bob issueshttps://gitlab.idiap.ch/groups/bob/-/issues2018-05-11T07:44:39Zhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/7Convert .npy and .png files in MR !17 to HDF52018-05-11T07:44:39ZAndré AnjosConvert .npy and .png files in MR !17 to HDF5Teodors EGLITISTeodors EGLITIShttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/6Tests skipped in master branch -- database is neither a resource for a 'datab...2018-05-11T07:44:39ZTeodors EGLITISTests skipped in master branch -- database is neither a resource for a 'database', nor an existing configuration fileTests for the databases using the new approach -- ``bob.bio.config`` are skipped:
```
bob.bio.vein.tests.test_databases.test_utfvp ... SKIP: Skipping test since the database bob.db.utfvp seems not to be available: The given command l...Tests for the databases using the new approach -- ``bob.bio.config`` are skipped:
```
bob.bio.vein.tests.test_databases.test_utfvp ... SKIP: Skipping test since the database bob.db.utfvp seems not to be available: The given command line option 'utfvp' is neither a resource for a 'database', nor an existing configuration file, nor could be interpreted as a command (error: name 'utfvp' is not defined)
bob.bio.vein.tests.test_databases.test_verafinger ... SKIP: Skipping test since the database bob.db.verafinger seems not to be available: The given command line option 'verafinger' is neither a resource for a 'database', nor an existing configuration file, nor could be interpreted as a command (error: name 'verafinger' is not defined)
```
https://gitlab.idiap.ch/bob/bob.bio.vein/builds/16343
Question is -- how this should be resolved and what would be a proper way to write tests?André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/5Can' t build locally `package-update` - **suggestions**?2018-05-11T07:44:39ZTeodors EGLITISCan' t build locally `package-update` - **suggestions**?I tried to build locally from branch `package-update` (after I merged branch `master` in to `package-update`), but get the error:
```
Makefile:76: recipe for target 'all' failed
make: *** [all] Error 2
error: CMake compilation stoppe...I tried to build locally from branch `package-update` (after I merged branch `master` in to `package-update`), but get the error:
```
Makefile:76: recipe for target 'all' failed
make: *** [all] Error 2
error: CMake compilation stopped with an error; stopping ...
While:
Installing.
Processing develop directory '/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/src/bob.math'.
An internal error occurred due to a bug in either zc.buildout or in a
recipe being used:
Traceback (most recent call last):
File "/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/eggs/zc.buildout-2.5.3-py2.7.egg/zc/buildout/buildout.py", line 1995, in main
getattr(buildout, command)(args)
File "/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/eggs/zc.buildout-2.5.3-py2.7.egg/zc/buildout/buildout.py", line 528, in install
installed_develop_eggs = self._develop()
File "/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/eggs/zc.buildout-2.5.3-py2.7.egg/zc/buildout/buildout.py", line 770, in _develop
zc.buildout.easy_install.develop(setup, dest)
File "/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/eggs/bob.buildout-2.0.14-py2.7.egg/bob/buildout/extension.py", line 213, in develop
zc.buildout.easy_install.call_subprocess(args)
File "/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/eggs/zc.buildout-2.5.3-py2.7.egg/zc/buildout/easy_install.py", line 160, in call_subprocess
% repr(args)[1:-1])
Exception: Failed to run command:
'/idiap/group/torch5spro/conda/envs/bob-2.3.4-py27_0/bin/python', '/tmp/tmpAtiCK5', '-v', 'develop', '-mxN', '-d', '/remote/idiap.svm/home.active/teglitis/Desktop/BOB/bob.bio.vein/develop-eggs/tmpceAGcmbuild'
```
Commands I executed:
```
git checkout package-update
source /idiap/group/torch5spro/conda/bin/activate bob-2.3.4-py27_0
python bootstrap-buildout.py
./bin/buildout -c develop.cfg
```
**Any suggestions?**
Branch is passing builds online -- https://gitlab.idiap.ch/bob/bob.bio.vein/commit/ba38c3c5dc69dc0d297f201ab1c5a77f567158a1/builds
Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/4ERROR: Failure: ImportError (No module named skimage.morphology)2018-05-11T07:44:39ZTeodors EGLITISERROR: Failure: ImportError (No module named skimage.morphology)Again import error in branch `package update`:
```
ERROR: Failure: ImportError (No module named skimage.morphology)
```
```
File "/local/gitlab-runner/builds/6b02994f/0/bob/bob.bio.vein/env/lib/python2.7/site-packages/bob/bio/vein...Again import error in branch `package update`:
```
ERROR: Failure: ImportError (No module named skimage.morphology)
```
```
File "/local/gitlab-runner/builds/6b02994f/0/bob/bob.bio.vein/env/lib/python2.7/site-packages/bob/bio/vein/preprocessors/TopographyCutRoi.py", line 13, in <module>
from skimage.morphology import convex_hull_image
ImportError: No module named skimage.morphology
```
E.g. - https://gitlab.idiap.ch/bob/bob.bio.vein/builds/12936Olegs NIKISINSOlegs NIKISINShttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/3Update to performances on documentation2018-05-11T07:44:39ZAndré AnjosUpdate to performances on documentation@pferrez provided the following table: [baselines.xlsx](/uploads/767d9c32c64d0bf612174913140d0815/baselines.xlsx)
It would be good to update the results on the documentation.@pferrez provided the following table: [baselines.xlsx](/uploads/767d9c32c64d0bf612174913140d0815/baselines.xlsx)
It would be good to update the results on the documentation.https://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/2Random process on RepeatedLineTracking algorithm is not reproducible2018-05-11T07:44:39ZAndré AnjosRandom process on RepeatedLineTracking algorithm is not reproducibleThere is a random walk inside this algorithm, with an unparameterized seed which makes it less reproducible on each try:
https://gitlab.idiap.ch/bob/bob.bio.vein/blob/master/bob/bio/vein/extractors/RepeatedLineTracking.py#L99
It wo...There is a random walk inside this algorithm, with an unparameterized seed which makes it less reproducible on each try:
https://gitlab.idiap.ch/bob/bob.bio.vein/blob/master/bob/bio/vein/extractors/RepeatedLineTracking.py#L99
It would be good to set a seed thorugh a parameter to the constructor.André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.bio.vein/-/issues/1Buildout issues2018-05-11T07:44:39ZAmir MOHAMMADIBuildout issuesCreate a directory called `my_exp_01` and put these files in it:
```sh
$ cd my_exp_01
$ curl -k --silent https://bootstrap.pypa.io/bootstrap-buildout.py > bootstrap-buildout.py
$ gedit buildout.cfg # content below
$ source /idiap/gr...Create a directory called `my_exp_01` and put these files in it:
```sh
$ cd my_exp_01
$ curl -k --silent https://bootstrap.pypa.io/bootstrap-buildout.py > bootstrap-buildout.py
$ gedit buildout.cfg # content below
$ source /idiap/group/torch5spro/conda/bin/activate bob-2.3.4-py27_0
$ python bootstrap-buildout.py
$ ./bin/buildout
```
```
[buildout]
parts = scripts
develop = src/bob.db.verafinger
src/bob.db.putvein
src/bob.bio.db
src/bob.bio.vein
eggs = bob.db.verafinger
bob.db.putvein
bob.bio.db
bob.bio.vein
extensions = bob.buildout
mr.developer
auto-checkout = *
debug = true
newest = false
verbose = true
[sources]
bob.bio.vein = git git@gitlab.idiap.ch:bob/bob.bio.vein branch=package-update
bob.bio.db = git git@gitlab.idiap.ch:bob/bob.bio.db
bob.db.verafinger = git git@gitlab.idiap.ch:bob/bob.db.verafinger
bob.db.putvein = git git@gitlab.idiap.ch:bob/bob.db.putvein
[scripts]
recipe = bob.buildout:scripts
dependent-scripts = true
```Refactoring 2016 and gitlab migration milestoneChristopher FINELLIChristopher FINELLIhttps://gitlab.idiap.ch/bob/nightlies/-/issues/35Nighlies are broken2018-05-14T09:17:55ZTiago de Freitas PereiraNighlies are brokenHi guys,
Nightlies are broken and I need some help to fix it.
Look at the logs
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/135856
We are pinning `hdf5` to `1.10.1` in `bob-devel` (https://gitlab.idiap.ch/bob/bob.conda/blob/master...Hi guys,
Nightlies are broken and I need some help to fix it.
Look at the logs
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/135856
We are pinning `hdf5` to `1.10.1` in `bob-devel` (https://gitlab.idiap.ch/bob/bob.conda/blob/master/conda/bob-devel/meta.yaml#L36), but it looks like `bob.io.base` is requiring something higher than `1.10.2`.
Sorry, but I don't know all the idiosyncrasies of conda packaging. Is this jinja variable https://gitlab.idiap.ch/bob/bob.io.base/blob/master/conda/meta.yaml#L32 forcing the conda package to pick the highest version available in the channels we point?
Nightlies are broken for 2 weeks.
Let's make an effort to make it green for this week, please.
ping @andre.anjos @amohammadi
Cheershttps://gitlab.idiap.ch/bob/bob.bio.face/-/issues/29Archiving bob.bio.csu2018-05-15T07:04:56ZTiago de Freitas PereiraArchiving bob.bio.csuSince we decided to archive `bob.bio.csu` (https://gitlab.idiap.ch/bob/bob.bio.csu/issues/3), we need to remove traces of it here.Since we decided to archive `bob.bio.csu` (https://gitlab.idiap.ch/bob/bob.bio.csu/issues/3), we need to remove traces of it here.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.ip.pytorch_extractor/-/issues/2PyTorch (0.3.0) has an unchecked dependency on pyyaml2018-05-15T08:33:02ZGuillaume HEUSCHPyTorch (0.3.0) has an unchecked dependency on pyyamlWhen running the CI locally on my machine for this package, I got the following error:
```bash
pkg_resources.DistributionNotFound: The 'pyyaml' distribution was not found and is required by torch
```
This is a known issue and it was fi...When running the CI locally on my machine for this package, I got the following error:
```bash
pkg_resources.DistributionNotFound: The 'pyyaml' distribution was not found and is required by torch
```
This is a known issue and it was fixed in the latest pyTorch version (0.4.0) (see https://github.com/pytorch/pytorch/commit/03f2ad9029165d20585d00b11f45fe50de6b687f). Unfortunately, this version is not available in conda (at least in our channels), so what is the procedure to adopt ? Add ```pyyaml``` in ```requirements.txt``` ?
Any piece of advice welcome @amohammadi @andre.anjos @tiago.pereira !
Thanks
https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/65evaluation script is too complicated and does not make use of the internal st...2018-05-15T11:39:57ZManuel Günthersiebenkopf@googlemail.comevaluation script is too complicated and does not make use of the internal structureBy now, we have to specify `--dev-files` and `--eval-files` using full paths. However, as most parts of the paths are common, it should be easily possible to simplify the parameters such that you only need to specify the `--result-direct...By now, we have to specify `--dev-files` and `--eval-files` using full paths. However, as most parts of the paths are common, it should be easily possible to simplify the parameters such that you only need to specify the `--result-directory` that you want to evaluate. The remaining parameters (check for the presence of `scores-dev` and `scores-eval` files), and even the `--protocol` or `--experiments` can automatically be estimated from the presence inside the `--results-directory`.
The current options `--dev-files` and `--eval-files` should IMHO still be present, so that we can plot together experiments from different directories. An exemplary evaluation call might be:
```
./bin/evaluate.py --result-directory results/mobio --protocol male --algorithms gmm ivector --dev-files other-results/mobio/isv/male/nonorm/scores-dev --eval-files other-results/mobio/isv/male/nonorm/scores-eval
```
In this case, the `--algorithms` could be automatically determined by the sub-directories inside `results/mobio`, and even the protocol might be automatically estimated, when only one common sub-directory is present inside `results/mobio/*`. In non-obvious cases, an error including proper instructions might be issued.
Another option would be to be able to provide several `--result-directories`, so that the same command line as above would be:
```
./bin/evaluate.py --result-directories results/mobio/gmm results/mobio/ivector other-results/mobio/isv --protocol male
```
This might be less confusing, but is longer to write, especially when you have several algorithms to evaluate.
@amohammadi @tiago.pereira Which option would you prefer?May 2017 HackathonGuillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.bio.face/-/issues/31Nightlies are failing because of this one2018-05-16T06:13:22ZTiago de Freitas PereiraNightlies are failing because of this oneHi guys,
The nightly builds are failing, because of this one https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/136039
The current `baseline` script is trying to run the `evaluate` script that was already deleted.
I'm offering three pos...Hi guys,
The nightly builds are failing, because of this one https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/136039
The current `baseline` script is trying to run the `evaluate` script that was already deleted.
I'm offering three possibilities to solve this one today:
- Disable the baseline unit tests until we solve the issues with the baseline script (https://gitlab.idiap.ch/bob/bob.bio.face/blob/49f48337ba2818dc8b3f64d88ccf76495209ac4b/bob/bio/face/test/test_scripts.py#L5)
- Completely remove the `baseline` script until we decide what to do with it
- Move forward with this one https://gitlab.idiap.ch/bob/bob.bio.face/merge_requests/49 . Here I'm offering a clean solution to solve the above issues. I could document it and merge it today to solve this issue, but I would appreciate a feedback
Feedback please.
2 weeks of red nightlies
ping @bob
Thankshttps://gitlab.idiap.ch/bob/bob.db.swan/-/issues/1Nightlies SAGA2018-05-16T11:16:00ZTiago de Freitas PereiraNightlies SAGAGuys,
Nightlies are broken here
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/136291
This is not even a conda package, why is it there?
Could you please take care of this @amohammadi ?
ThanksGuys,
Nightlies are broken here
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/136291
This is not even a conda package, why is it there?
Could you please take care of this @amohammadi ?
Thankshttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/113Follow-up from "Created the Baselines Concept"2018-05-16T14:01:25ZAmir MOHAMMADIFollow-up from "Created the Baselines Concept"The following discussion from !151 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/151#note_29783): (+10 comments)
> Just give the entry point group name here a...The following discussion from !151 should be addressed:
- [ ] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/151#note_29783): (+10 comments)
> Just give the entry point group name here and it will load the baseline for you. You don't need to load the baseline manually.https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/66Respect priority when loading entry-points2018-05-16T15:17:33ZAndré AnjosRespect priority when loading entry-pointsif one tries to run bob/bob.bio.base tests in an environment with bob/bob.bio.spear installed, the test `bob.bio.base.test.test_utils.test_grid` is not going to pass with the following error:
```text
====================================...if one tries to run bob/bob.bio.base tests in an environment with bob/bob.bio.spear installed, the test `bob.bio.base.test.test_utils.test_grid` is not going to pass with the following error:
```text
======================================================================
ERROR: bob.bio.base.test.test_utils.test_grid
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/bob/bio/base/test/test_utils.py", line 34, in test_grid
g = bob.bio.base.load_resource("demanding", "grid")
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/bob/bio/base/utils/resources.py", line 204, in load_resource
return entry_points[0].load()
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2291, in load
return self.resolve()
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2297, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/bob/bio/spear/config/grid/demanding.py", line 15, in <module>
scoring_queue = '8G-io-big'
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/bob/bio/base/grid.py", line 107, in __init__
self.training_queue = self.queue(training_queue)
File "/home/vagrant/anaconda/envs/bob_py27/lib/python2.7/site-packages/bob/bio/base/grid.py", line 140, in queue
raise ValueError("The given queue parameters '%s' are not in the predefined queues and neither a dictionary with values." % str(params))
ValueError: The given queue parameters '48G' are not in the predefined queues and neither a dictionary with values.
-------------------- >> begin captured logging << --------------------
bob.bio.base: WARNING: Under the desired name 'demanding', there are multiple entry points defined, we return the first one: ['bob.bio.spear.config.grid.demanding', 'bob.bio.base.config.grid.demanding']
--------------------- >> end captured logging << ---------------------
```
The reason for this error is that there is a resource called `demanding` on both packages. For some reason, the test is choosing the version on spear, which does not work.https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/47Usage of --environment is not clear2018-05-16T15:49:27ZAmir MOHAMMADIUsage of --environment is not clearOn the help message says:
```
-t [ENV [ENV ...]], --environment [ENV [ENV ...]]
Passes specific environment variables to the job.
(default: [])
```
but to get it to work you need to...On the help message says:
```
-t [ENV [ENV ...]], --environment [ENV [ENV ...]]
Passes specific environment variables to the job.
(default: [])
```
but to get it to work you need to use:
`verify.py -t "PATH=/mypath" "VARIABLE=001" `
Am I right?May 2017 HackathonTiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/83The of module `imp` is deprecated2018-05-16T16:13:52ZAndré AnjosThe of module `imp` is deprecatedSince python 3.3 came out, the module `imp` is being deprecated in favor of `importlib`. In python2 one can use an external package to mimick its behaviour (https://pypi.python.org/pypi/importlib2). This package is unfortunately not avai...Since python 3.3 came out, the module `imp` is being deprecated in favor of `importlib`. In python2 one can use an external package to mimick its behaviour (https://pypi.python.org/pypi/importlib2). This package is unfortunately not available in conda yet.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.learn.em/-/issues/13HMM2018-05-16T16:30:28ZAndré AnjosHMM*Created by: tiagofrepereira2012*
Our bob.learn.em package would be more complete with a HMM implementation, what do you think?
The options to approach this are the following:
- Implement it from scratch (We already have something ...*Created by: tiagofrepereira2012*
Our bob.learn.em package would be more complete with a HMM implementation, what do you think?
The options to approach this are the following:
- Implement it from scratch (We already have something for the emission probability distribution)
- We can try to bind the HTK library (http://htk.eng.cam.ac.uk/) or try to integrate this bind http://www.e-gymraeg.org/wispr/pyhtk.htm
- Try to integrate different software https://github.com/jmschrei/pomegranate or sklearn.
Worth the effort?
https://gitlab.idiap.ch/bob/bob.learn.em/-/issues/19constness issue in nose tests2018-05-16T16:31:20ZAndré Anjosconstness issue in nose tests*Created by: siebenkopf*
With the new constness initiative (see: bioidiap/bob.blitz#6) there is a nose tests failing:
https://travis-ci.org/bioidiap/bob.learn.em/builds/122338253
as it tries to modify values that are const. Please rev...*Created by: siebenkopf*
With the new constness initiative (see: bioidiap/bob.blitz#6) there is a nose tests failing:
https://travis-ci.org/bioidiap/bob.learn.em/builds/122338253
as it tries to modify values that are const. Please review both the test and also whether these values must be returned as const arrays.https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/111Follow-up from "Exposing the method groups in our FileDatabase API"2018-05-17T09:07:57ZAmir MOHAMMADIFollow-up from "Exposing the method groups in our FileDatabase API"The following discussion from !150 should be addressed:
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/150#note_29656):
> either the docs are wrong or you didn't implement the prot...The following discussion from !150 should be addressed:
- [x] @amohammadi started a [discussion](https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/150#note_29656):
> either the docs are wrong or you didn't implement the protocol parameter.Tiago de Freitas PereiraTiago de Freitas Pereira