Preparing release

.gitlab-ci.yml

@@ -29,11 +29,17 @@ variables:
     - git clean -ffdx
     - curl --silent https://gitlab.idiap.ch/bob/bob/snippets/7/raw | tr -d '\r' > bootstrap-conda.sh
     - chmod 755 ./bootstrap-conda.sh
+    - sed 1d -i requirements.txt # GAMBIT to remove pillow<3
     - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
   variables: &build_variables
     BOB_DOCUMENTATION_SERVER: "http://www.idiap.ch/software/bob/docs/latest/bob/%s/master/"
   script:
-    - ./bin/buildout
+    - ./bin/buildout -c buildout-before-patch.cfg
+    - wget https://www.idiap.ch/software/bob/databases/latest/PythonFaceEvaluation.tar.bz2
+    - mkdir PythonFaceEvaluation
+    - tar -xjf PythonFaceEvaluation.tar.bz2 -C PythonFaceEvaluation
+    - ./bin/patch_CSU.py PythonFaceEvaluation
+    - ./bin/buildout buildout:csu-dir=./PythonFaceEvaluation
     - if [ -x ./bin/bob_dbmanage.py ]; then ./bin/bob_dbmanage.py all download --force; fi
     - ./bin/sphinx-build doc sphinx
     - ./bin/python setup.py bdist_wheel --python-tag ${WHEEL_TAG}
@@ -45,6 +51,7 @@ variables:
       - bootstrap-conda.sh
       - dist/
       - sphinx/
+      - PythonFaceEvaluation/
 
 
 # Template for building on a Linux machine
@@ -74,11 +81,14 @@ variables:
 .test_template: &test_job
   stage: test
   before_script:
+    - sed 1d -i requirements.txt # GAMBIT to remove pillow<3 
     - ./bootstrap-conda.sh ${CONDA_FOLDER} ${PYTHON_VER} ${CONDA_PREFIX}
     - source ${CONDA_FOLDER}/bin/activate ${CONDA_PREFIX}
-    - pip install --use-wheel --no-index --pre dist/*.whl
+    - conda install --yes -c conda-forge -p ${CONDA_PREFIX} jpeg==9b opencv==2.4.12
+    - pip install --use-wheel --no-index --pre dist/*.whl    
   script:
-    - cd ${CONDA_PREFIX}
+    - cd ${CONDA_PREFIX}    
+    - export PYTHONPATH="../PythonFaceEvaluation/src:$PYTHONPATH"
     - python -c "from ${CI_PROJECT_NAME} import get_config; print(get_config())"
     - coverage run --source=${CI_PROJECT_NAME} ./bin/nosetests -sv ${CI_PROJECT_NAME}
     - coverage report
@@ -137,118 +147,17 @@ test_linux_27:
   tags:
     - conda-linux
 
-wheels_linux_27:
-  <<: *wheels_job
+docs_linux_27:
+  <<: *docs_job
   dependencies:
     - build_linux_27
   tags:
     - conda-linux
 
-
-# Linux + Python 3.4: Builds and tests
-build_linux_34:
-  <<: *linux_build_job
-  variables: &linux_34_build_variables
-    <<: *linux_build_variables
-    PYTHON_VER: "3.4"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-linux
-
-test_linux_34:
-  <<: *test_job
-  variables: *linux_34_build_variables
-  dependencies:
-    - build_linux_34
-  tags:
-    - conda-linux
-
-
-# Linux + Python 3.5: Builds, tests, uploads wheel
-build_linux_35:
-  <<: *linux_build_job
-  variables: &linux_35_build_variables
-    <<: *linux_build_variables
-    PYTHON_VER: "3.5"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-linux
-
-test_linux_35:
-  <<: *test_job
-  variables: *linux_35_build_variables
-  dependencies:
-    - build_linux_35
-  tags:
-    - conda-linux
-
-wheels_linux_35:
+wheels_linux_27:
   <<: *wheels_job
   dependencies:
-    - build_linux_35
-  tags:
-    - conda-linux
-
-docs_linux_35:
-  <<: *docs_job
-  dependencies:
-    - build_linux_35
+    - build_linux_27
   tags:
     - conda-linux
 
-
-# Mac OSX + Python 2.7: Builds and tests
-build_macosx_27:
-  <<: *macosx_build_job
-  variables: &macosx_27_build_variables
-    <<: *macosx_build_variables
-    PYTHON_VER: "2.7"
-    WHEEL_TAG: "py27"
-  tags:
-    - conda-macosx
-
-test_macosx_27:
-  <<: *test_job
-  variables: *macosx_27_build_variables
-  dependencies:
-    - build_macosx_27
-  tags:
-    - conda-macosx
-
-
-# Mac OSX + Python 3.4: Builds and tests
-build_macosx_34:
-  <<: *macosx_build_job
-  variables: &macosx_34_build_variables
-    <<: *macosx_build_variables
-    PYTHON_VER: "3.4"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-macosx
-
-test_macosx_34:
-  <<: *test_job
-  variables: *macosx_34_build_variables
-  dependencies:
-    - build_macosx_34
-  tags:
-    - conda-macosx
-
-
-# Mac OSX + Python 3.5: Builds and tests
-build_macosx_35:
-  <<: *macosx_build_job
-  variables: &macosx_35_build_variables
-    <<: *macosx_build_variables
-    PYTHON_VER: "3.5"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-macosx
-
-test_macosx_35:
-  <<: *test_job
-  variables: *macosx_35_build_variables
-  dependencies:
-    - build_macosx_35
-  tags:
-    - conda-macosx
\ No newline at end of file

bob/bio/csu/algorithm/LDAIR.py

@@ -7,7 +7,7 @@ import bob.bio.base
 from .. import utils
 
 class LDAIR (bob.bio.base.algorithm.Algorithm):
-  """This class defines a wrapper for the :py:class:`facerec2010.baseline.lda.LRLDA` class to be used as an image :py:class:`bob.bio.base.algorithm.Algorithm`.
+  """This class defines a wrapper for the `facerec2010.baseline.lda.LRLDA` class to be used as an image :py:class:`bob.bio.base.algorithm.Algorithm`.
 
   **Parameters:**
 
@@ -66,12 +66,12 @@ class LDAIR (bob.bio.base.algorithm.Algorithm):
 
     **Parameters:**
 
-    enroll_features : [:py:class:`facerec2010.baseline.common.FaceRecord`]
+    enroll_features : [`facerec2010.baseline.common.FaceRecord`]
       The features used to enroll the model.
 
     **Returns:**
 
-    model : [:py:class:`facerec2010.baseline.common.FaceRecord`]
+    model : [`facerec2010.baseline.common.FaceRecord`]
       The model, which is identical to the ``enroll_features``.
     """
     [self._check_feature(f) for f in enroll_features]
@@ -85,7 +85,7 @@ class LDAIR (bob.bio.base.algorithm.Algorithm):
 
     **Parameters:**
 
-    model : [:py:class:`facerec2010.baseline.common.FaceRecord`]
+    model : [`facerec2010.baseline.common.FaceRecord`]
       The model to be written.
 
     model_file : str
@@ -107,7 +107,7 @@ class LDAIR (bob.bio.base.algorithm.Algorithm):
 
     **Returns:**
 
-    model : [:py:class:`facerec2010.baseline.common.FaceRecord`]
+    model : [`facerec2010.baseline.common.FaceRecord`]
       The model read from file.
     """
     # just read the model from .pkl file
@@ -123,10 +123,10 @@ class LDAIR (bob.bio.base.algorithm.Algorithm):
 
     **Parameters:**
 
-    model : [:py:class:`facerec2010.baseline.common.FaceRecord`]
+    model : [`facerec2010.baseline.common.FaceRecord`]
       The model to compare, which is actually a list of extracted features.
 
-    probe : :py:class:`facerec2010.baseline.common.FaceRecord`
+    probe : `facerec2010.baseline.common.FaceRecord`
       The probe to compare.
 
     **Returns**:

bob/bio/csu/algorithm/LRPCA.py

@@ -9,7 +9,7 @@ from .. import utils
 
 
 class LRPCA (bob.bio.base.algorithm.Algorithm):
-  """This class defines a wrapper for the :py:class:`facerec2010.baseline.lda.LRPCA` class to be used as an image :py:class:`bob.bio.base.algorithm.Algorithm`.
+  """This class defines a wrapper for the `facerec2010.baseline.lda.LRPCA` class to be used as an image :py:class:`bob.bio.base.algorithm.Algorithm`.
 
   **Parameters:**
 
@@ -58,7 +58,7 @@ class LRPCA (bob.bio.base.algorithm.Algorithm):
 
     **Returns:**
 
-    model : [:py:class:`facerec2010.baseline.pca.FaceRecord`]
+    model : [`facerec2010.baseline.pca.FaceRecord`]
       The model, which a collection of face records, storing the given ``enroll_features``.
     """
     # no rule to enroll features in the LRPCA setup, so we just store all features
@@ -76,7 +76,7 @@ class LRPCA (bob.bio.base.algorithm.Algorithm):
 
     **Parameters:**
 
-    model : [:py:class:`facerec2010.baseline.pca.FaceRecord`]
+    model : [`facerec2010.baseline.pca.FaceRecord`]
       The model to be written.
 
     model_file : str
@@ -98,7 +98,7 @@ class LRPCA (bob.bio.base.algorithm.Algorithm):
 
     **Returns:**
 
-    model : [:py:class:`facerec2010.baseline.pca.FaceRecord`]
+    model : [`facerec2010.baseline.pca.FaceRecord`]
       The model read from file.
     """
     # just read the model from .pkl file
@@ -112,7 +112,7 @@ class LRPCA (bob.bio.base.algorithm.Algorithm):
 
     **Parameters:**
 
-    model : [:py:class:`facerec2010.baseline.pca.FaceRecord`]
+    model : [`facerec2010.baseline.pca.FaceRecord`]
       The model to compare, which is actually a list of extracted features.
 
     probe : :py:class:`numpy.ndarray`

bob/bio/csu/extractor/LDAIR.py

@@ -13,7 +13,7 @@ logger = logging.getLogger("bob.bio.csu")
 from .. import utils
 
 class LDAIR (bob.bio.base.extractor.Extractor):
-  """This class defines a wrapper for the :py:class:`facerec2010.baseline.lda.LRLDA` class to be used as an image :py:class:`bob.bio.base.extractor.Extractor`.
+  """This class defines a wrapper for the `facerec2010.baseline.lda.LRLDA` class to be used as an image :py:class:`bob.bio.base.extractor.Extractor`.
 
   **Parameters:**
 
@@ -127,7 +127,7 @@ class LDAIR (bob.bio.base.extractor.Extractor):
 
     **Returns:**
 
-    extracted : :py:class:`facerec2010.baseline.common.FaceRecord`
+    extracted : `facerec2010.baseline.common.FaceRecord`
       The extracted image feature.
     """
     self._check_image(image)
@@ -144,7 +144,7 @@ class LDAIR (bob.bio.base.extractor.Extractor):
 
     **Parameters:**
 
-    feature : :py:class:`facerec2010.baseline.common.FaceRecord`
+    feature : `facerec2010.baseline.common.FaceRecord`
       The extracted feature to be written.
 
     feature_file : str or :py:class:`bob.io.base.HDF5File`
@@ -167,7 +167,7 @@ class LDAIR (bob.bio.base.extractor.Extractor):
 
     **Returns:**
 
-    feature : :py:class:`facerec2010.baseline.common.FaceRecord`
+    feature : `facerec2010.baseline.common.FaceRecord`
       The read feature.
     """
     # read the feature from .pkl file

bob/bio/csu/extractor/LRPCA.py

@@ -13,7 +13,7 @@ import logging
 logger = logging.getLogger("bob.bio.csu")
 
 class LRPCA (bob.bio.base.extractor.Extractor):
-  """This class defines a wrapper for the :py:class:`facerec2010.baseline.lda.LRPCA` class to be used as an image :py:class:`bob.bio.base.extractor.Extractor`.
+  """This class defines a wrapper for the `facerec2010.baseline.lda.LRPCA` class to be used as an image :py:class:`bob.bio.base.extractor.Extractor`.
 
   **Parameters:**
 

bob/bio/csu/preprocessor/LDAIR.py

@@ -8,7 +8,7 @@ import bob.bio.base
 import bob.bio.face
 
 class LDAIR (bob.bio.face.preprocessor.FaceCrop):
-  """This class defines a wrapper for the :py:class:`facerec2010.baseline.lda.LRLDA` class to be used as an image :py:class:`bob.bio.base.preprocessor.Preprocessor`.
+  """This class defines a wrapper for the `facerec2010.baseline.lda.LRLDA` class to be used as an image :py:class:`bob.bio.base.preprocessor.Preprocessor`.
 
   **Parameters:**
 
@@ -24,11 +24,12 @@ class LDAIR (bob.bio.face.preprocessor.FaceCrop):
   """
 
   def __init__(self, REGION_ARGS = facerec2010.baseline.lda.CohortLDA_REGIONS, REGION_KEYWORDS = facerec2010.baseline.lda.CohortLDA_KEYWORDS, face_detector = None):
-    bob.bio.base.preprocessor.Preprocessor.__init__(self, REGION_ARGS=str(REGION_ARGS), REGION_KEYWORDS=str(REGION_KEYWORDS), face_detector=str(face_detector))
+    bob.bio.base.preprocessor.Preprocessor.__init__(self, REGION_ARGS=str(REGION_ARGS), REGION_KEYWORDS=str(REGION_KEYWORDS), face_detector=str(face_detector), read_original_data=self.read_original_data)
     self.ldair = facerec2010.baseline.lda.LRLDA(REGION_ARGS, **REGION_KEYWORDS)
     self.layers = len(REGION_ARGS)
     self.face_detector = bob.bio.face.preprocessor.utils.load_cropper(face_detector)
 
+
     if self.face_detector is not None:
       assert isinstance(self.face_detector, bob.bio.face.preprocessor.FaceDetect)
       # asign ourself to be the face cropper that should be used after face detection

bob/bio/csu/preprocessor/LRPCA.py

@@ -22,7 +22,7 @@ class LRPCA (bob.bio.face.preprocessor.FaceCrop):
   """
 
   def __init__(self, TUNING = facerec2010.baseline.lrpca.GBU_TUNING, face_detector = None):
-    bob.bio.base.preprocessor.Preprocessor.__init__(self, TUNING=str(TUNING), face_detector=str(face_detector))
+    bob.bio.base.preprocessor.Preprocessor.__init__(self, TUNING=str(TUNING), face_detector=str(face_detector), read_original_data=self.read_original_data)
     self.lrpca = facerec2010.baseline.lrpca.LRPCA(**TUNING)
     self.face_detector = bob.bio.face.preprocessor.utils.load_cropper(face_detector)
 

build.sh

+#!/usr/bin/env bash
+# Wed 21 Sep 2016 13:08:05 CEST
+
+source $(dirname ${0})/functions.sh
+
+run_cmd ./bin/buildout -c buildout-before-patch.cfg
+run_cmd wget https://www.idiap.ch/software/bob/databases/latest/PythonFaceEvaluation.tar.bz2
+run_cmd mkdir PythonFaceEvaluation
+run_cmd tar -xjf PythonFaceEvaluation.tar.bz2 -C PythonFaceEvaluation
+run_cmd ./bin/patch_CSU.py PythonFaceEvaluation
+run_cmd ./bin/buildout buildout:csu-dir=./PythonFaceEvaluation
+export PYTHONPATH="PythonFaceEvaluation:$PYTHONPATH"
+
+if [ -x ./bin/bob_dbmanage.py ]; then
+  run_cmd ./bin/bob_dbmanage.py all download --force;
+fi
+
+if [ -d ./doc ]; then
+  run_cmd ./bin/sphinx-build -n doc sphinx
+fi
+
+if [ -z "${WHEEL_TAG}" ]; then
+  # C/C++ extensions
+  run_cmd ./bin/python setup.py bdist_wheel
+else
+  # Python-only packages
+  run_cmd ./bin/python setup.py bdist_wheel --python-tag ${WHEEL_TAG}
+fi
+

buildout.cfg

@@ -4,11 +4,17 @@
 [buildout]
 parts = scripts
 develop = .
+          ${buildout:csu-dir}
+          
 eggs = bob.bio.csu
+       PythonFaceEvaluation
+       
 extensions = bob.buildout
 newest = false
 verbose = true
 
+csu-dir = [PATH_TO_YOUR_CSU_COPY]
+
 [scripts]
 recipe = bob.buildout:scripts
-dependent-scripts = true
+dependent-scripts = true
\ No newline at end of file

develop.cfg

@@ -30,7 +30,6 @@ develop = src/bob.extension
           src/bob.learn.em
           src/bob.measure
           src/bob.db.base
-          src/bob.bio.db
           src/bob.db.atnt
           src/bob.bio.base
           src/bob.learn.boosting
@@ -64,7 +63,6 @@ bob.learn.linear = git https://gitlab.idiap.ch/bob/bob.learn.linear
 bob.learn.em = git https://gitlab.idiap.ch/bob/bob.learn.em
 bob.measure = git https://gitlab.idiap.ch/bob/bob.measure
 bob.db.base = git https://gitlab.idiap.ch/bob/bob.db.base
-bob.bio.db = git https://gitlab.idiap.ch/bob/bob.bio.db
 bob.db.atnt = git https://gitlab.idiap.ch/bob/bob.db.atnt
 bob.bio.base = git https://gitlab.idiap.ch/bob/bob.bio.base
 bob.learn.boosting = git https://gitlab.idiap.ch/bob/bob.learn.boosting

doc/installation.rst

@@ -37,7 +37,7 @@ If you haven't patched it yet, please follow the set of instructions:
       $ ./bin/patch_CSU.py [PATH_TO_YOUR_CSU_COPY]
 
    If you get any error message, the sources of the CSU might have changed (the latest test was done in December 2012).
-   Please file a bug report in `our GitHub page <http://www.github.com/bioidiap/xfacereclib.extension.CSU>`_ to inform us so that we can provide a new patch.
+   Please file a bug report in `our google groups page <https://groups.google.com/forum/#!forum/bob-devel>`_ to inform us so that we can provide a new patch.
 
 
 4. Update the CSU toolkit path in the *buildout.cfg* file by setting the ``csu-dir`` variable via replacing the ``[PATH_TO_YOUR_CSU_COPY]`` with your actual directory:

requirements.txt

-setuptools
 pillow<3
+setuptools
 bob.extension
 bob.blitz
 bob.core
@@ -11,6 +11,5 @@ bob.sp
 bob.learn.em
 bob.measure
 bob.db.base
-bob.bio.db
 bob.bio.base
-bob.bio.face # for test purposes
+bob.bio.face

setup.py

@@ -20,8 +20,8 @@ setup(
 
     url = 'https://gitlab.idiap.ch/bob/bob.bio.csu',
     license = 'BSD',
-    author = 'Amir Mohammadi',
-    author_email = 'amir.mohammadi@idiap.ch',
+    author = 'Manuel Gunther',
+    author_email = 'siebenkopf@googlemail.com',
     keywords = 'bob',
 
     # If you have a better, long description of your package, place it on the

test.sh

+#!/usr/bin/env bash
+# Wed 21 Sep 2016 13:08:05 CEST
+
+source $(dirname ${0})/functions.sh
+
+run_cmd cd ${PREFIX}
+
+run_cmd export PYTHONPATH=\"../PythonFaceEvaluation/src:$PYTHONPATH\"
+
+# The tests:
+run_cmd ${PREFIX}/bin/python ${BOB_PREFIX_PATH}/bin/coverage run --source=${CI_PROJECT_NAME} ${BOB_PREFIX_PATH}/bin/nosetests -sv ${CI_PROJECT_NAME}
+run_cmd ${PREFIX}/bin/python ${BOB_PREFIX_PATH}/bin/coverage report
+run_cmd ${PREFIX}/bin/python ${BOB_PREFIX_PATH}/bin/sphinx-build -b doctest ${CI_PROJECT_DIR}/doc ${CI_PROJECT_NAME}/sphinx
+
+run_cmd cd ${CI_PROJECT_DIR}