening.patch
=
@@ -0,0 +1,22 @@
+--- a/Makefile
 b/Makefile
+@@ -1,8 +1,8 @@
+ CC ?= gcc
+ CXX ?= g++
+ AR ?= ar
+-CPPFLAGS=-g -Wall -fPIC
+-CFLAGS=-g -Wall -fPIC
++CPPFLAGS += -g -Wall -fPIC
++CFLAGS += -g -Wall -fPIC
+ 
+ # Enable to test with GCC 3.4
+ # CXX=g++34
+@@ -23,7 +23,7 @@
+ debug: clean all
+ 
+ libmmap_allocator.so: mmap_file_pool.o
+-  $(CXX) -shared -o libmmap_allocator.so mmap_file_pool.o
++  $(CXX) -shared -o libmmap_allocator.so mmap_file_pool.o $(LDFLAGS)
+ 
+ libmmap_allocator.a: mmap_file_pool.o
+   $(AR) r libmmap_allocator.a mmap_file_pool.o


=
debian/patches/series
=
@@ -1 +1,3 @@
 # soname.patch
+cross.patch
+hardening.patch


=
debian/rules
=
@@ -6,7 +6,7 @@
dh $@
 
 override_dh_auto_build:
-   $(MAKE) libmmap_allocator.so libmmap_allocator.a
+   dh_auto_build -- libmmap_allocator.so libmmap_allocator.a
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))



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[med-svn] [Git][med-team/libmmap-allocator][master] Bump Standards-Version to 4.7.0 (no changes needed)

2024-05-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / libmmap-allocator


Commits:
e083ff5f by Nilesh Patra at 2024-05-26T14:58:22+05:30
Bump Standards-Version to 4.7.0 (no changes needed)

- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
@@ -5,7 +5,7 @@ Section: libdevel
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
dh-exec
-Standards-Version: 4.5.0
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/libmmap-allocator
 Vcs-Git: https://salsa.debian.org/med-team/libmmap-allocator.git
 Homepage: https://github.com/ekg/mmap_allocator/



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[med-svn] [Git][med-team/blimps][master] 2 commits: Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066956)

2024-04-13 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / blimps


Commits:
e0ea8796 by Nilesh Patra at 2024-04-14T03:06:56+05:30
Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066956)

- - - - -
b304527b by Nilesh Patra at 2024-04-14T03:07:25+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fixup-implicit-function-declaration.patch
- debian/patches/series


Changes:

=
debian/changelog
=
@@ -1,3 +1,11 @@
+blimps (3.9+ds-2) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with
+implicit-function-declaration (Closes: #1066956)
+
+ -- Nilesh Patra   Sun, 14 Apr 2024 03:07:00 +0530
+
 blimps (3.9+ds-1) unstable; urgency=medium
 
   * Homepage vanished - point to waybackmachine as homepage


=
debian/patches/fixup-implicit-function-declaration.patch
=
@@ -0,0 +1,17 @@
+--- a/blimps/biassed_blocks_finder.c
 b/blimps/biassed_blocks_finder.c
+@@ -17,14 +17,8 @@
+ char *val;
+ } entry;
+ 
+-/* from util.c */
+-/*
+-char *makeword(char *line, char stop);
+-char *fmakeword(FILE *f, char stop, int *len);
+-char x2c(char *what);
+ void unescape_url(char *url);
+ void plustospace(char *str);
+-*/
+ // lkajan: very nice but util.c does not have an interface defined
+ // lkajan: can't figure out where this came from but it certainly picked up 
the wrong fmakeword
+ char *fmakeword(FILE *f, char stop, int *cl);


=
debian/patches/series
=
@@ -2,3 +2,4 @@ gets.patch
 makefile.patch
 hardening.patch
 avoid_privacy_breach.patch
+fixup-implicit-function-declaration.patch



View it on GitLab: 
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[med-svn] [Git][med-team/blimps] Pushed new tag debian/3.9+ds-2

2024-04-13 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/3.9+ds-2 at Debian Med / blimps

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[med-svn] [Git][med-team/maude][master] 5 commits: Drop patch file

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / maude


Commits:
e11f6096 by Nilesh Patra at 2024-04-07T16:22:20+05:30
Drop patch file

- - - - -
875abbea by Nilesh Patra at 2024-04-07T16:24:16+05:30
Update Builddep from libncurses5-dev => libncurses-dev (former is a virtual 
package)

- - - - -
d66e3a93 by Nilesh Patra at 2024-04-07T16:24:30+05:30
Bump Standards-Version to 4.6.2 (no changes needed)

- - - - -
e25c5880 by Nilesh Patra at 2024-04-07T16:27:50+05:30
Remove copyright for superfluous file

- - - - -
c1f2b3cc by Nilesh Patra at 2024-04-07T16:28:49+05:30
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/glibc-2.34.patch


Changes:

=
debian/changelog
=
@@ -1,10 +1,15 @@
-maude (3.4-1) UNRELEASED; urgency=medium
+maude (3.4-1) unstable; urgency=medium
 
   * Team Upload.
-  * New upstream version 3.4
+  * New upstream version 3.4 (Closes: #1067957)
   * Refresh, update patches
+  * Drop patch file
+  * Update Builddep from libncurses5-dev => libncurses-dev
+(former is a virtual package)
+  * Bump Standards-Version to 4.6.2 (no changes needed)
+  * Remove copyright for superfluous file
 
- -- Nilesh Patra   Sun, 07 Apr 2024 15:39:24 +0530
+ -- Nilesh Patra   Sun, 07 Apr 2024 16:28:11 +0530
 
 maude (3.2-2) unstable; urgency=medium
 


=
debian/control
=
@@ -11,9 +11,9 @@ Build-Depends: debhelper-compat (= 13),
libsigsegv-dev,
bison,
flex,
-   libncurses5-dev,
+   libncurses-dev,
libcvc4-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/maude
 Vcs-Git: https://salsa.debian.org/med-team/maude.git
 Homepage: http://maude.cs.uiuc.edu


=
debian/copyright
=
@@ -7,38 +7,6 @@ Files: *
 Copyright: 1997-2011 SRI International, Menlo Park, CA 94025, USA.
 License: GPL-2+
 
-Files: src/3rdParty/MersenneTwister.h
-Copyright: 2000 - 2003, Richard J. Wagner
-License: BSD-like
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- .
-  1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- .
-  2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- .
-  3. The names of its contributors may not be used to endorse or promote
- products derived from this software without specific prior written
- permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Comment: For citation information see
- file debian/upstream-metadata.yaml
-
 Files: debian/*
 Copyright: 2011 Scott Christley ,
 Andreas Tille 


=
debian/patches/glibc-2.34.patch deleted
=



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[med-svn] [Git][med-team/maude] Pushed new tag debian/3.4-1

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/3.4-1 at Debian Med / maude

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[med-svn] [Git][med-team/maude][pristine-tar] pristine-tar data for maude_3.4.orig.tar.gz

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch pristine-tar at Debian Med / maude


Commits:
3ed467bc by Nilesh Patra at 2024-04-07T16:29:47+05:30
pristine-tar data for maude_3.4.orig.tar.gz

- - - - -


2 changed files:

- + maude_3.4.orig.tar.gz.delta
- + maude_3.4.orig.tar.gz.id


Changes:

=
maude_3.4.orig.tar.gz.delta
=
Binary files /dev/null and b/maude_3.4.orig.tar.gz.delta differ


=
maude_3.4.orig.tar.gz.id
=
@@ -0,0 +1 @@
+e1a88830708fe1fcc46a0495f1f7f52c30dd91aa



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[med-svn] [Git][med-team/maude][master] 4 commits: New upstream version 3.4

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / maude


Commits:
5afd3e99 by Nilesh Patra at 2024-04-07T15:20:32+05:30
New upstream version 3.4
- - - - -
0420a331 by Nilesh Patra at 2024-04-07T15:20:32+05:30
Update upstream source from tag 'upstream/3.4'

Update to upstream version '3.4'
with Debian dir f5b81c0ca7d5e6216a57e9aba956fa3243b82864
- - - - -
02a2864e by Nilesh Patra at 2024-04-07T15:39:21+05:30
Refresh, update patches

- - - - -
781944d7 by Nilesh Patra at 2024-04-07T15:39:43+05:30
Interim d/ch

- - - - -


10 changed files:

- + .gitignore
- ChangeLog
- INSTALL
- Makefile.am
- Makefile.in
- NEWS
- − README
- + README.md
- compile
- config.guess


The diff was not included because it is too large.


View it on GitLab: 
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[med-svn] [Git][med-team/maude][upstream] New upstream version 3.4

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch upstream at Debian Med / maude


Commits:
5afd3e99 by Nilesh Patra at 2024-04-07T15:20:32+05:30
New upstream version 3.4
- - - - -


10 changed files:

- + .gitignore
- ChangeLog
- INSTALL
- Makefile.am
- Makefile.in
- NEWS
- − README
- + README.md
- compile
- config.guess


The diff was not included because it is too large.


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https://salsa.debian.org/med-team/maude/-/commit/5afd3e9923ca00d7aab807c93dd138f603b9fa77

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[med-svn] [Git][med-team/maude] Pushed new tag upstream/3.4

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag upstream/3.4 at Debian Med / maude

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[med-svn] [Git][med-team/fastdnaml][master] 3 commits: Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066709)

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / fastdnaml


Commits:
596df407 by Nilesh Patra at 2024-04-07T14:47:19+05:30
Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066709)

- - - - -
00d0112e by Nilesh Patra at 2024-04-07T14:47:38+05:30
Bump Standards-Version to 4.6.2 (no changes needed)

- - - - -
1ba1470a by Nilesh Patra at 2024-04-07T14:48:08+05:30
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/fixup-implicit-function-declaration.patch
- debian/patches/series


Changes:

=
debian/changelog
=
@@ -1,3 +1,12 @@
+fastdnaml (1.2.2-16) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with
+implicit-function-declaration (Closes: #1066709)
+  * Bump Standards-Version to 4.6.2 (no changes needed)
+
+ -- Nilesh Patra   Sun, 07 Apr 2024 14:47:48 +0530
+
 fastdnaml (1.2.2-15) unstable; urgency=medium
 
   * Standards-Version: 4.5.1 (routine-update)


=
debian/control
=
@@ -5,7 +5,7 @@ Uploaders: Andreas Tille ,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/fastdnaml
 Vcs-Git: https://salsa.debian.org/med-team/fastdnaml.git
 Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html


=
debian/patches/fixup-implicit-function-declaration.patch
=
@@ -0,0 +1,63 @@
+--- a/source/fastDNAml.h
 b/source/fastDNAml.h
+@@ -5,6 +5,7 @@
+ #define headerDate "March 9, 1998"
+ 
+ #ifndef dnaml_h
++#include 
+ 
+ /*  Compile time switches for various updates to program:
+  *0 gives original version
+@@ -218,7 +219,7 @@
+ 
+ #if  ANSI || MALLOC_VOID
+void *malloc();
+-#else
++#elif !defined(__STDC__)
+char *malloc();
+ #endif
+ 
+--- a/source/fastDNAml.c
 b/source/fastDNAml.c
+@@ -204,6 +204,8 @@
+ 
+ #include 
+ #include 
++#include 
++#include 
+ #include "fastDNAml.h"  /*  Requires version 1.2  */
+ 
+ #if Master || Slave
+@@ -2853,32 +2855,6 @@
+   } /* buildSimpleTree */
+ 
+ 
+-char * strchr (char *str, int chr)
+- { /* strchr */
+-int  c;
+-
+-while (c = *str)  {if (c == chr) return str; str++;}
+-return  (char *) NULL;
+- } /* strchr */
+-
+-
+-char * strstr (char *str1, char *str2)
+- { /* strstr */
+-char *s1, *s2;
+-int  c;
+-
+-while (*(s1 = str1)) {
+-  s2 = str2;
+-  do {
+-if (! (c = *s2++))  return str1;
+-} 
+-while (*s1++ == c);
+-  str1++;
+-  }
+-return  (char *) NULL;
+- } /* strstr */
+-
+-
+ boolean readKeyValue (char *string, char *key, char *format, void *value)
+   { /* readKeyValue */
+ 


=
debian/patches/series
=
@@ -2,3 +2,4 @@ Makefile.patch
 scripts.patch
 hardening.patch
 cross.patch
+fixup-implicit-function-declaration.patch



View it on GitLab: 
https://salsa.debian.org/med-team/fastdnaml/-/compare/45a7df96e9c18365a9aff09e55387a417ddf006f...1ba1470ac35cbc7b216893c907ac0aa43421e1d3

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[med-svn] [Git][med-team/fastdnaml] Pushed new tag debian/1.2.2-16

2024-04-07 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/1.2.2-16 at Debian Med / fastdnaml

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[med-svn] [Git][med-team/phast][master] Upload to unstable

2024-03-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / phast


Commits:
1ecf52be by Nilesh Patra at 2024-03-26T15:21:23+05:30
Upload to unstable

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
@@ -1,3 +1,12 @@
+phast (1.6+dfsg-5) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS due to -Werror-implicit-function-declaration
+(Closes: #1066451)
+  * Added B-D on lapacke-dev for porting functions to lapack equivalents
+
+ -- Nilesh Patra   Tue, 26 Mar 2024 15:19:11 +0530
+
 phast (1.6+dfsg-4) unstable; urgency=medium
 
   [ Andreas Tille ]



View it on GitLab: 
https://salsa.debian.org/med-team/phast/-/commit/1ecf52beedc6cab1372af683162a57c38c84d813

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[med-svn] [Git][med-team/phast] Pushed new tag debian/1.6+dfsg-5

2024-03-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/1.6+dfsg-5 at Debian Med / phast

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[med-svn] [Git][med-team/hmmer2][master] Upload to unstable

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / hmmer2


Commits:
74ad5321 by Nilesh Patra at 2024-03-25T18:17:26+05:30
Upload to unstable

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
@@ -1,3 +1,11 @@
+hmmer2 (2.3.2+dfsg-11) unstable; urgency=medium
+
+  * Team Upload.
+  * Fixup regression in autopkgtests introduced w/ previous
+upload.
+
+ -- Nilesh Patra   Mon, 25 Mar 2024 18:17:17 +0530
+
 hmmer2 (2.3.2+dfsg-10) unstable; urgency=medium
 
   * Team Upload.



View it on GitLab: 
https://salsa.debian.org/med-team/hmmer2/-/commit/74ad532194c54726b0b8172471d551fc5c8a5f03

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[med-svn] [Git][med-team/hmmer2] Pushed new tag debian/2.3.2+dfsg-11

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/2.3.2+dfsg-11 at Debian Med / hmmer2

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[med-svn] [Git][med-team/hmmer2][master] Fixup autopkgtests

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / hmmer2


Commits:
4429e204 by Nilesh Patra at 2024-03-25T18:07:42+05:30
Fixup autopkgtests

- - - - -


2 changed files:

- + debian/tests/Makefile.test
- debian/tests/run-unit-test


Changes:

=
debian/tests/Makefile.test
=
@@ -0,0 +1,79 @@
+
+# Makefile for HMMER testsuite
+# CVS $Id: Makefile.in,v 1.18 2003/06/13 20:05:31 eddy Exp $
+##
+# HMMER - Biological sequence analysis with profile HMMs
+# Copyright (C) 1992-2003 Washington University School of Medicine
+# All Rights Reserved
+# 
+# This source code is distributed under the terms of the
+# GNU General Public License. See the files COPYING and LICENSE
+# for details.
+###
+
+CC= gcc
+CFLAGS= -g -O2 -ffile-prefix-map=.=. -fstack-protector-strong 
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
+CPPFLAGS  = -Wdate-time -D_FORTIFY_SOURCE=2
+LDFLAGS   = -Wl,-z,relro -Wl,-z,now
+DEFS  = -DHAVE_CONFIG_H
+LIBS  =  -lm
+MYLIBS= -lhmmer `pkg-config --libs libsquid`
+
+# Configuration for optional pthreads multiprocessor support
+#
+PTHREAD_LIBS   = 
+PTHREAD_CFLAGS = 
+
+SHELL = /bin/sh
+
+SHIVA = alignalign_test\
+   evd_test\
+   masks_test\
+   parsingviterbi_test\
+   tophits_test\
+   trace_test\
+   viterbi_exercise\
+   weeviterbi_test
+
+###
+## Targets defining how to make Shiva executables.
+###
+
+.c.o:
+   $(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${CPPFLAGS} $(DEFS) `pkg-config 
--cflags libsquid` -I../src -I/usr/include/hmmer2 -c $<   
+
+all:   $(SHIVA)
+
+$(SHIVA): %: %.o
+   $(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${LDFLAGS} $(DEFS) -o $@ -L../src 
$@.o $(MYLIBS) $(PTHREAD_LIBS) $(LIBS)
+
+###
+## `make check` actually runs the tests.
+###
+
+check: 
+   @echo 
+   @echo Running test suite exercises.
+   @echo Warning: some tests may take several minutes to complete. 
+   @echo 
+   ./sqc 2 exercises.sqc . ../src
+
+
+###
+## Miscellaneous
+###
+
+clean:
+   -rm -f *.o *~ Makefile.bak core $(SHIVA) TAGS gmon.out
+
+distclean:
+   make clean
+   -rm -f Makefile
+
+binclean:
+   -rm -f *.o *~ Makefile.bak core TAGS gmon.out
+
+TAGS:
+   etags -t *.c *.h Makefile.in
+
+


=
debian/tests/run-unit-test
=
@@ -8,12 +8,12 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
 fi
 
 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+cp debian/tests/Makefile.test $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
 
 find . -name "*.gz" -exec gunzip \{\} \;
-sed -i 's|$(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${CPPFLAGS} $(DEFS) `pkg-config 
--cflags libsquid` -I../src -c $<|$(CC) $(CFLAGS) $(PTHREAD_CFLAGS) ${CPPFLAGS} 
$(DEFS) `pkg-config --cflags libsquid` -I../src -I/usr/include/hmmer2 -c $<|' 
Makefile 
-make
+make -f Makefile.test
 testnames=`cut -f2 -d '@' ./exercises.sqc | grep "_test\|_exercise"`
 
 chmod +x $testnames



View it on GitLab: 
https://salsa.debian.org/med-team/hmmer2/-/commit/4429e2043d2b33652d6ad3430e84cac8d2d5e938

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[med-svn] [Git][med-team/hmmer2] Pushed new tag debian/2.3.2+dfsg-10

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/2.3.2+dfsg-10 at Debian Med / hmmer2

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[med-svn] [Git][med-team/hmmer2][master] 6 commits: Add patch to fix FTBFS

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / hmmer2


Commits:
ca3a07cd by Nilesh Patra at 2024-03-25T13:08:20+05:30
Add patch to fix FTBFS

- - - - -
f6d21537 by Nilesh Patra at 2024-03-25T10:07:54+00:00
Pass GNU Test macro to resolve implicit function warning with pthread

- - - - -
5d9277d3 by Nilesh Patra at 2024-03-25T10:20:03+00:00
Also run dh_clean in addition to overriden ops

- - - - -
e63c921f by Nilesh Patra at 2024-03-25T10:31:21+00:00
Change exercises.sqc post installation - do not change files in source root

- - - - -
1a577145 by Nilesh Patra at 2024-03-25T16:09:07+05:30
Move from pkg-config => pkgconf

- - - - -
04766961 by Nilesh Patra at 2024-03-25T16:10:02+05:30
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/fixup-implicit-function-declaration.patch
- debian/patches/series
- debian/rules


Changes:

=
debian/changelog
=
@@ -1,3 +1,16 @@
+hmmer2 (2.3.2+dfsg-9) unstable; urgency=medium
+
+   * Team Upload.
+   * Add patch to fix FTBFS due to implicit-function-decl
+   * Pass GNU Test macro to resolve implicit function
+ warning with pthread. (Closes: #1066436)
+   * Also run dh_clean in addition to overridden ops
+   * Change exercises.sqc post installation - do not
+ change files in source root (Closes: #1046065, #1049476)
+   * Move from pkg-config => pkgconf
+
+ -- Nilesh Patra   Mon, 25 Mar 2024 16:09:47 +0530
+
 hmmer2 (2.3.2+dfsg-8) unstable; urgency=medium
 
   * Provide configure.ac as source for configure


=
debian/control
=
@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 13),
libperl4-corelibs-perl,
libsquid-dev,
-   pkg-config,
+   pkgconf,
dh-exec,
rename
 Standards-Version: 4.6.1


=
debian/patches/fixup-implicit-function-declaration.patch
=
@@ -0,0 +1,12 @@
+--- a/src/funcs.h
 b/src/funcs.h
+@@ -171,6 +171,9 @@
+ /* mathsupport.c
+  * Much of this code deals with Dirichlet prior mathematics. 
+  */
++
++extern double Gammln(double x);
++extern double IncompleteGamma(double a, double x);
+ extern int   Prob2Score(float p, float null);
+ extern float Score2Prob(int sc, float null);
+ extern float Scorify(int sc);


=
debian/patches/series
=
@@ -4,3 +4,4 @@ spelling.patch
 use_debian_packaged_biosquid.patch
 build_libhmmer.a_with-fPIC.patch
 add-runstatedir-option.patch
+fixup-implicit-function-declaration.patch


=
debian/rules
=
@@ -15,8 +15,9 @@ export AUTOHEADER = 'true'
dh $@
 
 override_dh_clean:
+   dh_clean
if [ -e configure_not_used ] ; then mv configure_not_used configure; fi
-   rm -f configure.ac
+   rm -f configure.ac src/config.h
 
 # Trying to address #1025739 but the resulting configure file does not work
 override_dh_autoreconf:
@@ -27,7 +28,7 @@ override_dh_autoreconf:
dh_autoreconf
 
 override_dh_auto_configure:
-   dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm
+   dh_auto_configure -- --enable-threads --enable-lfs 
PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm
# avoid duplicated definition of PACKAGE_NAME (basically conflicting 
with biosquid when used together)
sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \
   -e '/^#define PACKAGE_NAME /a #endif' \
@@ -68,9 +69,9 @@ endif
 override_dh_installexamples:
dh_installexamples
mkdir -p $(sampledir);
-   sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc
cp -a testsuite/* $(sampledir)/;
mkdir $(sampledir)/tutorial;
cp -a tutorial/* $(sampledir)/tutorial;
+   sed -i "s#hmm#hmm2#g" $(sampledir)/exercises.sqc
sed -i "s#../tut#./tut#g" $(sampledir)/exercises.sqc
find $(sampledir) -name 'Makefile' | xargs sed -i "s^$(CURDIR)^.^g"



View it on GitLab: 
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[med-svn] [Git][med-team/hmmer2] Pushed new tag debian/2.3.2+dfsg-9

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/2.3.2+dfsg-9 at Debian Med / hmmer2

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[med-svn] [Git][med-team/lagan][master] 2 commits: Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066580)

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / lagan


Commits:
8d2e6942 by Nilesh Patra at 2024-03-25T12:32:22+05:30
Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066580)

- - - - -
72adfc24 by Nilesh Patra at 2024-03-25T12:32:47+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fixup-implicit-function-declaration.patch
- debian/patches/series


Changes:

=
debian/changelog
=
@@ -1,3 +1,11 @@
+lagan (2.0-10) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with
+implicit-function-declaration (Closes: #1066580)
+
+ -- Nilesh Patra   Mon, 25 Mar 2024 12:32:30 +0530
+
 lagan (2.0-9) unstable; urgency=medium
 
   * Team upload.


=
debian/patches/fixup-implicit-function-declaration.patch
=
@@ -0,0 +1,63 @@
+--- a/src/utils/cstat.c
 b/src/utils/cstat.c
+@@ -3,6 +3,7 @@
+ #include 
+ #include 
+ #include 
++#include 
+ 
+ #define MAX_SEQ 31
+ #define MAX(a,b) ((a)>(b)?(a):(b))
+--- a/src/order.c
 b/src/order.c
+@@ -49,6 +49,8 @@
+ 
+ int substmatrix[256][256];
+ 
++int printXMFAAlign(char*, char*, align*, char*, char*);
++int printMFAAlign(char*, char*, align*, char*, char*);
+ 
+ seq* readfile(FILE* input, int seqnum) {
+   char* res = (char*) malloc(sizeof(char)*2);
+--- a/src/utils/scorecontigs.c
 b/src/utils/scorecontigs.c
+@@ -3,6 +3,7 @@
+ #include 
+ #include 
+ #include 
++#include 
+ 
+ #define MAX_SEQ 1024
+ #define MAX(a,b) ((a)>(b)?(a):(b))
+--- a/src/utils/overlay.c
 b/src/utils/overlay.c
+@@ -2,6 +2,7 @@
+ #include 
+ #include 
+ #include 
++#include 
+ 
+ #define MAX_SEQS 63
+ #define MIN2(y,z)((y)<(z))?(y):(z)
+--- a/src/mlagan.c
 b/src/mlagan.c
+@@ -31,6 +31,8 @@
+ static align *simaligns[MAX_SEQ];
+ static char* lagan_dir;
+ 
++extern int printXMFAAlign(FILE*, align*);
++
+ static int hptrcomp (const void *p1, const void *p2) {
+   int i = ((hptr*)p1)->number;
+   int j = ((hptr*)p2)->number;
+--- a/src/prolagan.c
 b/src/prolagan.c
+@@ -34,6 +34,8 @@
+ static align *profile1 = 0;
+ static align *profile2 = 0;
+ 
++extern int printXMFAAlign(FILE*, align*);
++
+ static int hptrcomp (const void *p1, const void *p2) {
+   int i = ((hptr*)p1)->number;
+   int j = ((hptr*)p2)->number;


=
debian/patches/series
=
@@ -8,3 +8,4 @@ cross.patch
 gcc9.patch
 gcc10.patch
 gcc-lto.patch
+fixup-implicit-function-declaration.patch



View it on GitLab: 
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[med-svn] [Git][med-team/lagan] Pushed new tag debian/2.0-10

2024-03-25 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/2.0-10 at Debian Med / lagan

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[med-svn] [Git][med-team/lucy] Pushed new tag debian/1.20-4

2024-03-24 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/1.20-4 at Debian Med / lucy

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[med-svn] [Git][med-team/lucy][master] 3 commits: Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066324)

2024-03-24 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / lucy


Commits:
5726e6aa by Nilesh Patra at 2024-03-24T22:14:21+05:30
Add patch to fix FTBFS with implicit-function-declaration (Closes: #1066324)

- - - - -
f9aba04e by Nilesh Patra at 2024-03-24T22:18:14+05:30
Add patch to remove .PU macro rather than trying to hack it in d/rules (Closes: 
#1047296)

- - - - -
f7058330 by Nilesh Patra at 2024-03-24T22:18:59+05:30
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/declare-function-prototypes-in-header.patch
- + debian/patches/fixup-manpage.patch
- debian/patches/series
- debian/rules


Changes:

=
debian/changelog
=
@@ -1,3 +1,14 @@
+lucy (1.20-4) unstable; urgency=medium
+
+  * Team Upload.
+  * Remove myself from Uploaders.
+  * Add patch to fix FTBFS with
+implicit-function-declaration (Closes: #1066324)
+  * Add patch to remove .PU macro rather than trying
+to hack it in d/rules (Closes: #1047296)
+
+ -- Nilesh Patra   Sun, 24 Mar 2024 22:18:20 +0530
+
 lucy (1.20-3) unstable; urgency=medium
 
   * Remove redundant files


=
debian/patches/declare-function-prototypes-in-header.patch
=
@@ -0,0 +1,83 @@
+--- a/abi.c
 b/abi.c
+@@ -5,6 +5,7 @@
+ *
+ /
+ 
++#include "utils.h"
+ #define VERYBAD 16
+ 
+ static struct stack_struct {
+--- a/lucy.c
 b/lucy.c
+@@ -10,6 +10,7 @@
+ #include 
+ #include 
+ #include 
++#include "utils.h"
+ 
+ #define TABLE_LENGTH 1023
+ #define BUFFER_LENGTH 4096
+--- a/poly.c
 b/poly.c
+@@ -5,6 +5,7 @@
+ *
+ /
+ 
++#include "utils.h"
+ #define A 0
+ #define T 3
+ 
+--- a/qual_trim.c
 b/qual_trim.c
+@@ -50,6 +50,7 @@
+ #include 
+ #include 
+ #include 
++#include "utils.h"
+ 
+ /* the highest quality value for which we have computed the */
+ /* corresponding probability of error */
+--- a/splice.c
 b/splice.c
+@@ -5,6 +5,7 @@
+ *
+ /
+ 
++#include "utils.h"
+ #define MAXIMUM_THREADS 32
+ 
+ #define NIL 0
+--- /dev/null
 b/utils.h
+@@ -0,0 +1,20 @@
++#ifndef UTILS_H
++#define UTILS_H
++
++#include 
++void giveup(char *msg);
++int abi_code(int);
++void abi_align(char*, int, char*, int, int*, int*);
++void prepare_abi_mask();
++void splice_align_left(int, char*, int, char*, int, int, int, int*);
++void splice_align_right(int, char*, int, char*, int, int, int, int*);
++void set_bracket(int, double);
++void default_windows(void);
++void quality_trim(int *, int, int, int*, int*);
++void construct_vector_tags(char*, int);
++int match_vector_tags(char*, int);
++void destroy_vector_tags();
++int poly_at_right(char*, int);
++int poly_at_left(char*, int);
++
++#endif
+--- a/vector.c
 b/vector.c
+@@ -6,6 +6,7 @@
+ /
+ #include 
+ #include 
++#include "utils.h"
+ 
+ extern void giveup(char *);
+ 


=
debian/patches/fixup-manpage.patch
=
@@ -0,0 +1,7 @@
+--- a/lucy.1
 b/lucy.1
+@@ -1,4 +1,3 @@
+-.PU
+ .TH LUCY 1 10/28/2000 "TIGR software" "Sequence Assembly Utilities"
+ .SH NAME
+ .B lucy 


=
debian/patches/series
=
@@ -1,2 +1,4 @@
 helpingMakefile.patch
 spellings.patch
+declare-function-prototypes-in-header.patch
+fixup-manpage.patch


=
debian/rules
=
@@ -7,7 +7,3 @@ export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
 
 %:
dh $@
-
-override_dh_installman:
-   sed 1d -i lucy.1
-   dh_installman



View it on GitLab: 
https://salsa.debian.org/med-team/lucy/-/compare/5a1de8b59df3ff869a08458c32815aa1623fa267...f705833078f506e052b0dba9caf91f5a8539d0e9

-- 
View it on GitLab: 
https://salsa.debian.org/med-team/lucy/-/compare/5a1de8b59df3ff869a08458c32815aa1623fa267...f705833078f506e052b0dba9caf91f5a8539d0e9
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[med-svn] [Git][med-team/lamassemble][master] [ci skip] Drop myself from uploaders field. Will not take care of its maintenance

2024-02-27 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / lamassemble


Commits:
fc7ff0b0 by Nilesh Patra at 2024-02-27T20:30:05+05:30
[ci skip] Drop myself from uploaders field. Will not take care of its 
maintenance

- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
@@ -2,9 +2,7 @@ Source: lamassemble
 Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team 

-Uploaders:
- Nilesh Patra ,
- Étienne Mollier ,
+Uploaders: Étienne Mollier 
 Build-Depends:
  debhelper-compat (= 13),
  dh-sequence-python3,



View it on GitLab: 
https://salsa.debian.org/med-team/lamassemble/-/commit/fc7ff0b0acea0161d78facb9acf9cc2086c5a7ae

-- 
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[med-svn] [Git][med-team/python-biom-format][master] 2 commits: Pull upstream patch to fix FTBFS (Closes: #1044074)

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / python-biom-format


Commits:
c11f2d26 by Nilesh Patra at 2024-02-05T00:46:28+05:30
Pull upstream patch to fix FTBFS (Closes: #1044074)

- - - - -
cdecfc8e by Nilesh Patra at 2024-02-05T00:46:46+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/adjust-pd-df-interaction-with-greater-than.patch
- debian/patches/series


Changes:

=
debian/changelog
=
@@ -1,3 +1,10 @@
+python-biom-format (2.1.15.2-3) unstable; urgency=medium
+
+  * Team Upload.
+  * Pull upstream patch to fix FTBFS (Closes: #1044074)
+
+ -- Nilesh Patra   Mon, 05 Feb 2024 00:46:33 +0530
+
 python-biom-format (2.1.15.2-2) unstable; urgency=medium
 
   * Drop python3-future from Build-Depends


=
debian/patches/adjust-pd-df-interaction-with-greater-than.patch
=
@@ -0,0 +1,45 @@
+From 5d1c921ca2cde5d7332508503ce990a7209d1fdc Mon Sep 17 00:00:00 2001
+From: Daniel McDonald 
+Date: Tue, 7 Nov 2023 16:36:07 -0800
+Subject: [PATCH] MAINT: adjust to change in pd.DataFrame interaction with >
+ (#940)
+
+* MAINT: adjust to change in pd.DataFrame interaction with >
+
+* STY: adjust for flake8
+---
+ biom/tests/test_table.py | 2 +-
+ biom/util.py | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/biom/tests/test_table.py b/biom/tests/test_table.py
+index 28d187e5..75675847 100644
+--- a/biom/tests/test_table.py
 b/biom/tests/test_table.py
+@@ -1593,7 +1593,7 @@ def test_to_dataframe_is_sparse(self):
+ df = example_table.to_dataframe()
+ density = (float(example_table.matrix_data.getnnz()) /
+np.prod(example_table.shape))
+-df_density = (df > 0).sum().sum() / np.prod(df.shape)
++df_density = (df.values > 0).sum().sum() / np.prod(df.shape)
+ assert np.allclose(df_density, density)
+ 
+ def test_to_dataframe_dense(self):
+diff --git a/biom/util.py b/biom/util.py
+index 879779dc..12700839 100644
+--- a/biom/util.py
 b/biom/util.py
+@@ -441,11 +441,11 @@ def biom_open(fp, permission='r'):
+ opener = h5py.File
+ 
+ if mode in ['U', 'r', 'rb'] and is_gzip(fp):
+-def opener(fp, mode):
++def opener(fp, mode):  # noqa
+ return codecs.getreader('utf-8')(gzip_open(fp, mode))
+ mode = 'rb' if permission in ['U', 'r'] else permission
+ elif mode in ['w', 'wb'] and str(fp).endswith('.gz'):
+-def opener(fp, mode):
++def opener(fp, mode):  # noqa
+ codecs.getwriter('utf-8')(gzip_open(fp, mode))
+ 
+ f = opener(fp, mode)


=
debian/patches/series
=
@@ -3,3 +3,4 @@ no-web-adds.patch
 fix_future_import.patch
 sphinx_1.6.patch
 posix_shell.patch
+adjust-pd-df-interaction-with-greater-than.patch



View it on GitLab: 
https://salsa.debian.org/med-team/python-biom-format/-/compare/7de41b27960ac73ede32397f30f5e897ef2c12e0...cdecfc8e4f0ddec9e28ddcd28a17a62cb7e9a933

-- 
View it on GitLab: 
https://salsa.debian.org/med-team/python-biom-format/-/compare/7de41b27960ac73ede32397f30f5e897ef2c12e0...cdecfc8e4f0ddec9e28ddcd28a17a62cb7e9a933
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[med-svn] [Git][med-team/python-biom-format] Pushed new tag debian/2.1.15.2-3

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/2.1.15.2-3 at Debian Med / python-biom-format

-- 
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[med-svn] [Git][med-team/python-nanoget][master] 2 commits: Versioned depends on pandas

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / python-nanoget


Commits:
d35ecc8a by Nilesh Patra at 2024-02-04T17:30:50+05:30
Versioned depends on pandas

- - - - -
c244775d by Nilesh Patra at 2024-02-04T12:05:33+00:00
Upload to unstable

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
@@ -1,10 +1,18 @@
-python-nanoget (1.19.3-1) UNRELEASED; urgency=medium
+python-nanoget (1.19.3-1) unstable; urgency=medium
 
-  * New upstream version
+  [ Andreas Tille ]
+  * Team Upload.
+  * New upstream version (Closes: #1044056)
   * Standards-Version: 4.6.2 (routine-update)
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
 
- -- Andreas Tille   Wed, 15 Nov 2023 11:25:46 +0100
+  [ Nilesh Patra ]
+  * Update missing source from nanotest repo
+  * Add missing-sources copyright
+  * gunzip mixed test suite file
+  * Versioned depends on pandas
+
+ -- Nilesh Patra   Sun, 04 Feb 2024 12:05:21 +
 
 python-nanoget (1.16.1-2) unstable; urgency=medium
 


=
debian/control
=
@@ -24,7 +24,8 @@ Depends: ${python3:Depends},
  ${misc:Depends},
  python3-biopython,
  python3-pysam,
- python3-nanomath
+ python3-nanomath,
+ python3-pandas (>= 2.0.0)
 Description: extract information from Oxford Nanopore sequencing data and 
alignments
  The Python3 module nanoget provides functions to extract useful metrics
  from Oxford Nanopore sequencing reads and alignments.



View it on GitLab: 
https://salsa.debian.org/med-team/python-nanoget/-/compare/08fb8a6215e332f63e1d2401b431b00782a6b154...c244775df69050978972acb05bd99eb6eadc3b78

-- 
View it on GitLab: 
https://salsa.debian.org/med-team/python-nanoget/-/compare/08fb8a6215e332f63e1d2401b431b00782a6b154...c244775df69050978972acb05bd99eb6eadc3b78
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[med-svn] [Git][med-team/python-nanoget] Pushed new tag debian/1.19.3-1

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/1.19.3-1 at Debian Med / python-nanoget

-- 
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[med-svn] [Git][med-team/python-nanoget][master] 3 commits: Update missing source from nanotest repo

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / python-nanoget


Commits:
57f4fbb1 by Nilesh Patra at 2024-02-04T16:38:14+05:30
Update missing source from nanotest repo

- - - - -
986f76e7 by Nilesh Patra at 2024-02-04T16:38:14+05:30
Add missing-sources copyright

- - - - -
08fb8a62 by Nilesh Patra at 2024-02-04T17:22:59+05:30
gunzip mixed test suite file

- - - - -


3 changed files:

- debian/copyright
- + debian/missing-source/nanotest/reads-mixed-timestamp.fastq
- debian/tests/run-unit-test


Changes:

=
debian/copyright
=
@@ -13,6 +13,11 @@ Copyright: 2020 Andreas Tille 
2022 Étienne Mollier 
 License: GPL-3+
 
+Files: debian/missing-source/*
+Copyright: 2016-2020 Wouter De Coster 
+License: GPL-3+
+Comment: Taken from https://github.com/wdecoster/nanotest
+
 License: GPL-3+
  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by


=
debian/missing-source/nanotest/reads-mixed-timestamp.fastq
=
@@ -0,0 +1,8 @@
+@b5b5833b-9341-4886-9ffd-7dd7f876c009 
runid=9ff0fede59c6669aa7f0d860aa73a4f0959d4b99 read=33 ch=5 
start_time=2023-09-12T22:36:47+00:00
+AGAAGGAGGAGGAGGAGGGAGGAGGAGGGAGGAGAAGGAGGGAGAGGAGGAGGAGGAGAGGAGGGAGGGAGGAGGAGGGAGGAGGAGGAGGGAGGAGGAGGGAGGGAGGGAGGAGGAGGGAGGGAGGGAGGGAGGAGGAGGAGGAGGGAGGAGGGAGGAGGAGGAGGAGGAGGGAGGAGGAGGGAGGAGGGAGGAGGAGGAGGAGGAGG
++
+%#&$#-(.-(.*&-)%*(+&./'/.(0++$+/&5/0+)$*+-1%).%/2/)/../.%)+%-/%+,&,.$)-*/.%+*)0--&,52&)0%)/&.0)'.-$(*%.3'/-+%-/)-+$,),&0,0%'.*%.-%'-%+-)$-+*$).-',-)%*+%*.%+-$*,%+,,(--$*)*./-%*)%..&*,%)0&.12(0,%,*$*)*$*2'*/-&/.&/.%*,%++%**%)'
+@76a5b578-7c92-458b-9981-437f48b82455 
runid=9ff0fede59c6669aa7f0d860aa73a4f0959d4b99 read=26 ch=438 
start_time=2023-09-13T14:17:12.357928+02:00
+ACGGTGTACTTCGTTCAGTTACGTATTGCTGTTTCGCAATCGTGAAACGCTTTCGCGTTCGTGCGCCGCTTCGTACGCCAGTGCCGCTACTGGTCACGCGTTTCTGAAGCGCGTAAGCGTTACAACAATGTTTGTAGCCATCATCGGCATATCGCCATGCTAATTGAAAGCCGGTCCGGGTTCCGGCGACAACGTTCAGATGATGCTGGTGGCCTACCGGCGATAATACGAACGCTTTAATCGCTGCAATCTTGTGGATTCAGATACACGCGATCAGGCGGTCCAAGGTCTGAATACCATCGATGACACTTTCGTCATTCACTTTGCATCAGAAATGAAGCGATCATGACCCGCGACTTGCGGTATCACCCACATTCAAAGTAGGTAGCACTTGGTTTCATTCGCCATGTATTCAGATCGATTTCTGAGTTTACCCACGCGGAATGCGCTAACGGCGCAAGTCGTGCGACAATCGTCTCTTCTTTGGGTAGTCAGTCGCGGCCATCGGCATCTTCGCGTGCGATTTCGGCGTCCACGGCAGGTTGCGAGCAGCCGTGCGCAGGCGAGACATGTTGACCGCCGGCTACGGTAGCAAACCGGTACGCCGCGACGCCATGAACGATTGTGTTGTTGTAAACCACAGAACTTCTTCTTCACCCGCGAACCACGAGAGAAGGTGTGCCTGTAAATGCCGAGGCACGGGATGATCGACCTGTGGTCCAGTTCGTAAGTTTACGACGGGAGAGGACAGATTTGTTCGATGACGGAAGGGCTTCTTAATCATGACGCGGTCTTCATTCTGGTAAACGACCGAAGTCGCTCTAGATCTAGTCATCTCTCAGCTTTATTTGGAGATGTGAAACGTCAAGAACTGTTAGAGAATGGCCAGACAGATTTGTCGTACCCGAGGATACCGGTTTCTAAAGTTGTCGTTCCGACATTGATACCAGCACAGCATCAAGGAAGTGCAACTTCGCCGTTAATCGGTAGCGAATACGTCATCTTCGGTGTAGCCCAGAACGCCCATTTCGCCAGCTGGCAGCAGCAGCGGCAGCTTGTTCCTTCGTAATTTGCGGCCCAGCGGTCAGGTCAACTACGAACCGTTCTCCGGAACGCGGAACGCCATACCAGTCGGTTGCCATTCAGTTCTGGCAGTACCTAATAGCAGCACCGGTAGAGGACGGGATGATGAGGCTTACCGCGACCGCGCGCCAGTCTTTGTAGACGGGCCATCAACGTTTCTGATAGCGATGAGTAGCGTGAACGGTGGTCATCAGACCTTCGATGATGCCAGAAGTTATCGTTGATAACTTTAGCCAGCGGTGCTGGTGGTGCAGGAAGCGTTGACCGATAATACTGACCATGTTGTCAACGCTGGTATCGGGCGTTGTCTTACTGAACGGACCAGTGCTTAACCACTTTCTTCGCACCAGCGGTGATGTGTTTACGAGCAGTTTCAGCCGGTGGGAACAGACCGGTTGCTTCGGCGACAACGTCAACACCGTTCCCATTTCAGGTTAGCCGGATGCGTTCAGCGGTAACACGCAGTTACCGTTAACGATCAGATGATAAATGCCGCTTCAACGACCGTCGAAACGGCCGTGGTAGGTCATAACTTCAGCCGTAAATCGGCGTCTAACAGGTCGTTGATTTGCAACGATCTCGATGTCAGGGCGTTTCGAGCAGCGAGCTAATGCGACCGACCGGTCCGTTGTTACCTACGATAGTCAACACTGTTCCTGTATATTTGATGAATGTTTGCCTGTTTACACCTTACGCAGCGTCGCGGAATCGTGTTCAATCGTGCGACAAATCAATCCTGTGCTAAGCATTACGCATTATTTCTCTCTTTCCTTGGGCTGGCAGACCATGGTCAAAAAAAAGAGGCCCGATATGTATTGACATCGATTTAGGTGCAGCATTTCGTCGGATCAGTTTACAGGACGCCAGTTGGTGTTATGTTTGTTAAGTGTGGTCACGTAATGGCGACACGATTAAAGTGAGATGTGAACATGGCTAATAAACCTTCGACGAAGAACTGAATTGTCGAGATGCAGGTGACGCAGTGGGACAGAGCCGCCATTTACGGGTGTTACTGCATAACAAGCGTGACGGCGTCTCACTGGTTGCGATCTGCACTGTTTCATTCCCAAACCAGAAATGTGATTCCGGCTGTGGCTGGCCCGGATTTCTACGAACCATTGAAGTGAAGAATCATTCGTTATAAAGACTTATCTCACATGGAATACGCGCATAGAAATTCGTTGCGGTAACTGTGATGCCATCTGGAACTATCTTGACAGACCCGCAGCCAACGGGCAGTATTTAACTGCCTGCTTTACGCTTTACACCGACTGGCAACGAAGAAATCAGCGGTTGACGATTCAGCAACTTATTCCACAGGGCAGGATTATGGTCTTGATGCGGCATTATCAACAGCATGATGCCCGTATACCAGCGTTTGACCTGCCGTTGAACTAAATGGCTGATGGCGTTGCGTTACGACGGAACAAGAACTGCCTGCAACTGGTGATGCGCCAGCAGGCTGCCACTATATCGAAGCATATGACAGTGACACAATGGTCAGATGATGTGAAGAGCAAACAGCAGTTAAGAGGGCACAATCTCGGCAGCCTATTGCCATGTTTAAGTAGGTTCTTCCCTGCCTCAAGCTATGAAATAATGACCCACGACTCATCTCAATTATCTCGCGGCTAGTCCCAAGTCGATCTTGCGTCCCGTTCGCCCTGACGACTTCCTGAACGAAGTCTCGAACCTATTGGCCGGCAATCCCTCTCGAATTTGCTCGCGCCCTTCCGTCAACCATAACAGACCCAGCCATTCTGCGTAATTGTGATGATCTGAGTTGTAAAGC

[med-svn] [Git][med-team/emperor][master] 2 commits: Add patch to fix FTBFS with pandas 2.0 (Closes: #1050144)

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / emperor


Commits:
276f8ee0 by Nilesh Patra at 2024-02-04T16:18:26+05:30
Add patch to fix FTBFS with pandas 2.0 (Closes: #1050144)

- - - - -
eac70e95 by Nilesh Patra at 2024-02-04T16:18:43+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/pandas-2.patch
- debian/patches/series


Changes:

=
debian/changelog
=
@@ -1,3 +1,10 @@
+emperor (1.0.3+ds-9) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with pandas 2.0 (Closes: #1050144)
+
+ -- Nilesh Patra   Sun, 04 Feb 2024 16:18:31 +0530
+
 emperor (1.0.3+ds-8) unstable; urgency=medium
 
   * Team upload.


=
debian/patches/pandas-2.patch
=
@@ -0,0 +1,80 @@
+Description: Replace pd.util.testing with pd.testing as the former has been 
pruned in pandas2.x
+Author: Nilesh Patra 
+Last-Update: 2024-02-04
+--- a/tests/test_core.py
 b/tests/test_core.py
+@@ -202,7 +202,7 @@
+ feature_mf['Second'] = ['No', 'Yes', 'Noes', 'N', 'Yep']
+ 
+ # it is redundant, but the mapping file should remain untouched
+-pd.util.testing.assert_frame_equal(feature_mf, emp.feature_mf,
++pd.testing.assert_frame_equal(feature_mf, emp.feature_mf,
+check_names=False)
+ 
+ self.assertEqual(emp.base_url, 
'https://cdn.rawgit.com/biocore/emperor'
+@@ -223,7 +223,7 @@
+'f.PC.481', 'f.PC.354'])
+ empty_mf['all'] = 'All elements'
+ 
+-pd.util.testing.assert_frame_equal(empty_mf, emp.feature_mf,
++pd.testing.assert_frame_equal(empty_mf, emp.feature_mf,
+check_names=False)
+ 
+ self.assertEqual(emp.base_url, 
'https://cdn.rawgit.com/biocore/emperor'
+@@ -291,7 +291,7 @@
+ 
+ expected.loc['PC.634'] = ['This element has no metadata'] * 3
+ 
+-pd.util.testing.assert_frame_equal(expected.sort_index(),
++pd.testing.assert_frame_equal(expected.sort_index(),
+emp.mf.sort_index(),
+check_names=False)
+ 
+@@ -313,7 +313,7 @@
+ 
+ expected.loc['f.PC.636'] = ['This element has no metadata'] * 2
+ 
+-pd.util.testing.assert_frame_equal(expected.sort_index(),
++pd.testing.assert_frame_equal(expected.sort_index(),
+emp.feature_mf.sort_index(),
+check_names=False)
+ 
+--- a/tests/test_pandas.py
 b/tests/test_pandas.py
+@@ -66,9 +66,9 @@
+ self.assertTrue(isinstance(emp, Emperor))
+ self.assertEqual(emp.dimensions, 4)
+ 
+-pd.util.testing.assert_frame_equal(self.df, emp.mf)
++pd.testing.assert_frame_equal(self.df, emp.mf)
+ 
+-pd.util.testing.assert_frame_equal(emp.ordination.samples,
++pd.testing.assert_frame_equal(emp.ordination.samples,
+self.samples)
+ 
+ def test_scatterplot_reordered(self):
+@@ -80,11 +80,11 @@
+ self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/'
+  'emperor/new-api/emperor/support_files')
+ 
+-pd.util.testing.assert_frame_equal(self.df, emp.mf)
++pd.testing.assert_frame_equal(self.df, emp.mf)
+ 
+ reordered = self.samples[['num_3', 'num_2', 'num_1', 'num_4']].copy()
+ 
+-pd.util.testing.assert_frame_equal(emp.ordination.samples,
++pd.testing.assert_frame_equal(emp.ordination.samples,
+reordered)
+ 
+ def test_bad_column_names(self):
+--- a/tests/test_util.py
 b/tests/test_util.py
+@@ -282,7 +282,7 @@
+ mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns)
+ obs = validate_and_process_custom_axes(mf, ['DOB'])
+ exp = pd.DataFrame(data=MAPPING_FILE_DATA_CONVERTED, columns=columns)
+-pd.util.testing.assert_frame_equal(obs, exp)
++pd.testing.assert_frame_equal(obs, exp)
+ 
+ def test_custom_axes_non_existent_names(self):
+ columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',


=
debian/patches/series
=
@@ -5,3 +5,4 @@ EditSectionTitle.patch
 8b803cd81586b832550eaa2428fa2d0dd581d35f.patch
 no_future_dependency.patch
 python3.12,patch
+pandas-2.patch



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[med-svn] [Git][med-team/emperor] Pushed new tag debian/1.0.3+ds-9

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/1.0.3+ds-9 at Debian Med / emperor

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[med-svn] [Git][med-team/mirtop] Pushed new tag debian/0.4.25-5

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed new tag debian/0.4.25-5 at Debian Med / mirtop

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[med-svn] [Git][med-team/mirtop][master] 4 commits: Revert "Enable experimental in salsa-ci.yml"

2024-02-04 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / mirtop


Commits:
f05fad48 by Nilesh Patra at 2024-02-04T14:45:11+05:30
Revert "Enable experimental in salsa-ci.yml"

This reverts commit 22554ec4496d11bbae115ef77c74608eed025690.

- - - - -
a16870eb by Nilesh Patra at 2024-02-04T14:45:19+05:30
Revert "Force pandas >= 2.0 to make sure the version from experimental 
will be taken"

This reverts commit 3eac0bc2e1bc3140be8321341e7d70c24ea417b3.

- - - - -
74187802 by Nilesh Patra at 2024-02-04T09:53:12+00:00
Add patch to fix FTBFS with pandas 2.0 (Closes: #1044055)

- - - - -
81d0909c by Nilesh Patra at 2024-02-04T09:53:12+00:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/pandas-2.patch
- debian/patches/series
- debian/salsa-ci.yml


Changes:

=
debian/changelog
=
@@ -1,9 +1,9 @@
-mirtop (0.4.25-5) UNRELEASED; urgency=medium
+mirtop (0.4.25-5) unstable; urgency=medium
 
-  * Team upload.
-  * Enable experimental in salsa-ci.yml
+  * Team Upload.
+  * Add patch to fix FTBFS with pandas 2.0 (Closes: #1044055)
 
- -- Andreas Tille   Mon, 29 Jan 2024 09:05:28 +0100
+ -- Nilesh Patra   Sun, 04 Feb 2024 14:47:21 +0530
 
 mirtop (0.4.25-4) unstable; urgency=medium
 


=
debian/control
=
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
python3-recommonmark,
python3-pysam,
python3-pybedtools,
-   python3-pandas (>= 2.0),
+   python3-pandas,
python3-biopython
 Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/mirtop
@@ -29,7 +29,7 @@ Depends: ${python3:Depends},
  ${sphinxdoc:Depends},
  python3-pysam,
  python3-pybedtools,
- python3-pandas (>= 2.0),
+ python3-pandas,
  python3-biopython
 Description: annotate miRNAs with a standard mirna/isomir naming (Python 3)
  The main goal of this project is to create a reflection group on metazoan


=
debian/patches/pandas-2.patch
=
@@ -0,0 +1,23 @@
+Description: Replace append with concat as per pandas changed API
+Author: Nilesh Patra 
+Last-Update: 2024-02-04
+--- a/mirtop/gff/stats.py
 b/mirtop/gff/stats.py
+@@ -107,13 +107,13 @@
+ # ref_miRNA_mean
+ category = "ref_miRNA_mean"
+ if sum(df['category']==category) == 0:
+-df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 
0}
+-df = df.append(df2, ignore_index = True)
++df2 = pd.DataFrame({'category': category, 'sample': 
df['sample'].iat[0], 'counts': 0}, index=[0])
++df = pd.concat([df, df2], ignore_index = True)
+ 
+ category = "isomiR_sum"
+ if sum(df['category']==category) == 0:
+-df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 
0}
+-df = df.append(df2, ignore_index = True)
++df2 = pd.DataFrame({'category': category, 'sample': 
df['sample'].iat[0], 'counts': 0}, index=[0])
++df = pd.concat([df, df2], ignore_index = True)
+ 
+ return df
+ 


=
debian/patches/series
=
@@ -2,3 +2,4 @@ spelling
 fix-circular-import.patch
 pytest.patch
 python3-syntax.patch
+pandas-2.patch


=
debian/salsa-ci.yml
=
@@ -2,7 +2,3 @@
 include:
   - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
   - 
https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
-
-variables:
-  # Build against pandas 2.x in experimental to recreate the test failure 
reported in bug #1044055
-  RELEASE: 'experimental'



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[med-svn] [Git][med-team/pydicom][pristine-tar] Deleted 1 commit: pristine-tar data for pydicom_2.4.4.orig.tar.gz

2024-01-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch pristine-tar at Debian Med / pydicom


WARNING: The push did not contain any new commits, but force pushed to delete 
the commits and changes below.


Deleted commits:
840bc84f by Andreas Tille at 2024-01-26T10:47:09+01:00
pristine-tar data for pydicom_2.4.4.orig.tar.gz

- - - - -


2 changed files:

- + pydicom_2.4.4.orig.tar.gz.delta
- + pydicom_2.4.4.orig.tar.gz.id


Changes:

=
pydicom_2.4.4.orig.tar.gz.delta
=
Binary files /dev/null and b/pydicom_2.4.4.orig.tar.gz.delta differ


=
pydicom_2.4.4.orig.tar.gz.id
=
@@ -0,0 +1 @@
+2c856cce92c647e4157bd0abb45dd5983a4ef509



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[med-svn] [Git][med-team/pydicom][master] 5 commits: Do not hack around sphinx. This is an issue w/ sphinx-gallery which has been fixed in latest upload

2024-01-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch master at Debian Med / pydicom


Commits:
055717d2 by Nilesh Patra at 2024-01-26T15:56:02+05:30
Do not hack around sphinx. This is an issue w/ sphinx-gallery which has been 
fixed in latest upload

- - - - -
9ad448bd by Nilesh Patra at 2024-01-26T16:25:16+05:30
Properly copy tests dir during build

- - - - -
51ccaaf8 by Nilesh Patra at 2024-01-26T17:22:51+05:30
Run tests after install step

- - - - -
3030db7d by Nilesh Patra at 2024-01-26T17:38:43+05:30
d/clean: Cleanup generated docs

- - - - -
590d8dfe by Nilesh Patra at 2024-01-26T17:38:51+05:30
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- + debian/clean
- debian/control
- debian/rules


Changes:

=
debian/changelog
=
@@ -1,5 +1,6 @@
-pydicom (2.4.3-1) UNRELEASED; urgency=medium
+pydicom (2.4.3-1) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Team upload.
   * New upstream version
   * Drop transitional package python3-dicom
@@ -11,7 +12,14 @@ pydicom (2.4.3-1) UNRELEASED; urgency=medium
 python3-mpl-sphinx-theme, python3-scipy
   * Hack around strange error of sphinx by simply ignoring it
 
- -- Andreas Tille   Wed, 16 Aug 2023 10:34:49 +0200
+  [ Nilesh Patra ]
+  * Add versioned Builddep against sphinx-gallery to fixup sphinx 7.2 issues
+Closes: #1042612
+  * Properly copy tests dir during build
+  * Run tests after install step
+  * d/clean: Cleanup generated docs
+
+ -- Nilesh Patra   Fri, 26 Jan 2024 17:38:13 +0530
 
 pydicom (2.3.1-1) unstable; urgency=medium
 


=
debian/clean
=
@@ -0,0 +1,5 @@
+doc/build/
+doc/generated/
+doc/auto_examples/
+doc/reference/generated/
+pydicom.egg-info/


=
debian/control
=
@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),
python3-docutils,
python3-pil,
python3-sphinx,
-   python3-sphinx-gallery,
+   python3-sphinx-gallery (>= 0.10.1-4~),
python3-sphinx-rtd-theme,
python3-sphinx-issues,
python3-sphinx-copybutton,


=
debian/rules
=
@@ -8,16 +8,26 @@ PYS = $(shell pyversions -r)
 export  http_proxy=http://127.0.0.1:9/
 export  https_proxy=http://127.0.0.1:9/
 
+# Copy the test package, as it is inside the root package (pydicom/tests).
+export PYBUILD_BEFORE_TEST=cp -r {dir}/pydicom/tests {build_dir}/pydicom
+# Cleanup the test package after dh_auto_test has run
+export PYBUILD_AFTER_TEST=rm -r {build_dir}/pydicom/tests
+
 %:
dh $@ --buildsystem=pybuild --with python3,sphinxdoc
 
 override_dh_auto_build:
dh_auto_build
-   cd doc; PYTHONPATH=.. python3 /usr/bin/sphinx-build -N -bhtml . 
build/html || true # FIXME: This ends in some error, but the doc seems OK so far
+   cd doc; PYTHONPATH=.. python3 /usr/bin/sphinx-build -N -bhtml . 
build/html
+
+override_dh_auto_test:
 
 override_dh_auto_install:
-find -name __pycache__ | xargs rm -r
dh_auto_install
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+   dh_auto_test
+endif
 
 override_dh_clean:
dh_clean



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[med-svn] [Git][med-team/pydicom][upstream] Deleted 1 commit: New upstream version 2.4.4

2024-01-26 Thread Nilesh Patra (@nilesh) 


Nilesh Patra pushed to branch upstream at Debian Med / pydicom


WARNING: The push did not contain any new commits, but force pushed to delete 
the commits and changes below.


Deleted commits:
d249a95a by Andreas Tille at 2024-01-26T10:47:03+01:00
New upstream version 2.4.4
- - - - -


5 changed files:

- doc/Makefile
- + doc/fix_search.py
- doc/make.bat
- pydicom/_version.py
- pyproject.toml


Changes:

=
doc/Makefile
=
@@ -59,6 +59,7 @@ html:
rm -rf $(BUILDDIR)/html/_images
#rm -rf _build/doctrees/
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+   python3 fix_search.py  # TODO remove when sphinx_rtd_theme fixes 
upstream
touch $(BUILDDIR)/html/.nojekyll
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."


=
doc/fix_search.py
=
@@ -0,0 +1,22 @@
+"""
+A temporary fix for https://github.com/pydicom/pydicom/issues/1965
+while waiting for upstream sphinx_rtd_theme to fix/remove their
+dependency on jQuery.
+"""
+from pathlib import Path
+import re
+
+
+search_html = Path("./_build/html/search.html")
+assert search_html.exists()
+
+with open(search_html) as fp:
+html = fp.read()
+
+pat = r"(\s+jQuery.+searchindex\.js.+\s+<\/script>)"
+repl = r'