date:20180204

[med-svn] [python-cobra] 03/06: Merge tag 'upstream/0.11.0'

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository python-cobra.

commit 030557f2cd3de31bb3a8c3f0e33058f2130fac28
Merge: ee24e38 362e088
Author: Afif Elghraoui 
Date:   Sun Feb 4 22:10:08 2018 -0500

Merge tag 'upstream/0.11.0'

Upstream version 0.11.0

 .gitignore|   1 +
 .travis.yml   | 128 +++--
 MANIFEST.in   |   2 +-
 README.rst|  17 +-
 appveyor.yml  |  83 +---
 appveyor/build_glpk.py|  60 ---
 appveyor/install.ps1  |  85 
 appveyor/run_with_env.cmd |  88 
 cobra/__init__.py |   4 +-
 cobra/core/arraybasedmodel.py | 435 
 cobra/core/dictlist.py|  17 +-
 cobra/core/model.py   | 149 ++
 cobra/core/reaction.py|  21 +-
 cobra/design/__init__.py  |   5 -
 cobra/design/design_algorithms.py |  17 -
 cobra/exceptions.py   |  33 +-
 cobra/flux_analysis/__init__.py   |  14 +-
 cobra/flux_analysis/deletion.py   | 362 ++
 cobra/flux_analysis/deletion_worker.py| 177 ---
 cobra/flux_analysis/double_deletion.py| 580 --
 cobra/flux_analysis/gapfilling.py |  35 +-
 cobra/flux_analysis/loopless.py   |  44 +-
 cobra/flux_analysis/moma.py   | 128 +
 cobra/flux_analysis/parsimonious.py   | 173 +--
 cobra/flux_analysis/phenotype_phase_plane.py  | 303 +--
 cobra/flux_analysis/reaction.py   |   8 +-
 cobra/flux_analysis/sampling.py   |  17 +-
 cobra/flux_analysis/single_deletion.py| 383 --
 cobra/flux_analysis/variability.py| 175 ++-
 cobra/io/dict.py  |  25 +-
 cobra/io/json.py  |  16 +-
 cobra/io/sbml3.py |   2 +-
 cobra/io/yaml.py  |  14 +-
 cobra/manipulation/__init__.py|   4 +-
 cobra/manipulation/modify.py  |  75 +--
 cobra/solvers/__init__.py | 134 -
 cobra/solvers/cglpk.pyx   | 566 -
 cobra/solvers/coin.py | 140 --
 cobra/solvers/cplex_solver.py | 347 -
 cobra/solvers/cplex_solver_java.py| 326 
 cobra/solvers/esolver.py  | 161 --
 cobra/solvers/glpk.pxd| 218 
 cobra/solvers/glpk_solver.py  | 276 --
 cobra/solvers/glpk_solver_java.py | 372 --
 cobra/solvers/gurobi_solver.py| 305 
 cobra/solvers/gurobi_solver_java.py   | 285 ---
 cobra/solvers/mosek.py| 245 -
 cobra/solvers/parameters.py   | 158 --
 cobra/solvers/wrappers.py |  49 --
 cobra/test/conftest.py|  31 +-
 cobra/test/test_flux_analysis.py  | 416 
 cobra/test/test_io.py |  12 +-
 cobra/test/test_io_order.py   |  92 
 cobra/test/test_manipulation.py   |  44 +-
 cobra/test/test_model.py  |  82 +--
 cobra/test/test_solver_model.py   | 133 ++---
 cobra/test/test_solver_utils.py   |  18 +-
 cobra/test/test_solvers.py| 271 --
 cobra/test/test_util.py   |   2 -
 cobra/topology/__init__.py|   5 -
 cobra/topology/reporter_metabolites.py|   9 -
 cobra/util/solver.py  |  45 +-
 config.sh |  68 ---
 develop-requirements.txt  |  20 +-
 documentation_builder/.gitignore  |   1 +
 documentation_builder/autodoc.sh  |   5 -
 documentation_builder/cobra.core.rst  |  94 
 documentation_builder/cobra.design.rst|  22 -
 documentation_builder/cobra.flux_analysis.rst | 110 
 documentation_builder/cobra.io.rst|  46 --
 documentation_builder/cobra.manipulation.rst  |  46 --
 documentation_builder/cobra.rst   |  43 --
 documentation_builder/cobra.topology.rst  |  22 -

[med-svn] [python-cobra] 05/06: Update patch

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository python-cobra.

commit 2e7e2707534a788e306ef05b0bcdb1f4d3b3a7a9
Author: Afif Elghraoui 
Date:   Mon Feb 5 00:31:56 2018 -0500

Update patch
---
 debian/patches/mathjax.patch | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/patches/mathjax.patch b/debian/patches/mathjax.patch
index a3da754..39401df 100644
--- a/debian/patches/mathjax.patch
+++ b/debian/patches/mathjax.patch
@@ -6,7 +6,7 @@ Last-Update: 2015-06-20
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- python-cobra.orig/documentation_builder/conf.py
 +++ python-cobra/documentation_builder/conf.py
-@@ -75,7 +75,7 @@
+@@ -95,7 +95,7 @@
  
  # -- Options for HTML output 
--
  

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[med-svn] [python-cobra] annotated tag upstream/0.11.0 created (now 9c80feb)

2018-02-04 Thread Afif Elghraoui

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afif pushed a change to annotated tag upstream/0.11.0
in repository python-cobra.

at  9c80feb   (tag)
   tagging  362e088175c39da41e7af86c1e146d7055b66433 (commit)
  replaces  upstream/0.9.0
 tagged by  Afif Elghraoui
on  Sun Feb 4 22:10:08 2018 -0500

- Log -
Upstream version 0.11.0

Afif Elghraoui (1):
  New upstream version 0.11.0

---

No new revisions were added by this update.

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[med-svn] [python-cobra] branch upstream updated (5444318 -> 362e088)

2018-02-04 Thread Afif Elghraoui

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afif pushed a change to branch upstream
in repository python-cobra.

  from  5444318   New upstream version 0.9.0
   new  362e088   New upstream version 0.11.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore|   1 +
 .travis.yml   | 128 +++--
 MANIFEST.in   |   2 +-
 README.rst|  17 +-
 appveyor.yml  |  83 +---
 appveyor/build_glpk.py|  60 ---
 appveyor/install.ps1  |  85 
 appveyor/run_with_env.cmd |  88 
 cobra/__init__.py |   4 +-
 cobra/core/arraybasedmodel.py | 435 
 cobra/core/dictlist.py|  17 +-
 cobra/core/model.py   | 149 ++
 cobra/core/reaction.py|  21 +-
 cobra/design/__init__.py  |   5 -
 cobra/design/design_algorithms.py |  17 -
 cobra/exceptions.py   |  33 +-
 cobra/flux_analysis/__init__.py   |  14 +-
 cobra/flux_analysis/deletion.py   | 362 ++
 cobra/flux_analysis/deletion_worker.py| 177 ---
 cobra/flux_analysis/double_deletion.py| 580 --
 cobra/flux_analysis/gapfilling.py |  35 +-
 cobra/flux_analysis/loopless.py   |  44 +-
 cobra/flux_analysis/moma.py   | 128 +
 cobra/flux_analysis/parsimonious.py   | 173 +--
 cobra/flux_analysis/phenotype_phase_plane.py  | 303 +--
 cobra/flux_analysis/reaction.py   |   8 +-
 cobra/flux_analysis/sampling.py   |  17 +-
 cobra/flux_analysis/single_deletion.py| 383 --
 cobra/flux_analysis/variability.py| 175 ++-
 cobra/io/dict.py  |  25 +-
 cobra/io/json.py  |  16 +-
 cobra/io/sbml3.py |   2 +-
 cobra/io/yaml.py  |  14 +-
 cobra/manipulation/__init__.py|   4 +-
 cobra/manipulation/modify.py  |  75 +--
 cobra/solvers/__init__.py | 134 -
 cobra/solvers/cglpk.pyx   | 566 -
 cobra/solvers/coin.py | 140 --
 cobra/solvers/cplex_solver.py | 347 -
 cobra/solvers/cplex_solver_java.py| 326 
 cobra/solvers/esolver.py  | 161 --
 cobra/solvers/glpk.pxd| 218 
 cobra/solvers/glpk_solver.py  | 276 --
 cobra/solvers/glpk_solver_java.py | 372 --
 cobra/solvers/gurobi_solver.py| 305 
 cobra/solvers/gurobi_solver_java.py   | 285 ---
 cobra/solvers/mosek.py| 245 -
 cobra/solvers/parameters.py   | 158 --
 cobra/solvers/wrappers.py |  49 --
 cobra/test/conftest.py|  31 +-
 cobra/test/test_flux_analysis.py  | 416 
 cobra/test/test_io.py |  12 +-
 cobra/test/test_io_order.py   |  92 
 cobra/test/test_manipulation.py   |  44 +-
 cobra/test/test_model.py  |  82 +--
 cobra/test/test_solver_model.py   | 133 ++---
 cobra/test/test_solver_utils.py   |  18 +-
 cobra/test/test_solvers.py| 271 --
 cobra/test/test_util.py   |   2 -
 cobra/topology/__init__.py|   5 -
 cobra/topology/reporter_metabolites.py|   9 -
 cobra/util/solver.py  |  45 +-
 config.sh |  68 ---
 develop-requirements.txt  |  20 +-
 documentation_builder/.gitignore  |   1 +
 documentation_builder/autodoc.sh  |   5 -
 documentation_builder/cobra.core.rst  |  94 
 documentation_builder/cobra.design.rst|  22 -
 documentation_builder/cobra.flux_analysis.rst | 110 
 documentation_builder/cobra.io.rst|  46 --
 documentation_builder/cobra.manipulation.rst  |  46 --

[med-svn] [python-cobra] 01/01: pristine-tar data for python-cobra_0.11.0.orig.tar.gz

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch pristine-tar
in repository python-cobra.

commit 96a42882d5378c60b7918c26ac13514ad35a679a
Author: Afif Elghraoui 
Date:   Sun Feb 4 22:10:08 2018 -0500

pristine-tar data for python-cobra_0.11.0.orig.tar.gz
---
 python-cobra_0.11.0.orig.tar.gz.delta | Bin 0 -> 5474 bytes
 python-cobra_0.11.0.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/python-cobra_0.11.0.orig.tar.gz.delta 
b/python-cobra_0.11.0.orig.tar.gz.delta
new file mode 100644
index 000..446adc5
Binary files /dev/null and b/python-cobra_0.11.0.orig.tar.gz.delta differ
diff --git a/python-cobra_0.11.0.orig.tar.gz.id 
b/python-cobra_0.11.0.orig.tar.gz.id
new file mode 100644
index 000..384497e
--- /dev/null
+++ b/python-cobra_0.11.0.orig.tar.gz.id
@@ -0,0 +1 @@
+6a7f0753a380ae9cf812e1bd2f833629e8be13d8

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[med-svn] [python-cobra] 01/06: TODO is to-done

2018-02-04 Thread Afif Elghraoui

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afif pushed a commit to branch master
in repository python-cobra.

commit ee24e38dd096b3fa867ae82b228432684b06425c
Author: Afif Elghraoui 
Date:   Sun Feb 4 22:07:34 2018 -0500

TODO is to-done
---
 debian/TODO | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/debian/TODO b/debian/TODO
deleted file mode 100644
index 6b44abf..000
--- a/debian/TODO
+++ /dev/null
@@ -1,3 +0,0 @@
-* package new dependencies:
-  - swiglpk https://github.com/biosustain/swiglpk
-  - optlang https://github.com/biosustain/optlang

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[med-svn] [nanopolish] branch master updated (9cfaa6b -> 64b18c3)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository nanopolish.

  from  9cfaa6b   releasing package nanopolish version 0.8.5-1
   new  0ad38d9   Remove all mentions of sse-support
   new  64b18c3   releasing package nanopolish version 0.8.5-2

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 6 ++
 debian/control   | 2 --
 2 files changed, 6 insertions(+), 2 deletions(-)

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[med-svn] [nanopolish] annotated tag debian/0.8.5-2 created (now b4fd7a6)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag debian/0.8.5-2
in repository nanopolish.

at  b4fd7a6   (tag)
   tagging  64b18c354b34ff0af1072ed7991e65d907d008e8 (commit)
  replaces  debian/0.8.5-1
 tagged by  Afif Elghraoui
on  Sun Feb 4 19:39:18 2018 -0500

- Log -
tagging package nanopolish version debian/0.8.5-2
-BEGIN PGP SIGNATURE-

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24ZgNMuyKt7MTcowb2eKL/u3MGd7+hMFfIiuDFmj4IfdG1ltC2QZZOHPT/A/TrhT
edU0A9Bj7/pQdOA+hgvIYERJTSD38krTrAZ8fauxhFvlCFA7EQq44+jccqB8Vi9B
7kSoy5T9AIQBZDS3HqaGIIBurx3B3c/vf7kTt5hmqSWlc95V0Tj7N/vqi+qtsLT+
xuoC5l7umR3J/vC7xufWV7Q6OnSNhCfXxThRt9uVqjkUhc0xw8sBh0phu6zxyrPi
S8YuW9aV9RXolzLfA1DwCYCL/F5pnZQDEqXjtjEBso87wITD+NLgZaM+wTrvrKf6
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qNw/eA8ihw==
=sR0l
-END PGP SIGNATURE-

Afif Elghraoui (2):
  Remove all mentions of sse-support
  releasing package nanopolish version 0.8.5-2

---

No new revisions were added by this update.

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[med-svn] [nanopolish] 02/02: releasing package nanopolish version 0.8.5-2

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 64b18c354b34ff0af1072ed7991e65d907d008e8
Author: Afif Elghraoui 
Date:   Sun Feb 4 19:39:18 2018 -0500

releasing package nanopolish version 0.8.5-2
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 542e63c..5a379bd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+nanopolish (0.8.5-2) unstable; urgency=low
+
+  * Remove dependency on nonexistent package sse-support [i386]
+
+ -- Afif Elghraoui   Sun, 04 Feb 2018 19:38:40 -0500
+
 nanopolish (0.8.5-1) unstable; urgency=medium
 
   * New upstream version

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[med-svn] [nanopolish] 01/01: pristine-tar data for nanopolish_0.8.5.orig.tar.gz

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch pristine-tar
in repository nanopolish.

commit fe0adc5b50a13fdd79bbfb8483b26ef0bec12356
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:05:34 2018 -0500

pristine-tar data for nanopolish_0.8.5.orig.tar.gz
---
 nanopolish_0.8.5.orig.tar.gz.delta | Bin 0 -> 6421 bytes
 nanopolish_0.8.5.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/nanopolish_0.8.5.orig.tar.gz.delta 
b/nanopolish_0.8.5.orig.tar.gz.delta
new file mode 100644
index 000..5eea073
Binary files /dev/null and b/nanopolish_0.8.5.orig.tar.gz.delta differ
diff --git a/nanopolish_0.8.5.orig.tar.gz.id b/nanopolish_0.8.5.orig.tar.gz.id
new file mode 100644
index 000..d488cc6
--- /dev/null
+++ b/nanopolish_0.8.5.orig.tar.gz.id
@@ -0,0 +1 @@
+6741bb21711da8a0baeae18186d86fd4b436d23f

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[med-svn] [nanopolish] 01/09: d/control: add sse-support to Build-Depends for i386

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit a3f03f0c98d2965daec3df37fce3d628c4d37404
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:02:26 2018 -0500

d/control: add sse-support to Build-Depends for i386

The package doesn't migrate due to not being installable
on i386.
---
 debian/control | 1 +
 1 file changed, 1 insertion(+)

diff --git a/debian/control b/debian/control
index e0227df..9f4f960 100644
--- a/debian/control
+++ b/debian/control
@@ -9,6 +9,7 @@ Build-Depends:
libfast5-dev (>= 0.6.4),
libhts-dev,
libeigen3-dev,
+   sse-support [any-i386],
 Standards-Version: 4.1.1
 Homepage: https://github.com/jts/nanopolish
 Vcs-Git: https://anonscm.debian.org/git/debian-med/nanopolish.git

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[med-svn] [nanopolish] 04/09: New upstream version 0.8.5

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 436609ff75aa5294791d7fd8433376eb27965f20
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:05:33 2018 -0500

New upstream version 0.8.5
---
 Makefile   |  26 +-
 README.md  |  11 +-
 docs/Makefile  |  20 +
 docs/source/_static/nanopolish-workflow.png| Bin 0 -> 318184 bytes
 .../_static/quickstart_methylation_results.png | Bin 0 -> 50765 bytes
 docs/source/conf.py| 168 +
 docs/source/debug.rst  | 170 +
 docs/source/index.rst  |  30 ++
 docs/source/installation.rst   |  45 +++
 docs/source/manual.rst | 413 +
 docs/source/quickstart_call_methylation.rst| 125 +++
 docs/source/quickstart_consensus.rst   | 115 ++
 docs/source/quickstart_eventalign.rst  | 103 +
 scripts/calculate_methylation_frequency.py |  11 +-
 scripts/extract_reads_aligned_to_region.py | 309 +++
 scripts/nanopolish_merge.py|  17 +-
 src/alignment/nanopolish_alignment_db.cpp  |   1 +
 src/alignment/nanopolish_eventalign.cpp| 134 ++-
 src/common/nanopolish_bam_processor.cpp|   3 +-
 src/common/nanopolish_common.h |   2 +-
 src/main/nanopolish.cpp|   9 +-
 src/nanopolish_call_variants.cpp   |   6 +-
 src/nanopolish_extract.cpp |  70 ++--
 src/nanopolish_index.cpp   |  18 +-
 src/nanopolish_raw_loader.cpp  |  12 +-
 src/nanopolish_read_db.cpp |  19 +-
 src/nanopolish_squiggle_read.cpp   |  46 ++-
 27 files changed, 1703 insertions(+), 180 deletions(-)

diff --git a/Makefile b/Makefile
index 5efffe6..3cab7a6 100644
--- a/Makefile
+++ b/Makefile
@@ -10,14 +10,15 @@ SUBDIRS := src src/hmm src/thirdparty 
src/thirdparty/scrappie src/common src/ali
 #Basic flags every build needs
 LIBS=-lz
 CXXFLAGS ?= -g -O3
-CXXFLAGS += -std=c++11 -fopenmp
+CXXFLAGS += -std=c++11 -fopenmp -fsigned-char
 CFLAGS ?= -O3 -std=c99
 CXX ?= g++
 CC ?= gcc
 
-# Change the value of HDF5 or EIGEN below to any value to disable compilation 
of bundled HDF5 code
-HDF5=install
-EIGEN=install
+# Change the value of HDF5, EIGEN, or HTS below to any value to disable 
compilation of bundled code
+HDF5?=install
+EIGEN?=install
+HTS?=install
 
 # Check operating system, OSX doesn't have -lrt
 UNAME_S := $(shell uname -s)
@@ -45,9 +46,14 @@ else
 EIGEN_CHECK=
 endif
 
-# Build and link the libhts submodule
-HTS_LIB=./htslib/libhts.a
-HTS_INCLUDE=-I./htslib
+# Default to build and link the libhts submodule
+ifeq ($(HTS), install)
+HTS_LIB=./htslib/libhts.a
+HTS_INCLUDE=-I./htslib
+else
+# Use system-wide htslib
+HTS_LIB=-lhts
+endif
 
 # Include the header-only fast5 library
 FAST5_INCLUDE=-I./fast5/include
@@ -116,15 +122,15 @@ include .depend
$(CXX) -o $@ -c $(CXXFLAGS) $(CPPFLAGS) -fPIC $<
 
 .c.o:
-   $(CC) -o $@ -c $(CFLAGS) $(H5_INCLUDE) -fPIC $<
+   $(CC) -o $@ -c $(CFLAGS) $(CPPFLAGS) $(H5_INCLUDE) -fPIC $<
 
 # Link main executable
 $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) 
$(EIGEN_CHECK)
-   $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) 
$(HTS_LIB) $(H5_LIB) $(LIBS)
+   $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) 
$(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
 
 # Link test executable
 $(TEST_PROGRAM): src/test/nanopolish_test.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) 
$(H5_LIB)
-   $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) 
$(HTS_LIB) $(H5_LIB) $(LIBS)
+   $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) 
$(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS)
 
 test: $(TEST_PROGRAM)
./$(TEST_PROGRAM)
diff --git a/README.md b/README.md
index 0564f32..b3433c4 100644
--- a/README.md
+++ b/README.md
@@ -6,15 +6,16 @@ Software package for signal-level analysis of Oxford Nanopore 
sequencing data. N
 
 ## Dependencies
 
-[libhdf5](http://www.hdfgroup.org/HDF5/release/obtain5.html) is automatically 
downloaded and compiled when running `make` but this can be disabled with: 
`HDF5=nofetch make`. The nanopolish binary will link libhdf5.a statically.
+A compiler that supports C++11 is needed to build nanopolish. Development of 
the code is performed using [gcc-4.8](https://gcc.gnu.org/gcc-4.8/).
 
-[eigen](http://eigen.tuxfamily.org) is also automatically downloaded and 
included when compiling with `make`.
+By default, nanopolish will download and compile all of its required 
dependencies. Some

[med-svn] [nanopolish] branch master updated (6927949 -> 9cfaa6b)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository nanopolish.

  from  6927949   releasing package nanopolish version 0.8.4-1
   new  a3f03f0   d/control: add sse-support to Build-Depends for i386
   new  1ca3539   d/control: Remove explicit declaration of x32
   new  649786e   Bump Standards-Version to 4.1.3
   new  436609f   New upstream version 0.8.5
   new  1b9384f   Merge tag 'upstream/0.8.5'
   new  4a135b3   Drop patches applied upstream
   new  14d3d48   Drop useless patch
   new  3e2a379   Bump copyright years
   new  9cfaa6b   releasing package nanopolish version 0.8.5-1

The 9 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 Makefile   |  26 +-
 README.md  |  11 +-
 debian/changelog   |  13 +
 debian/control |   5 +-
 debian/copyright   |   4 +-
 debian/patches/compiler-flags.patch|  27 --
 debian/patches/external-dependencies.patch |  38 --
 debian/patches/series  |   3 -
 debian/patches/write_return_values_ignored.patch   |  24 --
 docs/Makefile  |  20 +
 docs/source/_static/nanopolish-workflow.png| Bin 0 -> 318184 bytes
 .../_static/quickstart_methylation_results.png | Bin 0 -> 50765 bytes
 docs/source/conf.py| 168 +
 docs/source/debug.rst  | 170 +
 docs/source/index.rst  |  30 ++
 docs/source/installation.rst   |  45 +++
 docs/source/manual.rst | 413 +
 docs/source/quickstart_call_methylation.rst| 125 +++
 docs/source/quickstart_consensus.rst   | 115 ++
 docs/source/quickstart_eventalign.rst  | 103 +
 scripts/calculate_methylation_frequency.py |  11 +-
 scripts/extract_reads_aligned_to_region.py | 309 +++
 scripts/nanopolish_merge.py|  17 +-
 src/alignment/nanopolish_alignment_db.cpp  |   1 +
 src/alignment/nanopolish_eventalign.cpp| 134 ++-
 src/common/nanopolish_bam_processor.cpp|   3 +-
 src/common/nanopolish_common.h |   2 +-
 src/main/nanopolish.cpp|   9 +-
 src/nanopolish_call_variants.cpp   |   6 +-
 src/nanopolish_extract.cpp |  70 ++--
 src/nanopolish_index.cpp   |  18 +-
 src/nanopolish_raw_loader.cpp  |  12 +-
 src/nanopolish_read_db.cpp |  19 +-
 src/nanopolish_squiggle_read.cpp   |  46 ++-
 34 files changed, 1721 insertions(+), 276 deletions(-)
 delete mode 100644 debian/patches/compiler-flags.patch
 delete mode 100644 debian/patches/external-dependencies.patch
 delete mode 100644 debian/patches/write_return_values_ignored.patch
 create mode 100644 docs/Makefile
 create mode 100644 docs/source/_static/nanopolish-workflow.png
 create mode 100644 docs/source/_static/quickstart_methylation_results.png
 create mode 100644 docs/source/conf.py
 create mode 100644 docs/source/debug.rst
 create mode 100644 docs/source/index.rst
 create mode 100644 docs/source/installation.rst
 create mode 100644 docs/source/manual.rst
 create mode 100644 docs/source/quickstart_call_methylation.rst
 create mode 100644 docs/source/quickstart_consensus.rst
 create mode 100644 docs/source/quickstart_eventalign.rst
 mode change 100644 => 100755 scripts/calculate_methylation_frequency.py
 create mode 100755 scripts/extract_reads_aligned_to_region.py

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[med-svn] [nanopolish] 08/09: Bump copyright years

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 3e2a379d419b17f362625e98f68fa5d4c4c22802
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:12:16 2018 -0500

Bump copyright years
---
 debian/copyright | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 0a7b711..14fea05 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,7 @@ Upstream-Contact: Jared Simpson 
 Source: https://github.com/jts/nanopolish
 
 Files: *
-Copyright: 2015-2016 Ontario Institute for Cancer Research
+Copyright: 2015-2017 Ontario Institute for Cancer Research
 License: MIT
 
 Files: src/test/catch.hpp
@@ -27,7 +27,7 @@ Copyright: 2003-2006, 2008 Heng Li 
 License: MIT
 
 Files: debian/*
-Copyright: 2016 Afif Elghraoui 
+Copyright: 2016-2018 Afif Elghraoui 
 License: MIT
 
 License: MIT

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[med-svn] [nanopolish] 05/09: Merge tag 'upstream/0.8.5'

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 1b9384f5e36350e01d81b9965e812ae756f4788e
Merge: 649786e 436609f
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:05:34 2018 -0500

Merge tag 'upstream/0.8.5'

Upstream version 0.8.5

 Makefile   |  26 +-
 README.md  |  11 +-
 docs/Makefile  |  20 +
 docs/source/_static/nanopolish-workflow.png| Bin 0 -> 318184 bytes
 .../_static/quickstart_methylation_results.png | Bin 0 -> 50765 bytes
 docs/source/conf.py| 168 +
 docs/source/debug.rst  | 170 +
 docs/source/index.rst  |  30 ++
 docs/source/installation.rst   |  45 +++
 docs/source/manual.rst | 413 +
 docs/source/quickstart_call_methylation.rst| 125 +++
 docs/source/quickstart_consensus.rst   | 115 ++
 docs/source/quickstart_eventalign.rst  | 103 +
 scripts/calculate_methylation_frequency.py |  11 +-
 scripts/extract_reads_aligned_to_region.py | 309 +++
 scripts/nanopolish_merge.py|  17 +-
 src/alignment/nanopolish_alignment_db.cpp  |   1 +
 src/alignment/nanopolish_eventalign.cpp| 134 ++-
 src/common/nanopolish_bam_processor.cpp|   3 +-
 src/common/nanopolish_common.h |   2 +-
 src/main/nanopolish.cpp|   9 +-
 src/nanopolish_call_variants.cpp   |   6 +-
 src/nanopolish_extract.cpp |  70 ++--
 src/nanopolish_index.cpp   |  18 +-
 src/nanopolish_raw_loader.cpp  |  12 +-
 src/nanopolish_read_db.cpp |  19 +-
 src/nanopolish_squiggle_read.cpp   |  46 ++-
 27 files changed, 1703 insertions(+), 180 deletions(-)

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[med-svn] [nanopolish] 02/09: d/control: Remove explicit declaration of x32

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 1ca35396608efee7e69f3ff2f96a2438df9e15dd
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:04:06 2018 -0500

d/control: Remove explicit declaration of x32

It's included in any-amd64.
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 9f4f960..d9d1583 100644
--- a/debian/control
+++ b/debian/control
@@ -16,7 +16,7 @@ Vcs-Git: 
https://anonscm.debian.org/git/debian-med/nanopolish.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/nanopolish.git
 
 Package: nanopolish
-Architecture: any-amd64 any-i386 x32
+Architecture: any-amd64 any-i386
 Depends:
${shlibs:Depends},
${misc:Depends},

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[med-svn] [nanopolish] 03/09: Bump Standards-Version to 4.1.3

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 649786ec015f699b0955f0509df2777c61b46c8c
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:04:44 2018 -0500

Bump Standards-Version to 4.1.3
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index d9d1583..d7bd02c 100644
--- a/debian/control
+++ b/debian/control
@@ -10,7 +10,7 @@ Build-Depends:
libhts-dev,
libeigen3-dev,
sse-support [any-i386],
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Homepage: https://github.com/jts/nanopolish
 Vcs-Git: https://anonscm.debian.org/git/debian-med/nanopolish.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/nanopolish.git

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[med-svn] [nanopolish] 07/09: Drop useless patch

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 14d3d4882de82b558ceb4044ab417d9f1aed0d19
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:11:04 2018 -0500

Drop useless patch
---
 debian/patches/series|  1 -
 debian/patches/write_return_values_ignored.patch | 24 
 2 files changed, 25 deletions(-)

diff --git a/debian/patches/series b/debian/patches/series
index d2144c0..bfc5783 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 add-shebang-to-script.patch
 reproducible.patch
-write_return_values_ignored.patch
diff --git a/debian/patches/write_return_values_ignored.patch 
b/debian/patches/write_return_values_ignored.patch
deleted file mode 100644
index c933766..000
--- a/debian/patches/write_return_values_ignored.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Author: Steffen Moeller
-Last-Updated: 2017-09-16 02:14:07 +0200
-Description: Do not ignore return values of samtool functions
-
 nanopolish.orig/src/alignment/nanopolish_eventalign.cpp
-+++ nanopolish/src/alignment/nanopolish_eventalign.cpp
-@@ -229,7 +229,7 @@
- 
- void emit_sam_header(samFile* fp, const bam_hdr_t* hdr)
- {
--sam_hdr_write(fp, hdr);
-+int r = sam_hdr_write(fp, hdr);
- }
- 
- std::string cigar_ops_to_string(const std::vector& ops)
-@@ -368,7 +368,7 @@
- int stride = alignments.front().event_idx < alignments.back().event_idx ? 
1 : -1;
- bam_aux_append(event_record, "ES", 'i', 4, 
reinterpret_cast());
- 
--sam_write1(fp, base_hdr, event_record);
-+int r = sam_write1(fp, base_hdr, event_record);
- bam_destroy1(event_record); // automatically frees malloc'd segment
- }
- 

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[med-svn] [nanopolish] annotated tag upstream/0.8.5 created (now 3bdb1b4)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag upstream/0.8.5
in repository nanopolish.

at  3bdb1b4   (tag)
   tagging  436609ff75aa5294791d7fd8433376eb27965f20 (commit)
  replaces  upstream/0.8.4
 tagged by  Afif Elghraoui
on  Sun Feb 4 16:05:34 2018 -0500

- Log -
Upstream version 0.8.5

Afif Elghraoui (1):
  New upstream version 0.8.5

---

No new revisions were added by this update.

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[med-svn] [nanopolish] branch pristine-tar updated (0282462 -> fe0adc5)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch pristine-tar
in repository nanopolish.

  from  0282462   pristine-tar data for nanopolish_0.8.4.orig.tar.gz
   new  fe0adc5   pristine-tar data for nanopolish_0.8.5.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 nanopolish_0.8.5.orig.tar.gz.delta | Bin 0 -> 6421 bytes
 nanopolish_0.8.5.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 nanopolish_0.8.5.orig.tar.gz.delta
 create mode 100644 nanopolish_0.8.5.orig.tar.gz.id

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[med-svn] [nanopolish] 09/09: releasing package nanopolish version 0.8.5-1

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository nanopolish.

commit 9cfaa6b79728858bb7e60a9a27759ba1c0da3da2
Author: Afif Elghraoui 
Date:   Sun Feb 4 16:18:27 2018 -0500

releasing package nanopolish version 0.8.5-1
---
 debian/changelog | 13 +
 1 file changed, 13 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 44290ab..542e63c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,16 @@
+nanopolish (0.8.5-1) unstable; urgency=medium
+
+  * New upstream version
+  * d/control:
++ Add sse-support to Build-Depends for i386
++ Remove explicit declaration of x32
+  * Bump Standards-Version to 4.1.3
+  * Drop patches applied upstream
+  * Drop useless patch
+  * Bump copyright years
+
+ -- Afif Elghraoui   Sun, 04 Feb 2018 16:17:01 -0500
+
 nanopolish (0.8.4-1) unstable; urgency=medium
 
   [ Steffen Moeller ]

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[med-svn] [nanopolish] annotated tag debian/0.8.4-1 created (now 88ed6d5)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag debian/0.8.4-1
in repository nanopolish.

at  88ed6d5   (tag)
   tagging  69279491c07dc0c863f601e434f5ae0b3544b880 (commit)
  replaces  debian/0.5.0-1
 tagged by  Afif Elghraoui
on  Sat Nov 11 01:01:03 2017 -0500

- Log -
tagging package nanopolish version debian/0.8.4-1
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Afif Elghraoui (11):
  New upstream version 0.8.4
  Merge tag 'upstream/0.8.4'
  Update and refine patches
  Improve handling of external dependencies and build flags
  d/rules Set the correct variable to use system htslib
  d/rules: Remove redundant LDFLAGS setting
  Remove obsolete patches
  d/rules: don't override upstream optimization flags and move Steffen's 
-flto
  Bump Standards-Version to 4.1.1
  Bump fast5 minimum version
  releasing package nanopolish version 0.8.4-1

Andreas Tille (14):
  debhelper 10
  Standards-Version: 4.1.0 (no changes needed)
  Make sure abs() gets int arguments
  More abs() replacements
  New upstream version 0.7.2
  Updated version 0.7.2 from 'upstream/0.7.2'
  New upstream version
  Refresh patches
  Hack around broken clean target which tries to build dependencies from 
external sources
  DEP3
  Fix path tp hdf5 lib on i386
  Remove paragraph about never released version and move changelog entries
  Restrict Architectures: any-amd64 any-i386 x32
  Upload to unstable

Steffen Moeller (6):
  Added references to registries.
  New upstream version 0.8.1
  Updated version 0.8.1 from 'upstream/0.8.1'
  Proceeded to version 0.8.1
  upstream/metadata RRID->SciCrunch
  Merge branch 'master' of 
git+ssh://anonscm.debian.org:/git/debian-med/nanopolish

---

No new revisions were added by this update.

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[med-svn] [hinge] 05/05: releasing package hinge version 0.5.0-3

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository hinge.

commit bc918b771f33fcda1bcf64582f177eb644dd4899
Author: Afif Elghraoui 
Date:   Sun Feb 4 14:09:56 2018 -0500

releasing package hinge version 0.5.0-3
---
 debian/changelog | 10 ++
 1 file changed, 10 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index dec84a2..718774e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+hinge (0.5.0-3) unstable; urgency=low
+
+  * Mark spdlog patch as forwarded upstream
+  * d/control: copy Depends into Build-Depends
+to allow migration to Testing
+  * Bump Standards-Version to 4.1.3
+  * Bump copyright year
+
+ -- Afif Elghraoui   Sun, 04 Feb 2018 14:07:59 -0500
+
 hinge (0.5.0-2) unstable; urgency=medium
 
   * Team upload.

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[med-svn] [hinge] 04/05: Bump copyright year

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository hinge.

commit 3c7ede5fc6c0792c7adfd4bd64212267d7791d86
Author: Afif Elghraoui 
Date:   Sun Feb 4 14:03:34 2018 -0500

Bump copyright year
---
 debian/copyright | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/copyright b/debian/copyright
index ecf2e19..1168830 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -40,7 +40,7 @@ Copyright: 2011-2014 Pacific Biosciences of California
 License: BSD-3-Clause/PacBio
 
 Files: debian/*
-Copyright: 2017 Afif Elghraoui 
+Copyright: 2017-2018 Afif Elghraoui 
 License: BSD-3-Clause
 
 License: BSD-3-Clause

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[med-svn] [hinge] annotated tag debian/0.5.0-3 created (now 7cd9735)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag debian/0.5.0-3
in repository hinge.

at  7cd9735   (tag)
   tagging  bc918b771f33fcda1bcf64582f177eb644dd4899 (commit)
  replaces  debian/0.5.0-2
 tagged by  Afif Elghraoui
on  Sun Feb 4 14:09:56 2018 -0500

- Log -
tagging package hinge version debian/0.5.0-3
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Afif Elghraoui (6):
  Mark spdlog patch as forwarded upstream
  d/control: remove placeholder for dextractor
  d/control: copyy Depends into Build-Depends
  Bump Standards-Version to 4.1.3
  Bump copyright year
  releasing package hinge version 0.5.0-3

---

No new revisions were added by this update.

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[med-svn] [hinge] 02/05: d/control: copyy Depends into Build-Depends

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository hinge.

commit e4bbb4dc5ad23e0a3f76bfdb2e02576eb1f9e4ee
Author: Afif Elghraoui 
Date:   Sun Feb 4 14:01:29 2018 -0500

d/control: copyy Depends into Build-Depends

a hack to prevent building on architectures where it won't be installable,
which would then prevent migration to Testing.
---
 debian/control | 13 +
 1 file changed, 13 insertions(+)

diff --git a/debian/control b/debian/control
index 3f99b50..4a5c9b1 100644
--- a/debian/control
+++ b/debian/control
@@ -12,6 +12,19 @@ Build-Depends:
libhdf5-dev,
zlib1g-dev,
pandoc,
+# Run-Time-Depends:
+# (to prevent building where not installable)
+   python,
+   daligner,
+   dazzdb,
+   dascrubber,
+   python-numpy,
+   python-ujson,
+   python-configparser,
+   python-colormap,
+   python-pbcore,
+   python-networkx,
+   python-matplotlib,
 Standards-Version: 4.1.1
 Homepage: https://github.com/HingeAssembler/HINGE
 Vcs-Git: https://anonscm.debian.org/git/debian-med/hinge.git

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[med-svn] [hinge] branch master updated (49d285a -> bc918b7)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository hinge.

  from  49d285a   Mark spdlog patch as forwarded upstream
   new  26c1142   d/control: remove placeholder for dextractor
   new  e4bbb4d   d/control: copyy Depends into Build-Depends
   new  4589edd   Bump Standards-Version to 4.1.3
   new  3c7ede5   Bump copyright year
   new  bc918b7   releasing package hinge version 0.5.0-3

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 10 ++
 debian/control   | 16 ++--
 debian/copyright |  2 +-
 3 files changed, 25 insertions(+), 3 deletions(-)

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[med-svn] [hinge] 01/05: d/control: remove placeholder for dextractor

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository hinge.

commit 26c1142d0a2225f8630c3fd1ac2a5a4bcbb5cbf1
Author: Afif Elghraoui 
Date:   Sun Feb 4 14:01:17 2018 -0500

d/control: remove placeholder for dextractor
---
 debian/control | 1 -
 1 file changed, 1 deletion(-)

diff --git a/debian/control b/debian/control
index 907be93..3f99b50 100644
--- a/debian/control
+++ b/debian/control
@@ -26,7 +26,6 @@ Depends:
daligner,
dazzdb,
dascrubber,
-#  dextractor,
python-numpy,
python-ujson,
python-configparser,

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[med-svn] [dascrubber] branch master updated (11d817c -> 54329ea)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository dascrubber.

  from  11d817c   releasing package dascrubber version 0~20171015-1
   new  717ed48   New upstream version 0~20180108
   new  9e204fa   Merge tag 'upstream/0_20180108'
   new  538f0cd   Bump copyright years
   new  0289e0e   Bump Standards-Version to 4.1.3
   new  54329ea   releasing package dascrubber version 0~20180108-1

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DASedit.c|  21 ++-
 DASmap.c |   6 +-
 DASpatch.c   |  44 +++--
 DASqv.c  |  28 ++--
 DASrealign.c |  23 +--
 DAStrim.c| 497 ++-
 DB.c | 325 +++-
 DB.h | 208 +++
 REPqv.c  |   4 +-
 REPtrim.c|  89 ++
 align.c  | 128 ++
 align.h  |  13 +-
 debian/changelog |   8 +
 debian/control   |   2 +-
 debian/copyright |   4 +-
 15 files changed, 1001 insertions(+), 399 deletions(-)

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[med-svn] [dascrubber] 04/05: Bump Standards-Version to 4.1.3

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository dascrubber.

commit 0289e0e5651c831807bab6b85d928d95c966d332
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:53:02 2018 -0500

Bump Standards-Version to 4.1.3
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 6fc2580..aa37a26 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: Debian Med Packaging Team 

 Uploaders: Afif Elghraoui 
 Build-Depends: debhelper (>=10)
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Homepage: https://dazzlerblog.wordpress.com/
 Vcs-Git: https://anonscm.debian.org/git/debian-med/dascrubber.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/dascrubber.git

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[med-svn] [dascrubber] annotated tag debian/0_20180108-1 created (now 96843d4)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag debian/0_20180108-1
in repository dascrubber.

at  96843d4   (tag)
   tagging  54329ea09d2a7180f2429b337ba641c7cff1d29c (commit)
  replaces  debian/0_20171015-1
 tagged by  Afif Elghraoui
on  Sun Feb 4 13:55:06 2018 -0500

- Log -
tagging package dascrubber version debian/0_20180108-1
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Afif Elghraoui (5):
  New upstream version 0~20180108
  Merge tag 'upstream/0_20180108'
  Bump copyright years
  Bump Standards-Version to 4.1.3
  releasing package dascrubber version 0~20180108-1

---

No new revisions were added by this update.

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[med-svn] [dascrubber] branch pristine-tar updated (b792e8b -> 8b11cbd)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch pristine-tar
in repository dascrubber.

  from  b792e8b   pristine-tar data for dascrubber_0~20171015.orig.tar.gz
   new  8b11cbd   pristine-tar data for dascrubber_0~20180108.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 dascrubber_0~20180108.orig.tar.gz.delta | Bin 0 -> 1337 bytes
 dascrubber_0~20180108.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 dascrubber_0~20180108.orig.tar.gz.delta
 create mode 100644 dascrubber_0~20180108.orig.tar.gz.id

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[med-svn] [dascrubber] 01/01: pristine-tar data for dascrubber_0~20180108.orig.tar.gz

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch pristine-tar
in repository dascrubber.

commit 8b11cbde23b64e0ec63173cbcb34231ce9c27586
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:51:30 2018 -0500

pristine-tar data for dascrubber_0~20180108.orig.tar.gz
---
 dascrubber_0~20180108.orig.tar.gz.delta | Bin 0 -> 1337 bytes
 dascrubber_0~20180108.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/dascrubber_0~20180108.orig.tar.gz.delta 
b/dascrubber_0~20180108.orig.tar.gz.delta
new file mode 100644
index 000..3589b48
Binary files /dev/null and b/dascrubber_0~20180108.orig.tar.gz.delta differ
diff --git a/dascrubber_0~20180108.orig.tar.gz.id 
b/dascrubber_0~20180108.orig.tar.gz.id
new file mode 100644
index 000..f5714e8
--- /dev/null
+++ b/dascrubber_0~20180108.orig.tar.gz.id
@@ -0,0 +1 @@
+ebd55e1ec5e06edfdb02c9bfcf1e9e760c13ab05

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[med-svn] [dascrubber] 02/05: Merge tag 'upstream/0_20180108'

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository dascrubber.

commit 9e204fa2b17639055521019138ecbaa32cc6857a
Merge: 11d817c 717ed48
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:51:30 2018 -0500

Merge tag 'upstream/0_20180108'

Upstream version 0~20180108

 DASedit.c|  21 ++-
 DASmap.c |   6 +-
 DASpatch.c   |  44 +++---
 DASqv.c  |  28 ++--
 DASrealign.c |  23 +--
 DAStrim.c| 497 ---
 DB.c | 325 +-
 DB.h | 208 -
 REPqv.c  |   4 +-
 REPtrim.c|  89 ++-
 align.c  | 128 +++
 align.h  |  13 +-
 12 files changed, 990 insertions(+), 396 deletions(-)

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[med-svn] [dascrubber] 03/05: Bump copyright years

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository dascrubber.

commit 538f0cde6a878ea811c1d455cf7252f291633d81
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:52:49 2018 -0500

Bump copyright years
---
 debian/copyright | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 60b7f2e..e49f18f 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,11 +4,11 @@ Upstream-Contact: Eugene W. Myers, Jr. 
 Source: https://github.com/thegenemyers/DASCRUBBER
 
 Files: *
-Copyright: 2014-2017 Eugene W. Myers, Jr. 
+Copyright: 2014-2018 Eugene W. Myers, Jr. 
 License: BSD-3-Clause-EWM
 
 Files: debian/*
-Copyright: 2016-2017 Afif Elghraoui 
+Copyright: 2016-2018 Afif Elghraoui 
 License: BSD-3-Clause-EWM
 
 License: BSD-3-Clause-EWM

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[med-svn] [dazzdb] annotated tag upstream/1.0+20180115 created (now a3a932c)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag upstream/1.0+20180115
in repository dazzdb.

at  a3a932c   (tag)
   tagging  eb6be9a3ec71ec159ce78d2c4cb35dd0643fd6f5 (commit)
  replaces  upstream/1.0+20171014
 tagged by  Afif Elghraoui
on  Sun Feb 4 13:34:40 2018 -0500

- Log -
Upstream version 1.0+20180115

Afif Elghraoui (1):
  New upstream version 1.0+20180115

---

No new revisions were added by this update.

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[med-svn] [dazzdb] annotated tag debian/1.0+20180115-1 created (now 5aaa6fb)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag debian/1.0+20180115-1
in repository dazzdb.

at  5aaa6fb   (tag)
   tagging  463fc2284a84d46be84e927855385df64623fcb3 (commit)
  replaces  debian/1.0+20171014-1
 tagged by  Afif Elghraoui
on  Sun Feb 4 13:46:18 2018 -0500

- Log -
dazzdb (1.0+20180115-1) unstable; urgency=medium

  * New upstream snapshot (git 7104852)
  * Bump copyright years
  * Bump Standards-Version to 4.1.3
  * Update and refresh patches

 -- Afif Elghraoui   Sun, 04 Feb 2018 13:43:31 -0500
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-END PGP SIGNATURE-

Afif Elghraoui (6):
  New upstream version 1.0+20180115
  Merge tag 'upstream/1.0+20180115'
  Bump copyright years
  Bump Standards-Version to 4.1.3
  Update and refresh patches
  releasing package dazzdb version 1.0+20180115-1

---

No new revisions were added by this update.

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[med-svn] [dazzdb] 02/06: Merge tag 'upstream/1.0+20180115'

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository dazzdb.

commit 92e5b52b774c684dd4bdafc22d1d493265dfbd11
Merge: 2e04978 eb6be9a
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:34:40 2018 -0500

Merge tag 'upstream/1.0+20180115'

Upstream version 1.0+20180115

 Catrack.c   | 251 ++
 DAM2fasta.c |  46 +
 DB.c| 325 ++--
 DB.h| 208 +++---
 DB2arrow.c  |  39 
 DB2fasta.c  |  39 
 DB2quiva.c  |  38 +++
 DBdump.c| 137 +
 DBdust.c|  35 ---
 DBmv.c  |  95 ++
 DBrm.c  |  47 +++--
 DBshow.c| 108 +++-
 DBsplit.c   |  68 +++--
 DBstats.c   |  14 ++-
 DBtrim.c|  60 +--
 DBwipe.c|  32 --
 Makefile|   7 +-
 README.md   |  35 ---
 arrow2DB.c  |  17 ++--
 fasta2DAM.c |  22 ++--
 fasta2DB.c  |  62 
 quiva2DB.c  |  26 ++---
 simulator.c |  34 +++
 23 files changed, 1202 insertions(+), 543 deletions(-)

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[med-svn] [dazzdb] 05/06: Update and refresh patches

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository dazzdb.

commit f766c80d3bff1ebe9c82d1e0590ea7cad2d12e31
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:41:40 2018 -0500

Update and refresh patches
---
 debian/patches/append-cflags.patch  | 4 ++--
 debian/patches/compiler-flags.patch | 9 ++---
 debian/patches/destdir.patch| 2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/debian/patches/append-cflags.patch 
b/debian/patches/append-cflags.patch
index 1de1856..a60b7c7 100644
--- a/debian/patches/append-cflags.patch
+++ b/debian/patches/append-cflags.patch
@@ -10,5 +10,5 @@ Last-Update: 2015-09-13
 -CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
 +CFLAGS += -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
  
- ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow 
DBstats DBrm simulator \
-   fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim
+ ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow 
DBstats DBrm DBmv \
+   simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe 
DBtrim
diff --git a/debian/patches/compiler-flags.patch 
b/debian/patches/compiler-flags.patch
index cd1c368..4d38d98 100644
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -10,9 +10,9 @@ Last-Update: 2017-01-18
  CFLAGS += -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
 +LDLIBS = -lm
  
- ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow 
DBstats DBrm simulator \
-   fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe DBtrim
-@@ -8,61 +9,46 @@
+ ALL = fasta2DB DB2fasta quiva2DB DB2quiva DBsplit DBdust Catrack DBshow 
DBstats DBrm DBmv \
+   simulator fasta2DAM DAM2fasta DBdump rangen arrow2DB DB2arrow DBwipe 
DBtrim
+@@ -8,64 +9,48 @@
  all: $(ALL)
  
  fasta2DB: fasta2DB.c DB.c DB.h QV.c QV.h
@@ -60,6 +60,9 @@ Last-Update: 2017-01-18
  DBrm: DBrm.c DB.c DB.h QV.c QV.h
 -  gcc $(CFLAGS) -o DBrm DBrm.c DB.c QV.c -lm
  
+ DBmv: DBmv.c DB.c DB.h QV.c QV.h
+-  gcc $(CFLAGS) -o DBmv DBmv.c DB.c QV.c -lm
+ 
  simulator: simulator.c DB.c DB.h QV.c QV.h
 -  gcc $(CFLAGS) -o simulator simulator.c DB.c QV.c -lm
  
diff --git a/debian/patches/destdir.patch b/debian/patches/destdir.patch
index ac2be15..82ca8eb 100644
--- a/debian/patches/destdir.patch
+++ b/debian/patches/destdir.patch
@@ -5,7 +5,7 @@ Forwarded: no
 Last-Update: 2015-09-13
 --- dazzdb.orig/Makefile
 +++ dazzdb/Makefile
-@@ -57,7 +57,8 @@
+@@ -59,7 +59,8 @@
rm -f dazz.db.tar.gz
  
  install:

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[med-svn] [dazzdb] 01/01: pristine-tar data for dazzdb_1.0+20180115.orig.tar.gz

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch pristine-tar
in repository dazzdb.

commit bea3905fc8200a0829f035ca93f877f1b2e40d08
Author: Afif Elghraoui 
Date:   Sun Feb 4 13:34:40 2018 -0500

pristine-tar data for dazzdb_1.0+20180115.orig.tar.gz
---
 dazzdb_1.0+20180115.orig.tar.gz.delta | Bin 0 -> 1654 bytes
 dazzdb_1.0+20180115.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/dazzdb_1.0+20180115.orig.tar.gz.delta 
b/dazzdb_1.0+20180115.orig.tar.gz.delta
new file mode 100644
index 000..27dd684
Binary files /dev/null and b/dazzdb_1.0+20180115.orig.tar.gz.delta differ
diff --git a/dazzdb_1.0+20180115.orig.tar.gz.id 
b/dazzdb_1.0+20180115.orig.tar.gz.id
new file mode 100644
index 000..b8c9abe
--- /dev/null
+++ b/dazzdb_1.0+20180115.orig.tar.gz.id
@@ -0,0 +1 @@
+da7c5a2f30ce9224b53cda2ee578463011f0921e

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[med-svn] [python-fitbit] 01/01: Build new package python3-fitbit (Python 3)

2018-02-04 Thread Dylan Aïssi

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository python-fitbit.

commit e9e9733c8b54c107ac0ce72e5c19d39698a49cd1
Author: Dylan Aïssi 
Date:   Sun Feb 4 16:27:45 2018 +0100

Build new package python3-fitbit (Python 3)
---
 debian/changelog |  1 +
 debian/control   | 27 +--
 debian/rules |  2 +-
 3 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index dadb3dc..47e084e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ python-fitbit (0.3.0-2) UNRELEASED; urgency=medium
   * Move documentation into a new package python-fitbit-doc.
   * Bump Standards-Version: 4.1.3 (no changes needed).
   * Update debhelper compat to 11.
+  * Build new package python3-fitbit (Python 3).
 
  -- Dylan Aïssi   Sun, 04 Feb 2018 15:55:33 +0100
 
diff --git a/debian/control b/debian/control
index 1f4876d..8c777e4 100644
--- a/debian/control
+++ b/debian/control
@@ -10,12 +10,22 @@ Build-Depends: debhelper (>= 11~),
python-requests-oauthlib (>= 0.7),
python-dateutil,
python-mock,
-   python-sphinx,
python-docutils,
python-nose,
python-coverage,
python-freezegun (>= 0.3.8),
-   python-requests-mock (>= 1.2.0)
+   python-requests-mock (>= 1.2.0),
+   python3,
+   python3-setuptools,
+   python3-requests-oauthlib (>= 0.7),
+   python3-dateutil,
+   python3-mock,
+   python3-sphinx,
+   python3-docutils,
+   python3-nose,
+   python3-coverage,
+   python3-freezegun (>= 0.3.8),
+   python3-requests-mock (>= 1.2.0)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-fitbit.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/python-fitbit.git
@@ -34,6 +44,19 @@ Description: FitBit REST API Client Implementation - Python 2
  .
  This package contains the Python 2 module.
 
+Package: python3-fitbit
+Architecture: all
+Depends: ${python3:Depends},
+ ${misc:Depends},
+ python3-dateutil,
+ python3-requests-oauthlib
+Description: FitBit REST API Client Implementation - Python 3
+ A Python module containing an implementation of a client for the FitBit
+ REST API. It uses OAuth for authentication, it supports both US and SI
+ units.
+ .
+ This package contains the Python 3 module.
+
 Package: python-fitbit-doc
 Section: doc
 Architecture: all
diff --git a/debian/rules b/debian/rules
index e057c81..04526c6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,7 @@
 export PYBUILD_NAME=fitbit
 
 %:
-   dh $@ --with python2,sphinxdoc --buildsystem=pybuild
+   dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
 
 override_dh_auto_build:
dh_auto_build

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[med-svn] [python-fitbit] branch master updated (1bce71d -> e9e9733)

2018-02-04 Thread Dylan Aïssi

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a change to branch master
in repository python-fitbit.

  from  1bce71d   Correction of path in doc-base
   new  e9e9733   Build new package python3-fitbit (Python 3)

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repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog |  1 +
 debian/control   | 27 +--
 debian/rules |  2 +-
 3 files changed, 27 insertions(+), 3 deletions(-)

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[med-svn] [python-fitbit] branch master updated (a4f86b5 -> 1bce71d)

2018-02-04 Thread Dylan Aïssi

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a change to branch master
in repository python-fitbit.

  from  a4f86b5   Upload to unstable
   new  53d012a   Move documentation into a new package python-fitbit-doc
   new  76576e9   Bump Standards-Version: 4.1.3 (no changes needed)
   new  301ba6c   Update debhelper compat to 11
   new  1bce71d   Correction of path in doc-base

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog   |  8 
 debian/compat  |  2 +-
 debian/control | 23 --
 ...-fitbit.doc-base => python-fitbit-doc.doc-base} |  0
 debian/{docs => python-fitbit-doc.docs}|  0
 debian/python-fitbit.links |  2 --
 debian/python-markdown-doc.docs|  1 -
 debian/rules   | 10 --
 8 files changed, 30 insertions(+), 16 deletions(-)
 rename debian/{python-fitbit.doc-base => python-fitbit-doc.doc-base} (100%)
 rename debian/{docs => python-fitbit-doc.docs} (100%)
 delete mode 100644 debian/python-fitbit.links
 delete mode 100644 debian/python-markdown-doc.docs

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[med-svn] [python-fitbit] 01/04: Move documentation into a new package python-fitbit-doc

2018-02-04 Thread Dylan Aïssi

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository python-fitbit.

commit 53d012a6895c3b8f578113a41a9c8f3c8dae6dd9
Author: Dylan Aïssi 
Date:   Sun Feb 4 15:56:35 2018 +0100

Move documentation into a new package python-fitbit-doc
---
 debian/changelog  |  6 ++
 debian/control| 19 +++
 ...hon-fitbit.doc-base => python-fitbit-doc.doc-base} |  4 ++--
 debian/{docs => python-fitbit-doc.docs}   |  0
 debian/python-fitbit.links|  2 --
 debian/python-markdown-doc.docs   |  1 -
 debian/rules  | 10 --
 7 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index bca664a..1b4f5d4 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+python-fitbit (0.3.0-2) UNRELEASED; urgency=medium
+
+  * Move documentation into a new package python-fitbit-doc.
+
+ -- Dylan Aïssi   Sun, 04 Feb 2018 15:55:33 +0100
+
 python-fitbit (0.3.0-1) unstable; urgency=medium
 
   * New upstream release.
diff --git a/debian/control b/debian/control
index b560e59..d266831 100644
--- a/debian/control
+++ b/debian/control
@@ -24,13 +24,24 @@ Homepage: https://github.com/orcasgit/python-fitbit/
 Package: python-fitbit
 Architecture: all
 Depends: ${python:Depends},
- ${sphinxdoc:Depends},
  ${misc:Depends},
- libjs-jquery,
- libjs-underscore,
  python-dateutil,
  python-requests-oauthlib
-Description: FitBit REST API Client Implementation
+Description: FitBit REST API Client Implementation - Python 2
  A Python module containing an implementation of a client for the FitBit
  REST API. It uses OAuth for authentication, it supports both US and SI
  units.
+ .
+ This package contains the Python 2 module.
+
+Package: python-fitbit-doc
+Section: doc
+Architecture: all
+Depends: ${sphinxdoc:Depends},
+ ${misc:Depends}
+Description: FitBit REST API Client Implementation - Documentation
+ A Python module containing an implementation of a client for the FitBit
+ REST API. It uses OAuth for authentication, it supports both US and SI
+ units.
+ .
+  This package contains the documentation.
diff --git a/debian/python-fitbit.doc-base b/debian/python-fitbit-doc.doc-base
similarity index 65%
rename from debian/python-fitbit.doc-base
rename to debian/python-fitbit-doc.doc-base
index 8989283..7bf9e43 100644
--- a/debian/python-fitbit.doc-base
+++ b/debian/python-fitbit-doc.doc-base
@@ -5,5 +5,5 @@ Abstract: This manual describes the functions provided by the 
Python FitBit REST
 Section: Programming
 
 Format: html
-Index: /usr/share/doc/python-fitbit/html/index.html
-Files: /usr/share/doc/python-fitbit/html/*.html
+Index: /usr/share/doc/python-fitbit-doc/html/index.html
+Files: /usr/share/doc/python-fitbit-doc/html/*.html
diff --git a/debian/docs b/debian/python-fitbit-doc.docs
similarity index 100%
rename from debian/docs
rename to debian/python-fitbit-doc.docs
diff --git a/debian/python-fitbit.links b/debian/python-fitbit.links
deleted file mode 100644
index 7e4be00..000
--- a/debian/python-fitbit.links
+++ /dev/null
@@ -1,2 +0,0 @@
-usr/share/javascript/jquery/jquery.js 
usr/share/doc/python-fitbit/html/_static/jquery.js
-usr/share/javascript/underscore/underscore.js 
usr/share/doc/python-fitbit/html/_static/underscore.js
diff --git a/debian/python-markdown-doc.docs b/debian/python-markdown-doc.docs
deleted file mode 100644
index 6d28621..000
--- a/debian/python-markdown-doc.docs
+++ /dev/null
@@ -1 +0,0 @@
-build/html
diff --git a/debian/rules b/debian/rules
index 6ac3cbc..e057c81 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,14 +2,12 @@
 
 export PYBUILD_NAME=fitbit
 
+%:
+   dh $@ --with python2,sphinxdoc --buildsystem=pybuild
+
 override_dh_auto_build:
dh_auto_build
-   PYTHONPATH=. http_proxy='localhost' sphinx-build -N -bhtml docs/ 
build/html  # HTML generator
-   rm -rf build/html/.doctrees
-   rm build/html/_static/jquery.js # Remove JQuery, this is linked in 
d/*.links
-   rm build/html/_static/underscore.js # Remove underscore, this is linked 
in d/*.links
-%:
-   dh $@ --with python2 --buildsystem=pybuild
+   PYTHONPATH=. http_proxy='localhost' sphinx-build -N -bhtml docs/ 
build/html # HTML generator
 
 override_dh_auto_test:
echo "Skipping tests: Tests require network access..."

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[med-svn] [python-fitbit] 03/04: Update debhelper compat to 11

2018-02-04 Thread Dylan Aïssi

This is an automated email from the git hooks/post-receive script.

bob.dybian-guest pushed a commit to branch master
in repository python-fitbit.

commit 301ba6cc0b083e07469df6b3ef9bb89538d4a075
Author: Dylan Aïssi 
Date:   Sun Feb 4 16:03:18 2018 +0100

Update debhelper compat to 11
---
 debian/changelog | 1 +
 debian/compat| 2 +-
 debian/control   | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index fc801ce..dadb3dc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ python-fitbit (0.3.0-2) UNRELEASED; urgency=medium
 
   * Move documentation into a new package python-fitbit-doc.
   * Bump Standards-Version: 4.1.3 (no changes needed).
+  * Update debhelper compat to 11.
 
  -- Dylan Aïssi   Sun, 04 Feb 2018 15:55:33 +0100
 
diff --git a/debian/compat b/debian/compat
index f599e28..b4de394 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
diff --git a/debian/control b/debian/control
index 67a7cdf..1f4876d 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team 

 Section: python
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
dh-python,
python,
python-setuptools,

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[med-svn] [mummer] branch master updated (9e62338 -> d1c4158)

2018-02-04 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository mummer.

  from  9e62338   improve performance of delta2maf
  adds  06ee7ad   d/watch: point to new upstream repository at GitHub
   new  d1c4158   Merge branch 'watch'

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/watch | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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[med-svn] [mummer] 05/07: Commit as per 3.23+dfsg-2 upload

2018-02-04 Thread Andreas Tille

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository mummer.

commit 3fd3ad1f69ede037c829d70a51c2f8921e91df08
Author: Andreas Tille 
Date:   Sun Feb 4 16:01:44 2018 +0100

Commit as per 3.23+dfsg-2 upload
---
 .../0009-improve-performance-of-delta2maf.patch| 56 --
 debian/patches/series  |  2 -
 debian/upstream/edam   | 21 
 3 files changed, 10 insertions(+), 69 deletions(-)

diff --git a/debian/patches/0009-improve-performance-of-delta2maf.patch 
b/debian/patches/0009-improve-performance-of-delta2maf.patch
deleted file mode 100644
index 885c402..000
--- a/debian/patches/0009-improve-performance-of-delta2maf.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= 
-Date: Fri, 5 Aug 2016 14:14:02 +0200
-Subject: improve performance of delta2maf
-

- src/tigr/delta2maf.cc | 23 ---
- 1 file changed, 20 insertions(+), 3 deletions(-)
-
-diff --git a/src/tigr/delta2maf.cc b/src/tigr/delta2maf.cc
-index f397f35..f47d797 100644
 a/src/tigr/delta2maf.cc
-+++ b/src/tigr/delta2maf.cc
-@@ -378,8 +378,8 @@ void printAlignments
- 
- {
- 
--  const char * IdR;
--  const char * IdQ;
-+  const char * IdR, *previous_IdR = NULL;
-+  const char * IdQ, *previous_IdQ = NULL;
- 
-   map::iterator finditer;
- 
-@@ -405,6 +405,7 @@ void printAlignments
-   long int sR, eR, sQ, eQ;
-   long int Apos, Bpos;
-   long int SeqLenR, SeqLenQ;
-+  long int previous_SeqLenR = 0, previous_SeqLenQ = 0;
-   int frameR, frameQ;
- 
-   //for ( i = 0; i < LINE_PREFIX_LEN; i ++ )
-@@ -426,7 +427,23 @@ void printAlignments
-   //printf("Looking for R:\"%s\" in map of size %d\n",IdR,seqsMap.size());
-   assert(finditer != seqsMap.end());
-   R = finditer->second;
--  SeqLenR = strlen(R+1);
-+  // SeqLenR = strlen(R+1);
-+
-+  /**
-+   * We don't want to recompute the length of a sequence for each
-+   * iteration. This is especially important as many pairwise alignments
-+   * are split into blocks and we thus do the same thing over and over
-+   * again.
-+   *
-+   * My solution is to simply cache the current length value and reuse
-+   * it in the next iteration given the IDs are equal. This speeds up
-+   * the code by a factor of 20 (in words: twenty).
-+   *
-+   * -- Fabian Klötzl 2016-03-11
-+   */
-+  SeqLenR = IdR == previous_IdR ? previous_SeqLenR : strlen(R + 1);
-+  previous_IdR = IdR;
-+  previous_SeqLenR = SeqLenR;
- 
-   if(DATA_TYPE == NUCMER_DATA){
-   seqsiter = seqsMapArray.find(make_pair(Ap->idR,1));
diff --git a/debian/patches/series b/debian/patches/series
index 8214868..72bcb76 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,6 +5,4 @@ fix_sf_privacy_breach_issue.patch
 hardening.patch
 spelling.patch
 addition_from_mugsy.patch
-addition_from_report_duplicates.patch
-0009-improve-performance-of-delta2maf.patch
 # most probably broken see bug #843621 addition_from_report_duplicates.patch
diff --git a/debian/upstream/edam b/debian/upstream/edam
index 8577214..b7659bc 100644
--- a/debian/upstream/edam
+++ b/debian/upstream/edam
@@ -1,19 +1,18 @@

 ontology: EDAM (1.12)
 topic:
   - Sequence analysis
 scopes:
   - name: summary
 function:
-  - Local sequence alignment
-  - Genome alignment
+ - Local sequence alignment
+ - Genome alignment
 inputs:
-  - data: Sequence
-formats: [FASTA]
+ - data:   Sequence
+   formats: [FASTA]
 outputs:
-  - data: Sequence alignment
-formats: [Alignment format (text)]
-  - data: Sequence
-formats: [FASTA]
-  - data: Sequence variations
-formats: [Textual format]
+ - data:   Sequence alignment
+   formats: [Alignment format (text)]
+ - data:   Sequence
+   formats: [FASTA]
+ - data:   Sequence variations
+   formats: [Textual format]

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[med-svn] [mummer] 06/07: Fix edam syntax

2018-02-04 Thread Andreas Tille

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commit 1467d86b5847a3d08ff59900a22812a2790a3eee
Author: Andreas Tille 
Date:   Sun Feb 4 16:04:39 2018 +0100

Fix edam syntax
---
 debian/upstream/edam | 21 +++--
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/debian/upstream/edam b/debian/upstream/edam
index b7659bc..8577214 100644
--- a/debian/upstream/edam
+++ b/debian/upstream/edam
@@ -1,18 +1,19 @@
+---
 ontology: EDAM (1.12)
 topic:
   - Sequence analysis
 scopes:
   - name: summary
 function:
- - Local sequence alignment
- - Genome alignment
+  - Local sequence alignment
+  - Genome alignment
 inputs:
- - data:   Sequence
-   formats: [FASTA]
+  - data: Sequence
+formats: [FASTA]
 outputs:
- - data:   Sequence alignment
-   formats: [Alignment format (text)]
- - data:   Sequence
-   formats: [FASTA]
- - data:   Sequence variations
-   formats: [Textual format]
+  - data: Sequence alignment
+formats: [Alignment format (text)]
+  - data: Sequence
+formats: [FASTA]
+  - data: Sequence variations
+formats: [Textual format]

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[med-svn] [mummer] 07/07: improve performance of delta2maf

2018-02-04 Thread Andreas Tille

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in repository mummer.

commit 9e623381055a56b8264265d19772867e5f4394f5
Author: Andreas Tille 
Date:   Sun Feb 4 16:06:43 2018 +0100

improve performance of delta2maf
---
 debian/changelog   |  6 +++
 .../0009-improve-performance-of-delta2maf.patch| 56 ++
 debian/patches/series  |  1 +
 3 files changed, 63 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 49ee10a..2cc077e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+mummer (3.23+dfsg-3) UNRELEASED; urgency=medium
+
+  * improve performance of delta2maf
+
+ -- Fabian Klötzl   Thu, 17 Nov 2016 21:44:58 +0200
+
 mummer (3.23+dfsg-2) unstable; urgency=medium
 
   * Deactivate broken patch from mugsy that was taken over in last Debian
diff --git a/debian/patches/0009-improve-performance-of-delta2maf.patch 
b/debian/patches/0009-improve-performance-of-delta2maf.patch
new file mode 100644
index 000..885c402
--- /dev/null
+++ b/debian/patches/0009-improve-performance-of-delta2maf.patch
@@ -0,0 +1,56 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= 
+Date: Fri, 5 Aug 2016 14:14:02 +0200
+Subject: improve performance of delta2maf
+
+---
+ src/tigr/delta2maf.cc | 23 ---
+ 1 file changed, 20 insertions(+), 3 deletions(-)
+
+diff --git a/src/tigr/delta2maf.cc b/src/tigr/delta2maf.cc
+index f397f35..f47d797 100644
+--- a/src/tigr/delta2maf.cc
 b/src/tigr/delta2maf.cc
+@@ -378,8 +378,8 @@ void printAlignments
+ 
+ {
+ 
+-  const char * IdR;
+-  const char * IdQ;
++  const char * IdR, *previous_IdR = NULL;
++  const char * IdQ, *previous_IdQ = NULL;
+ 
+   map::iterator finditer;
+ 
+@@ -405,6 +405,7 @@ void printAlignments
+   long int sR, eR, sQ, eQ;
+   long int Apos, Bpos;
+   long int SeqLenR, SeqLenQ;
++  long int previous_SeqLenR = 0, previous_SeqLenQ = 0;
+   int frameR, frameQ;
+ 
+   //for ( i = 0; i < LINE_PREFIX_LEN; i ++ )
+@@ -426,7 +427,23 @@ void printAlignments
+   //printf("Looking for R:\"%s\" in map of size %d\n",IdR,seqsMap.size());
+   assert(finditer != seqsMap.end());
+   R = finditer->second;
+-  SeqLenR = strlen(R+1);
++  // SeqLenR = strlen(R+1);
++
++  /**
++   * We don't want to recompute the length of a sequence for each
++   * iteration. This is especially important as many pairwise alignments
++   * are split into blocks and we thus do the same thing over and over
++   * again.
++   *
++   * My solution is to simply cache the current length value and reuse
++   * it in the next iteration given the IDs are equal. This speeds up
++   * the code by a factor of 20 (in words: twenty).
++   *
++   * -- Fabian Klötzl 2016-03-11
++   */
++  SeqLenR = IdR == previous_IdR ? previous_SeqLenR : strlen(R + 1);
++  previous_IdR = IdR;
++  previous_SeqLenR = SeqLenR;
+ 
+   if(DATA_TYPE == NUCMER_DATA){
+   seqsiter = seqsMapArray.find(make_pair(Ap->idR,1));
diff --git a/debian/patches/series b/debian/patches/series
index 72bcb76..9cb30cf 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,4 +5,5 @@ fix_sf_privacy_breach_issue.patch
 hardening.patch
 spelling.patch
 addition_from_mugsy.patch
+0009-improve-performance-of-delta2maf.patch
 # most probably broken see bug #843621 addition_from_report_duplicates.patch

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[med-svn] [mummer] 01/07: Deactivate broken patch from mugsy that was taken over in last Debian release

2018-02-04 Thread Andreas Tille

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tille pushed a commit to branch master
in repository mummer.

commit b8a636802fc6f51b99c75df85cc34fcb55c2cc49
Author: Andreas Tille 
Date:   Thu Nov 17 21:29:26 2016 +0100

Deactivate broken patch from mugsy that was taken over in last Debian 
release
---
 debian/changelog | 10 +++---
 debian/patches/addition_from_report_duplicates.patch |  6 +-
 debian/patches/series|  1 +
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 57fb619..49ee10a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
-mummer (3.23+dfsg-2) UNRELEASED; urgency=medium
+mummer (3.23+dfsg-2) unstable; urgency=medium
 
-  * improve performance of delta2maf
+  * Deactivate broken patch from mugsy that was taken over in last Debian
+release
+Closes: #843621
+  * debhelper 10
+  * d/watch: version=4
 
- -- Fabian Klötzl   Fri, 05 Aug 2016 14:44:58 +0200
+ -- Andreas Tille   Thu, 17 Nov 2016 21:32:47 +0100
 
 mummer (3.23+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/patches/addition_from_report_duplicates.patch 
b/debian/patches/addition_from_report_duplicates.patch
index 8e0d7d6..bee0768 100644
--- a/debian/patches/addition_from_report_duplicates.patch
+++ b/debian/patches/addition_from_report_duplicates.patch
@@ -1,6 +1,10 @@
 Author: Andreas Tille 
 Last-Update: Mon, 13 Apr 2015 21:50:34 +0200
-Description: The tool mugsy provides an old mummer code copy (version 3.20)
+Description: This patch is deactivated since it is most probably broken.
+ .
+ See bug #843621
+ .
+ The tool mugsy provides an old mummer code copy (version 3.20)
  with modifications to include delta-filter -b for reporting duplications.
  Since the mummer copy in mugsy does not feature all the mummer patches we
  rather inject the additional tool right into the Debian package.
diff --git a/debian/patches/series b/debian/patches/series
index 693d3e5..8214868 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ spelling.patch
 addition_from_mugsy.patch
 addition_from_report_duplicates.patch
 0009-improve-performance-of-delta2maf.patch
+# most probably broken see bug #843621 addition_from_report_duplicates.patch

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[med-svn] [mummer] 04/07: Update d/copyright

2018-02-04 Thread Andreas Tille

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tille pushed a commit to branch master
in repository mummer.

commit ab93d40b3fcebb27f247f74221795aa88d316de8
Author: Andreas Tille 
Date:   Thu Nov 17 21:31:41 2016 +0100

Update d/copyright
---
 debian/copyright | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 0472c0a..1467b11 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: MUMmer
 Source: https://sourceforge.net/projects/mummer/files/mummer/
 Files-Excluded: */M*.pdf
@@ -13,7 +13,8 @@ Comment: MUMmer 1.0 code and documentation are copyright (c) 
1999 by The
  Arthur Delcher.
 
 Files: debian/*
-Copyright: © 2005-2007, Steffen Moeller , and 
Andreas Tille 
+Copyright: 2005-2007 Steffen Moeller ,
+   2007-2016 Andreas Tille 
 License: GPL
  Available at `/usr/share/common-licenses/GPL'.
 

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[med-svn] [mummer] branch master updated (19b498a -> 9e62338)

2018-02-04 Thread Andreas Tille

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tille pushed a change to branch master
in repository mummer.

  from  19b498a   Corrected EDAM annotation file
   new  b8a6368   Deactivate broken patch from mugsy that was taken over in 
last Debian release
   new  df4da7e   Debhelper 10
   new  e047a34   d/watch: version=4
   new  ab93d40   Update d/copyright
   new  3fd3ad1   Commit as per 3.23+dfsg-2 upload
   new  1467d86   Fix edam syntax
   new  9e62338   improve performance of delta2maf

The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 14 --
 debian/compat|  2 +-
 debian/control   |  2 +-
 debian/copyright |  5 +++--
 debian/patches/addition_from_report_duplicates.patch |  6 +-
 debian/patches/series|  2 +-
 debian/watch |  2 +-
 7 files changed, 24 insertions(+), 9 deletions(-)

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[med-svn] [mummer] 02/07: Debhelper 10

2018-02-04 Thread Andreas Tille

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tille pushed a commit to branch master
in repository mummer.

commit df4da7e8763c820dd29fd31bc5f2b21930ea1146
Author: Andreas Tille 
Date:   Thu Nov 17 21:29:58 2016 +0100

Debhelper 10
---
 debian/compat  | 2 +-
 debian/control | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index aecebd7..6509a49 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Uploaders: Steffen Moeller ,
Charles Plessy 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
texlive-latex-base,
texlive-latex-recommended,
texlive-fonts-recommended

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[med-svn] [dcm2niix] branch debian/master updated (b3f5285 -> 672b618)

2018-02-04 Thread Ghislain Vaillant

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ghisvail-guest pushed a change to branch debian/master
in repository dcm2niix.

  from  b3f5285   Release to unstable
   new  a95f70c   Ensure tags are signed
   new  da6a7e8   New upstream version 1.0.20171215
   new  c095374   Update upstream source from tag 'upstream/1.0.20171215'
   new  8ac3d79   Bump the debhelper version to 11
   new  88cd557   Bump the standards version to 4.1.3
   new  95e4644   Drop get-orig-source target, use uscan instead
   new  672b618   Release to unstable

The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 README.md   |   5 +-
 VERSIONS.md |   9 +
 console/main_console.cpp|  69 +-
 console/makefile|  11 +-
 console/nii_dicom.cpp   | 534 +---
 console/nii_dicom.h |   8 +-
 console/nii_dicom_batch.cpp | 187 
 console/nii_dicom_batch.h   |   3 +
 debian/changelog|  10 +
 debian/compat   |   2 +-
 debian/control  |   4 +-
 debian/gbp.conf |   1 +
 debian/rules|   3 -
 13 files changed, 709 insertions(+), 137 deletions(-)

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[med-svn] [dcm2niix] annotated tag upstream/1.0.20171215 created (now ad2e329)

2018-02-04 Thread Ghislain Vaillant

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ghisvail-guest pushed a change to annotated tag upstream/1.0.20171215
in repository dcm2niix.

at  ad2e329   (tag)
   tagging  da6a7e864029464a35ffeb262451ede3e657c59b (commit)
  replaces  upstream/1.0.20171017
 tagged by  Ghislain Antony Vaillant
on  Sun Feb 4 14:10:48 2018 +

- Log -
Upstream version 1.0.20171215
-BEGIN PGP SIGNATURE-

iQFHBAABCgAxFiEEWJjgycCqM1Izl5WcRM3alqEvFrYFAlp3FGgTHGdoaXN2YWls
QGdtYWlsLmNvbQAKCRBEzdqWoS8Wtp4jB/wPnZeA42BOlQhEMcs1HnRwXLj2aJaT
sBzX5FZN9PNSWMCKA/R/hyHW8RNFEkfosjS6rZsytfwT3N2VMF5Y1xWnDD2/pYqg
IpYBnhT1frHAZmc3v5nAMLnqD1vSQKnD3977M0q/fd0LA/Vl8EBwDhpfAszTrlPW
RMVCCxJ1Xmo3D7jkd06bslfPGLpFPw2ako3jkKZJB/ZqN/gSAmlqpqAPgbmI0NjO
YfEwsAOjwED5odk+P7IKko36rIA0AJjGCb4sqK+mMLlOLx0wikQ9MPQGww7yz3SG
WkHLYOfDwGcjhr7dt3lyPazlCAycZ26RjXm+aKn7f2ghppZg/+C/cz+Y
=ZGnV
-END PGP SIGNATURE-

Ghislain Antony Vaillant (1):
  New upstream version 1.0.20171215

---

No new revisions were added by this update.

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[med-svn] [dcm2niix] 07/07: Release to unstable

2018-02-04 Thread Ghislain Vaillant

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a commit to branch debian/master
in repository dcm2niix.

commit 672b618d8f0e5ffdaa047a8237343323e3b041f0
Author: Ghislain Antony Vaillant 
Date:   Sun Feb 4 14:21:47 2018 +

Release to unstable
---
 debian/changelog | 10 ++
 1 file changed, 10 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 40d1731..e414e86 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+dcm2niix (1.0.20171215-1) unstable; urgency=medium
+
+  * Ensure tags are signed
+  * New upstream version 1.0.20171215
+  * Bump the debhelper version to 11
+  * Bump the standards version to 4.1.3
+  * Drop get-orig-source target, use uscan instead
+
+ -- Ghislain Antony Vaillant   Sun, 04 Feb 2018 14:21:38 
+
+
 dcm2niix (1.0.20171017-1) unstable; urgency=medium
 
   * New upstream version 1.0.20171017

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[med-svn] [dcm2niix] 02/07: New upstream version 1.0.20171215

2018-02-04 Thread Ghislain Vaillant

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a commit to branch debian/master
in repository dcm2niix.

commit da6a7e864029464a35ffeb262451ede3e657c59b
Author: Ghislain Antony Vaillant 
Date:   Sun Feb 4 14:10:46 2018 +

New upstream version 1.0.20171215
---
 README.md   |   5 +-
 VERSIONS.md |   9 +
 console/main_console.cpp|  69 +-
 console/makefile|  11 +-
 console/nii_dicom.cpp   | 534 +---
 console/nii_dicom.h |   8 +-
 console/nii_dicom_batch.cpp | 187 
 console/nii_dicom_batch.h   |   3 +
 8 files changed, 695 insertions(+), 131 deletions(-)

diff --git a/README.md b/README.md
index 97eb97b..d1f42ec 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,7 @@ mkdir build && cd build
 cmake ..
 make
 ```
-`dcm2niix` will be created in the `bin` subfolder. To install on the system 
run `make install`.
+`dcm2niix` will be created in the `bin` subfolder. To install on the system 
run `make install` instead of `make` - this will copy the executable to your 
path so you do not have to provide the full path to the executable.
 
 **optional building with OpenJPEG:**
 
@@ -70,7 +70,8 @@ If you have any problems with the cmake build script 
described above or want to
   - [dcm2niir](https://github.com/muschellij2/dcm2niir) R wrapper for 
dcm2niix/dcm2nii.
   - [divest](https://github.com/jonclayden/divest) R interface to dcm2niix.
   - [sci-tran dcm2niix](https://github.com/scitran-apps/dcm2niix) docker.
-  - [neuro_docker](https://github.com/Neurita/neuro_docker) includes dcm2niix 
as part of a provides a single, static Dockerfile.
+  - [neuro_docker](https://github.com/Neurita/neuro_docker) includes dcm2niix 
as part of a single, static Dockerfile.
+  - [https://github.com/lalet/boutiques-dcm2niix boutiques-dcm2niix] is a 
dockerfile for installing and validating dcm2niix.
   - [neurodocker](https://github.com/kaczmarj/neurodocker) generates 
[custom](https://github.com/rordenlab/dcm2niix/issues/138) Dockerfiles given 
specific versions of neuroimaging software.
   - 
[dcm2niix_afni](https://afni.nimh.nih.gov/pub/dist/doc/program_help/dcm2niix_afni.html)
 is a version of dcm2niix included with the [AFNI](https://afni.nimh.nih.gov/) 
distribution.
   - [MRIcroGL](https://github.com/neurolabusc/MRIcroGL) is available for 
MacOS, Linux and Windows and provides a graphical interface for dcm2niix. You 
can get compiled copies from the [MRIcroGL NITRC web 
site](https://www.nitrc.org/projects/mricrogl/).
\ No newline at end of file
diff --git a/VERSIONS.md b/VERSIONS.md
index 43ef2d4..0d8b611 100644
--- a/VERSIONS.md
+++ b/VERSIONS.md
@@ -1,5 +1,14 @@
 ## Versions
 
+15-Dec-2017
+ - Support [Siemens XA10 
images](https://github.com/rordenlab/dcm2niix/pull/145).
+ - [Ability to select specific series to 
convert](https://github.com/rordenlab/dcm2niix/pull/146).
+
+4-Dec-2017
+ - Handle implicit VR DICOMs where [critical values nested in sequence groups 
(SQ)](https://github.com/rordenlab/dcm2niix/commit/7f5649c6fe6ed366d07776aa54397b50f6641aff)
+ - Better support for [PAR/REC files with segmented 3D 
EPI](https://github.com/rordenlab/dcm2niix/commit/66cdf2dcc60d55a6ef37f5a6db8d500d3eeb7c88).
+ - Allow Protocol Name to be 
[empty](https://github.com/rordenlab/dcm2niix/commit/94f3129898ba83bf310c9ff28e994f29feb13068).
+
 17-Oct-2017
  - Swap [phase-encoding direction 
polarity](https://github.com/rordenlab/dcm2niix/issues/125) for Siemens images 
where PE is in the Column direction.
  - Sort diffusion volumes by [B-value 
amplitude](https://www.nitrc.org/forum/forum.php?thread_id=8396_id=4703) 
(use "-d n"/"-d y" to turn the feature off/on).
diff --git a/console/main_console.cpp b/console/main_console.cpp
index 3608038..a784d2d 100644
--- a/console/main_console.cpp
+++ b/console/main_console.cpp
@@ -89,11 +89,15 @@ void showHelp(const char * argv[], struct TDCMopts opts) {
 printf("  -h : show help\n");
 printf("  -i : ignore derived, localizer and 2D images (y/n, default 
n)\n");
 printf("  -m : merge 2D slices from same series regardless of study time, 
echo, coil, orientation, etc. (y/n, default n)\n");
+printf("  -n : only convert this series number - can be used up to %i 
times (default convert all)\n", MAX_NUM_SERIES);
 printf("  -o : output directory (omit to save to input folder)\n");
 printf("  -p : Philips precise float (not display) scaling (y/n, default 
y)\n");
 printf("  -s : single file mode, do not convert other images in folder 
(y/n, default n)\n");
 printf("  -t : text notes includes private patient details (y/n, default 
n)\n");
-printf("  -v : verbose (n/y or 0/1/2 [no, yes, logorrheic], default 0)\n");
+#if !defined(_WIN64) && !defined(_WIN32) //shell script for Unix only
+   printf("  -u : up-to-date check\n");
+   #endif
+   printf("  -v : verbose (n/y or

[med-svn] [dcm2niix] 06/07: Drop get-orig-source target, use uscan instead

2018-02-04 Thread Ghislain Vaillant

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a commit to branch debian/master
in repository dcm2niix.

commit 95e46443388c479ec216b4f226403da4fb8c72e1
Author: Ghislain Antony Vaillant 
Date:   Sun Feb 4 14:15:51 2018 +

Drop get-orig-source target, use uscan instead
---
 debian/rules | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/debian/rules b/debian/rules
index c040e09..3545880 100755
--- a/debian/rules
+++ b/debian/rules
@@ -28,6 +28,3 @@ override_dh_auto_build:
 
 override_dh_installchangelogs:
dh_installchangelogs VERSIONS.md
-
-get-orig-source:
-   uscan --download-current-version --force-download --no-symlink

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[med-svn] [dcm2niix] branch pristine-tar updated (29ccb99 -> 836ce3d)

2018-02-04 Thread Ghislain Vaillant

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ghisvail-guest pushed a change to branch pristine-tar
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  from  29ccb99   pristine-tar data for dcm2niix_1.0.20171017.orig.tar.gz
   new  836ce3d   pristine-tar data for dcm2niix_1.0.20171215.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
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listed as "adds" were already present in the repository and have only
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Summary of changes:
 dcm2niix_1.0.20171215.orig.tar.gz.delta | Bin 0 -> 4419 bytes
 dcm2niix_1.0.20171215.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 dcm2niix_1.0.20171215.orig.tar.gz.delta
 create mode 100644 dcm2niix_1.0.20171215.orig.tar.gz.id

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[med-svn] [dcm2niix] annotated tag debian/1.0.20171215-1 created (now 79aa75f)

2018-02-04 Thread Ghislain Vaillant

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a change to annotated tag debian/1.0.20171215-1
in repository dcm2niix.

at  79aa75f   (tag)
   tagging  672b618d8f0e5ffdaa047a8237343323e3b041f0 (commit)
  replaces  debian/1.0.20171017-1
 tagged by  Ghislain Antony Vaillant
on  Sun Feb 4 14:35:51 2018 +

- Log -
dcm2niix Debian release 1.0.20171215-1
-BEGIN PGP SIGNATURE-

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dsH28EhAcAYJypAwTI3BDeXKmWyejdTTtM3mx60ws7ckA/QZiOgz5tjbecQO0roc
xxyrZ0clRBZ0kXGXtFYymay10/ZU7BsXG4nS5jLCxxW6Z+Af9+IT+lHjO6mUzohv
vWohCeBQQh31S4U6QsOvY5V0dAX6oGsATF5LM7Px2oeLdisJmQFQA3sG1Skl8WYO
9vS55bNFzOduDF2MRzeJ1cugA3fczdChy88KkV9Nm4GB7ntR11ejyQ3PWV1fOZ3C
d41W9/qXaVrEPDP6o/qC4TsA8xjCpxP7OKubXIWFEhbZEYNkwranM3aA
=uieF
-END PGP SIGNATURE-

Ghislain Antony Vaillant (7):
  Ensure tags are signed
  New upstream version 1.0.20171215
  Update upstream source from tag 'upstream/1.0.20171215'
  Bump the debhelper version to 11
  Bump the standards version to 4.1.3
  Drop get-orig-source target, use uscan instead
  Release to unstable

---

No new revisions were added by this update.

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[med-svn] [dcm2niix] 04/07: Bump the debhelper version to 11

2018-02-04 Thread Ghislain Vaillant

This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a commit to branch debian/master
in repository dcm2niix.

commit 8ac3d797dcad13508002815ecf49c0934c9c7c4f
Author: Ghislain Antony Vaillant 
Date:   Sun Feb 4 14:11:42 2018 +

Bump the debhelper version to 11
---
 debian/compat  | 2 +-
 debian/control | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/compat b/debian/compat
index f599e28..b4de394 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
diff --git a/debian/control b/debian/control
index 243a0c5..e99578c 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Ghislain Antony Vaillant 
 Section: science
 Priority: optional
 Build-Depends: cmake,
-   debhelper (>= 10),
+   debhelper (>= 11),
libopenjp2-7-dev,
libturbojpeg0-dev,
libyaml-cpp-dev,

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[med-svn] [daligner] annotated tag upstream/1.0+20180108 created (now 1c1d7a4)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag upstream/1.0+20180108
in repository daligner.

at  1c1d7a4   (tag)
   tagging  153de3c928622a637859f8a43c6ccd416675a9fd (commit)
  replaces  upstream/1.0+20171010
 tagged by  Afif Elghraoui
on  Sun Feb 4 05:22:21 2018 -0500

- Log -
Upstream version 1.0+20180108

Afif Elghraoui (1):
  New upstream version 1.0+20180108

---

No new revisions were added by this update.

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[med-svn] [daligner] branch upstream updated (3c46bb0 -> 153de3c)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch upstream
in repository daligner.

  from  3c46bb0   New upstream version 1.0+20171010
   new  153de3c   New upstream version 1.0+20180108

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DB.c   | 325 +++--
 DB.h   | 208 +---
 HPC.daligner.c |  20 ++--
 LAcat.c|  16 +--
 LAcheck.c  |  12 +--
 LAdump.c   |  30 +++---
 LAindex.c  |   4 +-
 LAmerge.c  |  12 +--
 LAshow.c   |  17 ++-
 LAsort.c   |  14 +--
 LAsplit.c  |  18 ++--
 align.c| 128 +--
 align.h|  13 ++-
 daligner.c |  38 +++
 filter.c   |  20 ++--
 filter.h   |   4 +-
 16 files changed, 638 insertions(+), 241 deletions(-)

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[med-svn] [daligner] annotated tag debian/1.0+20180108-1 created (now 63c3ad1)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to annotated tag debian/1.0+20180108-1
in repository daligner.

at  63c3ad1   (tag)
   tagging  26e4cb4f9012c3b18e11bd1eb6245d2090471e79 (commit)
  replaces  debian/1.0+20171010-2
 tagged by  Afif Elghraoui
on  Sun Feb 4 05:27:41 2018 -0500

- Log -
tagging package daligner version debian/1.0+20180108-1
-BEGIN PGP SIGNATURE-

iQJEBAABCAAuFiEE6rcjomb2J+aAVWFfWbIwbzr53cEFAlp24B0QHGFmaWZAZGVi
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jQQr7PnXYrx+IzZ0UPT1V3mHxnLNjPWJaK3B4tAHTZuXp/LVsiYJwtq1ghDSjDxf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=bGP3
-END PGP SIGNATURE-

Afif Elghraoui (5):
  New upstream version 1.0+20180108
  Merge tag 'upstream/1.0+20180108'
  Bump Standards-Version to 4.1.3
  Bump copyright years
  releasing package daligner version 1.0+20180108-1

---

No new revisions were added by this update.

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[med-svn] [daligner] 03/05: Bump Standards-Version to 4.1.3

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository daligner.

commit 0053b3539758821576f7591b2e1a241544435b57
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:24:42 2018 -0500

Bump Standards-Version to 4.1.3
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 4e6f986..788b459 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Maintainer: Debian Med Packaging Team 

 Build-Depends:
debhelper (>= 10),
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Homepage: https://dazzlerblog.wordpress.com
 Vcs-Git: https://anonscm.debian.org/git/debian-med/daligner.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/daligner.git

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[med-svn] [daligner] 01/01: pristine-tar data for daligner_1.0+20180108.orig.tar.gz

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch pristine-tar
in repository daligner.

commit caa9a8223e264c86024274c723419a25629b660f
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:22:21 2018 -0500

pristine-tar data for daligner_1.0+20180108.orig.tar.gz
---
 daligner_1.0+20180108.orig.tar.gz.delta | Bin 0 -> 1506 bytes
 daligner_1.0+20180108.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/daligner_1.0+20180108.orig.tar.gz.delta 
b/daligner_1.0+20180108.orig.tar.gz.delta
new file mode 100644
index 000..3bfbc84
Binary files /dev/null and b/daligner_1.0+20180108.orig.tar.gz.delta differ
diff --git a/daligner_1.0+20180108.orig.tar.gz.id 
b/daligner_1.0+20180108.orig.tar.gz.id
new file mode 100644
index 000..b811865
--- /dev/null
+++ b/daligner_1.0+20180108.orig.tar.gz.id
@@ -0,0 +1 @@
+7875fef282de2fc0b33aba1ba6080eea8b957037

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[med-svn] [daligner] branch master updated (211ed00 -> 26e4cb4)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository daligner.

  from  211ed00   releasing package daligner version 1.0+20171010-2
   new  153de3c   New upstream version 1.0+20180108
   new  aff34d9   Merge tag 'upstream/1.0+20180108'
   new  0053b35   Bump Standards-Version to 4.1.3
   new  0739436   Bump copyright years
   new  26e4cb4   releasing package daligner version 1.0+20180108-1

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DB.c | 325 ++-
 DB.h | 208 +--
 HPC.daligner.c   |  20 ++--
 LAcat.c  |  16 +--
 LAcheck.c|  12 +-
 LAdump.c |  30 +++--
 LAindex.c|   4 +-
 LAmerge.c|  12 +-
 LAshow.c |  17 ++-
 LAsort.c |  14 +--
 LAsplit.c|  18 +--
 align.c  | 128 --
 align.h  |  13 ++-
 daligner.c   |  38 +++
 debian/changelog |   8 ++
 debian/control   |   2 +-
 debian/copyright |   4 +-
 filter.c |  20 ++--
 filter.h |   4 +-
 19 files changed, 649 insertions(+), 244 deletions(-)

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[med-svn] [daligner] 04/05: Bump copyright years

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository daligner.

commit 07394366d640050b11fc8c574f98573fd806b0b0
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:24:57 2018 -0500

Bump copyright years
---
 debian/copyright | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index b6c391a..1788141 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,11 +4,11 @@ Upstream-Contact: Eugene W. Myers, Jr. 
 Source: http://github.com/thegenemyers/DALIGNER
 
 Files: *
-Copyright: 2013-2017 Eugene W. Myers, Jr. 
+Copyright: 2013-2018 Eugene W. Myers, Jr. 
 License: BSD-3-Clause~EWM
 
 Files: debian/*
-Copyright: 2015-2017 Afif Elghraoui 
+Copyright: 2015-2018 Afif Elghraoui 
 License: BSD-3-Clause~EWM
 
 License: BSD-3-Clause~EWM

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[med-svn] [daligner] 02/05: Merge tag 'upstream/1.0+20180108'

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository daligner.

commit aff34d9887a57824ab9079dd3475141ad8acda4f
Merge: 211ed00 153de3c
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:22:21 2018 -0500

Merge tag 'upstream/1.0+20180108'

Upstream version 1.0+20180108

 DB.c   | 325 +++--
 DB.h   | 208 +---
 HPC.daligner.c |  20 ++--
 LAcat.c|  16 +--
 LAcheck.c  |  12 +--
 LAdump.c   |  30 +++---
 LAindex.c  |   4 +-
 LAmerge.c  |  12 +--
 LAshow.c   |  17 ++-
 LAsort.c   |  14 +--
 LAsplit.c  |  18 ++--
 align.c| 128 +--
 align.h|  13 ++-
 daligner.c |  38 +++
 filter.c   |  20 ++--
 filter.h   |   4 +-
 16 files changed, 638 insertions(+), 241 deletions(-)

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[med-svn] [daligner] 05/05: releasing package daligner version 1.0+20180108-1

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository daligner.

commit 26e4cb4f9012c3b18e11bd1eb6245d2090471e79
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:27:41 2018 -0500

releasing package daligner version 1.0+20180108-1
---
 debian/changelog | 8 
 1 file changed, 8 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 4c03d1c..ba8db30 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+daligner (1.0+20180108-1) unstable; urgency=medium
+
+  * New upstream snapshot (git 233274a)
+  * Bump Standards-Version to 4.1.3
+  * Bump copyright years
+
+ -- Afif Elghraoui   Sun, 04 Feb 2018 05:26:26 -0500
+
 daligner (1.0+20171010-2) unstable; urgency=low
 
   [ Steffen Moeller ]

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[med-svn] [daligner] branch pristine-tar updated (08a86ea -> caa9a82)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch pristine-tar
in repository daligner.

  from  08a86ea   pristine-tar data for daligner_1.0+20171010.orig.tar.gz
   new  caa9a82   pristine-tar data for daligner_1.0+20180108.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 daligner_1.0+20180108.orig.tar.gz.delta | Bin 0 -> 1506 bytes
 daligner_1.0+20180108.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 daligner_1.0+20180108.orig.tar.gz.delta
 create mode 100644 daligner_1.0+20180108.orig.tar.gz.id

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[med-svn] [sprai] branch master updated (c687bdb -> ccf82fa)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository sprai.

  from  c687bdb   releasing package sprai version 0.9.9.22+dfsg-1
  adds  0d163af   New upstream version 0.9.9.23+dfsg
  adds  9bf810f   Merge tag 'upstream/0.9.9.23+dfsg'
  adds  f80586e   Bump Standards-Version to 4.1.3
  adds  ccf82fa   releasing package sprai version 0.9.9.23+dfsg-1

No new revisions were added by this update.

Summary of changes:
 debian/changelog  |  7 +++
 debian/control|  2 +-
 doc/_build/html/_sources/Download.txt |  4 +++-
 dumbbell_filter.pl| 11 +++
 ec.spec   |  2 +-
 makefile  |  2 +-
 wscript   |  2 +-
 7 files changed, 25 insertions(+), 5 deletions(-)

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[med-svn] [sprai] branch pristine-tar updated (578c7bb -> 0619fbb)

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch pristine-tar
in repository sprai.

  from  578c7bb   pristine-tar data for sprai_0.9.9.22+dfsg.orig.tar.gz
   new  0619fbb   pristine-tar data for sprai_0.9.9.23+dfsg.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 sprai_0.9.9.23+dfsg.orig.tar.gz.delta | Bin 0 -> 4775 bytes
 sprai_0.9.9.23+dfsg.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 sprai_0.9.9.23+dfsg.orig.tar.gz.delta
 create mode 100644 sprai_0.9.9.23+dfsg.orig.tar.gz.id

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[med-svn] [sprai] 04/04: releasing package sprai version 0.9.9.23+dfsg-1

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to annotated tag debian/0.9.9.23+dfsg-1
in repository sprai.

commit ccf82fa77116e41a5897c42bfe40c886a39ce3fa
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:12:36 2018 -0500

releasing package sprai version 0.9.9.23+dfsg-1
---
 debian/changelog | 7 +++
 1 file changed, 7 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 396649d..9e9c8b0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+sprai (0.9.9.23+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Bump Standards-Version to 4.1.3
+
+ -- Afif Elghraoui   Sun, 04 Feb 2018 05:10:53 -0500
+
 sprai (0.9.9.22+dfsg-1) unstable; urgency=low
 
   * Add example data

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[med-svn] [sprai] 02/04: Merge tag 'upstream/0.9.9.23+dfsg'

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to annotated tag debian/0.9.9.23+dfsg-1
in repository sprai.

commit 9bf810f706f4d0ef38b470f109214883bb8c1c14
Merge: c687bdb 0d163af
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:05:04 2018 -0500

Merge tag 'upstream/0.9.9.23+dfsg'

Upstream version 0.9.9.23+dfsg

 doc/_build/html/_sources/Download.txt |  4 +++-
 dumbbell_filter.pl| 11 +++
 ec.spec   |  2 +-
 makefile  |  2 +-
 wscript   |  2 +-
 5 files changed, 17 insertions(+), 4 deletions(-)

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[med-svn] [sprai] 03/04: Bump Standards-Version to 4.1.3

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to annotated tag debian/0.9.9.23+dfsg-1
in repository sprai.

commit f80586edffc34ba3d9c3dcd07f9492090d116e49
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:10:41 2018 -0500

Bump Standards-Version to 4.1.3
---
 debian/control | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index f03de21..0286ce4 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Uploaders: Afif Elghraoui 
 Build-Depends:
debhelper (>= 9),
python,
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Homepage: http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html
 Vcs-Git: https://anonscm.debian.org/git/debian-med/sprai.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sprai.git

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[med-svn] [sprai] 01/04: New upstream version 0.9.9.23+dfsg

2018-02-04 Thread Afif Elghraoui

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to annotated tag debian/0.9.9.23+dfsg-1
in repository sprai.

commit 0d163af0aed80a5d4a866dab98e1d2a873a99dbd
Author: Afif Elghraoui 
Date:   Sun Feb 4 05:05:04 2018 -0500

New upstream version 0.9.9.23+dfsg
---
 doc/_build/html/_sources/Download.txt |  4 +++-
 dumbbell_filter.pl| 11 +++
 ec.spec   |  2 +-
 makefile  |  2 +-
 wscript   |  2 +-
 5 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/doc/_build/html/_sources/Download.txt 
b/doc/_build/html/_sources/Download.txt
index c65687c..4befd04 100644
--- a/doc/_build/html/_sources/Download.txt
+++ b/doc/_build/html/_sources/Download.txt
@@ -1,11 +1,13 @@
 ===
 Download The Latest Version
 ===
-http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.21.tar.gz
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.22.tar.gz
 
 ==
 Older releases
 ==
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.21.tar.gz
+
 http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.20.tar.gz
 
 http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.19.tar.gz
diff --git a/dumbbell_filter.pl b/dumbbell_filter.pl
index 6187f93..f943e3b 100755
--- a/dumbbell_filter.pl
+++ b/dumbbell_filter.pl
@@ -149,6 +149,16 @@ sub flush(){
 
   my $longest = length($reads[0]);
   my $i_adequate=0;
+  # use longest subread
+  if(@reads > 1){
+for(my $i=1; $i<@reads; ++$i){
+  if(length($reads[$i]) > $longest){
+$longest = length($reads[$i]);
+$i_adequate = $i;
+  }
+}
+  }
+=pod
   # discard last one (because it may have low quality)
   # if # of subreads > 2, then use 1st or 2nd read.
   # else use 1st read
@@ -158,6 +168,7 @@ sub flush(){
   $i_adequate = 1; 
 }
   }
+=cut
   printf("\@%s\n",$names[$i_adequate]);
   printf("%s\n",$reads[$i_adequate]);
   printf("%s\n",$opts[$i_adequate]);
diff --git a/ec.spec b/ec.spec
index 1c16fd3..452bd6b 100644
--- a/ec.spec
+++ b/ec.spec
@@ -53,7 +53,7 @@ max_target_seqs 100
 trim 42
 
 # if not 0, use only one subread per one molecule
-use_one_subread 0
+use_one_subread 1
 
 # direct_vote & copy_blastdb are used by ezez4makefile_v4.pl
 direct_vote 0
diff --git a/makefile b/makefile
index 78ff75f..ccc8a99 100644
--- a/makefile
+++ b/makefile
@@ -1,5 +1,5 @@
 APPNAME = 'sprai'
-VERSION = '0.9.9.22'
+VERSION = '0.9.9.23'
 
 PREFIX=$(PWD)
 COMPILED= \
diff --git a/wscript b/wscript
index e0b432d..f0292c8 100644
--- a/wscript
+++ b/wscript
@@ -1,5 +1,5 @@
 APPNAME = 'sprai'
-VERSION = '0.9.9.22'
+VERSION = '0.9.9.23'
 
 srcdir = '.'
 blddir = 'build'

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