RE:Packaging python-xrayutilities

2019-03-21 Thread MARIE Alexandre
Hello,

I'm still working on the package python-xrayutilities for debian.

I've come to a point where the package can be built but when generating the doc,
lintian comes with a bunch of privacy-generic-breach tags like this :

W: python-xrayutilities-doc: privacy-breach-generic 
usr/share/doc/python-xrayutilities/html/_modules/index.html 

RE:Packaging python-xrayutilities

2019-03-21 Thread MARIE Alexandre
> Hi,
> 
> I didn't have time to look into issue, but may be looking on how other
> people solve similar problems will give you a hint:
>
>  https://codesearch.debian.net/search?q=path%3Adebian%2Frules+mathjax
>
> Best,
> Alex

Hello,
Thanks for the hint, 
this is where I am looking to deal with the issue, 
but there are things that I don't understand,
thus I'm asking it here.

Cheers,

Alex



RE:Packaging python-xrayutilities

2019-03-21 Thread MARIE Alexandre
> Is there really the leading tab only on the second line?

In fact I am trying to figure out where should I install the doc, and how could 
I avoid the lintian tag : privacy-breach-generic.

> What exactly doesn't seem to work?

The code I paste before wasn't working because the path was not good, I should 
have cleaned that before, sorry.

First I have this overrided to use the right method : 
_
override_dh_installdocs-indep:
PYTONPATH=$(CURDIR)/debian python3 setup.py build_doc
dh_installdocs
_

Then I want to deal with mathjax causing the privacy-breach-generic.
But I really don't know how to do that.

Cheers,

Alex




RE:Packaging python-xrayutilities

2019-03-21 Thread MARIE Alexandre
> Wild guessing: The files to be changed might reside in debian/tmp - thus
>
> 
> find debian ...
> 
> could be the solution.

I am trying to do so, thanks for your response.

Cheers,

Alex



Packaging debian xRayUtilities

2019-03-25 Thread MARIE Alexandre
Hello,

I am working on the salsa/debian CI tests, after the build.
Lintian, blhc and puiparts are working fine.
I am trying to fix the autopkgtest, but I am stuck with an error:

```
File 
"/usr/lib/python3/dist-packages/xrayutilities/materials/_create_database.py", 
line 70, in 
add_mass_from_NIST(dbf, os.path.join(dataroot, 'nist_atom.dat'), verbose)
  File "/usr/lib/python3/dist-packages/xrayutilities/materials/database.py", 
line 727, in add_mass_from_NIST
with open(nistfile, "r") as nf:
FileNotFoundError: [Errno 2] No such file or directory: 
'/tmp/autopkgtest.ZEJOsL/autopkgtest_tmp/tests/../xrayutilities/materials/data/nist_atom.dat'
```

This error happens only with python3 and python3-dbg.
I have tried to copy xrayutilities/ (recursively) in "$AUTOPKGTEST_TMP" and 
tried to only copy nist_atom.dat.
But this causes import issues because of the "xrayutilities" dir.

It makes the autopkgtest to fail..

Thanks for your time.

Cheers,

Alexandre


xRayUtilities Package

2019-02-22 Thread MARIE Alexandre
Hello,

I'm trying to package xrayutilities new version (1.5.1) as the one in Debian is 
the 1.2.0.
I cleaned the conflicts and edited d/changelog.
Now when I run "dgit sbuild" I get this error message : 



dgit: error: --quilt=gbp specified, implying patches-unapplied git tree
dgit:  but git tree differs from orig in upstream files.
dgit: For full diff showing the problem(s), type:
dgit:  git diff 6d8103f84ac364be0fb53f7ceb8748b0d5ee63da HEAD -- :/ ':!debian' 
':!/.gitignore' ':!*/.gitignore'



And when I run the git diff command, I get a message that I don't understand :



diff --git a/CHANGES.txt b/CHANGES.txt
index 9c905fa..693a199 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -154,14 +154,14 @@ v1.2.1, 2016-01-08
 v1.2.0, 2015-08-03
 
 * Radicon file support was removed (no test scripts available!)
-* replace pytables by faster and more convenient h5py
-* bug fixes/improvements in the file parsers (discovered by the unit tests!)
-* new unittests for file parsers (spec, edf, xrdml, esg, nja, fio, cbf, tif)
-* added different oxidation states of the chemical elements to the database
-* huge speed improvements for the database access, especially when querying
-  multiple values at the same time
-* add PseudoVoigtAsym option in xu.math.peakfit
-* memory usage optimization in FastScanCCD
+* replace pytables by faster and more convenient h5py bug
+* fixes/improvements in the file parsers (discovered by the unit
+* tests!)  new unittests for file parsers (spec, edf, xrdml, esg, nja,
+* fio, cbf, tif) added different oxidation states of the chemical
+* elements to the database huge speed improvements for the database
+* access, especially when querying multiple values at the same time
+* add PseudoVoigtAsym option in xu.math.peakfit memory usage
+* optimization in FastScanCCD
 
 v1.1.2, 2015-04-22
 
diff --git a/PKG-INFO b/PKG-INFO
new file mode 100644
index 000..8e3faac
--- /dev/null
+++ b/PKG-INFO
@@ -0,0 +1,196 @@
+Metadata-Version: 1.1
+Name: xrayutilities
+Version: 1.5.1
+Summary: package for x-ray diffraction data evaluation
+Home-page: http://xrayutilities.sourceforge.net
+Author: Dominik Kriegner
+Author-email: dominik.krieg...@gmail.com
+License: GPLv2
+Description:
+=
+xrayutilities
+=
+
+xrayutilities is a collection of scripts used to analyze x-ray 
diffraction
+data.  It consists of a Python package and several routines coded in 
C. It is
+especially useful for the reciprocal space conversion of diffraction 
data
+taken with linear and area detectors.
+


I don't see what I am missing here, thus I'm looking for your help !
Thanks you for reading.

Cheers,

Alexandre Marie


RE:xRayUtilities Package

2019-02-22 Thread MARIE Alexandre
Sorry, my mistake, the name of the package is python-xrayutilities !*

The routine I had to upgrade this package was :

 - gbp clone  https://salsa.debian.org/science-team/python-xrayutilities

Then go into the folder that have been created : cd python-xrayutilities

 - gbp import-orig --uscan --pristine-tar
 
 - gbp dch -a

Solve conflicts

Edit d/changelog

Commit

And run :

 -  dgit sbuild : This command creates the error in the previous mail.

Dgit then advice me to run : 

 - git diff 6d8103f84ac364be0fb53f7ceb8748b0d5ee63da HEAD -- :/ ':!debian' 
':!/.gitignore' ':!*/.gitignore'

And this is the command that shows the additions and deletions that I pasted to 
you.

I don't know if it's clearer, but I hope it is !

Thanks for your time,

Alexandre Marie

De : Andrey Rahmatullin [w...@debian.org]
Envoyé : vendredi 22 février 2019 15:03
À : debian-python@lists.debian.org
Objet : Re: xRayUtilities Package

Telling us the commands you used to get to this stage would be helpful, I
think. Right now it's only clear that the listed files are different in
the upstream and in the master branches, but dgit already told you that.
Also, what is the package name? "apt search xrayutilities" returns nothing
for me.

--
WBR, wRAR



RE:Packaging python-xrayutilities

2019-03-18 Thread MARIE Alexandre
>  You need to find why there are conflicts and fix them. Good first steps
>  are running gbp with --no-rollback and/or finding what upstream files are
>  modified in the master branch in the current state.

When I do so, I only have one conflict on the file .gitignore.
I solved it and tried to commit all the staged changes in git gui, I get this 
message :

```commit-tree failed: fatal: 5d93.. is not a valid 'commit object'```

This error prevents me from doing anything more.

Thanks in advance for response.

Cheers,

Alex


RE:Packaging python-xrayutilities

2019-03-18 Thread MARIE Alexandre


Thanks again for the response !

I am resending an answer as the first one was sent to Florian Pelgrim only.

> Try to replace all http links to https in your package.
Changing http to https didn't solve the issue.

I still get this error :
__
What is the upstream version? [1.5.1] 
gbp:info: Importing '../python-xrayutilities_1.5.1.orig.tar.gz' to branch 
'upstream'...
gbp:info: Source package is python-xrayutilities
gbp:info: Upstream version is 1.5.1
Branch pristine-tar set up to track remote branch pristine-tar from origin.
gbp:info: Merging to 'master'
gbp:error: Automatic merge failed.
gbp:error: Error detected, Will roll back changes.
gbp:info: Rolling back branch upstream by resetting it to 
a6a78543327c683bda62802445a37132d18af730
gbp:info: Rolling back branch pristine-tar by deleting it
gbp:info: Rolling back tag upstream/1.5.1 by deleting it
gbp:info: Rolling back branch master by resetting it to 
c64c56e88836df1e54a8cd1926dfd621c3161254
gbp:info: Rolling back failed merge of upstream/1.5.1
gbp:error: Rolled back changes after import error.
__

Thanks for your time.

Cheers, 

Alex


RE:Packaging python-xrayutilities

2019-03-19 Thread MARIE Alexandre
Hello,

I resolved my git issue, but when I build the package doc with sphinx-build :

```
make[1]: Entering directory '/<>'
pybuild --build -s custom -p 3.7 --build-args="env PYTHONPATH={build_dir} 
sphinx-build -bhtml doc/source build/sphinx/html"
I: pybuild base:217: env 
PYTHONPATH=/<>/.pybuild/cpython3_3.7_xrayutilities/build 
sphinx-build -bhtml doc/source build/sphinx/html
```

I get this error :

```
/<>/doc/source/examples.rst:7: WARNING: Duplicate explicit target 
name: "here".
WARNING: autodoc: failed to import module 'xrayutilities'; the following 
exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/sphinx/ext/autodoc/importer.py", line 
154, in import_module
__import__(modname)
  File 
"/<>/.pybuild/cpython3_3.7_xrayutilities/build/xrayutilities/__init__.py",
 line 74, in 
__version__ = pkg_resources.get_distribution("xrayutilities").version
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 481, in 
get_distribution
dist = get_provider(dist)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 357, in 
get_provider
return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0]
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 900, in 
require
needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 786, in 
resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'xrayutilities' distribution was not 
found and is required by the application
```

Does someone know how to deal with this kind of issue ?

Thanks in advance. Cheers,

Alex


Packaging python-xrayutilities

2019-03-18 Thread MARIE Alexandre
Hello,

I'm sorry if this is in the wrong place.
I've already asked for help but I had not explained well how I was encountering 
my problem and couldn't answer before today.
So here it is, i'm trying to update the debian package of python-xrayutilities.

The problem is when I run:```gbp import-orig --uscan --pristine-tar```

I get this error :
__
uscan warn: In directory ., downloading
  
https://qa.debian.org/watch/sf.php/xrayutilities/xrayutilities-testdata-20171020.tar.gz
 failed: 500 SSL upgrade failed: SSL wants a read first
uscan warn: No upstream tarball downloaded. No further processing with 
mk_origtargz ...
gbp:error: Uscan failed: In directory ., downloading
  
https://qa.debian.org/watch/sf.php/xrayutilities/xrayutilities-testdata-20171020.tar.gz
 failed: 500 SSL upgrade failed: SSL wants a read first
No upstream tarball downloaded. No further processing with 
mk_origtargz ...
__

So what I've done is update d/watch from :

```version=3 
opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/ \ 
http://sf.net/xrayutilities/xrayutilities-(.+)\.tar\.gz```

to : 

```version=4
opts="uversionmangle=s/-pre/~pre/, \
  filenamemangle=s%(?:.*)xrayutilities-(.+)\.tar\.gz/download%\
  xrayutilities-$1.tar.gz%" \
  http://sourceforge.net/projects/xrayutilities/files/v([\d\.]+)/ \
  (?:.*)xrayutilities-([\d\.]+)\.tar\.gz/download debian uupdate
```

that I got in the uscan man.

Thus I can run again : ```gbp import-orig --uscan --pristine-tar```

And then the command is able to find the right version.

The fact is when I choose the latest version to update debian's one, I get this 
error :
___
What is the upstream version? [1.5.1] 1.5.1
gbp:info: Importing '../python-xrayutilities_1.5.1.orig.tar.gz' to branch 
'upstream'...
gbp:info: Source package is python-xrayutilities
gbp:info: Upstream version is 1.5.1
Branch pristine-tar set up to track remote branch pristine-tar from origin.
gbp:info: Merging to 'master'
gbp:error: Automatic merge failed.
gbp:error: Error detected, Will roll back changes.
gbp:info: Rolling back branch upstream by resetting it to 
5ce1c0bf0d95a9ffd7321a5065041596f05a8fe0
gbp:info: Rolling back branch pristine-tar by deleting it
gbp:info: Rolling back tag upstream/1.5.1 by deleting it
gbp:info: Rolling back branch master by resetting it to 
121347cb1309a8ce3821ed3efdd3646442e59ca3
gbp:info: Rolling back failed merge of upstream/1.5.1
gbp:error: Rolled back changes after import error.
___

Here is where I am stuck and where I am asking for some help please !

Thanks in advance for a response.

Cheers,

Alexandre Marie


[no subject]

2019-11-18 Thread MARIE Alexandre
Hello,

I am trying to fix lmfit-py and python-fabio packages as the first can't be 
built with python 3.8 and the second can't make it through autopkgtest.

As I am not importing a new version but fixing one, I don't have the orig.tar 
or debian.tar file and the error:

```
dpkg-source: error: missing orig.tar or debian.tar file in v2.0 source package
```

occurs when I run the dgit sbuild line.

I don't know how could I import these files without touching my version of the 
packages.

Sorry if this question is basic.

Cheers,

===

Alexandre MARIE
Engineer in training – IT field
Synchrotron SOLEIL – Beamline DiffAbs
L’Orme des Merisiers Saint-Aubin BP48
91192 Gif-sur-Yvette Cédex
Mobile : +33(0)6.58.74.02.36
E-Mail : alexandre.ma...@synchrotron-soleil.fr


[packaging] wurlitzer

2019-10-21 Thread MARIE Alexandre
Hi everybody,

I am creating a package to release wurlitzer in debian.

But, I am facing an issue in the d/watch file [0] when uscan [1] seeks for the 
latest version to download on the pypi redirector [2].


[0] debian/watch file :

version=4
opts=pasv,repacksuffix=+dfsg1,\
pgpsigurlmangle=s/$/.asc/,\
uversionmangle=s/(rc|a|b|c)/~$1/,\
dversionmangle=s/\+dfsg\d*// \
https://www.pypi.org/project/wurlitzer/\
@PACKAGE@-@ANY_VERSION@(?:_src)?@ARCHIVE_EXT@ debian uupdate



[1]

scan info: uscan (version 2.19.5+deb10u1) See uscan(1) for help
uscan info: Scan watch files in .
uscan info: Check debian/watch and debian/changelog in .
uscan info: package="wurlitzer" version="1.0.3-1" (as seen in debian/changelog)
uscan info: package="wurlitzer" version="1.0.3" (no epoch/revision)
uscan info: ./debian/changelog sets package="wurlitzer" version="1.0.3"
uscan info: Process watch file at: debian/watch
package = wurlitzer
version = 1.0.3
pkg_dir = .
uscan info: opts: 
pasv,repacksuffix=+dfsg1,pgpsigurlmangle=s/$/.asc/,uversionmangle=s/(rc|a|b|c)/~$1/,dversionmangle=s/\+dfsg\d*//
uscan info: line: 
https://www.pypi.org/project/wurlitzer/wurlitzer\-1.0.3\.tar\.gz
uscan info: Parsing pasv
uscan info: Set passive mode: 1
uscan info: Parsing repacksuffix=+dfsg1
uscan info: Parsing pgpsigurlmangle=s/$/.asc/
uscan info: Parsing uversionmangle=s/(rc|a|b|c)/~$1/
uscan info: Parsing dversionmangle=s/\+dfsg\d*//
uscan info: line: 
https://www.pypi.org/project/wurlitzer/wurlitzer\-1.0.3\.tar\.gz
Use of uninitialized value $filepattern in pattern match (m//) at 
/usr/share/perl5/Devscripts/Uscan/WatchLine.pm line 582.
uscan warn: Tag pattern missing version delimiters () in debian/watch, skipping:
  https://www.pypi.org/project/wurlitzer/wurlitzer\-1.0.3\.tar\.gz
uscan info: Scan finished
__

[2] https://pypi.org/project/wurlitzer/


I do not seem to be able to deal with that issue so I am asking your help.

Cheers, 

Alexandre Marie


RE:[packaging] wurlitzer

2019-10-21 Thread MARIE Alexandre
Thanks for your fast answer, but I made a mistake when I pasted the error from 
the bash.

Here is the real error (according to the d/watch file I gave you) :

___

uscan info: uscan (version 2.19.5+deb10u1) See uscan(1) for help
uscan info: Scan watch files in .
uscan info: Check debian/watch and debian/changelog in .
uscan info: package="wurlitzer" version="1.0.3-1" (as seen in debian/changelog)
uscan info: package="wurlitzer" version="1.0.3" (no epoch/revision)
uscan info: ./debian/changelog sets package="wurlitzer" version="1.0.3"
uscan info: Process watch file at: debian/watch
package = wurlitzer
version = 1.0.3
pkg_dir = .
uscan info: opts: 
pasv,repacksuffix=+dfsg1,pgpsigurlmangle=s/$/.asc/,uversionmangle=s/(rc|a|b|c)/~$1/,dversionmangle=s/\+dfsg\d*//
uscan info: line: 
https://www.pypi.org/project/wurlitzer/wurlitzer-((?:[-_]?(\d[\-+\.:\~\da-zA-Z]*)))(?:_src)?(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|zip|tgz|tbz|txz))
 debian uupdate
uscan info: Parsing pasv
uscan info: Set passive mode: 1
uscan info: Parsing repacksuffix=+dfsg1
uscan info: Parsing pgpsigurlmangle=s/$/.asc/
uscan info: Parsing uversionmangle=s/(rc|a|b|c)/~$1/
uscan info: Parsing dversionmangle=s/\+dfsg\d*//
uscan info: line: 
https://www.pypi.org/project/wurlitzer/wurlitzer-((?:[-_]?(\d[\-+\.:\~\da-zA-Z]*)))(?:_src)?(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|zip|tgz|tbz|txz))
 debian uupdate
uscan info: Last orig.tar.* tarball version (from debian/changelog): 1.0.3
uscan info: Last orig.tar.* tarball version (dversionmangled): 1.0.3
uscan info: Requesting URL:
   https://www.pypi.org/project/wurlitzer/
uscan info: redirections: https://pypi.org/project/wurlitzer/
uscan info: Matching pattern:
   
(?:(?:https://www.pypi.org)?\/project\/wurlitzer\/)?wurlitzer-((?:[-_]?(\d[\-+\.:\~\da-zA-Z]*)))(?:_src)?(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|zip|tgz|tbz|txz))
 
(?:(?:https://pypi.org)?\/project\/wurlitzer\/)?wurlitzer-((?:[-_]?(\d[\-+\.:\~\da-zA-Z]*)))(?:_src)?(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|zip|tgz|tbz|txz))
uscan warn: In debian/watch no matching files for watch line
  
https://www.pypi.org/project/wurlitzer/wurlitzer-((?:[-_]?(\d[\-+\.:\~\da-zA-Z]*)))(?:_src)?(?i)(?:\.(?:tar\.xz|tar\.bz2|tar\.gz|zip|tgz|tbz|txz))
 debian uupdate
___

Have a good day,

Alexandre Marie

De : Andrius Merkys [andrius.mer...@gmail.com]
Envoyé : lundi 21 octobre 2019 14:53
À : debian-python@lists.debian.org
Objet : Re: [packaging] wurlitzer

Hi Alexandre,

On 2019-10-21 15:47, MARIE Alexandre wrote:
> @PACKAGE@-@ANY_VERSION@(?:_src)?@ARCHIVE_EXT@ debian uupdate

Try putting @ANY_VERSION@ inside parenthesis:

@PACKAGE@-(@ANY_VERSION@)(?:_src)?@ARCHIVE_EXT@ debian uupdate

Hope this helps,
Andrius



RE:[packaging] wurlitzer

2019-10-21 Thread MARIE Alexandre
This one works perfectly fine, thanks a lot for giving me some time to help !

Have a nice day,

Alexandre Marie

De : Andrius Merkys [andrius.mer...@gmail.com]
Envoyé : lundi 21 octobre 2019 15:26
À : debian-python@lists.debian.org
Objet : Re: [packaging] wurlitzer

On 2019-10-21 16:15, MARIE Alexandre wrote:
> I tried it as you said but I still get the same error :

Hmm. The layout on PyPI seems to have changed. Could you try this now?:

version=4
opts="pgpmode=none" \
 https://pypi.python.org/pypi/wurlitzer/ \
 https://files.pythonhosted.org/packages/.*/.*/.*/\
 wurlitzer-([\d\.]+).tar.gz debian uupdate



[Request]

2019-10-22 Thread MARIE Alexandre
Hello,

I woud like to join debian-python team in order to maintain and package a bunch 
of modules :
 - wurlitzer
 - jupyter_sphinx

Wich are dependecies of scientific softwares.

My username is : alexandre.marie-guest.

I read the python policy [0] and I accept it.

Thanks,

Alexandre Marie


[0] 
https://salsa.debian.org/python-team/tools/python-modules/blob/master/policy.rst