bob issueshttps://gitlab.idiap.ch/groups/bob/-/issues2019-03-20T12:37:41Zhttps://gitlab.idiap.ch/bob/bob.pad.face/-/issues/27fix CASIA-SURF tests2019-03-20T12:37:41ZGuillaume HEUSCHfix CASIA-SURF testsGuillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.devtools/-/issues/27Unable to build the docs package for BEAT locally2019-06-03T14:32:52ZZohreh MOSTAANIUnable to build the docs package for BEAT locallyI am trying to build the docs package for BEAT locally, however it seems that bob.devtools only assumes that docs is on the CI. I assume the same will apply to bob.docs.I am trying to build the docs package for BEAT locally, however it seems that bob.devtools only assumes that docs is on the CI. I assume the same will apply to bob.docs.https://gitlab.idiap.ch/bob/bob.learn.em/-/issues/32Remove score normalization from here2020-11-05T14:56:37ZTiago de Freitas PereiraRemove score normalization from hereScore normalization mechanisms are implemented as a pipeline in `bob.bio.base` (https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/dask-pipelines/bob/bio/base/script/vanilla_biometrics_ztnorm.py).
Shall we remove the score-normalization bi...Score normalization mechanisms are implemented as a pipeline in `bob.bio.base` (https://gitlab.idiap.ch/bob/bob.bio.base/-/blob/dask-pipelines/bob/bio/base/script/vanilla_biometrics_ztnorm.py).
Shall we remove the score-normalization bits from here?
The score-normalization bits are placed here for historical reasons.
ThanksBob 9.0.0https://gitlab.idiap.ch/bob/bob.pipelines/-/issues/27The `DelayedSampleCall` makes pipelines memory greedy.2020-11-26T18:06:00ZTiago de Freitas PereiraThe `DelayedSampleCall` makes pipelines memory greedy.The way we delay transformer calls (look https://gitlab.idiap.ch/bob/bob.pipelines/-/blob/master/bob/pipelines/wrappers.py#L132) makes our pipeline super memory greedy.
I'm running a simple experiment **LOCALLY**, no dask involved, on `...The way we delay transformer calls (look https://gitlab.idiap.ch/bob/bob.pipelines/-/blob/master/bob/pipelines/wrappers.py#L132) makes our pipeline super memory greedy.
I'm running a simple experiment **LOCALLY**, no dask involved, on `bob.bio.base` wrapping everything with the `CheckpointWrapper`; and my experiment blows 32GB of my RAM + my swap without writing one single file from mine experiment.
Do you have any thoughts on this @amohammadi ?
Do you think is a good call the `DelayedSampleCall`?
Thanks
ping @ydayerBob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.base/-/issues/62preprocessing, extraction and projection will not stop if files are missing2017-08-07T13:07:35ZManuel Günthersiebenkopf@googlemail.compreprocessing, extraction and projection will not stop if files are missingWhen there is an issue preprocessing the file or extracting/projecting features and the tool returns `None`, a message is written, but the file is silently skipped. This should be the default behavior when the `--allow-missing-files` fla...When there is an issue preprocessing the file or extracting/projecting features and the tool returns `None`, a message is written, but the file is silently skipped. This should be the default behavior when the `--allow-missing-files` flag is set. However, even without the flag, currently the processing just emits an error message, but continues. This is especially annoying when running in the grid and, thus, getting the error messages written into log files instead of to console.
The problem is that the `continue`: https://gitlab.idiap.ch/bob/bob.bio.base/blob/master/bob/bio/base/tools/extractor.py#L129 is not what we want.
I think, when the processing fails and `None` is returned, we should raise an exception rather than skipping.https://gitlab.idiap.ch/bob/bob.extension/-/issues/47Relative imports are not supported by Python configuration loading system2018-01-15T17:17:22ZAndré AnjosRelative imports are not supported by Python configuration loading systemIf a configuration file is a resource in a package, it should be possible to do relative imports. For that, the module name should be correctly set (and not be a fixed string).If a configuration file is a resource in a package, it should be possible to do relative imports. For that, the module name should be correctly set (and not be a fixed string).André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.bio.spear/-/issues/30The demanding grid configuration is shadowed by the one in bob.bio.base2018-04-16T14:59:56ZAmir MOHAMMADIThe demanding grid configuration is shadowed by the one in bob.bio.baseSee:
```
bob.bio.base@2018-01-10 15:41:33,306 -- WARNING: Under the desired name 'demanding', there are multiple entry points defined, we return the first one: ['bob.bio.base.config.grid.demanding', 'bob.bio.spear.config.grid.demanding']...See:
```
bob.bio.base@2018-01-10 15:41:33,306 -- WARNING: Under the desired name 'demanding', there are multiple entry points defined, we return the first one: ['bob.bio.base.config.grid.demanding', 'bob.bio.spear.config.grid.demanding']
```
I think the best approach is to rename the demanding one here.https://gitlab.idiap.ch/bob/nightlies/-/issues/33bob.io.image broken at nightlies2018-02-28T17:47:06ZAndré Anjosbob.io.image broken at nightliesThe current version of bob.io.image is not compiling properly at the nightlies and that is despite the fact nothing really changed that could break it.
The problem happens on all architectures and Python variants (see, e.g.: https://git...The current version of bob.io.image is not compiling properly at the nightlies and that is despite the fact nothing really changed that could break it.
The problem happens on all architectures and Python variants (see, e.g.: https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/125060)
The error:
```text
OSError: libgif.so.7: cannot open shared object file: No such file or directory
```
What is strange:
* bob.io.image has not changed since last week where we managed to build it successfuly
* There are no changes on its dependencies and giflib, in particular giflib 1.5.4-3 has not changed for a few months
Any clues?Conda-based CIAndré AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob/-/issues/249Make bob, bob again!2018-04-17T11:31:52ZAmir MOHAMMADIMake bob, bob again!:) it means we want to remove this idea of core and extra packages and make everything a part of bob.
To do so we need:
* Make sure bob is only a meta package (both in PyPI and conda) with only optional dependencies.
* Bob will (opti...:) it means we want to remove this idea of core and extra packages and make everything a part of bob.
To do so we need:
* Make sure bob is only a meta package (both in PyPI and conda) with only optional dependencies.
* Bob will (optionally) depend on all core and extra packages. There will be no concept of core and extra packages anymore.
* We will still use semantic versioning in Bob and follow semantic versioning. This means with every release, we could easily be releasing a new major version of Bob: bob 4, bob 5, bob 6
* We could remove bob/bob.nightlies and bob/docs repositories as well and do everything here.
* Since the bob package is not going to install anything, we could potentially list private stable packages here too. However, I am not sure we can build the docs here then.
Here is the idea for its conda recipe at least:
```yaml
{% set name = 'bob' %}
{% set project_dir = environ.get('RECIPE_DIR') + '/..' %}
package:
name: {{ name }}
version: {{ environ.get('BOB_PACKAGE_VERSION', '0.0.1') }}
build:
number: {{ environ.get('BOB_BUILD_NUMBER', 0) }}
run_exports:
- {{ pin_subpackage(name) }}
script:
- cd {{ project_dir }}
{% if environ.get('BUILD_EGG') %}
- python setup.py sdist --formats=zip
{% endif %}
- python setup.py install --single-version-externally-managed --record record.txt
requirements:
run:
- python {{ python }}
- setuptools {{ setuptools }}
- bob.extension
- bob.blitz
...
- bob.ip.flandmark
- bob.bio.base
...
- gridtk
- bob.pad.voice
...
- bob.buildout # even bob.buildout
test:
imports:
- {{ name }}
commands:
- nosetests --with-coverage --cover-package={{ name }} -sv {{ name }}
- conda inspect linkages -p $PREFIX {{ name }} # [not win]
- conda inspect objects -p $PREFIX {{ name }} # [osx]
requires:
- bob-devel {{ bob_devel }}.*
- nose
- coverage
- sphinx
- sphinx_rtd_theme
- pkgtools
- cmake
- pkg-config
- freetype
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- bob.buildout
...
```
Then we run `conda render`, and create a new recipe based on that while converting `run` to `run_constrained`. I have explained this in https://gitlab.idiap.ch/bob/bob.conda/issues/46#note_25677Conda-based CIAmir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.face/-/issues/30Script broken by bob.bio.base merge2018-05-17T14:18:33ZTheophile GENTILHOMMEScript broken by bob.bio.base mergeBroken by https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/146
baselines.py is using evaluate.py that has been removed.Broken by https://gitlab.idiap.ch/bob/bob.bio.base/merge_requests/146
baselines.py is using evaluate.py that has been removed.Theophile GENTILHOMMETheophile GENTILHOMMEhttps://gitlab.idiap.ch/bob/bob.measure/-/issues/56Limitations of matplotlib's constrained layout are not taken into account2018-08-27T14:55:54ZAmir MOHAMMADILimitations of matplotlib's constrained layout are not taken into accountPlease see: https://matplotlib.org/tutorials/intermediate/constrainedlayout_guide.html#limitations
Basically we should not be using `plt.subplot` and should be using `GridSpec`.
I think this was recently added to the documentation so w...Please see: https://matplotlib.org/tutorials/intermediate/constrainedlayout_guide.html#limitations
Basically we should not be using `plt.subplot` and should be using `GridSpec`.
I think this was recently added to the documentation so we didn't know before.
Another thing that we did not know is that `plt.subplots_adjust` and `plt.tight_layout` should not be used when constrained_layout is True.
In matplotlib 2.2.3 now constrained_layout is automatically is set to False if either of those is used. See: https://github.com/matplotlib/matplotlib/pull/11588/files
I think we should rethink our usage to make sure we don't go out of supported bounds of matplotlib's constrained layout. Probably then, we can remove a lot of hacks that we had to do.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.pad.base/-/issues/30Nightlies broken2019-03-22T12:53:58ZTiago de Freitas PereiraNightlies brokenHi guys,
Nightlies are broken because of this one.
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/160177
There's a test case with CASIA-SURF database that is failing.
Can someone check this?
ThanksHi guys,
Nightlies are broken because of this one.
https://gitlab.idiap.ch/bob/bob.nightlies/-/jobs/160177
There's a test case with CASIA-SURF database that is failing.
Can someone check this?
ThanksGuillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.pad.face/-/issues/28Unnecessary logger warning?2022-06-03T15:08:14ZAnjith GEORGEanjith.george@idiap.chUnnecessary logger warning?@heusch Do you actually need this warning?
`https://gitlab.idiap.ch/bob/bob.pad.face/blob/master/bob/pad/face/preprocessor/FaceCropAlign.py#L627`
It pops up every time when I have RGB image as input and I want grayscale as the output.@heusch Do you actually need this warning?
`https://gitlab.idiap.ch/bob/bob.pad.face/blob/master/bob/pad/face/preprocessor/FaceCropAlign.py#L627`
It pops up every time when I have RGB image as input and I want grayscale as the output.Guillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.devtools/-/issues/28The build number for the docs package is not increasing2019-06-17T15:12:12ZAmir MOHAMMADIThe build number for the docs package is not increasingOur docs package keeps failing to deploy:
* https://gitlab.idiap.ch/bob/docs/pipelines/30854
* https://gitlab.idiap.ch/bob/docs/pipelines/30855
* https://gitlab.idiap.ch/bob/docs/pipelines/30877
Looks like the build number is always 22.Our docs package keeps failing to deploy:
* https://gitlab.idiap.ch/bob/docs/pipelines/30854
* https://gitlab.idiap.ch/bob/docs/pipelines/30855
* https://gitlab.idiap.ch/bob/docs/pipelines/30877
Looks like the build number is always 22.https://gitlab.idiap.ch/bob/bob.measure/-/issues/25Moving biometrics-related functionality to bob.bio.base2018-10-16T06:34:31ZAndré AnjosMoving biometrics-related functionality to bob.bio.baseAs Bob keeps its trajectory to serve more types of systems, it becomes less and less obvious to keep biometrics-related functionality inside this package. I'm proposing we move those into `bob.bio.base`, which is the place they should ha...As Bob keeps its trajectory to serve more types of systems, it becomes less and less obvious to keep biometrics-related functionality inside this package. I'm proposing we move those into `bob.bio.base`, which is the place they should have been in the first place.
A few things that come to mind:
* All score loading/saving functionality
* OpenBR exchange support
* The scripts, which are tunned for Biometrics-style reporting (and can only load biometric score files)
* Not sure about all the identification stuff, maybe generic enough to keep here?
Thanks for your feedback.May 2017 HackathonGuillaume HEUSCHGuillaume HEUSCHhttps://gitlab.idiap.ch/bob/bob.bio.base/-/issues/61FAIL: bob.bio.base.test.test_algorithms.test_plda2017-08-07T13:07:35ZAmir MOHAMMADIFAIL: bob.bio.base.test.test_algorithms.test_plda```
======================================================================
FAIL: bob.bio.base.test.test_algorithms.test_plda
----------------------------------------------------------------------
Traceback (most recent call last):
File...```
======================================================================
FAIL: bob.bio.base.test.test_algorithms.test_plda
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/gitlab-runner/builds/0d638152/2/bob/bob.bio.base/build-prefix/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/gitlab-runner/builds/0d638152/2/bob/bob.bio.base/build-prefix/lib/python2.7/site-packages/bob/bio/base/test/test_algorithms.py", line 340, in test_plda
assert plda1.plda_base.is_similar_to(plda3.plda_base)
AssertionError:
-------------------- >> begin captured logging << --------------------
bob.bio.base: INFO: -> Training LinearMachine using PCA
bob.bio.base: INFO: -> limiting PCA subspace to 10 dimensions
bob.bio.base: INFO: -> Training PLDA base machine
bob.learn.em: INFO: Iteration = 0/1
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
```
@tiago.pereira could this because of our changes in bob.math? related to https://gitlab.idiap.ch/bob/bob.math/issues/10Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.extension/-/issues/48Do not include -isystem /usr/include in compile parameters2018-05-02T07:49:13ZAmir MOHAMMADIDo not include -isystem /usr/include in compile parametersSee: https://groups.google.com/forum/#!topic/bob-devel/vDCKfTWEh-s
>Environment: archlinux with gcc 7.2.1
Have installed bob.extension successfully by `pip install --user bob.extension`.
Then, when I `pip install --user bob.blitz`, got ...See: https://groups.google.com/forum/#!topic/bob-devel/vDCKfTWEh-s
>Environment: archlinux with gcc 7.2.1
Have installed bob.extension successfully by `pip install --user bob.extension`.
Then, when I `pip install --user bob.blitz`, got the following error:
```
running install
running bdist_egg
running egg_info
creating bob.blitz.egg-info
writing bob.blitz.egg-info/PKG-INFO
writing dependency_links to bob.blitz.egg-info/dependency_links.txt
writing requirements to bob.blitz.egg-info/requires.txt
writing top-level names to bob.blitz.egg-info/top_level.txt
writing manifest file 'bob.blitz.egg-info/SOURCES.txt'
reading manifest file 'bob.blitz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'bob.blitz.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/bob
copying bob/__init__.py -> build/lib.linux-x86_64-3.6/bob
creating build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/__init__.py -> build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/extension.py -> build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/test.py -> build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/api.cpp -> build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/array.cpp -> build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/main.cpp -> build/lib.linux-x86_64-3.6/bob/blitz
copying bob/blitz/version.cpp -> build/lib.linux-x86_64-3.6/bob/blitz
creating build/lib.linux-x86_64-3.6/bob/blitz/include
creating build/lib.linux-x86_64-3.6/bob/blitz/include/bob.blitz
copying bob/blitz/include/bob.blitz/capi.h -> build/lib.linux-x86_64-3.6/bob/blitz/include/bob.blitz
copying bob/blitz/include/bob.blitz/cleanup.h -> build/lib.linux-x86_64-3.6/bob/blitz/include/bob.blitz
copying bob/blitz/include/bob.blitz/config.h -> build/lib.linux-x86_64-3.6/bob/blitz/include/bob.blitz
copying bob/blitz/include/bob.blitz/cppapi.h -> build/lib.linux-x86_64-3.6/bob/blitz/include/bob.blitz
running build_ext
building 'bob.blitz.version' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/bob
creating build/temp.linux-x86_64-3.6/bob/blitz
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstac$
-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -Wno-strict-aliasing -DBOB_EXT_MODULE_PREFIX="bob.blitz" -DBOB_EXT_MODULE_NAME="version" $
DBOB_EXT_ENTRY_NAME=PyInit_version -DBOB_EXT_MODULE_VERSION="2.0.15b0" -DHAVE_BOOST=1 -DBOOST_VERSION="1.66.0" -DHAVE_BLITZ=1 -DBLITZ_VERSION="0.10" -DPY_ARRAY_UNIQUE_SYMBOL=BOB_BLITZ_NUMPY_C_API
-DNO_IMPORT_ARRAY=1 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/home/yuxinwu/install/bob.blitz/bob/blitz/include -I/home/yuxinwu/.local/lib/python3.6/site-packages/bob/extension/include -I/usr$
include/python3.6m -c bob/blitz/version.cpp -o build/temp.linux-x86_64-3.6/bob/blitz/version.o -std=c++0x -isystem /home/yuxinwu/.local/lib/python3.6/site-packages/numpy/core/include -isystem /us$
/include
In file included from /usr/include/boost/config/platform/linux.hpp:15:0,
from /usr/include/boost/config.hpp:57,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:17,
from /usr/include/boost/shared_ptr.hpp:17,
from /home/yuxinwu/install/bob.blitz/bob/blitz/include/bob.blitz/cleanup.h:13,
from /home/yuxinwu/install/bob.blitz/bob/blitz/include/bob.blitz/config.h:22,
from bob/blitz/version.cpp:10:
/usr/include/c++/7.2.1/cstdlib:75:15: fatal error: stdlib.h: No such file or directory
#include_next <stdlib.h>
^~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1
```
>The reason is because, the command line has `-isystem /usr/include`.
>For new version of gcc, you should not compile with `-isystem /usr/include`. See: https://stackoverflow.com/questions/37218953/isystem-on-a-system-include-directory-causes-errors
>By looking at `bob.extension` source code, I found that `/usr/include` comes from `boost.include_directory`, defined in `bob.extension.boost`. It is then added as a system-include directory inside `bob.extension.__init__`.
>I think this is an abuse of `-isystem`. Please fix. Thanks.André AnjosAndré Anjoshttps://gitlab.idiap.ch/bob/bob.bio.spear/-/issues/31Mod 4Hz preprocessor cannot handle mute files properly2018-05-18T15:14:16ZAmir MOHAMMADIMod 4Hz preprocessor cannot handle mute files properlyI tested this preprocessor on a mute audio file (all `0` numbers) and the labels are all `1`.
This is wrong. I have not tested other preprocessor but they should be tested too.I tested this preprocessor on a mute audio file (all `0` numbers) and the labels are all `1`.
This is wrong. I have not tested other preprocessor but they should be tested too.https://gitlab.idiap.ch/bob/bob/-/issues/250Compilation instructions from source have an extra `bob` item2018-04-17T11:31:56ZManuel Günthersiebenkopf@googlemail.comCompilation instructions from source have an extra `bob` itemFor installing bob from source, there is a script provided here:
https://gitlab.idiap.ch/bob/bob/blob/10e4995c5f68f79f2ddbba4feb4b1cc52880753c/doc/source.rst
In this script, 8 levels of bob packages are listed. While the first seven lev...For installing bob from source, there is a script provided here:
https://gitlab.idiap.ch/bob/bob/blob/10e4995c5f68f79f2ddbba4feb4b1cc52880753c/doc/source.rst
In this script, 8 levels of bob packages are listed. While the first seven levels of packages install all bob packages in the latest versions, the last level, which only includes `bob` removes some of the previously installed packages and replaces them with older versions, which are pin-pointed in the `bob` package.
Is there any reason why the `bob` package is mentioned in the last stage? Wouldn't it make more sense to remove that?https://gitlab.idiap.ch/bob/nightlies/-/issues/34We need to update the README2018-05-08T08:22:25ZTiago de Freitas PereiraWe need to update the READMEThe README content is obsoleteThe README content is obsoleteTiago de Freitas PereiraTiago de Freitas Pereira