[Blends-commit] [Git][blends-team/med][master] r-cran-rniftilib removed from Debian

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
a005bab1 by Andreas Tille at 2024-05-28T07:21:24+02:00
r-cran-rniftilib removed from Debian

- - - - -


2 changed files:

- debian/changelog
- tasks/imaging-dev


Changes:

=
debian/changelog
=
@@ -5,6 +5,7 @@ debian-med (3.8.2) UNRELEASED; urgency=medium
   * aeskulap removed from Debian
   * miaviewit removed from Debian
   * Remove dicomnifti (see bug #1070243)
+  * r-cran-rniftilib removed from Debian
 
  -- Andreas Tille   Tue, 04 Jul 2023 10:23:01 +0200
 


=
tasks/imaging-dev
=
@@ -54,8 +54,6 @@ Recommends: python3-mia
 
 Recommends: libopenigtlink-dev
 
-Recommends: r-cran-rniftilib
-
 Recommends: libmni-perllib-perl
 Homepage: http://packages.bic.mni.mcgill.ca/tgz/
 License: Artistic License



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/a005bab1b98fff60857b1d4936843fec728cfdc9

-- 
This project does not include diff previews in email notifications.
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/a005bab1b98fff60857b1d4936843fec728cfdc9
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] r-cran-eco will be removed since it is not supported on CRAN any more

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
b44477cb by Andreas Tille at 2024-05-28T07:12:58+02:00
r-cran-eco will be removed since it is not supported on CRAN any more

- - - - -


2 changed files:

- debian/changelog
- tasks/statistics


Changes:

=
debian/changelog
=
@@ -1,3 +1,13 @@
+debian-science (1.14.7) UNRELEASED; urgency=medium
+
+  [ Sébastien Villemot ]
+  * Drop octave-mpi
+
+  [ Andreas Tille ]
+  * Drop r-cran-eco
+
+ -- Andreas Tille   Tue, 28 May 2024 07:12:16 +0200
+
 debian-science (1.14.6) unstable; urgency=medium
 
   * Remove r-cran-maptools from geography task since its removed from CRAN


=
tasks/statistics
=
@@ -15,7 +15,7 @@ Recommends: r-cran-mapproj, r-cran-abind, r-cran-arm, 
r-cran-bayesm,
 r-cran-boot, r-cran-cairodevice, r-cran-ca, r-cran-car, 
r-cran-caret, r-cran-chron,
 r-cran-cluster, r-cran-coda, r-cran-codetools,
 r-cran-date, r-cran-dbi,
-r-cran-eco, r-cran-effects, r-cran-erm,
+r-cran-effects, r-cran-erm,
 r-cran-fbasics, r-cran-fcopulae, r-cran-fecofin, r-cran-fextremes,
 r-cran-fmultivar, r-cran-foptions, r-cran-foreign, 
r-cran-fportfolio,
 r-cran-gam, r-cran-gdata, r-cran-geepack, r-cran-glmnet, 
r-cran-gmodels,



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/b44477cbdddcaf5a23580c0baf31730c70284c2a

-- 
This project does not include diff previews in email notifications.
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/b44477cbdddcaf5a23580c0baf31730c70284c2a
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 2 commits: Really fix spacing

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
f0726bcc by Andreas Tille at 2024-04-22T19:57:17+02:00
Really fix spacing

- - - - -
5729e18a by Andreas Tille at 2024-04-22T20:26:06+02:00
Work around possibly missing key conflicts

- - - - -


1 changed file:

- devtools/tasks_diff


Changes:

=
devtools/tasks_diff
=
@@ -89,10 +89,10 @@ def load_task(path_to_task):
if "recommends" in paragraph:
taskinfo["recommends"] += 
clean_up_packages(paragraph["recommends"])
 
-   if "conflicts" in paragraph:
+   if "conflicts" in paragraph:
taskinfo["conflicts"] += 
clean_up_packages(paragraph["conflicts"])
 
-   if "breaks" in paragraph:
+   if "breaks" in paragraph:
taskinfo["breaks"] += 
clean_up_packages(paragraph["breaks"])
 
if "ignore" in paragraph:
@@ -118,7 +118,10 @@ def compare_tasks(tasks, tasks_compare, taskprefix):
task_first = True 
first_add = True
for header in ["depends", "recommends", "suggests", 
"conflicts", "breaks", "ignore", "avoid"]:
-   added =  set(tasks[task][header]) - 
set(tasks_compare[task][header])
+   try:
+   added =  set(tasks[task][header]) - 
set(tasks_compare[task][header])
+   except:
+   continue # if some key is missing
if added:
if first_print:
print(START_FLAG, "\n")
@@ -135,7 +138,10 @@ def compare_tasks(tasks, tasks_compare, taskprefix):

first_remove = True
for header in ["depends", "recommends", "suggests", 
"conflicts", "breaks", "ignore", "avoid"]:
-   removed =  set(tasks_compare[task][header]) - 
set(tasks[task][header])
+   try:
+   removed =  set(tasks_compare[task][header]) - 
set(tasks[task][header])
+   except:
+   continue # if some key is missing
if removed:
if first_print:
print(START_FLAG, "\n")



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/cacbc3f4e856c5bea51783aa4c23fbafdc2a3031...5729e18a2f70df486bdc7041cbd13c0cfca2557b

-- 
This project does not include diff previews in email notifications.
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/cacbc3f4e856c5bea51783aa4c23fbafdc2a3031...5729e18a2f70df486bdc7041cbd13c0cfca2557b
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science] Pushed new tag debian/1.14.6

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.14.6 at Debian Blends Team / science

-- 
This project does not include diff previews in email notifications.
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/tree/debian/1.14.6
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 2 commits: Standards-Version: 4.7.0

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
2ec6b611 by Andreas Tille at 2024-05-18T22:44:46+02:00
Standards-Version: 4.7.0

- - - - -
d3b60e43 by Andreas Tille at 2024-05-18T22:47:56+02:00
Upload to unstable

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
@@ -1,8 +1,9 @@
-blends (0.7.7) UNRELEASED; urgency=medium
+blends (0.7.7) unstable; urgency=medium
 
   * Fix spacing in tasks_diff
+  * Standards-Version: 4.7.0
 
- -- Andreas Tille   Mon, 22 Apr 2024 19:32:19 +0200
+ -- Andreas Tille   Sat, 18 May 2024 22:44:52 +0200
 
 blends (0.7.6) unstable; urgency=medium
 


=
debian/control
=
@@ -17,7 +17,7 @@ Build-Depends-Indep: dblatex,
  python3-sphinx,
  w3m,
  xmlto
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/blends-team/blends
 Vcs-Git: https://salsa.debian.org/blends-team/blends.git
 Homepage: https://www.debian.org/blends/



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/5729e18a2f70df486bdc7041cbd13c0cfca2557b...d3b60e43aab34e5cd38da7f04b5dcb2f249096c3

-- 
This project does not include diff previews in email notifications.
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/5729e18a2f70df486bdc7041cbd13c0cfca2557b...d3b60e43aab34e5cd38da7f04b5dcb2f249096c3
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends] Pushed new tag debian/0.7.7

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/0.7.7 at Debian Blends Team / blends

-- 
This project does not include diff previews in email notifications.
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/tree/debian/0.7.7
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Remove dicomnifti (see bug #1070243)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
2bb33099 by Andreas Tille at 2024-05-03T11:53:32+02:00
Remove dicomnifti (see bug #1070243)

- - - - -


2 changed files:

- debian/changelog
- tasks/imaging


Changes:

=
debian/changelog
=
@@ -4,6 +4,7 @@ debian-med (3.8.2) UNRELEASED; urgency=medium
   * r-cran-treescape replaced by r-cran-treespace
   * aeskulap removed from Debian
   * miaviewit removed from Debian
+  * Remove dicomnifti (see bug #1070243)
 
  -- Andreas Tille   Tue, 04 Jul 2023 10:23:01 +0200
 


=
tasks/imaging
=
@@ -11,7 +11,7 @@ Description: Debian Med image processing and visualization 
packages
  - either from a graphical user interface, the command  line, or implemented in
  workflows.
 
-Recommends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, 
python3-nibabel, python3-pydicom, xmedcon, dcmtk
+Recommends: amide, ctsim, ctn, imagej, minc-tools, medcon, python3-nibabel, 
python3-pydicom, xmedcon, dcmtk
 
 Suggests: imagemagick, pngquant, imview, trimage
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/2bb33099a7bf052a7cf058fdd621c5d1c4638940

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/2bb33099a7bf052a7cf058fdd621c5d1c4638940
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 2 commits: Fix spacing in tasks_diff

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
23182dfe by Andreas Tille at 2024-04-22T19:32:43+02:00
Fix spacing in tasks_diff

- - - - -
cacbc3f4 by Andreas Tille at 2024-04-22T19:54:56+02:00
Fix lintian-overrides

- - - - -


4 changed files:

- debian/blends-common.lintian-overrides
- − debian/blends-dev.lintian-overrides
- debian/changelog
- devtools/tasks_diff


Changes:

=
debian/blends-common.lintian-overrides
=
@@ -4,8 +4,8 @@
 # That's why neither postinst nor prerm will call update-menus and
 # if they would it would just be a useless call because it just exits 0
 # if called by root.
-blends-common: postinst-does-not-call-updatemenus usr/share/menu/blend-menu
+blends-common: postinst-does-not-call-updatemenus [usr/share/menu/blend-menu]
 
 # For obvious reasons the script has to be executable which is the
 # intended use for scripts which dynamically create menu entries.
-blends-common: executable-menu-file usr/share/menu/blend-menu 0755
+blends-common: executable-menu-file 0755 [usr/share/menu/blend-menu]


=
debian/blends-dev.lintian-overrides deleted
=
@@ -1,2 +0,0 @@
-# Dependency on debhelper is intended
-blends-dev: binary-package-depends-on-toolchain-package depends: debhelper (>= 
9)


=
debian/changelog
=
@@ -1,3 +1,9 @@
+blends (0.7.7) UNRELEASED; urgency=medium
+
+  * Fix spacing in tasks_diff
+
+ -- Andreas Tille   Mon, 22 Apr 2024 19:32:19 +0200
+
 blends (0.7.6) unstable; urgency=medium
 
   [ Gianfranco Costamagna ]


=
devtools/tasks_diff
=
@@ -89,10 +89,10 @@ def load_task(path_to_task):
if "recommends" in paragraph:
taskinfo["recommends"] += 
clean_up_packages(paragraph["recommends"])
 
-if "conflicts" in paragraph:
+   if "conflicts" in paragraph:
taskinfo["conflicts"] += 
clean_up_packages(paragraph["conflicts"])
 
-if "breaks" in paragraph:
+   if "breaks" in paragraph:
taskinfo["breaks"] += 
clean_up_packages(paragraph["breaks"])
 
if "ignore" in paragraph:



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/fe167e03b6fd0199dcc534bb4f3b12391aa96c78...cacbc3f4e856c5bea51783aa4c23fbafdc2a3031

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/fe167e03b6fd0199dcc534bb4f3b12391aa96c78...cacbc3f4e856c5bea51783aa4c23fbafdc2a3031
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/imaging][master] Add fim

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / imaging


Commits:
f9d18899 by Andreas Tille at 2024-03-16T23:50:34+01:00
Add fim

- - - - -


1 changed file:

- tasks/imageviewer


Changes:

=
tasks/imageviewer
=
@@ -2,7 +2,7 @@ Task: Image viewer
 Description: Image viewers in Debian
  Debian contains a lot of image viewers. Here you can have an overview.
 
-Depends: feh, gliv, gpicview, mirage, qiv, pqiv, xli
+Depends: feh, fim, gliv, gpicview, mirage, qiv, pqiv, xli
 
 Depends: eog | gthumb | gwenview | showfoto | preview.app
 



View it on GitLab: 
https://salsa.debian.org/blends-team/imaging/-/commit/f9d188998319cc9bf1832af7a55a9fe3123f541e

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/imaging/-/commit/f9d188998319cc9bf1832af7a55a9fe3123f541e
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] 2 commits: Fix accidentally created absolute symlinks

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
fe7d5471 by Guido Berhoerster at 2024-02-23T16:34:31+01:00
Fix accidentally created absolute symlinks

- - - - -
32ff89a7 by Andreas Tille at 2024-02-23T15:37:01+00:00
Merge branch master into master

Fix accidentally created absolute symlinks

See merge request blends-team/website!14
- - - - -


11 changed files:

- www/edu/img
- www/edu/index.html.de
- www/edu/index.html.en
- www/edu/index.html.fr
- www/edu/index.html.gl
- www/edu/index.html.id
- www/edu/index.html.nb
- www/edu/index.html.nl
- www/edu/index.html.no
- www/edu/index.html.ru
- www/edu/index.no.html


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/2adee13b8b37ae55f451fe8ef5897df88693eb42...32ff89a73fe907b2c7b3edb62e2d65ccf24b1b8f

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/2adee13b8b37ae55f451fe8ef5897df88693eb42...32ff89a73fe907b2c7b3edb62e2d65ccf24b1b8f
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] 4 commits: Update DebianEdu page for the bookworm release

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
92ef8297 by Guido Berhoerster at 2024-02-23T15:51:58+01:00
Update DebianEdu page for the bookworm release

- - - - -
bc01c7db by Guido Berhoerster at 2024-02-23T15:53:31+01:00
Update DebianEdu translations

- - - - -
47e440ae by Guido Berhoerster at 2024-02-23T15:59:05+01:00
Update de and id translations for DebianEdu

- - - - -
2adee13b by Andreas Tille at 2024-02-23T15:16:04+00:00
Merge branch master into master

Update DebianEdu page for the Bookworm release

See merge request blends-team/website!13
- - - - -


30 changed files:

- www/edu/de.po
- www/edu/fr.po
- www/edu/gl.po
- www/edu/id.po
- www/edu/img
- www/edu/index.de.html
- www/edu/index.en.html
- www/edu/index.fr.html
- www/edu/index.gl.html
- www/edu/index.html.de
- www/edu/index.html.en
- www/edu/index.html.fr
- www/edu/index.html.gl
- www/edu/index.html.id
- www/edu/index.html.nb
- www/edu/index.html.nl
- www/edu/index.html.no
- www/edu/index.html.ru
- www/edu/index.id.html
- www/edu/index.nb.html
- www/edu/index.nl.html
- www/edu/index.no.html
- www/edu/index.pot
- www/edu/index.ru.html
- www/edu/nb.po
- www/edu/nl.po
- www/edu/ru.po
- www/img/de/27-Tjener-Xfce_Desktop.png
- www/img/en/27-Tjener-Xfce_Desktop.png
- www/img/fr/27-Tjener-Xfce_Desktop.png


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/298f2e8441235a53840b8c3b3c28709d38778f5e...2adee13b8b37ae55f451fe8ef5897df88693eb42

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/298f2e8441235a53840b8c3b3c28709d38778f5e...2adee13b8b37ae55f451fe8ef5897df88693eb42
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] Add visidata

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
27553b64 by Andreas Tille at 2024-02-08T13:42:35+01:00
Add visidata

- - - - -


1 changed file:

- tasks/datamanagement


Changes:

=
tasks/datamanagement
=
@@ -35,3 +35,5 @@ Recommends: python3-pyzoltan
 Recommends: virtuoso-opensource
 
 Recommends: python3-mdp
+
+Recommends: visidata



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/27553b64b0c1026ba28f2c990b6ea1b7197fe4d4

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/27553b64b0c1026ba28f2c990b6ea1b7197fe4d4
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Keep libbiojava4-java suggested

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
57943436 by Andreas Tille at 2024-01-31T08:14:46+01:00
Keep libbiojava4-java suggested

- - - - -
10431e30 by Andreas Tille at 2024-01-31T08:48:49+01:00
Add further uncategorized packages

- - - - -


3 changed files:

- tasks/bio
- tasks/bio-dev
- tasks/psychology


Changes:

=
tasks/bio
=
@@ -620,6 +620,8 @@ X-Category: Sequencing
 
 Recommends: crux-toolkit
 
+Recommends: ctffind
+
 Recommends: cutadapt
 
 Recommends: cutesv


=
tasks/bio-dev
=
@@ -16,7 +16,7 @@ Recommends: biosquid
 
 Recommends: cwltool, snakemake, python3-wdlparse
 
-Suggests: cwlformat
+Suggests: cwlformat, cwltest
 
 Recommends: libvibrant6-dev
 
@@ -42,6 +42,8 @@ Recommends: ruby-bio
 
 Recommends: libbiojava-java, libbiojava6-java
 
+Suggests: libbiojava4-java
+
 Recommends: libgenome-dev, libmuscle-dev, libmems-dev
 
 Recommends: libhtsjdk-java


=
tasks/psychology
=
@@ -39,3 +39,5 @@ Comment: Several related R packages are listed at CRAN:
  http://cran.r-project.org/web/views/Psychometrics.html
 
 Recommends: python3-bioxtasraw
+
+Suggests: python3-pynwb



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/0f9cbb90ed3f6e3dbf53c53e794a3bd0a6cbd692...10431e30f6da773300da344251ec923b58e24549

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/0f9cbb90ed3f6e3dbf53c53e794a3bd0a6cbd692...10431e30f6da773300da344251ec923b58e24549
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] Do not report pure unrelated helpers in Debian Med as uncategorized

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
298f2e84 by Andreas Tille at 2024-01-31T08:49:16+01:00
Do not report pure unrelated helpers in Debian Med as uncategorized

- - - - -


1 changed file:

- misc/sql/0-uncategorised.sh


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/298f2e8441235a53840b8c3b3c28709d38778f5e

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/298f2e8441235a53840b8c3b3c28709d38778f5e
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] Add python3-hmmlearn and python3-trx-python

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
1e7e71c4 by Andreas Tille at 2024-01-31T08:47:41+01:00
Add python3-hmmlearn and python3-trx-python

- - - - -


2 changed files:

- tasks/dataacquisition-dev
- tasks/statistics


Changes:

=
tasks/dataacquisition-dev
=
@@ -42,3 +42,5 @@ Recommends: mseed2sac
 Recommends: libopen3d-dev, python3-open3d
 
 Recommends: libvnlog-dev, libvnlog-perl, python3-vnlog
+
+Recommends: python3-trx-python


=
tasks/statistics
=
@@ -170,3 +170,5 @@ Suggests: node-shiny-server-client
 Recommends: libdistlib-java
 
 Suggests: libicb-utils-java
+
+Recommends: python3-hmmlearn



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/1e7e71c49bdc525895a28fa47ba41b5b53c64918

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/1e7e71c49bdc525895a28fa47ba41b5b53c64918
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] Add liblibleidenalg-dev, fix name of libigraph-dev

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
392093fc by Andreas Tille at 2024-01-31T08:22:27+01:00
Add liblibleidenalg-dev, fix name of libigraph-dev

- - - - -


1 changed file:

- tasks/mathematics-dev


Changes:

=
tasks/mathematics-dev
=
@@ -184,7 +184,7 @@ Why: solver
 Recommends: libdogleg-dev
 Why: solver
 
-Recommends: libigraph0-dev
+Recommends: libigraph-dev, liblibleidenalg-dev
 
 Recommends: libalglib-dev
 



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/392093fc84b1a0dacbd00a445705108c201d7b19

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/392093fc84b1a0dacbd00a445705108c201d7b19
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add deblur

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
0f9cbb90 by Andreas Tille at 2024-01-31T07:13:52+01:00
Add deblur

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -648,6 +648,8 @@ Remark: There is no intend to keep continue the existing 
packaging since
 
 Recommends: dendroscope
 
+Recommends: deblur
+
 Recommends: diann
 
 Recommends: dnarrange



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/0f9cbb90ed3f6e3dbf53c53e794a3bd0a6cbd692

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/0f9cbb90ed3f6e3dbf53c53e794a3bd0a6cbd692
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add python3-bioxtasraw

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
218e350e by Andreas Tille at 2024-01-06T16:19:11+01:00
Add python3-bioxtasraw

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -171,6 +171,8 @@ Recommends: tophat,
 
 Recommends: umap
 
+Recommends: python3-bioxtasraw
+
 Suggests: python3-intake
 
 Suggests: python3-ncls



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/218e350e299cffdbdf67d815be12abeb718f20d2

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/218e350e299cffdbdf67d815be12abeb718f20d2
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Drop libbiococoa-dev since asked for removal

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
5c1b8eb1 by Andreas Tille at 2023-12-10T16:32:11+01:00
Drop libbiococoa-dev since asked for removal

- - - - -


1 changed file:

- tasks/bio-dev


Changes:

=
tasks/bio-dev
=
@@ -75,8 +75,6 @@ Recommends: libbio-alignio-stockholm-perl, 
libbio-cluster-perl,
 
 Recommends: libace-perl
 
-Recommends: libbiococoa-dev
-
 Recommends: libcifpp-dev
 
 Recommends: libstaden-read-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/5c1b8eb1c8bc0824df5048e73bc54e38faa94eff

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/5c1b8eb1c8bc0824df5048e73bc54e38faa94eff
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] Add three Python3 modules that are great to develop views on scientific data. ...

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
7491d7ad by Andreas Tille at 2023-11-29T08:01:55+01:00
Add three Python3 modules that are great to develop views on scientific data.  
Unfortunately these all require python3-bokeh which is hard to package.

- - - - -


1 changed file:

- tasks/viewing-dev


Changes:

=
tasks/viewing-dev
=
@@ -76,3 +76,9 @@ Recommends: python3-symfit
 Recommends: libtulip-dev
 
 Recommends: python3-vedo
+
+Recommends: python3-gneiss
+
+Recommends: python3-hvplot
+
+Recommends: python3-holoviews



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/7491d7ade49c39b35c4d5f784bbf501b2eedcd3e

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/7491d7ade49c39b35c4d5f784bbf501b2eedcd3e
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] Fix date in doc

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
fe167e03 by Andreas Tille at 2023-11-27T08:38:00+01:00
Fix date in doc

- - - - -


1 changed file:

- doc/en/00_titletoc.xml


Changes:

=
doc/en/00_titletoc.xml
=
@@ -14,14 +14,14 @@


v1
-   19 Jun 2013
+   01 Nov 2023



 
 
-   2004 - 2013 Andreas Tille, Ben Armstrong, 
Emmanouil Kiagias
+   2004 - 2023 Andreas Tille, Ben Armstrong, 
Emmanouil Kiagias
 
 




View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/commit/fe167e03b6fd0199dcc534bb4f3b12391aa96c78

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/commit/fe167e03b6fd0199dcc534bb4f3b12391aa96c78
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior] Pushed new tag debian/1.32

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.32 at Debian Blends Team / junior

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/tree/debian/1.32
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior][master] Upload to unstable

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / junior


Commits:
cf14bd71 by Andreas Tille at 2023-11-11T19:17:23+01:00
Upload to unstable

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
@@ -1,4 +1,4 @@
-debian-junior (1.32) UNRELEASED; urgency=medium
+debian-junior (1.32) unstable; urgency=medium
 
   * Team upload.
   * Drop junior-tasks from desktop task since it is in Depends



View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/commit/cf14bd7145141b2c89b5e9526b82acdd192afa13

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/commit/cf14bd7145141b2c89b5e9526b82acdd192afa13
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add bifrost

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
e0ffb099 by Andreas Tille at 2023-11-08T20:21:52+01:00
Add bifrost

- - - - -


2 changed files:

- tasks/bio
- tasks/bio-dev


Changes:

=
tasks/bio
=
@@ -551,6 +551,8 @@ Recommends: biosyntax
 
 Recommends: bismark
 
+Recommends: bifrost
+
 Recommends: bitseq
 
 Recommends: blat


=
tasks/bio-dev
=
@@ -685,3 +685,5 @@ Recommends: python3-bioframe
 Suggests: python3-cgelib
 
 Recommends: libwfa2-dev
+
+Suggests: libbifrost-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e0ffb099e4d3423cbd2eb008be6b6ab16e4c0a0e

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e0ffb099e4d3423cbd2eb008be6b6ab16e4c0a0e
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior][master] 4 commits: Trim trailing whitespace.

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / junior


Commits:
da046df2 by Andreas Tille at 2023-10-26T15:28:32+02:00
Trim trailing whitespace.

Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html

- - - - -
2189f167 by Andreas Tille at 2023-10-26T15:28:32+02:00
debian/copyright: use spaces rather than tabs to start continuation lines.

Changes-By: lintian-brush
Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html

- - - - -
f94eef75 by Andreas Tille at 2023-10-26T15:29:25+02:00
Use secure URI in Homepage field.

Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html

- - - - -
7134405c by Andreas Tille at 2023-10-26T15:31:40+02:00
Rules-Requires-Root: no

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/control.stub
- debian/copyright


Changes:

=
debian/changelog
=
@@ -3,6 +3,10 @@ debian-junior (1.32) UNRELEASED; urgency=medium
   * Team upload.
   * Drop junior-tasks from desktop task since it is in Depends
 automatically
+  * Trim trailing whitespace.
+  * debian/copyright: use spaces rather than tabs to start continuation lines.
+  * Use secure URI in Homepage field.
+  * Rules-Requires-Root: no
 
  -- Andreas Tille   Thu, 26 Oct 2023 15:09:27 +0200
 
@@ -19,8 +23,8 @@ debian-junior (1.31) unstable; urgency=low
   [ Andreas Tille ]
   * Standards-Version: 4.6.2
 
-  * start of automatic changelog entry * 
-  
+  * start of automatic changelog entry *
+
   * Changes in metapackage dependencies
-junior-art
 added:
@@ -132,8 +136,8 @@ debian-junior (1.29) unstable; urgency=medium
   * Remove myself from Uploaders
   * Depends: ${misc:Depends} for junior-tasks
 
-  * start of automatic changelog entry * 
-  
+  * start of automatic changelog entry *
+
   * Changes in metapackage dependencies
-junior-programming
 removed:
@@ -178,8 +182,8 @@ debian-junior (1.26) unstable; urgency=medium
   * Dropped Ben Armstrong from Uploaders
   * Bump Standards-Version
 
-  * start of automatic changelog entry * 
-  
+  * start of automatic changelog entry *
+
   * Changes in metapackage dependencies
-junior-art
 added:


=
debian/control
=
@@ -11,7 +11,8 @@ Build-Depends-Indep: blends-dev (>= 0.7~)
 Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/blends-team/junior
 Vcs-Git: https://salsa.debian.org/blends-team/junior.git
-Homepage: http://blends.debian.org/junior/tasks/
+Homepage: https://blends.debian.org/junior/tasks/
+Rules-Requires-Root: no
 
 Package: junior-tasks
 Architecture: all
@@ -582,4 +583,3 @@ Description: Debian Jr. writing
  This metapackage will install tools for your budding young
  writer. It includes a text editor, spell-checker, dictionary client,
  word processor, and educational writing software.
-


=
debian/control.stub
=
@@ -10,7 +10,8 @@ Build-Depends-Indep: blends-dev (>= 0.7~)
 Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/blends-team/junior
 Vcs-Git: https://salsa.debian.org/blends-team/junior.git
-Homepage: http://blends.debian.org/junior/tasks/
+Homepage: https://blends.debian.org/junior/tasks/
+Rules-Requires-Root: no
 
 Package: junior-tasks
 Architecture: all
@@ -19,4 +20,3 @@ Description: Debian Jr. tasks for tasksel
  This package provides Debian Jr. tasks in tasksel.
  .
  These tasks are described in detail at http://blends.debian.org/junior/tasks/
-


=
debian/copyright
=
@@ -6,7 +6,7 @@ Files: *
 Copyright: 2001-2008 Ben Armstrong 
2008-2010, 2012, 2014, 2015 Andreas Tille 
2014, 2016 Per Andersson 
-  2019 Jonathan Carter 
+   2019 Jonathan Carter 
 License: GPL-3+
 
 License: GPL-3+



View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/compare/1a6ce22384a61c3f2e6a6efd08e5ea235dde203e...7134405ccd718e7b07881504cc2008452e298cfa

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/compare/1a6ce22384a61c3f2e6a6efd08e5ea235dde203e...7134405ccd718e7b07881504cc2008452e298cfa
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior][master] Drop junior-tasks from desktop task since it is in Depends automatically (fixing lintian warning)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / junior


Commits:
1a6ce223 by Andreas Tille at 2023-10-26T15:11:18+02:00
Drop junior-tasks from desktop task since it is in Depends automatically 
(fixing lintian warning)

- - - - -


2 changed files:

- debian/changelog
- tasks/desktop


Changes:

=
debian/changelog
=
@@ -1,3 +1,11 @@
+debian-junior (1.32) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Drop junior-tasks from desktop task since it is in Depends
+automatically
+
+ -- Andreas Tille   Thu, 26 Oct 2023 15:09:27 +0200
+
 debian-junior (1.31) unstable; urgency=low
 
   [ Stefan Kropp ]


=
tasks/desktop
=
@@ -7,7 +7,7 @@ Recommends: icewm, dino-im, eog, epiphany-browser, evolution
 
 Recommends: gnome-calculator, gnome-clocks, gnome-dictionary
 
-Recommends: goldendict, gpxviewer, grun, junior-doc, junior-tasks
+Recommends: goldendict, gpxviewer, grun, junior-doc
 
 Recommends: libreoffice, lightdm, mousepad, paprefs, pavucontrol
 



View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/commit/1a6ce22384a61c3f2e6a6efd08e5ea235dde203e

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/commit/1a6ce22384a61c3f2e6a6efd08e5ea235dde203e
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior] Pushed new tag debian/1.31

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.31 at Debian Blends Team / junior

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/tree/debian/1.31
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 3 commits: Basically add Conflicts and Breaks relationships

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
4da66604 by Dominik George at 2023-08-27T09:28:58+00:00
Basically add Conflicts and Breaks relationships

- - - - -
388be5bc by Dominik George at 2023-08-27T10:18:24+00:00
Amend d/changelog

- - - - -
4408f93e by Andreas Tille at 2023-08-27T17:39:26+00:00
Merge branch feature/support-conflicts into master

Support Conflicts and Breaks

See merge request blends-team/blends!14
- - - - -


3 changed files:

- blends.py
- debian/changelog
- devtools/tasks_diff


Changes:

=
blends.py
=
@@ -252,8 +252,8 @@ class Task:
 self.format_upgraded = True
 
 # Create package dependencies
-dep_types = ["Depends", "Recommends", "Suggests"]
-dep_attrs = ["dependencies", "recommends", "suggests"]
+dep_types = ["Depends", "Recommends", "Suggests", "Conflicts", 
"Breaks"]
+dep_attrs = ["dependencies", "recommends", "suggests", "conflicts", 
"breaks"]
 for dep_type, dep_attr in zip(dep_types, dep_attrs):
 setattr(self, dep_attr, list(itertools.chain(
 *(list(Dependency(dep_type, s.strip(), par)
@@ -380,6 +380,14 @@ class Task:
 d['Suggests'] = ",\n  ".join(sorted(
 set(d.rawstr for d in self.suggests)
 ))
+if self.conflicts:
+d['Conflicts'] = ",\n   ".join(sorted(
+set(d.rawstr for d in self.conflicts)
+))
+if self.breaks:
+d['Breaks'] = ",\n".join(sorted(
+set(d.rawstr for d in self.breaks)
+))
 d['Description'] = self.summary + '\n ' + \
 "\n ".join(self.description.replace("\n\n", "\n.\n").split("\n"))
 return d


=
debian/changelog
=
@@ -1,7 +1,12 @@
 blends (0.7.6) UNRELEASED; urgency=medium
 
+  [ Gianfranco Costamagna ]
   * Add "ubuntu devel", an alias for the latest development release
 
+  [ Dominik George ]
+  * Add support for Conflicts and Breaks in task meta-packages
+(Closes: #1050621)
+
  -- Gianfranco Costamagna   Mon, 06 Jun 2022 
09:32:29 +0200
 
 blends (0.7.5) unstable; urgency=medium


=
devtools/tasks_diff
=
@@ -76,7 +76,7 @@ def load_task(path_to_task):
task = os.path.basename(path_to_task)
taskinfo = {}
 
-   for header in ["depends", "suggests", "recommends", "ignore", "avoid"]:
+   for header in ["depends", "suggests", "recommends", "conflicts", 
"breaks", "ignore", "avoid"]:
taskinfo[header] = []
 
for paragraph in deb822.Sources.iter_paragraphs(ftask, 
shared_storage=False):
@@ -89,6 +89,12 @@ def load_task(path_to_task):
if "recommends" in paragraph:
taskinfo["recommends"] += 
clean_up_packages(paragraph["recommends"])
 
+if "conflicts" in paragraph:
+   taskinfo["conflicts"] += 
clean_up_packages(paragraph["conflicts"])
+
+if "breaks" in paragraph:
+   taskinfo["breaks"] += 
clean_up_packages(paragraph["breaks"])
+
if "ignore" in paragraph:
taskinfo["ignore"] += 
clean_up_packages(paragraph["ignore"])
 
@@ -111,7 +117,7 @@ def compare_tasks(tasks, tasks_compare, taskprefix):

task_first = True 
first_add = True
-   for header in ["depends", "recommends", "suggests", "ignore", 
"avoid"]:
+   for header in ["depends", "recommends", "suggests", 
"conflicts", "breaks", "ignore", "avoid"]:
added =  set(tasks[task][header]) - 
set(tasks_compare[task][header])
if added:
if first_print:
@@ -128,7 +134,7 @@ def compare_tasks(tasks, tasks_compare, taskprefix):
print(", ".join(added))

first_remove = True
-   for header in ["depends", "recommends", "suggests", "ignore", 
"avoid"]:
+   for header in ["depends", "recommends", "suggests", 
"conflicts", "breaks", "ignore", "avoid"]:
removed =  set(tasks_compare[task][header]) - 
set(tasks[task][header])
if removed:
if first_print:



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/b643bb0b41a5de3c3f1e002e360b5a48d486b0b7...4408f93e5cd4eb7d65eb7611ce24f018c56ffa86

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/b643bb0b41a5de3c3f1e002e360b5a48d486b0b7...4408f93e5cd4eb7d65eb7611ce24f018c56ffa86
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list

[Blends-commit] [Git][blends-team/med][master] miaviewit removed from Debian

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
e717fd3e by Andreas Tille at 2023-08-02T08:58:17+02:00
miaviewit removed from Debian

- - - - -


2 changed files:

- debian/changelog
- tasks/imaging-dev


Changes:

=
debian/changelog
=
@@ -3,6 +3,7 @@ debian-med (3.8.2) UNRELEASED; urgency=medium
   * mriconvert removed from Debian
   * r-cran-treescape replaced by r-cran-treespace
   * aeskulap removed from Debian
+  * miaviewit removed from Debian
 
  -- Andreas Tille   Tue, 04 Jul 2023 10:23:01 +0200
 


=
tasks/imaging-dev
=
@@ -48,7 +48,7 @@ Recommends: libgiftiio-dev
 
 Recommends: libvistaio-dev
 
-Recommends: libmia-2.4-dev, libmiaviewit-dev, libmialm-dev
+Recommends: libmia-2.4-dev, libmialm-dev
 
 Recommends: python3-mia
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e717fd3ef604d6a19a7062adb24cbcba5bf834a9

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e717fd3ef604d6a19a7062adb24cbcba5bf834a9
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] aeskulap removed from Debian

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
8ae286d1 by Andreas Tille at 2023-07-10T10:54:14+02:00
aeskulap removed from Debian

- - - - -


3 changed files:

- debian/changelog
- tasks/covid-19
- tasks/imaging


Changes:

=
debian/changelog
=
@@ -2,6 +2,7 @@ debian-med (3.8.2) UNRELEASED; urgency=medium
 
   * mriconvert removed from Debian
   * r-cran-treescape replaced by r-cran-treespace
+  * aeskulap removed from Debian
 
  -- Andreas Tille   Tue, 04 Jul 2023 10:23:01 +0200
 


=
tasks/covid-19
=
@@ -368,8 +368,6 @@ X-Mark:  
 
 X-Mark:  
 
-Recommends: aeskulap
-
 Recommends: conquest-common
 
 Recommends: dcmtk


=
tasks/imaging
=
@@ -21,8 +21,6 @@ Recommends: nifti-bin
 
 Recommends: heudiconv
 
-Recommends: aeskulap
-
 Recommends: fsl
 
 Recommends: fslview



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/8ae286d1d981be382e3ca7e4cd2c48367cf1b93e

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/8ae286d1d981be382e3ca7e4cd2c48367cf1b93e
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add veryfasttree

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
b16e529a by Andreas Tille at 2023-07-04T10:23:11+02:00
Add veryfasttree

- - - - -


4 changed files:

- debian/changelog
- tasks/bio
- tasks/bio-phylogeny
- tasks/cloud


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+debian-med (3.8.2) UNRELEASED; urgency=medium
+
+  * 
+
+ -- Andreas Tille   Tue, 04 Jul 2023 10:23:01 +0200
+
 debian-med (3.8.1) unstable; urgency=medium
 
   * Standards-Version: 4.6.2


=
tasks/bio
=
@@ -676,7 +676,7 @@ Recommends: fasta3
 
 Recommends: fastani
 
-Recommends: fasttree
+Recommends: fasttree, veryfasttree
 
 Recommends: fastahack
 


=
tasks/bio-phylogeny
=
@@ -15,6 +15,8 @@ Recommends: altree
 
 Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
 
+Recommends: fasttree, veryfasttree
+
 Recommends: probalign
 
 Recommends: treeviewx


=
tasks/cloud
=
@@ -7,7 +7,8 @@ Description: Debian Med bioinformatics applications usable in 
cloud computing
 
 X-Begin-Category: Phylogenetic analysis
 Recommends: altree, clearcut, fastdnaml, fasttree, parsinsert, phyml,
-phyutility, prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle
+phyutility, prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle,
+veryfasttree
 X-End-Category: Phylogenetic analysis
 
 X-Begin-Category: Genetics and genomics



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/b16e529a8ff9e89622b21bdd031dd7af59909ba3

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/b16e529a8ff9e89622b21bdd031dd7af59909ba3
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] mriconvert removed from Debian; r-cran-treescape replaced by r-cran-treespace

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
9cbc707f by Andreas Tille at 2023-07-06T09:38:11+02:00
mriconvert removed from Debian; r-cran-treescape replaced by r-cran-treespace

- - - - -


3 changed files:

- debian/changelog
- tasks/bio
- tasks/imaging


Changes:

=
debian/changelog
=
@@ -1,6 +1,7 @@
 debian-med (3.8.2) UNRELEASED; urgency=medium
 
-  * 
+  * mriconvert removed from Debian
+  * r-cran-treescape replaced by r-cran-treespace
 
  -- Andreas Tille   Tue, 04 Jul 2023 10:23:01 +0200
 


=
tasks/bio
=
@@ -1361,7 +1361,7 @@ Recommends: r-cran-seqinr
 
 Recommends: r-cran-spp
 
-Recommends: r-cran-treescape
+Recommends: r-cran-treespace
 
 Recommends: r-cran-tsne
 


=
tasks/imaging
=
@@ -497,8 +497,6 @@ Recommends: ants
 
 Recommends: itksnap
 
-Recommends: mriconvert
-
 Recommends: mia-tools, mialmpick, mia-viewit
 
 Recommends: ismrmrd-tools



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/9cbc707f2560f4366ff66e46e1f51461dd92a64f

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/9cbc707f2560f4366ff66e46e1f51461dd92a64f
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] Use phototools mailing list instead of my own

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
18769d1a by Andreas Tille at 2023-05-29T20:54:40+02:00
Use phototools mailing list instead of my own

- - - - -


1 changed file:

- webtools/webconf/debian-imaging.conf


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/18769d1a866cc4cc9091551c9c9b8b680a0ccee0

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/18769d1a866cc4cc9091551c9c9b8b680a0ccee0
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science] Pushed new tag debian/1.14.5

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.14.5 at Debian Blends Team / science

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/tree/debian/1.14.5
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] Recommends: python3-mdp

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
afbffa0b by Andreas Tille at 2023-04-18T10:16:29+02:00
Recommends: python3-mdp

- - - - -


1 changed file:

- tasks/datamanagement


Changes:

=
tasks/datamanagement
=
@@ -33,3 +33,5 @@ Recommends: python3-jdata
 Recommends: python3-pyzoltan
 
 Recommends: virtuoso-opensource
+
+Recommends: python3-mdp



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/afbffa0ba5e0ece63c8514653eabeb0baf470239

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/afbffa0ba5e0ece63c8514653eabeb0baf470239
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] Catch more exceptions

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
755ee077 by Andreas Tille at 2023-03-15T19:11:59+01:00
Catch more exceptions

- - - - -


1 changed file:

- misc/machine_readable/fetch-machine-readable_salsa.py


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/755ee077caaf0b342715e0f4cf88a680d7cd3e6a

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/755ee077caaf0b342715e0f4cf88a680d7cd3e6a
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] 2 commits: Ignore more packages that do not need categorisation

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
7368031c by Andreas Tille at 2023-03-15T15:13:55+01:00
Ignore more packages that do not need categorisation

- - - - -
a51cf1cf by Andreas Tille at 2023-03-15T15:15:20+01:00
Increase time between attempts to fetch data; add more exceptions

- - - - -


2 changed files:

- misc/machine_readable/fetch-machine-readable_salsa.py
- misc/sql/0-uncategorised.sh


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/848970ca4913eeb28ce8b77d5d81d3aded66e979...a51cf1cfeadc4693aaacfb5e74113805a286ebe1

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/848970ca4913eeb28ce8b77d5d81d3aded66e979...a51cf1cfeadc4693aaacfb5e74113805a286ebe1
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/pan][master] 3 commits: Fix license

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / pan


Commits:
3151934d by Andreas Tille at 2023-03-05T17:57:01+01:00
Fix license

- - - - -
fa5c066b by Andreas Tille at 2023-03-05T17:59:38+01:00
Upload to experimental

- - - - -
f1cd08bc by Andreas Tille at 2023-03-05T21:29:07+01:00
 * Spelling issues
 * Fix description of data-reduction-frameworks-dev

- - - - -


8 changed files:

- debian/changelog
- debian/copyright
- tasks/coherent-diffraction
- tasks/data-reduction-frameworks-dev
- tasks/diffraction
- tasks/laue
- tasks/mx
- tasks/powder


Changes:

=
debian/changelog
=
@@ -1,4 +1,12 @@
-debian-pan (0.4) unstable; urgency=medium
+debian-pan (0.4) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Spelling issues
+  * Fix description of data-reduction-frameworks-dev
+
+ -- Andreas Tille   Sun, 05 Mar 2023 21:28:26 +0100
+
+debian-pan (0.4~exp) experimental; urgency=medium
 
   * Team upload.
 


=
debian/copyright
=
@@ -6,16 +6,6 @@ Source: https://salsa.debian.org/blends-team/pan
 Files: *
 Copyright: © 2013-2021 Picca Frédéric-Emmanuel 
  Andreas Tille  and others
-License: GPL-2+
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
- .
+License: GPL-3
  On Debian systems, the complete text of the GNU General Public
- License can be found in `/usr/share/common-licenses/GPL-2'.
+ License can be found in `/usr/share/common-licenses/GPL-3'.


=
tasks/coherent-diffraction
=
@@ -1,6 +1,6 @@
 Format: https://blends.debian.org/blends/1.1
 Task: coherent-diffraction
-Description: coherent diffraction softwares
+Description: coherent diffraction software
  This metapackage will install X-ray photons-and-neutrons PAN Blend coherent
  diffraction packages.
 Comment: Improve the Description


=
tasks/data-reduction-frameworks-dev
=
@@ -1,9 +1,8 @@
 Format: https://blends.debian.org/blends/1.1
 Task: data-reduction-frameworks-dev
 Description: PAN Debian data reduction frameworks dev
- This metapackage will install all PAN Blend packages. This is
- a temporary package until we sort all packages into the right
- categories.
+ This metapackage will install X-ray photons-and-neutrons PAN frameworks
+ dedicated to data reduction development.
 comment: Improve the description
 
 Depends: pan-data-reduction-frameworks


=
tasks/diffraction
=
@@ -1,8 +1,8 @@
 Format: https://blends.debian.org/blends/1.1
 Task: diffraction
-Description: diffraction softwares suit
+Description: diffraction software suit
  This metapackage will install all X-ray photons-and-neutrons PAN diffraction
- softwares
+ software
 Comment: Improve the description
 
 Recommends: binoculars, binoculars-doc, python3-binoculars


=
tasks/laue
=
@@ -1,7 +1,7 @@
 Format: https://blends.debian.org/blends/1.1
 Task: laue
 Description: laue software suit
- This metapackage will install all -ray photons-and-neutrons PAN laue softwares
+ This metapackage will install all X-ray photons-and-neutrons PAN laue software
 Comment: Improve the description
 
 Suggests: esmeralda


=
tasks/mx
=
@@ -1,7 +1,7 @@
 Format: https://blends.debian.org/blends/1.1
 Task: mx
 Description: Macro Molecular diffraction
- This metapackage will install all MX diffraction softwares for X-ray
+ This metapackage will install all MX diffraction software for X-ray
  photons-and-neutrons PAN.
 Comment: Improve the description
 


=
tasks/powder
=
@@ -2,7 +2,7 @@ Format: https://blends.debian.org/blends/1.1
 Task: powder
 Description: powder diffraction
  This metapackage will install all X-ray photons-and-neutrons PAN powder
- diffraction softwares.
+ diffraction software.
 Comment: Improve the description
 
 



View it on GitLab: 
https://salsa.debian.org/blends-team/pan/-/compare/f92c39974c9ad28ac228a50ad4bc693294e966e0...f1cd08bc69a1832d24905c355b84856f3c81348c

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/pan/-/compare/f92c39974c9ad28ac228a50ad4bc693294e966e0...f1cd08bc69a1832d24905c355b84856f3c81348c
You're receiving this email because of your 

[Blends-commit] [Git][blends-team/pan] Pushed new tag debian/0.4

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/0.4 at Debian Blends Team / pan

-- 
View it on GitLab: https://salsa.debian.org/blends-team/pan/-/tree/debian/0.4
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science] Pushed new tag debian/1.14.4

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.14.4 at Debian Blends Team / science

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/tree/debian/1.14.4
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/pan] Deleted tag debian/0.4

[Andreas Tille (@tille)]

Andreas Tille deleted tag debian/0.4 at Debian Blends Team / pan

-- 

You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/pan] Pushed new tag debian/0.4

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/0.4 at Debian Blends Team / pan

-- 
View it on GitLab: https://salsa.debian.org/blends-team/pan/-/tree/debian/0.4
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] 3 commits: Exclude some more packages that are not relevant

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
8e5ba8b8 by Andreas Tille at 2023-02-01T10:12:03+01:00
Exclude some more packages that are not relevant

- - - - -
9ab90a48 by Andreas Tille at 2023-02-01T10:24:49+01:00
Do not merge Science and Electronics any more

- - - - -
848970ca by Andreas Tille at 2023-02-24T11:54:12+01:00
Whitelist some more Science packages

- - - - -


1 changed file:

- misc/sql/0-uncategorised.sh


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/f753503c489d74d49d6061aa071eacc78a0c9f23...848970ca4913eeb28ce8b77d5d81d3aded66e979

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/f753503c489d74d49d6061aa071eacc78a0c9f23...848970ca4913eeb28ce8b77d5d81d3aded66e979
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Recommends: libwfa2-dev

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
c5df24bc by Andreas Tille at 2023-02-08T11:27:57+01:00
Recommends: libwfa2-dev

- - - - -


1 changed file:

- tasks/bio-dev


Changes:

=
tasks/bio-dev
=
@@ -684,3 +684,5 @@ Recommends: python3-pyfastx
 Recommends: python3-bioframe
 
 Suggests: python3-cgelib
+
+Recommends: libwfa2-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/c5df24bcd391871419e0cec224671b2036689236

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/c5df24bcd391871419e0cec224671b2036689236
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] [skip ci] Standards-Version: 4.6.2

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
d74719d2 by Andreas Tille at 2023-02-08T11:26:01+01:00
[skip ci] Standards-Version: 4.6.2

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/control.stub


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+debian-med (3.8.1) UNRELEASED; urgency=medium
+
+  * Standards-Version: 4.6.2
+
+ -- Andreas Tille   Wed, 08 Feb 2023 11:25:36 +0100
+
 debian-med (3.8) unstable; urgency=medium
 
   * nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed


=
debian/control
=
@@ -6,7 +6,7 @@ Section: misc
 Priority: optional
 Build-Depends-Indep: blends-dev (>= 0.7.5~),
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 


=
debian/control.stub
=
@@ -5,7 +5,7 @@ Section: misc
 Priority: optional
 Build-Depends-Indep: blends-dev (>= 0.7.5~),
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/d74719d275063ab41a0a3b967ecfaf23a2b9d409

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/d74719d275063ab41a0a3b967ecfaf23a2b9d409
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med] Pushed new tag debian/3.8

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/3.8 at Debian Blends Team / med

-- 
View it on GitLab: https://salsa.debian.org/blends-team/med/-/tree/debian/3.8
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Replace: msxpertsuite by massxpert, minexpert2 (see #1024780)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
e60a1f68 by Andreas Tille at 2023-02-08T09:11:01+01:00
Replace: msxpertsuite by massxpert, minexpert2 (see #1024780)

- - - - -


2 changed files:

- debian/changelog
- tasks/bio


Changes:

=
debian/changelog
=
@@ -3,6 +3,7 @@ debian-med (3.7.4) UNRELEASED; urgency=medium
   * nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed
 from Debian thus removed from tasks
   * Suggests: libgatk-native-bindings-java
+  * Replace: msxpertsuite by massxpert, minexpert2 (see #1024780)
 
  -- Andreas Tille   Mon, 07 Nov 2022 07:27:02 +0100
 


=
tasks/bio
=
@@ -199,7 +199,7 @@ Recommends: adun-core
 
 Suggests:adun.app
 
-Recommends: avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, 
r-cran-bio3d, msxpertsuite
+Recommends: avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, 
r-cran-bio3d, massxpert, minexpert2
 
 Recommends: gromacs
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e60a1f685a68c0eff597778ab8a5ef777a6f7fd9

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e60a1f685a68c0eff597778ab8a5ef777a6f7fd9
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Suggests: libgatk-native-bindings-java

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
f2bf6683 by Andreas Tille at 2023-02-07T11:14:15+01:00
Suggests: libgatk-native-bindings-java

- - - - -


2 changed files:

- debian/changelog
- tasks/bio-dev


Changes:

=
debian/changelog
=
@@ -2,6 +2,7 @@ debian-med (3.7.4) UNRELEASED; urgency=medium
 
   * nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed
 from Debian thus removed from tasks
+  * Suggests: libgatk-native-bindings-java
 
  -- Andreas Tille   Mon, 07 Nov 2022 07:27:02 +0100
 


=
tasks/bio-dev
=
@@ -659,7 +659,7 @@ X-Category: Genomics; Clustering analysis (+GUI)
 
 Suggests: capsule-nextflow, libcapsule-maven-nextflow-java
 
-Suggests: libgatk-bwamem-java, libgatk-bwamem-jni, libgatk-fermilite-java, 
libgatk-fermilite-jni, libgenomicsdb-java, libgenomicsdb-dev
+Suggests: libgatk-bwamem-java, libgatk-bwamem-jni, libgatk-fermilite-java, 
libgatk-fermilite-jni, libgenomicsdb-java, libgenomicsdb-dev, 
libgatk-native-bindings-java
 
 Suggests: libicb-utils-java
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/f2bf66831d23cd49593aae48c97e8f14962c2658

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/f2bf66831d23cd49593aae48c97e8f14962c2658
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add metaeuk and not xet classified packages

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
66037cc8 by Andreas Tille at 2023-02-02T20:52:47+01:00
Add metaeuk and not xet classified packages

- - - - -


3 changed files:

- tasks/bio
- tasks/imaging-dev
- tasks/psychology


Changes:

=
tasks/bio
=
@@ -599,6 +599,8 @@ Recommends: chromimpute
 
 Recommends: codonw
 
+Recommends: comet-ms
+
 Recommends: condetri
 
 Recommends: contrafold
@@ -901,6 +903,8 @@ Recommends: metastudent
 
 Suggests: metastudent-data, metastudent-data-2
 
+Recommends: metaeuk
+
 Recommends: microbegps
 
 Recommends: mindthegap


=
tasks/imaging-dev
=
@@ -153,3 +153,5 @@ Recommends: libxdf-dev
 Recommends: python3-torchvision
 
 Recommends: libsight-dev
+
+Recommends: python3-bioxtasraw


=
tasks/psychology
=
@@ -37,3 +37,5 @@ Recommends: orthanc-neuro
 
 Comment: Several related R packages are listed at CRAN:
  http://cran.r-project.org/web/views/Psychometrics.html
+
+Recommends: python3-bioxtasraw



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/66037cc85e5da4d50a4631f66c4cb2259a0f526c

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/66037cc85e5da4d50a4631f66c4cb2259a0f526c
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add libbio-db-seqfeature-perl

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
f4b62c36 by Andreas Tille at 2023-01-30T10:13:02+01:00
Add libbio-db-seqfeature-perl

- - - - -


1 changed file:

- tasks/bio-dev


Changes:

=
tasks/bio-dev
=
@@ -70,7 +70,7 @@ Recommends: libbio-graphics-perl, libbio-coordinate-perl
 Recommends: libbio-primerdesigner-perl
 
 Recommends: libbio-alignio-stockholm-perl, libbio-cluster-perl,
-libbio-db-biofetch-perl, libbio-db-embl-perl, libbio-db-hts-perl, 
libbio-db-ncbihelper-perl,
+libbio-db-biofetch-perl, libbio-db-embl-perl, libbio-db-hts-perl, 
libbio-db-ncbihelper-perl, libbio-db-seqfeature-perl,
 libbio-featureio-perl, libbio-tools-run-remoteblast-perl, 
libbio-variation-perl
 
 Recommends: libace-perl



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/f4b62c36feac832cdeb0617f5902c6709875a261

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/f4b62c36feac832cdeb0617f5902c6709875a261
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Add new packages

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
1a1e8b99 by Andreas Tille at 2023-01-17T20:00:22+01:00
Add new packages

- - - - -
46123031 by Andreas Tille at 2023-01-17T20:01:40+01:00
Add python3-cgelib

- - - - -


2 changed files:

- tasks/bio
- tasks/bio-dev


Changes:

=
tasks/bio
=
@@ -1123,6 +1123,8 @@ Recommends: pycorrfit
 
 Recommends: pyensembl
 
+Recommends: pyfastx
+
 Recommends: pyscanfcs
 
 Suggests: python3-alignlib


=
tasks/bio-dev
=
@@ -4,7 +4,7 @@ Description: Debian Med packages for development of 
bioinformatics applications
  This metapackage will install Debian packages which might be helpful
  for development of applications for biological research.
 
-Suggests: conda-package-handling
+Suggests: conda-package-handling, python3-conda-package-streaming
 
 Recommends: bioperl, bioperl-run, libncbi6-dev
 
@@ -678,3 +678,9 @@ Suggests: libterraces-dev
 Suggests: libbtllib-dev
 
 Suggests: libsavvy-dev
+
+Recommends: python3-pyfastx
+
+Recommends: python3-bioframe
+
+Suggests: python3-cgelib



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/34e2039de3df20241025fc6097a21b338275abd8...461230318bd03da09c0918937e00786c373ae9b8

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/34e2039de3df20241025fc6097a21b338275abd8...461230318bd03da09c0918937e00786c373ae9b8
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med] Pushed new tag debian/3.7.3

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/3.7.3 at Debian Blends Team / med

-- 
View it on GitLab: https://salsa.debian.org/blends-team/med/-/tree/debian/3.7.3
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Add muscle3 to tasks

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
bc3ae844 by Andreas Tille at 2023-01-12T09:09:38+01:00
Add muscle3 to tasks

- - - - -
34e2039d by Andreas Tille at 2023-01-12T09:09:38+01:00
Add libbiojava6-java

- - - - -


5 changed files:

- tasks/bio
- tasks/bio-dev
- tasks/bio-phylogeny
- tasks/cloud
- tasks/covid-19


Changes:

=
tasks/bio
=
@@ -48,7 +48,7 @@ Remark: Dead upstream
  
 Suggests: conda-package-handling
 
-Recommends: boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+Recommends: boxshade, gff2aplot, muscle, muscle3, sim4, sibsim4, tabix, 
wise
 
 Recommends: maqview
 


=
tasks/bio-dev
=
@@ -40,7 +40,7 @@ Recommends: python3-tinyalign
 
 Recommends: ruby-bio
 
-Recommends: libbiojava-java, libbiojava4-java, libbiojava5-java
+Recommends: libbiojava-java, libbiojava4-java, libbiojava5-java, 
libbiojava6-java
 
 Recommends: libgenome-dev, libmuscle-dev, libmems-dev
 


=
tasks/bio-phylogeny
=
@@ -29,7 +29,7 @@ X-Comment: treetool is removed from Debian because it is not 
maintained upstream
 
 X-Begin-Category: Sequence alignments and related programs.
 
-Recommends: muscle
+Recommends: muscle, muscle3
 
 Recommends: t-coffee
 


=
tasks/cloud
=
@@ -20,7 +20,7 @@ Recommends: amap-align, blast2, biosquid, boxshade, 
cassiopee, cdbfasta,
 cd-hit, clustalo, clustalw, conservation-code, dialign, dialign-tx,
 emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch,
 embassy-phylip, exonerate, gff2aplot, gff2ps, glam2, gmap, hmmer,
-jellyfish, kalign, mafft, mlv-smile, mummer, muscle, neobio, poa,
+jellyfish, kalign, mafft, mlv-smile, mummer, muscle, muscle3, 
neobio, poa,
 prank, probcons, proda, sibsim4, sigma-align, sim4, snap,
 squizz, t-coffee, wise
 X-End-Category: Sequence alignments and related programs.


=
tasks/covid-19
=
@@ -192,7 +192,7 @@ Recommends: porechop
 
 Recommends: changeo
 
-Recommends: muscle
+Recommends: muscle, muscle3
 
 Recommends: plasmidid
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/1392694949d36956a79743ef1caa7cd071f3f593...34e2039de3df20241025fc6097a21b338275abd8

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/1392694949d36956a79743ef1caa7cd071f3f593...34e2039de3df20241025fc6097a21b338275abd8
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] 2 commits: Fix typo

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
77d74d57 by Andreas Tille at 2023-01-03T16:10:12+01:00
Fix typo

- - - - -
b4ca1737 by Andreas Tille at 2023-01-03T16:15:16+01:00
Trim trailing whitespace

- - - - -


2 changed files:

- debian/changelog
- tasks/meteorology


Changes:

=
debian/changelog
=
@@ -28,8 +28,8 @@ debian-science (1.14.3) unstable; urgency=medium
 debian/compat.
   * Set debhelper-compat version in Build-Depends.
 
-  * start of automatic changelog entry * 
-  
+  * start of automatic changelog entry *
+
   * Changes in metapackage dependencies
-science-chemistry
 added:


=
tasks/meteorology
=
@@ -28,7 +28,7 @@ Why: Units translation utility
 Recommends: libemos-bin
 Why: Interpolation tool for ECMWF software
 
-Recommands: odc
+Recommends: odc
 Why: Tools for Observation database (ECMWF) handling
 
 Recommends: cdo
@@ -107,7 +107,7 @@ Recommends: python3-gsw
 
 Recommends: python3-iapws
 
-Recommands: python3-magics++
+Recommends: python3-magics++
 
 Recommends: python3-gsw
 



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/5457099d210f1827a3bc49814aeaa174d10c1707...b4ca173780028fbfe92ffa9d5f0253c5b60e7817

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/5457099d210f1827a3bc49814aeaa174d10c1707...b4ca173780028fbfe92ffa9d5f0253c5b60e7817
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] Mention some packages maintained by Debian Med team

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
a35176ee by Andreas Tille at 2022-11-28T15:08:35+01:00
Mention some packages maintained by Debian Med team

- - - - -


4 changed files:

- tasks/dataacquisition-dev
- tasks/machine-learning
- tasks/statistics
- tasks/workflow


Changes:

=
tasks/dataacquisition-dev
=
@@ -29,6 +29,8 @@ Recommends: python3-guidata
 
 Recommends: python3-segyio
 
+Recommends: python3-datacache
+
 Recommends: python3-aws-xray-sdk
 
 Recommends: python3-csvkit


=
tasks/machine-learning
=
@@ -157,3 +157,5 @@ Remark: Needed for chime which is COVID-19 relevant.
  Help for packaging is needed.
 
 Suggests: libxgboost-predictor-java
+
+Suggests: python3-imblearn


=
tasks/statistics
=
@@ -127,6 +127,10 @@ Suggests: r-cran-futile.logger, r-cran-futile.options
 
 Suggests: r-cran-igraph
 
+Suggests: python3-leidenalg
+
+Suggests: python3-pynndescent
+
 Suggests: r-cran-lambda.r
 
 Suggests: r-cran-magrittr
@@ -164,3 +168,5 @@ Recommends: python3-bayespy
 Suggests: node-shiny-server-client
 
 Recommends: libdistlib-java
+
+Suggests: libicb-utils-java


=
tasks/workflow
=
@@ -24,4 +24,6 @@ Recommends: toil
 
 Suggests: libbenchmark-tools
 
-Recommends: python3-wdlparse
\ No newline at end of file
+Recommends: python3-wdlparse
+
+Recommends: capsule-nextflow



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/a35176eea0d950825b1c1afee46dbd90752ec9a4

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/commit/a35176eea0d950825b1c1afee46dbd90752ec9a4
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] 2 commits: Update control: remove msxpertsuite

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
34c28546 by Filippo Rusconi at 2022-11-27T11:21:40+00:00
Update control: remove msxpertsuite
- - - - -
6f275fee by Andreas Tille at 2022-11-27T18:35:55+00:00
Merge branch master into master

Update control: remove msxpertsuite

See merge request blends-team/science!12
- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
@@ -214,7 +214,6 @@ Recommends: adun.app,
 katomic,
 libcdk-java,
 mopac7-bin,
-msxpertsuite,
 openbabel,
 openfoam,
 pdb2pqr,



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/1d5a1f22092ba9ca1e6e04888cf8ad49db6d9dc8...6f275feeec417e178db9171c7970ec7666954c62

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/1d5a1f22092ba9ca1e6e04888cf8ad49db6d9dc8...6f275feeec417e178db9171c7970ec7666954c62
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Update control: remove msxpertsuite

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
dffdecae by Filippo Rusconi at 2022-11-27T11:07:57+00:00
Update control: remove msxpertsuite
- - - - -
13926949 by Andreas Tille at 2022-11-27T18:34:54+00:00
Merge branch master into master

Update control: remove msxpertsuite

See merge request blends-team/med!7
- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
@@ -843,7 +843,6 @@ Suggests: acacia,
   mpsqed,
   mrs,
   msatfinder,
-  msxpertsuite,
   mugsy,
   mummergpu,
   mview,



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/b770685b381588e853261aa718e143715203e334...1392694949d36956a79743ef1caa7cd071f3f593

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/b770685b381588e853261aa718e143715203e334...1392694949d36956a79743ef1caa7cd071f3f593
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] 2 commits: The source package should be ignored

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
a99b8120 by Andreas Tille at 2022-10-12T09:27:09+02:00
The source package should be ignored

- - - - -
f753503c by Andreas Tille at 2022-11-24T13:09:01+01:00
Exclude some non-Med stuff

- - - - -


1 changed file:

- misc/sql/0-uncategorised.sh


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/79ec0c681ed257e4331d0d7547d612b68d847287...f753503c489d74d49d6061aa071eacc78a0c9f23

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/79ec0c681ed257e4331d0d7547d612b68d847287...f753503c489d74d49d6061aa071eacc78a0c9f23
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add some new packages

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
b770685b by Andreas Tille at 2022-11-16T08:16:24+01:00
Add some new packages

- - - - -


2 changed files:

- tasks/bio
- tasks/bio-dev


Changes:

=
tasks/bio
=
@@ -291,7 +291,7 @@ Recommends: mira-assembler
 
 Recommends: alien-hunter
 
-Recommends: seqan-apps
+Recommends: seqan-apps, seqan-needle, seqan-raptor
 
 Recommends: ncoils
 
@@ -470,6 +470,8 @@ Remark: Mentioned at http://www.renard.it/, developed in RKI
 
 Recommends: bio-vcf
 
+Recommends: btllib-tools
+
 Recommends: cnvkit
 
 Recommends: csb
@@ -1419,6 +1421,8 @@ Recommends: sap
 Remark: Precondition for T-Coffee
  see http://wiki.debian.org/DebianMed/TCoffee
 
+Recommends: savvy-util
+
 Recommends: scrappie
 
 Recommends: scrm
@@ -1442,18 +1446,6 @@ Recommends: seqsero
 
 Recommends: seqtk
 
-Recommends: sequenceconverter.app
-Remark: Formerly part of Debian as biococoa.app but removed
- The package was part of Debian under the name biococoa.app which is confusing
- because biococoa is actually a library for working with sequences under 
GNUstep.
- There was an attempt to reupload under the name sequenceconverter.app but
- ftpmaster did not accepted the package.  The reasons can be read here:
- 
http://lists.alioth.debian.org/pipermail/debian-med-packaging/2009-May/003430.html
- .
- Version 1.6 is the last upstream version that works with GNUstep.  If
- newer versions are needed to work under Linux try to convince upstream to
- support GNUstep.
-
 Recommends: seqwish
 
 Suggests: seqcluster


=
tasks/bio-dev
=
@@ -674,3 +674,7 @@ Suggests: python3-bioblend
 Recommends: python3-gtfparse
 
 Suggests: libterraces-dev
+
+Suggests: libbtllib-dev
+
+Suggests: libsavvy-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/b770685b381588e853261aa718e143715203e334

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/b770685b381588e853261aa718e143715203e334
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed from...

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
64b4ab4f by Andreas Tille at 2022-11-07T07:29:06+01:00
nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed from 
Debian thus removed from tasks

- - - - -


3 changed files:

- debian/changelog
- tasks/imaging
- tasks/imaging-dev


Changes:

=
debian/changelog
=
@@ -1,3 +1,10 @@
+debian-med (3.7.4) UNRELEASED; urgency=medium
+
+  * nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed
+from Debian thus removed from tasks
+
+ -- Andreas Tille   Mon, 07 Nov 2022 07:27:02 +0100
+
 debian-med (3.7.3) unstable; urgency=medium
 
   * Build-Depends-Indep: blends-dev (>= 0.7.5~)


=
tasks/imaging
=
@@ -41,8 +41,6 @@ Comment: removed from Debian and only available in Wheezy or 
snapshot.debian.org
 
 Recommends: gwyddion
 
-Recommends: nifti2dicom, qnifti2dicom
-
 Recommends: sofa-apps
 
 Recommends: python3-nipy


=
tasks/imaging-dev
=
@@ -150,8 +150,6 @@ Recommends: libcifti-dev
 
 Recommends: libxdf-dev
 
-Recommends: libsimpleitk1-dev, python3-simpleitk
-
 Recommends: python3-torchvision
 
 Recommends: libsight-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/64b4ab4f73a446a3ade1266654c246dbd84dadab

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/64b4ab4f73a446a3ade1266654c246dbd84dadab
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] Exclude some generic source package from check whether all is mentioned in Debian Med tasks

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
79ec0c68 by Andreas Tille at 2022-10-10T13:40:12+02:00
Exclude some generic source package from check whether all is mentioned in 
Debian Med tasks

- - - - -


1 changed file:

- misc/sql/0-uncategorised.sh


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/79ec0c681ed257e4331d0d7547d612b68d847287

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/79ec0c681ed257e4331d0d7547d612b68d847287
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] dicompyler removed from Debian thus from oncology task

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
5c1c7d45 by Andreas Tille at 2022-08-12T15:05:05+02:00
dicompyler removed from Debian thus from oncology task

- - - - -


2 changed files:

- debian/changelog
- tasks/oncology


Changes:

=
debian/changelog
=
@@ -2,6 +2,7 @@ debian-med (3.7.3) UNRELEASED; urgency=medium
 
   * Build-Depends-Indep: blends-dev (>= 0.7.5~)
 Closes: #1012341
+  * dicompyler removed from Debian thus from oncology task
 
  -- Andreas Tille   Fri, 03 Jun 2022 12:06:56 +0200
 


=
tasks/oncology
=
@@ -25,8 +25,6 @@ Pkg-Description: tools for radiotherapy treatment planning
  therapy, and to support RTP training for dosimetrists, physicists,
  radiation therapists, and radiation oncology residents.
 
-Recommends: dicompyler
-
 Suggests: python3-dicompylercore
 
 Recommends: simrisc



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/5c1c7d45c2f873d80048d103063585fab64391e9

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/5c1c7d45c2f873d80048d103063585fab64391e9
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Remove falcon (see Bug#1015978)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
091b9043 by Andreas Tille at 2022-08-05T09:37:56+02:00
Remove falcon (see Bug#1015978)

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -664,8 +664,6 @@ Recommends: exabayes
 
 Recommends: berkeley-express
 
-Recommends: falcon
-
 Recommends: fasta3
 
 Recommends: fastani



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/091b90438f72a38df30499cf74e8b1f7e828e634

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/091b90438f72a38df30499cf74e8b1f7e828e634
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Do not suggest vtk7 any more

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
9eede0fb by Andreas Tille at 2022-07-22T10:08:34+02:00
Do not suggest vtk7 any more

- - - - -


1 changed file:

- tasks/imaging-dev


Changes:

=
tasks/imaging-dev
=
@@ -6,8 +6,6 @@ Description: Debian Med image processing and visualization 
packages development
 
 Recommends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev, libvtk9-dev
 
-Suggests: libvtk7-dev
-
 Recommends: libnifti2-dev
 
 Recommends: libinsighttoolkit5-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/9eede0fb5a6563321547b28795d5f385d92a12a5

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/9eede0fb5a6563321547b28795d5f385d92a12a5
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science] Pushed new tag debian/1.14.3

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.14.3 at Debian Blends Team / science

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/tree/debian/1.14.3
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] 3 commits: Build-Depends-Indep: blends-dev (>= 0.7.5~)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
67743cde by Andreas Tille at 2022-06-06T07:06:59+02:00
Build-Depends-Indep: blends-dev (= 0.7.5~)

- - - - -
1204e02e by Andreas Tille at 2022-06-06T07:08:19+02:00
Build-Depends: debhelper-compat (= 13)

- - - - -
7517c46a by Andreas Tille at 2022-06-06T07:08:57+02:00
Standards-Version: 4.6.0

- - - - -


4 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/control.stub


Changes:

=
debian/changelog
=
@@ -1,6 +1,10 @@
 debian-science (1.14.3) UNRELEASED; urgency=medium
 
   * Re-enable packages that were portet to Python3
+  * Build-Depends-Indep: blends-dev (>= 0.7.5~)
+Closes: #1011982
+  * Build-Depends: debhelper-compat (= 13)
+  * Standards-Version: 4.6.0
 
  -- Andreas Tille   Thu, 04 Nov 2021 08:42:40 +0100
 


=
debian/compat deleted
=
@@ -1 +0,0 @@
-13


=
debian/control
=
@@ -5,9 +5,9 @@ Priority: optional
 Maintainer: Debian Science Team 

 Uploaders: Andreas Tille ,
Ole Streicher 
-Build-Depends-Indep: blends-dev (>= 0.7~)
-Build-Deoends: debhelper (>= 13)
-Standards-Version: 4.5.0
+Build-Depends-Indep: blends-dev (>= 0.7.5~)
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/science
 Vcs-Git: https://salsa.debian.org/blends-team/science.git
 Homepage: https://wiki.debian.org/DebianScience/


=
debian/control.stub
=
@@ -4,9 +4,9 @@ Priority: optional
 Maintainer: Debian Science Team 

 Uploaders: Andreas Tille ,
Ole Streicher 
-Build-Depends-Indep: blends-dev (>= 0.7~)
-Build-Deoends: debhelper (>= 13)
-Standards-Version: 4.5.0
+Build-Depends-Indep: blends-dev (>= 0.7.5~)
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/science
 Vcs-Git: https://salsa.debian.org/blends-team/science.git
 Homepage: https://wiki.debian.org/DebianScience/



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/af4593682d3f7c40e81ec9481ecebaee4bcea6d8...7517c46ae7db835b85e68a27a5fd5615e09b250a

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/af4593682d3f7c40e81ec9481ecebaee4bcea6d8...7517c46ae7db835b85e68a27a5fd5615e09b250a
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 3 commits: Add "ubuntu devel", an alias for the latest development release

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
7691ddee by Gianfranco Costamagna at 2022-06-06T09:32:16+02:00
Add ubuntu devel, an alias for the latest development release

- - - - -
374f9a60 by Gianfranco Costamagna at 2022-06-06T09:32:58+02:00
Update changelog

- - - - -
b643bb0b by Andreas Tille at 2022-06-06T08:29:43+00:00
Merge branch master into master

add ubuntu devel

See merge request blends-team/blends!13
- - - - -


2 changed files:

- debian/changelog
- + sources.list.devel


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+blends (0.7.6) UNRELEASED; urgency=medium
+
+  * Add "ubuntu devel", an alias for the latest development release
+
+ -- Gianfranco Costamagna   Mon, 06 Jun 2022 
09:32:29 +0200
+
 blends (0.7.5) unstable; urgency=medium
 
   [ Andreas Tille ]


=
sources.list.devel
=
@@ -0,0 +1 @@
+deb http://archive.ubuntu.com/ubuntu/ devel main universe



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/059737eeecd4b4f1890e15bb83eb5afacd788a6f...b643bb0b41a5de3c3f1e002e360b5a48d486b0b7

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/059737eeecd4b4f1890e15bb83eb5afacd788a6f...b643bb0b41a5de3c3f1e002e360b5a48d486b0b7
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Build-Depends-Indep: blends-dev (>= 0.7.5~)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
de82acac by Andreas Tille at 2022-06-05T08:25:44+02:00
Build-Depends-Indep: blends-dev (= 0.7.5~)

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/control.stub


Changes:

=
debian/changelog
=
@@ -1,6 +1,7 @@
 debian-med (3.7.3) UNRELEASED; urgency=medium
 
-  * 
+  * Build-Depends-Indep: blends-dev (>= 0.7.5~)
+Closes: #1012341
 
  -- Andreas Tille   Fri, 03 Jun 2022 12:06:56 +0200
 


=
debian/control
=
@@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team 

 Section: misc
 Priority: optional
-Build-Depends-Indep: blends-dev (>= 0.7.2~),
+Build-Depends-Indep: blends-dev (>= 0.7.5~),
 Build-Depends: debhelper-compat (= 13)
 Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/med


=
debian/control.stub
=
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team 

 Section: misc
 Priority: optional
-Build-Depends-Indep: blends-dev (>= 0.7.2~),
+Build-Depends-Indep: blends-dev (>= 0.7.5~),
 Build-Depends: debhelper-compat (= 13)
 Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/med



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/de82acac21bd2fe8085227723d4ad3b3e0974bb4

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/de82acac21bd2fe8085227723d4ad3b3e0974bb4
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 2 commits: Add missing semikolon in templates/apt.conf (preventing bugs like #1012341)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
fb24cd3e by Andreas Tille at 2022-06-05T07:59:21+02:00
Add missing semikolon in templates/apt.conf (preventing bugs like #1012341)

- - - - -
059737ee by Andreas Tille at 2022-06-05T08:04:41+02:00
Upload to unstable

- - - - -


2 changed files:

- debian/changelog
- templates/apt.conf


Changes:

=
debian/changelog
=
@@ -1,8 +1,9 @@
-blends (0.7.5) UNRELEASED; urgency=medium
+blends (0.7.5) unstable; urgency=medium
 
   [ Andreas Tille ]
   * Add Homepage
 Closes: #999579
+  * Add missing semikolon in templates/apt.conf (preventing bugs like #1012341)
 
   [ Stefan Kropp ]
   * Fixed some links (alioth)
@@ -13,7 +14,7 @@ blends (0.7.5) UNRELEASED; urgency=medium
   [ Daniele Forsi ]
   * Fix spelling errors found with codespell
 
- -- Gianfranco Costamagna   Tue, 28 Dec 2021 
10:24:22 +0100
+ -- Andreas Tille   Sun, 05 Jun 2022 07:59:36 +0200
 
 blends (0.7.4) unstable; urgency=medium
 


=
templates/apt.conf
=
@@ -4,4 +4,4 @@
 
 DPkg {
Post-Invoke {"test -f /var/run/#BLEND#-config.usermenu && if [ -x 
/usr/sbin/blend-update-usermenus ] ; then /usr/sbin/blend-update-usermenus 
#BLEND# ; fi ; rm -f /var/run/#BLEND#-config.usermenu";};
-}
+};



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/2148a25e502aed914b026b9d98af410bd240c468...059737eeecd4b4f1890e15bb83eb5afacd788a6f

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/2148a25e502aed914b026b9d98af410bd240c468...059737eeecd4b4f1890e15bb83eb5afacd788a6f
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends] Pushed new tag debian/0.7.5

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/0.7.5 at Debian Blends Team / blends

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/tree/debian/0.7.5
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Create new changelog entry

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
e29ca0d0 by Andreas Tille at 2022-06-03T12:07:05+02:00
Create new changelog entry

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+debian-med (3.7.3) UNRELEASED; urgency=medium
+
+  * 
+
+ -- Andreas Tille   Fri, 03 Jun 2022 12:06:56 +0200
+
 debian-med (3.7.2) unstable; urgency=medium
 
   * opensurgsim is removed from Debian



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e29ca0d09af4a5e2d0f113888edc07656fc8495f

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/e29ca0d09af4a5e2d0f113888edc07656fc8495f
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med] Pushed new tag debian/3.7.2

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/3.7.2 at Debian Blends Team / med

-- 
View it on GitLab: https://salsa.debian.org/blends-team/med/-/tree/debian/3.7.2
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add lamassemble and dnarrange

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
4fb1feef by Andreas Tille at 2022-05-31T16:12:56+02:00
Add lamassemble and dnarrange

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -638,6 +638,8 @@ Recommends: dendroscope
 
 Recommends: diann
 
+Recommends: dnarrange
+
 Recommends: drop-seq-tools
 
 Recommends: dwgsim
@@ -815,6 +817,8 @@ Recommends: kraken, kraken2
 Recommends: lagan
 X-Category: Comparative genomics
 
+Recommends: lamassemble
+
 Recommends: lambda-align, lambda-align2
 
 Recommends: lastz



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/4fb1feeffee10388ddacc0a34cdfecebbe2bca3b

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/4fb1feeffee10388ddacc0a34cdfecebbe2bca3b
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add r-cran-prevalence

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
282985ae by Andreas Tille at 2022-05-24T14:02:38+02:00
Add r-cran-prevalence

- - - - -


1 changed file:

- tasks/epi


Changes:

=
tasks/epi
=
@@ -25,8 +25,9 @@ Recommends: r-cran-epi
 
 Recommends: r-cran-diagnosismed, r-cran-epicalc, r-cran-epir
 
+Recommends: r-cran-prevalence
+
 Recommends: r-cran-seroincidence
-X-Comment: Needs to wait for processing of r-cran-knitr
 
 Suggests: r-cran-cmprsk
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/282985ae80efbc55705a90b26b0007f8e94d4e07

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/282985ae80efbc55705a90b26b0007f8e94d4e07
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Recommends: provean

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
3cc8ceb8 by Andreas Tille at 2022-05-18T11:54:20+02:00
Recommends: provean

- - - - -
189c132e by Andreas Tille at 2022-05-18T11:56:00+02:00
opensurgsim is removed from Debian

- - - - -


3 changed files:

- debian/changelog
- tasks/bio
- tasks/imaging-dev


Changes:

=
debian/changelog
=
@@ -1,6 +1,6 @@
 debian-med (3.7.2) UNRELEASED; urgency=medium
 
-  * 
+  * opensurgsim is removed from Debian
 
  -- Andreas Tille   Tue, 18 Jan 2022 16:28:04 +0100
 


=
tasks/bio
=
@@ -1091,6 +1091,8 @@ Recommends: proteinortho
 
 Recommends: prottest
 
+Recommends: provean
+
 Recommends: psortb
 
 Recommends: pscan-tfbs, pscan-chip


=
tasks/imaging-dev
=
@@ -24,8 +24,6 @@ Recommends: python3-gdcm
 
 Suggests: libics-dev
 
-Recommends: libopensurgsim-dev
-
 Recommends: libmaxflow-dev
 
 Suggests: liblimereg-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/4fc5c292644544d86002d2c3c695f30409573580...189c132e11569dbe88cf09661363830c1164baf7

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/4fc5c292644544d86002d2c3c695f30409573580...189c132e11569dbe88cf09661363830c1164baf7
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/imaging][master] Add fotoxx to imageorganizer

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / imaging


Commits:
36c81ad3 by Andreas Tille at 2022-02-25T18:12:40+01:00
Add fotoxx to imageorganizer

- - - - -


1 changed file:

- tasks/imageorganizer


Changes:

=
tasks/imageorganizer
=
@@ -26,6 +26,8 @@ Depends: gallery-uploader
 
 Depends: f-spot
 
+Depends: fotoxx
+
 Depends: imgseek
 
 Depends: shotwell



View it on GitLab: 
https://salsa.debian.org/blends-team/imaging/-/commit/36c81ad34bc2e2f5818650e0662747bb15354ef3

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/imaging/-/commit/36c81ad34bc2e2f5818650e0662747bb15354ef3
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add ntcard

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
d424cf5f by Andreas Tille at 2022-02-20T21:27:54+01:00
Add ntcard

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -964,6 +964,8 @@ Recommends: ngmlr
 
 Recommends: ngsqctoolkit
 
+Recommends: ntcard
+
 Recommends: nw-align
 
 Recommends: oases



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/d424cf5f92d90605c8a7e422e3786dbb4e810dc7

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/d424cf5f92d90605c8a7e422e3786dbb4e810dc7
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add twopaco

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
bef72108 by Andreas Tille at 2022-02-20T14:51:31+01:00
Add twopaco

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -874,6 +874,8 @@ Recommends: mecat2
 
 Recommends: medaka
 
+Recommends: megan-ce
+
 Recommends: meme
 License: non-free for commercial purpose 
(http://meme.nbcr.net/meme/COPYRIGHT.html)
 
@@ -1562,6 +1564,8 @@ Recommends: trf
 
 Recommends: trinityrnaseq
 
+Recommends: twopaco
+
 Recommends: uc-echo
 X-Category: NGS
 
@@ -2788,8 +2792,6 @@ Pkg-Description: JCVI Metagenomics Reports
  at various functional and taxonomic levels applying statistical tests as
  well as hierarchical clustering, multidimensional scaling and heatmaps.
 
-Recommends: megan-ce
-
 Recommends: arachne
 Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
 License: free



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/bef72108aa175b1f1221dc624899e09c92479cd5

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/bef72108aa175b1f1221dc624899e09c92479cd5
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] No need to specify additional information for accepted package megan-ce

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
66967ab7 by Andreas Tille at 2022-02-19T07:37:51+01:00
No need to specify additional information for accepted package megan-ce

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -2788,19 +2788,7 @@ Pkg-Description: JCVI Metagenomics Reports
  at various functional and taxonomic levels applying statistical tests as
  well as hierarchical clustering, multidimensional scaling and heatmaps.
 
-
 Recommends: megan-ce
-License: Registriation required
-Homepage: http://www-ab.informatik.uni-tuebingen.de/software/megan
-Pkg-Description: MEtaGenome ANalyzer
- In metagenomics, the aim is to understand the composition and operation
- of complex microbial consortia in environmental samples through
- sequencing and analysis of their DNA. Similarly, metatranscriptomics and
- metaproteomics target the RNA and proteins obtained from such samples.
- Technological advances in next-generation sequencing methods are fueling
- a rapid increase in the number and scope of environmental sequencing
- projects. In consequence, there is a dramatic increase in the volume of
- sequence data to be analyzed.
 
 Recommends: arachne
 Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/66967ab772e7e9a0a18811ed71892ff5ba4ad86b

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/66967ab772e7e9a0a18811ed71892ff5ba4ad86b
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Fix several names and remove packages that will probably never be touched

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
b3de1805 by Andreas Tille at 2022-02-18T11:44:48+01:00
Fix several names and remove packages that will probably never be touched

- - - - -


5 changed files:

- tasks/bio
- tasks/bio-dev
- tasks/covid-19
- tasks/imaging
- tasks/imaging-dev


Changes:

=
tasks/bio
=
@@ -868,7 +868,7 @@ X-Importance: efficient
 
 Recommends: mauve-aligner
 
-Suggests: mcaller
+Recommends: mcaller
 
 Recommends: mecat2
 


=
tasks/bio-dev
=
@@ -24,9 +24,7 @@ Recommends: python3-biopython
 
 Suggests: python3-biopython-sql, python-biopython-doc
 
-Suggests: python3-cogent3
-
-Suggests: python3-mcaller
+Recommends: python3-cogent3
 
 Suggests: python3-joypy
 


=
tasks/covid-19
=
@@ -103,8 +103,7 @@ Recommends: bedtools
 
 Recommends: multiqc
 
-Recommends: artic
-Homepage: 
https://github.com/nf-core/artic/blob/dev/bin/scrape_software_versions.py
+Recommends: nf-core-artic
 
 Recommends: viralrecon
 Homepage: 
https://github.com/nf-core/viralrecon/blob/dev/bin/scrape_software_versions.py
@@ -119,7 +118,7 @@ Recommends: ivar
 
 Recommends: varscan
 
-Recommends: snpeff, snpsift
+Recommends: snpeff
 
 Recommends: bcftools
 


=
tasks/imaging
=
@@ -43,9 +43,6 @@ Recommends: nifti2dicom, qnifti2dicom
 
 Recommends: sofa-apps
 
-Recommends: python3-mvpa2
-Why: Suggested by maintainer Michael Hanke 
-
 Recommends: python3-nipy
 Why: Although listed in -dev task, it also has a strong focus on interactive
  data analysis.


=
tasks/imaging-dev
=
@@ -30,9 +30,6 @@ Recommends: libmaxflow-dev
 
 Suggests: liblimereg-dev
 
-Recommends: python3-mvpa2
-Why: Suggested by maintainer Michael Hanke 
-
 Recommends: python3-nipy
 
 Recommends: python3-nipype
@@ -43,7 +40,7 @@ Recommends: libvia-dev
 
 Recommends: odin
 
-Recommends: libcv-dev
+Recommends: libopencv-dev
 
 Recommends: libteem-dev
 
@@ -157,6 +154,6 @@ Recommends: libxdf-dev
 
 Recommends: libsimpleitk1-dev, python3-simpleitk
 
-Recommends: pytorch-vision
+Recommends: python3-torchvision
 
 Recommends: libsight-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/b3de1805c50daae9e5d82f51e0ab0887d7402ba0

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/b3de1805c50daae9e5d82f51e0ab0887d7402ba0
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add rockhopper

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
95662702 by Andreas Tille at 2022-02-16T14:34:44+01:00
Add rockhopper

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -1367,6 +1367,8 @@ Recommends: roadtrips
 
 Recommends: roary
 
+Recommends: rockhopper
+
 Recommends: roguenarok
 
 Recommends: rosa



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/95662702f5c0b16d39e61d6e25b1b813072ebc2a

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/95662702f5c0b16d39e61d6e25b1b813072ebc2a
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: alphabeitc sorting

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
38d86f5e by Andreas Tille at 2022-01-20T14:51:31+01:00
alphabeitc sorting

- - - - -
b0988400 by Andreas Tille at 2022-01-20T14:52:23+01:00
Add libpwiz (Proteowizard) for Proteomic data anylyses

- - - - -


2 changed files:

- tasks/bio
- tasks/bio-dev


Changes:

=
tasks/bio
=
@@ -792,10 +792,16 @@ Recommends: jbrowse
 
 Recommends: jmodeltest
 
+Recommends: kallisto
+
 Recommends: kaptive, kleborate
 
 Recommends: kempbasu
 
+Recommends: khmer
+
+Recommends: kmer
+
 Recommends: kineticstools
 
 Recommends: kissplice
@@ -823,16 +829,13 @@ Recommends: ltrsift
 
 Recommends: lofreq
 
-Recommends: kallisto
-
-Recommends: khmer
-
-Recommends: kmer
 
 Recommends: radiant
 
 Recommends: lefse
 
+Recommends: libpwiz-tools
+
 Recommends: lighter
 
 Recommends: lumpy-sv


=
tasks/bio-dev
=
@@ -333,6 +333,8 @@ Remark: This is a part of Bioconductor project
 
 Recommends: libffindex0-dev
 
+Recommends: libpwiz-dev
+
 Recommends: librostlab3-dev
 
 Suggests: librostlab-doc



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/eed508f407762e674cf81caf4cf0dd50ab4ced72...b098840062c65281c21aade8fc3477599c6c8755

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/eed508f407762e674cf81caf4cf0dd50ab4ced72...b098840062c65281c21aade8fc3477599c6c8755
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Add diann

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
eed508f4 by Andreas Tille at 2022-01-18T16:29:04+01:00
Add diann

- - - - -


2 changed files:

- debian/changelog
- tasks/bio


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+debian-med (3.7.2) UNRELEASED; urgency=medium
+
+  * 
+
+ -- Andreas Tille   Tue, 18 Jan 2022 16:28:04 +0100
+
 debian-med (3.7.1) unstable; urgency=medium
 
   * Remove libbiod-dev


=
tasks/bio
=
@@ -636,6 +636,8 @@ Remark: There is no intend to keep continue the existing 
packaging since
 
 Recommends: dendroscope
 
+Recommends: diann
+
 Recommends: drop-seq-tools
 
 Recommends: dwgsim



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/eed508f407762e674cf81caf4cf0dd50ab4ced72

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/eed508f407762e674cf81caf4cf0dd50ab4ced72
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med] Pushed new tag debian/3.7.1

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/3.7.1 at Debian Blends Team / med

-- 
View it on GitLab: https://salsa.debian.org/blends-team/med/-/tree/debian/3.7.1
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Replace libinsighttoolkit4-dev by libinsighttoolkit5-dev

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
9bccbe30 by Andreas Tille at 2022-01-12T15:20:07+01:00
Replace libinsighttoolkit4-dev by libinsighttoolkit5-dev

- - - - -
e3424cb2 by Andreas Tille at 2022-01-12T15:21:37+01:00
Do not suggest vtk6-dev any more, Recommend libvtk9-dev, Suggests: libvtk7-dev

- - - - -


1 changed file:

- tasks/imaging-dev


Changes:

=
tasks/imaging-dev
=
@@ -4,13 +4,13 @@ Description: Debian Med image processing and visualization 
packages development
  for developing applications for medical image processing and
  visualization.
 
-Recommends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev, libvtk7-dev
+Recommends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev, libvtk9-dev
 
-Suggests: libvtk6-dev
+Suggests: libvtk7-dev
 
 Recommends: libnifti2-dev
 
-Recommends: libinsighttoolkit4-dev
+Recommends: libinsighttoolkit5-dev
 
 Suggests: libnifti-doc
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/f5c187e70d6645b2fa51d0e952aa0e678ae17214...e3424cb2671cf7102de4ca19bd2e5b7100c837a5

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/f5c187e70d6645b2fa51d0e952aa0e678ae17214...e3424cb2671cf7102de4ca19bd2e5b7100c837a5
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 4 commits: Remove r-cran-rsgcc (see #1002794)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
e1fa888b by Andreas Tille at 2021-12-30T16:32:06+01:00
Remove r-cran-rsgcc (see #1002794)

- - - - -
512e5a47 by Andreas Tille at 2021-12-30T16:32:36+01:00
Standards-Version: 4.6.0

- - - - -
9bb691ef by Andreas Tille at 2021-12-30T16:33:05+01:00
Just use version 3.7.1

- - - - -
f5c187e7 by Andreas Tille at 2021-12-30T16:38:07+01:00
Remove r-other-hms-dbmi-spp since it is r-cran-spp

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/control.stub
- tasks/bio
- tasks/bio-dev


Changes:

=
debian/changelog
=
@@ -1,6 +1,9 @@
-debian-med (3.8) UNRELEASED; urgency=medium
+debian-med (3.7.1) unstable; urgency=medium
 
   * Remove libbiod-dev
+  * Remove r-cran-rsgcc (see #1002794)
+  * Remove r-other-hms-dbmi-spp since it is r-cran-spp
+  * Standards-Version: 4.6.0
 
  -- Andreas Tille   Tue, 23 Nov 2021 08:04:35 +0100
 


=
debian/control
=
@@ -6,7 +6,7 @@ Section: misc
 Priority: optional
 Build-Depends-Indep: blends-dev (>= 0.7.2~),
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 


=
debian/control.stub
=
@@ -5,7 +5,7 @@ Section: misc
 Priority: optional
 Build-Depends-Indep: blends-dev (>= 0.7.2~),
 Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 


=
tasks/bio
=
@@ -1310,8 +1310,6 @@ Recommends: r-cran-pscbs
 
 Suggests: r-cran-rcpphnsw
 
-Suggests: r-cran-rsgcc
-
 Suggests: r-cran-sctransform
 
 Recommends: r-cran-seurat


=
tasks/bio-dev
=
@@ -290,8 +290,6 @@ Suggests: r-cran-rcpphnsw
 
 Recommends: r-cran-rentrez
 
-Suggests: r-cran-rsgcc
-
 Recommends: r-cran-rncl, r-cran-rnexml
 
 Suggests: r-cran-robustrankaggreg
@@ -324,8 +322,6 @@ Suggests: r-cran-venndiagram
 
 Recommends: r-cran-webgestaltr
 
-Recommends: r-other-hms-dbmi-spp
-
 Recommends: r-other-apmswapp
 
 Suggests: ruby-rgfa



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/771f16c10023eb9139a3e573a031dc8b389876a6...f5c187e70d6645b2fa51d0e952aa0e678ae17214

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/771f16c10023eb9139a3e573a031dc8b389876a6...f5c187e70d6645b2fa51d0e952aa0e678ae17214
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] Ignore subprojects covering backports only

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
e59b595b by Andreas Tille at 2021-12-29T13:31:10+01:00
Ignore subprojects covering backports only

- - - - -


1 changed file:

- misc/machine_readable/fetch-machine-readable_salsa.py


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/e59b595b5d8ad82396478995754a0ed5ddbd1676

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/e59b595b5d8ad82396478995754a0ed5ddbd1676
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/science][master] 2 commits: Update robotics-dev and simulation for Gazebo and Ignition

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / science


Commits:
6cb9853c by Jose Luis Rivero at 2021-12-20T17:14:57+00:00
Update robotics-dev and simulation for Gazebo and Ignition

Update package names for Gazebo simulator and other robotics libraries:
 * Some packages now use an unversioned -dev
 * Kido project was renamed to DART
 * Add new ignition libraries available

- - - - -
19f203e0 by Andreas Tille at 2021-12-28T06:08:59+00:00
Merge branch jrivero/update_simulation_dec_2021 into master

Update robotics-dev and simulation for Gazebo and Ignition

See merge request blends-team/science!8
- - - - -


3 changed files:

- debian/control
- tasks/robotics-dev
- tasks/simulations


Changes:

=
debian/control
=
@@ -2210,7 +2210,7 @@ Depends: ${misc:Depends},
  science-config (= ${source:Version}),
  science-tasks (= ${source:Version})
 Recommends: aseba,
-gazebo9,
+gazebo,
 joint-state-publisher,
 liburdfdom-tools,
 octomap-tools,
@@ -2257,20 +2257,23 @@ Architecture: all
 Depends: ${misc:Depends},
  science-config (= ${source:Version}),
  science-tasks (= ${source:Version})
-Recommends: libapriltag-dev,
+Recommends: ignition-tools,
+libapriltag-dev,
 libccd-dev,
 libcomedi-dev,
 libconsole-bridge-dev,
 libfcl-dev,
-libgazebo9-dev,
+libgazebo-dev,
 libignition-cmake-dev,
 libignition-common-dev,
-libignition-fuel-tools1-dev,
-libignition-math4-dev,
+libignition-fuel-tools-dev,
+libignition-math-dev,
 libignition-msgs-dev,
+libignition-plugin-dev,
 libignition-transport-dev,
+libignition-utils-dev,
 libkdl-parser-dev,
-libkido-dev,
+libdart-dev,
 liboctomap-dev,
 libode-dev,
 libompl-dev,
@@ -2280,6 +2283,7 @@ Recommends: libapriltag-dev,
 libpcl-dev,
 librobottestingframework-dev,
 librosconsole-dev,
+libsdformat-dev,
 libsimbody-dev,
 libslicot-dev,
 liburdfdom-dev,
@@ -2297,9 +2301,7 @@ Recommends: libapriltag-dev,
 ros-simulators-dev
 Suggests: libcnoid-dev,
   libcv-dev,
-  libignition-math2-dev,
   libroboptim-core-dev,
-  libsdformat4-dev,
   visp-images-data
 Description: Debian Robotics development packages
  This metapackage is part of the Debian Pure Blend "Debian Science"
@@ -2315,7 +2317,7 @@ Depends: ${misc:Depends},
 Recommends: calculix-ccx,
 calculix-cgx,
 esys-particle,
-gazebo9,
+gazebo,
 getdp,
 lammps,
 libceres-dev,


=
tasks/robotics-dev
=
@@ -27,7 +27,7 @@ Recommends: liburdfdom-dev, liburdfdom-headers-dev
 
 Recommends: libslicot-dev
 
-Recommends: libsdformat4-dev
+Recommends: libsdformat-dev
 
 Recommends: libconsole-bridge-dev
 
@@ -35,23 +35,21 @@ Recommends: libcomedi-dev, python3-comedilib
 
 Recommends: libccd-dev
 
-Recommends: libgazebo9-dev
+Recommends: libgazebo-dev
 
 Recommends: libsimbody-dev
 
-Recommends: libignition-common-dev
-
-Recommends: libignition-cmake-dev
-
-Recommends: libignition-transport-dev
-
-Recommends: libignition-math2-dev, libignition-math4-dev
-
-Recommends: libignition-msgs-dev
-
-Recommends: libignition-fuel-tools1-dev
-
-Recommends: libkido-dev
+Recommends: libignition-cmake-dev,
+libignition-common-dev,
+libignition-fuel-tools-dev,
+libignition-math-dev,
+libignition-msgs-dev,
+libignition-plugin-dev,
+libignition-transport-dev,
+libignition-utils-dev,
+ignition-tools
+
+Recommends: libdart-dev
 
 Recommends: ros-desktop-full-dev,
  ros-desktop-dev,


=
tasks/simulations
=
@@ -41,7 +41,7 @@ Recommends: python3-woo
 
 Recommends: libceres-dev
 
-Recommends: gazebo9
+Recommends: gazebo
 
 Suggests: ceres-solver-doc
 
@@ -53,3 +53,5 @@ Suggests: libgismo-dev
 Recommends: libkim-api-v2-models
 
 Recommends: occt-draw, occt-misc
+
+Recommends: libdart-dev



View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/cac2fd811aa765e11ffa2d0bb876afa319f62262...19f203e0dd43399def247b6080afcdfcf8557328

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/science/-/compare/cac2fd811aa765e11ffa2d0bb876afa319f62262...19f203e0dd43399def247b6080afcdfcf8557328
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list

[Blends-commit] [Git][blends-team/blends][master] 2 commits: Drop cosmic/disco/eoan old Ubuntu releases, add focal and jammy

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
ed3e7c24 by Gianfranco Costamagna at 2021-12-27T22:40:19+01:00
Drop cosmic/disco/eoan old Ubuntu releases, add focal and jammy

- - - - -
fcae74a0 by Andreas Tille at 2021-12-27T21:50:56+00:00
Merge branch master into master

Drop cosmic/disco/eoan old Ubuntu releases, add focal and jammy

See merge request blends-team/blends!10
- - - - -


5 changed files:

- − sources.list.cosmic
- − sources.list.disco
- − sources.list.eoan
- + sources.list.focal
- + sources.list.jammy


Changes:

=
sources.list.cosmic deleted
=
@@ -1 +0,0 @@
-deb http://archive.ubuntu.com/ubuntu/ cosmic main universe


=
sources.list.disco deleted
=
@@ -1 +0,0 @@
-deb http://archive.ubuntu.com/ubuntu/ disco main universe


=
sources.list.eoan deleted
=
@@ -1 +0,0 @@
-deb http://archive.ubuntu.com/ubuntu/ eoan main universe


=
sources.list.focal
=
@@ -0,0 +1 @@
+deb http://archive.ubuntu.com/ubuntu/ focal main universe


=
sources.list.jammy
=
@@ -0,0 +1 @@
+deb http://archive.ubuntu.com/ubuntu/ jammy main universe



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/2b6a829475cc613f4e76f001c219a20a2f354505...fcae74a0d2eb050ef067c12f221ba2532734d7e9

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/2b6a829475cc613f4e76f001c219a20a2f354505...fcae74a0d2eb050ef067c12f221ba2532734d7e9
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] 2 commits: Fixed some links (alioth)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
702018d9 by Stefan Kropp at 2021-12-24T20:50:40+01:00
Fixed some links (alioth)

- - - - -
2b6a8294 by Andreas Tille at 2021-12-24T21:31:48+00:00
Merge branch master into master

Fixed some links (alioth)

See merge request blends-team/blends!9
- - - - -


4 changed files:

- debian/blends-common.README.Debian
- doc/en/00_titletoc.xml
- doc/en/09_todo.xml
- templates/README.Debian


Changes:

=
debian/blends-common.README.Debian
=
@@ -17,7 +17,7 @@ menu files which are provided by each single med-* 
metapackage in
 If you do not want to install the suggested blends-doc package you might read
 the online version at
 
-   http://blends.alioth.debian.org/blends/
+   http://blends.debian.org/blends/
 
 which is frequently updated.
 


=
doc/en/00_titletoc.xml
=
@@ -49,7 +49,7 @@


  You can find the source of this article 
- http://git.debian.org/?p=blends/blends.git;a=tree;f=doc/en;>in the Git 
repository at git.debian.org.
+ https://salsa.debian.org/blends-team/blends/-/tree/master/doc;>in the Git 
repository at salsa.debian.org.
  It is also available as Debian package 
blends-doc.

 
@@ -75,4 +75,4 @@
vitality and quality of Debian.
 
 
-
\ No newline at end of file
+


=
doc/en/09_todo.xml
=
@@ -149,7 +149,7 @@ up to date at any time.
Debian Package Tags
 
 
-http://debtags.alioth.debian.org/;>Debian
+http://debtags.debian.org/;>Debian
 Package Tags  is a work to add more metadata to Debian packages.
 At the beginning it could be seen as a way to allow to specify
 multiple sections (called "tags") per package where now only one can


=
templates/README.Debian
=
@@ -7,7 +7,7 @@ packages, you have to remove this package as well. The other 
packages won't be
 touched.
 
 There exists an comprehensive documentation about Debian Pure Blends
-which can be found at http://blends.alioth.debian.org/blends/.
+which can be found at http://blends.debian.org/blends/.
 
 The metapackages should always be installable on a Debian system.
 Thus no dependency on a non-available package (ie. a package available



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/406b34ddd681b23c5e6a8ced27db7fb0f77e4e9a...2b6a829475cc613f4e76f001c219a20a2f354505

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/compare/406b34ddd681b23c5e6a8ced27db7fb0f77e4e9a...2b6a829475cc613f4e76f001c219a20a2f354505
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior][master] 3 commits: Bump debhelper to 13

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / junior


Commits:
3c31467c by Andreas Tille at 2021-12-22T09:11:44+01:00
Bump debhelper to 13

- - - - -
6c27b303 by Andreas Tille at 2021-12-22T09:12:24+01:00
Upload to unstable

- - - - -
d7a392d4 by Andreas Tille at 2021-12-22T09:38:59+01:00
lintian-override for no-dh-sequencer

- - - - -


5 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/control.stub
- + debian/source/lintian-overrides


Changes:

=
debian/changelog
=
@@ -1,6 +1,6 @@
 debian-junior (1.30) unstable; urgency=low
 
-  * Team upload.
+  [ Stefan Kropp ]
   * Added myself to Uploader.
   * Changed iceweasel to firefox-esr
   * Downgraded 13 missing packages to Suggests
@@ -39,6 +39,10 @@ debian-junior (1.30) unstable; urgency=low
 removed:
   Recommends:  bloopsaphone
 
+  [ Andreas Tille ]
+  * Bump debhelper to 13
+  * lintian-override for no-dh-sequencer
+
  -- Stefan Kropp   Sat, 11 Dec 2021 13:58:13 +0100
 
 debian-junior (1.29) unstable; urgency=medium


=
debian/compat deleted
=
@@ -1,2 +0,0 @@
-11
-


=
debian/control
=
@@ -6,8 +6,8 @@ Maintainer: Debian Junior 
 Uploaders: Per Andersson ,
   Jonathan Carter ,
   Stefan Kropp 
-Build-Depends-Indep: debhelper (>= 11~),
- blends-dev (>= 0.7~)
+Build-Depends: debhelper-compat (= 13),
+Build-Depends-Indep: blends-dev (>= 0.7~)
 Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/junior
 Vcs-Git: https://salsa.debian.org/blends-team/junior.git


=
debian/control.stub
=
@@ -5,8 +5,8 @@ Maintainer: Debian Junior 
 Uploaders: Per Andersson ,
   Jonathan Carter ,
   Stefan Kropp 
-Build-Depends-Indep: debhelper (>= 11~),
- blends-dev (>= 0.7~)
+Build-Depends: debhelper-compat (= 13),
+Build-Depends-Indep: blends-dev (>= 0.7~)
 Standards-Version: 4.6.0 
 Vcs-Browser: https://salsa.debian.org/blends-team/junior
 Vcs-Git: https://salsa.debian.org/blends-team/junior.git


=
debian/source/lintian-overrides
=
@@ -0,0 +1,2 @@
+# the dh-sequencer is called in /usr/share/blends-dev/rules
+debian-junior source: no-dh-sequencer



View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/compare/7c38e192881b4ccb1e04a5ca1989dfbbca9ef319...d7a392d4ebc5b64b233e5a2067fcea18195d6025

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/compare/7c38e192881b4ccb1e04a5ca1989dfbbca9ef319...d7a392d4ebc5b64b233e5a2067fcea18195d6025
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/junior] Pushed new tag debian/1.30

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/1.30 at Debian Blends Team / junior

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/junior/-/tree/debian/1.30
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] If at all compclust should be python3-compclust

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
771f16c1 by Andreas Tille at 2021-12-08T17:36:25+01:00
If at all compclust should be python3-compclust

- - - - -


2 changed files:

- tasks/bio
- tasks/bio-dev


Changes:

=
tasks/bio
=
@@ -2652,10 +2652,6 @@ Pkg-Description: heuristic computer program to identify 
prophage regions within
  will facilitate future studies on the biology and evolution of these 
prophages by providing
  a level of microbial genome annotation that was previously void.
 
-Recommends: compclust
-X-Category: Genomics; Clustering analysis (+GUI)
-Pkg-URL: http://woldlab.caltech.edu/compclust/debian_install.shtml
-
 Recommends: treebuilder3d
 Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder
 License: GPL


=
tasks/bio-dev
=
@@ -649,3 +649,6 @@ Suggests: libsuma-dev
 Recommends: python3-scanpy
 
 Recommends: python3-cigar
+
+Recommends: python3-compclust
+X-Category: Genomics; Clustering analysis (+GUI)



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/771f16c10023eb9139a3e573a031dc8b389876a6

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/771f16c10023eb9139a3e573a031dc8b389876a6
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] 2 commits: Remove python3-hyphy (which is removed from Debian) and fix name of python3-pangolearn

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
d6e11f17 by Andreas Tille at 2021-11-17T14:24:56+01:00
Remove python3-hyphy (which is removed from Debian) and fix name of 
python3-pangolearn

- - - - -
6fa9629e by Andreas Tille at 2021-11-23T08:04:50+01:00
Remove libbiod-dev

- - - - -


3 changed files:

- debian/changelog
- tasks/bio-dev
- tasks/covid-19


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+debian-med (3.8) UNRELEASED; urgency=medium
+
+  * Remove libbiod-dev
+
+ -- Andreas Tille   Tue, 23 Nov 2021 08:04:35 +0100
+
 debian-med (3.7) unstable; urgency=medium
 
   * Re-render metapackages according the package pool in bullseye


=
tasks/bio-dev
=
@@ -448,8 +448,6 @@ Suggests: python3-networkx
 
 Recommends: python3-ruffus
 
-Recommends: python3-hyphy
-
 Recommends: python3-dendropy
 
 Recommends: python3-skbio
@@ -555,8 +553,6 @@ Recommends: python3-biomaj3
 
 Suggests: python3-pyflow
 
-Recommends: libbiod-dev
-
 Recommends: python3-ete3
 
 Recommends: python3-gfapy
@@ -630,7 +626,7 @@ Suggests: libbbhash-dev
 
 Recommends: python3-cooler, python3-pairix
 
-Recommends: pangolearn
+Recommends: python3-pangolearn
 
 Recommends: python3-pyranges
 


=
tasks/covid-19
=
@@ -28,7 +28,7 @@ Recommends: fieldbioinformatics
 
 Recommends: megahit
 
-Recommends: idseq-dag
+Recommends: python3-idseq-dag
 
 Recommends: nextstrain-ncov
 Remark: needs auspice



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/52bac3cf8fe5cd2a9bee07fb620e46a6da355cca...6fa9629e3ff50541f8c4f29f97d5c569e1312d09

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/compare/52bac3cf8fe5cd2a9bee07fb620e46a6da355cca...6fa9629e3ff50541f8c4f29f97d5c569e1312d09
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/debug][master] Debug issues with bbmap and idba

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / debug


Commits:
92af7ba7 by Andreas Tille at 2021-11-18T12:33:51+01:00
Debug issues with bbmap and idba

- - - - -


2 changed files:

- − tasks/covid-19
- tasks/debug


Changes:

=
tasks/covid-19 deleted
=
@@ -1,17 +0,0 @@
-Task: Covid-19
-Metapackage: false
-Description: This task exists only for tagging COVID-19 relevant cases
- The Debian Med team intends to take part at the
-  COVID-19 Biohackathon (April 5-11, 2020)
- This task was created only for the purpose to list relevant packages.
-
-Recommends: abacas
-
-Recommends: bwa
-
-Recommends: covtobed
-
-Recommends: lastz
-
-Recommends: acacia
-


=
tasks/debug
=
@@ -3,5 +3,5 @@ Description: Some unclassified problematic descriptions
  Here some new techniques are tested - currently the
  new database query method is tested
 
-Depends: seaview, tree-puzzle
-Remark: tree-puzzle is duplicated in QA
+Depends: bbmap, idba
+Remark: Some issues for these packages - possibly duplicated in return



View it on GitLab: 
https://salsa.debian.org/blends-team/debug/-/commit/92af7ba7d65f0423c1f14dc7786368b0472224ef

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/debug/-/commit/92af7ba7d65f0423c1f14dc7786368b0472224ef
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] Avoid capital letters in directory names

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
a8255672 by Andreas Tille at 2021-11-18T08:53:17+01:00
Avoid capital letters in directory names

- - - - -


1 changed file:

- misc/machine_readable/fetch-machine-readable_salsa.py


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/a8255672e6c82521247c185ee65e6d4c27af6c91

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/commit/a8255672e6c82521247c185ee65e6d4c27af6c91
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/website][master] 2 commits: Add some comment to declare basic usage

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / website


Commits:
a62d017d by Andreas Tille at 2021-11-17T17:36:45+01:00
Add some comment to declare basic usage

- - - - -
0b2f4e9f by Andreas Tille at 2021-11-17T17:38:00+01:00
Add Debian Math team

- - - - -


1 changed file:

- misc/machine_readable/fetch-machine-readable_salsa.py


View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/1df0611d5ce8aa372b7893fb98a654125d1cb9fb...0b2f4e9f55c46d9d96b74b69d91a0c7f2ac686c5

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/website/-/compare/1df0611d5ce8aa372b7893fb98a654125d1cb9fb...0b2f4e9f55c46d9d96b74b69d91a0c7f2ac686c5
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Recommends: r-cran-kernelheaping

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
52bac3cf by Andreas Tille at 2021-11-17T13:54:10+01:00
Recommends: r-cran-kernelheaping

- - - - -


2 changed files:

- tasks/covid-19
- tasks/epi


Changes:

=
tasks/covid-19
=
@@ -49,6 +49,8 @@ Suggests: r-bioc-rsubread
 
 Recommends: r-bioc-tcgabiolinks
 
+Recommends: r-cran-kernelheaping
+
 Recommends: r-cran-mediana
 
 Recommends: r-cran-spp


=
tasks/epi
=
@@ -32,6 +32,8 @@ Suggests: r-cran-cmprsk
 
 Recommends: r-cran-incidence, r-cran-epiestim
 
+Recommends: r-cran-kernelheaping
+
 Recommends: ushahidi
 
 Suggests: shiny-server



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/52bac3cf8fe5cd2a9bee07fb620e46a6da355cca

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/52bac3cf8fe5cd2a9bee07fb620e46a6da355cca
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/med][master] Fix names in metapackages

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
1a6beeae by Andreas Tille at 2021-11-14T09:56:44+01:00
Fix names in metapackages

- - - - -


1 changed file:

- tasks/bio


Changes:

=
tasks/bio
=
@@ -278,7 +278,8 @@ Recommends: staden-io-lib-utils
 
 Recommends: samtools, bedtools, datamash
 
-Recommends: gassst
+#Recommends: gassst
+# Removed in bug #689957
 
 Recommends: hinge
 
@@ -562,7 +563,8 @@ Recommends: cassiopee
 
 Recommends: cat-bat
 
-Recommends: ccs
+# Recommends: ccs
+# Removed https://tracker.debian.org/news/592502/ccs-removed-from-testing/
 
 Recommends: cdbfasta
 
@@ -748,7 +750,7 @@ Recommends: gwama
 
 Recommends: gubbins
 
-Recommends: haploview-cran-amap
+Recommends: haploview
 
 Recommends: harvest-tools
 
@@ -1096,7 +1098,7 @@ Recommends: pyscanfcs
 
 Suggests: python3-alignlib
 
-Recommends: python3-cogent
+Recommends: python3-cogent3
 
 Suggests: python3-cgecore 
 
@@ -1231,7 +1233,10 @@ Recommends: r-bioc-multiassayexperiment
 
 Recommends: r-bioc-mutationalpatterns
 
-Suggests: r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db, r-bioc-org.rn.eg.db, 
r-bioc-org.ce.eg.db
+Suggests: r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db
+
+# No metadata for these packages
+#, r-bioc-org.rn.eg.db, r-bioc-org.ce.eg.db
 
 Recommends: r-bioc-pcamethods
 
@@ -1327,7 +1332,7 @@ Recommends: r-cran-webgestaltr
 
 Recommends: r-other-apmswapp
 
-Recommends: r-other-hms-dbmi-spp
+Recommends: r-cran-spp
 
 Recommends: r-cran-wgcna
 
@@ -1610,7 +1615,7 @@ Recommends: dnaclust
 
 Recommends: r-cran-tcr, r-cran-tigger, r-cran-alakazam, r-cran-shazam, igor, 
r-cran-sdmtools, presto, changeo
 
-Recommends: ncbi-igblast
+Recommends: igblast
 
 Recommends: pigx-rnaseq, pigx-scrnaseq
 



View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/1a6beeae290b85bcdf7b3dc8ca4348c18407b705

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/med/-/commit/1a6beeae290b85bcdf7b3dc8ca4348c18407b705
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit

[Blends-commit] [Git][blends-team/blends][master] Add Homepage

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / blends


Commits:
406b34dd by Andreas Tille at 2021-11-13T18:21:42+01:00
Add Homepage

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
@@ -1,3 +1,10 @@
+blends (0.7.5) UNRELEASED; urgency=medium
+
+  * Add Homepage
+Closes: #999579
+
+ -- Andreas Tille   Sat, 13 Nov 2021 18:21:08 +0100
+
 blends (0.7.4) unstable; urgency=medium
 
   [ Gianfranco Costamagna ]


=
debian/control
=
@@ -20,6 +20,7 @@ Build-Depends-Indep: dblatex,
 Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/blends-team/blends
 Vcs-Git: https://salsa.debian.org/blends-team/blends.git
+Homepage: https://www.debian.org/blends/
 
 Package: blends-dev
 Architecture: all



View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/commit/406b34ddd681b23c5e6a8ced27db7fb0f77e4e9a

-- 
View it on GitLab: 
https://salsa.debian.org/blends-team/blends/-/commit/406b34ddd681b23c5e6a8ced27db7fb0f77e4e9a
You're receiving this email because of your account on salsa.debian.org.


___
Blends-commit mailing list
Blends-commit@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit