Merge branch 'issue-16' into 'master'

Port to new CI (closes #16)

Closes #16

See merge request !40

.gitlab-ci.yml

-# This build file heavily uses template features from YAML so it is generic
-# enough for any Bob project. Don't modify it unless you know what you're
-# doing.
+# This build file uses template features from YAML so it is generic enough for
+# any Bob project. Don't modify it unless you know what you're doing.
 
+# Definition of global variables (all stages)
+variables:
+  CONDA_ROOT: "${CI_PROJECT_DIR}/miniconda"
 
-# Definition of our build pipeline
+
+# Definition of our build pipeline order
 stages:
   - build
-  - test
-  - docs
-  - wheels
   - deploy
+  - pypi
 
 
-# ---------
-# Templates
-# ---------
-
-# Template for the build stage
-# Needs to run on all supported architectures, platforms and python versions
+# Build targets
 .build_template: &build_job
   stage: build
   before_script:
-    - git clean -ffdx
     - mkdir _ci
     - curl --silent "https://gitlab.idiap.ch/bob/bob.admin/raw/master/gitlab/install.sh" > _ci/install.sh
     - chmod 755 _ci/install.sh
-    - ./_ci/install.sh _ci #updates
+    - ./_ci/install.sh _ci master #installs ci support scripts
     - ./_ci/before_build.sh
   script:
     - ./_ci/build.sh
   after_script:
     - ./_ci/after_build.sh
-  artifacts:
-    expire_in: 1 week
+  cache: &build_caches
     paths:
-      - _ci/
-      - dist/
-      - sphinx/
-
-
-# Template for the test stage - re-installs from uploaded wheels
-# Needs to run on all supported architectures, platforms and python versions
-.test_template: &test_job
-  stage: test
-  before_script:
-    - ./_ci/install.sh _ci #updates
-    - ./_ci/before_test.sh
-  script:
-    - ./_ci/test.sh
-  after_script:
-    - ./_ci/after_test.sh
-
-
-# Template for the wheel uploading stage
-# Needs to run against one supported architecture, platform and python version
-.wheels_template: &wheels_job
-  stage: wheels
-  environment: intranet
-  only:
-    - master
-    - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
-  before_script:
-    - ./_ci/install.sh _ci #updates
-    - ./_ci/before_wheels.sh
-  script:
-    - ./_ci/wheels.sh
-  after_script:
-    - ./_ci/after_wheels.sh
-
-
-# Template for (latest) documentation upload stage
-# Only one real job needs to do this
-.docs_template: &docs_job
-  stage: docs
-  environment: intranet
-  only:
-    - master
-  before_script:
-    - ./_ci/install.sh _ci #updates
-    - ./_ci/before_docs.sh
-  script:
-    - ./_ci/docs.sh
-  after_script:
-    - ./_ci/after_docs.sh
-
-
-# Template for the deployment stage - re-installs from uploaded wheels
-# Needs to run on a single architecture only
-# Will deploy your package to PyPI and other required services
-# Only runs for tags
-.deploy_template: &deploy_job
-  stage: deploy
-  environment: internet
-  only:
-    - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
-  except:
-    - branches
-  before_script:
-    - ./_ci/install.sh _ci #updates
-    - ./_ci/before_deploy.sh
-  script:
-    - ./_ci/deploy.sh
-  after_script:
-    - ./_ci/after_deploy.sh
-
+      - miniconda.sh
+      - ${CONDA_ROOT}/pkgs/*.tar.bz2
+      - ${CONDA_ROOT}/pkgs/urls.txt
 
-# -------------
-# Build Targets
-# -------------
 
-# Linux + Python 2.7: Builds, tests, uploads wheel and deploys (if needed)
-build_linux_27:
+.build_linux_template: &linux_build_job
   <<: *build_job
-  variables: &linux_27_build_variables
-    PYTHON_VERSION: "2.7"
-    WHEEL_TAG: "py27"
-  tags:
-    - conda-linux
-
-test_linux_27:
-  <<: *test_job
-  variables: *linux_27_build_variables
-  dependencies:
-    - build_linux_27
-  tags:
-    - conda-linux
-
-wheels_linux_27:
-  <<: *wheels_job
-  variables: *linux_27_build_variables
-  dependencies:
-    - build_linux_27
-  tags:
-    - conda-linux
-
-deploy_linux_27:
-  <<: *deploy_job
-  variables: *linux_27_build_variables
-  dependencies:
-    - build_linux_27
   tags:
-    - conda-linux
+    - docker
+  image: continuumio/conda-concourse-ci
+  artifacts:
+    expire_in: 1 week
+    paths:
+      - _ci/
+      - ${CONDA_ROOT}/conda-bld/linux-64/*.tar.bz2
+  cache:
+    <<: *build_caches
+    key: "linux-cache"
 
 
-# Linux + Python 3.5: Builds, tests and uploads wheel
-build_linux_35:
+.build_macosx_template: &macosx_build_job
   <<: *build_job
-  variables: &linux_35_build_variables
-    PYTHON_VERSION: "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
+    - macosx
+  artifacts:
+    expire_in: 1 week
+    paths:
+      - _ci/
+      - ${CONDA_ROOT}/conda-bld/osx-64/*.tar.bz2
+  cache:
+    <<: *build_caches
+    key: "macosx-cache"
 
-wheels_linux_35:
-  <<: *wheels_job
-  variables: *linux_35_build_variables
-  dependencies:
-    - build_linux_35
-  tags:
-    - conda-linux
 
-docs_linux_35:
-  <<: *docs_job
-  variables: *linux_35_build_variables
-  dependencies:
-    - build_linux_35
-  tags:
-    - conda-linux
+build_linux_27:
+  <<: *linux_build_job
+  variables:
+    PYTHON_VERSION: "2.7"
 
 
-# Linux + Python 3.6: Builds and tests
 build_linux_36:
-  <<: *build_job
-  variables: &linux_36_build_variables
+  <<: *linux_build_job
+  variables:
     PYTHON_VERSION: "3.6"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-linux
-
-test_linux_36:
-  <<: *test_job
-  variables: *linux_36_build_variables
-  dependencies:
-    - build_linux_36
-  tags:
-    - conda-linux
+    BUILD_EGG: "true"
+  artifacts:
+    expire_in: 1 week
+    paths:
+      - _ci/
+      - dist/*.zip
+      - sphinx
+      - ${CONDA_ROOT}/conda-bld/linux-64/*.tar.bz2
 
 
-# Mac OSX + Python 2.7: Builds and tests
 build_macosx_27:
-  <<: *build_job
-  variables: &macosx_27_build_variables
+  <<: *macosx_build_job
+  variables:
     PYTHON_VERSION: "2.7"
-    WHEEL_TAG: "py27"
-  tags:
-    - conda-macosx
 
-test_macosx_27:
-  <<: *test_job
-  variables: *macosx_27_build_variables
+
+build_macosx_36:
+  <<: *macosx_build_job
+  variables:
+    PYTHON_VERSION: "3.6"
+
+
+# Deploy targets
+.deploy_template: &deploy_job
+  stage: deploy
+  before_script:
+    - ./_ci/install.sh _ci master #updates ci support scripts
+  script:
+    - ./_ci/deploy.sh
   dependencies:
+    - build_linux_27
+    - build_linux_36
     - build_macosx_27
+    - build_macosx_36
   tags:
-    - conda-macosx
+    - deployer
 
 
-# Mac OSX + Python 3.5: Builds and tests
-build_macosx_35:
-  <<: *build_job
-  variables: &macosx_35_build_variables
-    PYTHON_VERSION: "3.5"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-macosx
+deploy_beta:
+  <<: *deploy_job
+  environment: beta
+  only:
+    - master
 
-test_macosx_35:
-  <<: *test_job
-  variables: *macosx_35_build_variables
-  dependencies:
-    - build_macosx_35
-  tags:
-    - conda-macosx
 
+deploy_stable:
+  <<: *deploy_job
+  environment: stable
+  only:
+    - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
+  except:
+    - branches
 
-# Mac OSX + Python 3.6: Builds and tests
-build_macosx_36:
-  <<: *build_job
-  variables: &macosx_36_build_variables
-    PYTHON_VERSION: "3.6"
-    WHEEL_TAG: "py3"
-  tags:
-    - conda-macosx
 
-test_macosx_36:
-  <<: *test_job
-  variables: *macosx_36_build_variables
+pypi:
+  stage: pypi
+  environment: pypi
+  only:
+    - /^v\d+\.\d+\.\d+([abc]\d*)?$/  # PEP-440 compliant version (tags)
+  except:
+    - branches
+  before_script:
+    - ./_ci/install.sh _ci master #updates ci support scripts
+  script:
+    - ./_ci/pypi.sh
   dependencies:
-    - build_macosx_36
+    - build_linux_36
   tags:
-    - conda-macosx
+    - deployer

bob/bio/vein/database/utfvp.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-# Fri 04 Nov 2016 14:46:53 CET
+# Tue 27 Sep 2016 16:48:57 CEST
+
 
 from bob.bio.base.database import BioFile, BioDatabase
 
+from . import AnnotatedArray
+from ..preprocessor.utils import poly_to_mask
+
 
 class File(BioFile):
     """
-    Implements extra properties of vein files for the UTFVP Fingervein database
+    Implements extra properties of vein files for the UTFVP database
 
 
     Parameters:
 
-      f (object): Low-level file (or sample) object that is kept inside
+        f (object): Low-level file (or sample) object that is kept inside
 
     """
 
     def __init__(self, f):
 
-        super(File, self).__init__(client_id=f.client_id, path=f.path,
-                                   file_id=f.id)
+        super(File, self).__init__(client_id=f.unique_finger_name, path=f.path,
+            file_id=f.id)
         self.__f = f
 
 
+    def load(self, *args, **kwargs):
+        """(Overrides base method) Loads both image and mask"""
+
+        image = super(File, self).load(*args, **kwargs)
+        roi = self.__f.roi()
+        return AnnotatedArray(image, metadata=dict(roi=roi))
+
+
 class Database(BioDatabase):
     """
-    Implements verification API for querying UTFVP Fingervein database.
+    Implements verification API for querying UTFVP database.
     """
 
     def __init__(self, **kwargs):
@@ -34,22 +46,38 @@ class Database(BioDatabase):
         from bob.db.utfvp.query import Database as LowLevelDatabase
         self._db = LowLevelDatabase()
 
+        self.low_level_group_names = ('train', 'dev')
+        self.high_level_group_names = ('world', 'dev')
+
+    def groups(self):
+
+        return self.convert_names_to_highlevel(self._db.groups(),
+            self.low_level_group_names, self.high_level_group_names)
+
+    def client_id_from_model_id(self, model_id, group='dev'):
+        """Required as ``model_id != client_id`` on this database"""
+
+        return self._db.finger_name_from_model_id(model_id)
+
+
     def model_ids_with_protocol(self, groups=None, protocol=None, **kwargs):
-        protocol = protocol if protocol is not None else self.protocol
+
+        groups = self.convert_names_to_lowlevel(groups,
+            self.low_level_group_names, self.high_level_group_names)
         return self._db.model_ids(groups=groups, protocol=protocol)
 
+
     def objects(self, groups=None, protocol=None, purposes=None,
                 model_ids=None, **kwargs):
 
+        groups = self.convert_names_to_lowlevel(groups,
+            self.low_level_group_names, self.high_level_group_names)
         retval = self._db.objects(groups=groups, protocol=protocol,
-            purposes=purposes, model_ids=model_ids, **kwargs)
+                                  purposes=purposes, model_ids=model_ids,
+                                  **kwargs)
 
         return [File(f) for f in retval]
 
+
     def annotations(self, file):
         return None
-
-    def client_id_from_model_id(self, model_id, group='dev'):
-        """Required as ``model_id != client_id`` on this database"""
-
-        return self._db.get_client_id_from_model_id(model_id)

bob/bio/vein/tests/test_databases.py

@@ -14,8 +14,8 @@ def test_utfvp():
     module = bob.bio.base.load_resource('utfvp', 'config',
         preferred_package='bob.bio.vein')
     try:
-        check_database(module.database, protocol=module.protocol,
-            groups=('dev', 'eval'))
+        check_database(module.database, protocol='nomLeftIndex', groups=('dev',
+          'eval'))
     except IOError as e:
         raise SkipTest(
             "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
@@ -52,4 +52,4 @@ def test_putvein():
         check_database(module.database, protocol='wrist-LR_1', groups=('dev',))
     except IOError as e:
         raise SkipTest(
-            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)
\ No newline at end of file
+            "The database could not queried; probably the db.sql3 file is missing. Here is the error: '%s'" % e)

conda/meta.yaml

+{% set name = 'bob.bio.vein' %}
+{% set project_dir = environ.get('RECIPE_DIR') + '/..' %}
+
+package:
+  name: {{ name }}
+  version: {{ environ.get('BOB_PACKAGE_VERSION', '0.0.1') }}
+
+build:
+  entry_points:
+    - compare_rois.py = bob.bio.vein.script.compare_rois:main
+    - view_sample.py = bob.bio.vein.script.view_sample:main
+    - blame.py = bob.bio.vein.script.blame:main
+    - markdet.py = bob.bio.vein.script.markdet:main
+    - watershed_mask.py = bob.bio.vein.script.watershed_mask:main
+  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:
+  host:
+    - python {{ python }}
+    - setuptools {{ setuptools }}
+    - numpy {{ numpy }}
+    - scipy {{ scipy }}
+    - pillow {{ pillow }}
+    - schema {{ schema }}
+    - docopt {{ docopt }}
+    - scikit-image {{ scikit_image }}
+    - matplotlib {{ matplotlib }}
+    - bob.extension
+    - bob.core
+    - bob.io.base
+    - bob.io.matlab
+    - bob.io.image
+    - bob.ip.base
+    - bob.ip.color
+    - bob.bio.base
+    - bob.learn.linear
+    - bob.learn.activation
+    - bob.learn.mlp
+
+  run:
+    - python
+    - setuptools
+    - {{ pin_compatible('numpy') }}
+    - {{ pin_compatible('scipy') }}
+    - {{ pin_compatible('pillow') }}
+    - {{ pin_compatible('schema') }}
+    - {{ pin_compatible('docopt') }}
+    - {{ pin_compatible('scikit-image') }}
+    - {{ pin_compatible('matplotlib') }}
+
+test:
+  imports:
+    - {{ name }}
+  commands:
+    - compare_rois.py --help
+    - view_sample.py --help
+    - blame.py --help
+    - markdet.py --help
+    - watershed_mask.py --help
+    - nosetests --with-coverage --cover-package={{ name }} -sv {{ name }}
+    - sphinx-build -aEW {{ project_dir }}/doc {{ project_dir }}/sphinx
+    - sphinx-build -aEb doctest {{ project_dir }}/doc sphinx
+    - 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
+    - bob.db.utfvp
+    - bob.db.verafinger
+    - bob.db.fv3d
+    - bob.db.putvein
+
+about:
+  home: https://www.idiap.ch/software/bob/
+  license: GNU General Public License v3 (GPLv3)
+  summary: Vein Recognition Library
+  license_family: GPL

doc/conf.py

@@ -25,15 +25,9 @@ extensions = [
     'sphinx.ext.intersphinx',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
+    'sphinx.ext.mathjax',
     ]
 
-import sphinx
-if sphinx.__version__ >= "1.4.1":
-    extensions.append('sphinx.ext.imgmath')
-    imgmath_image_format = 'svg'
-else:
-    extensions.append('sphinx.ext.pngmath')
-
 # Be picky about warnings
 nitpicky = True
 

doc/index.rst

 .. vim: set fileencoding=utf-8 :
-.. date: Wed Jan 14 11:58:57 CEST 2015
 
+.. _bob.bio.vein:
 
 ====================================
  Biometric Vein Recognition Library

doc/references.rst

@@ -5,21 +5,21 @@
  References
 ============
 
-.. [KUU02] *M. Kono, H. Ueki and S. Umemura*, **Near-infrared finger vein patterns for personal identification**, Applied Optics, Vol. 41, Issue 35, pp. 7429-7436 (2002).
+.. #not used [KUU02] *M. Kono, H. Ueki and S. Umemura*, **Near-infrared finger vein patterns for personal identification**, Applied Optics, Vol. 41, Issue 35, pp. 7429-7436 (2002).
 
 .. [MNM04] *N. Miura, A. Nagasaka, and T. Miyatake*, **Feature extraction of finger vein patterns based on repeated line tracking and its application to personal identification. Machine Vision and Applications**, Vol. 15, Num. 4, pp. 194--203, 2004.
 
 .. [MNM05] *N. Miura, A. Nagasaka, and T. Miyatake*, **Extraction of Finger-Vein Pattern Using Maximum Curvature Points in Image Profiles**, Proceedings on IAPR conference on machine vision applications, Vol. 9 , pp. 347--350, 2005.
 
-.. [LLP09] *E.C. Lee, H.C. Lee and K.R. Park*, **Finger vein recognition using minutia-based alignment and local binary pattern-based feature extraction**, International Journal of Imaging Systems and Technology. Vol. 19, No. 3, pp. 175-178, September 2009.
+.. #not used [LLP09] *E.C. Lee, H.C. Lee and K.R. Park*, **Finger vein recognition using minutia-based alignment and local binary pattern-based feature extraction**, International Journal of Imaging Systems and Technology. Vol. 19, No. 3, pp. 175-178, September 2009.
 
-.. [ZY09] *J. Zhang and J. Yang*, **Finger-vein image enhancement based on combination of gray-level grouping and circular gabor filter** In International Conference on Information Engineering and Computer Science (ICIECS), pp. 1-4, Dec 2009.
+.. #not used [ZY09] *J. Zhang and J. Yang*, **Finger-vein image enhancement based on combination of gray-level grouping and circular gabor filter** In International Conference on Information Engineering and Computer Science (ICIECS), pp. 1-4, Dec 2009.
 
-.. [ZTXL09] *Jianjun Zhao, Hogliang Tian, Weixing Xu, and Xin Li*, **A New Approach to Hand Vein Image Enhancement**. In IEEE Second International Conference on Intelligent Computation Technology and Automation, ICICTA. Vol. 1, pp. 499-501. 2009.
+.. #not used [ZTXL09] *Jianjun Zhao, Hogliang Tian, Weixing Xu, and Xin Li*, **A New Approach to Hand Vein Image Enhancement**. In IEEE Second International Conference on Intelligent Computation Technology and Automation, ICICTA. Vol. 1, pp. 499-501. 2009.
 
 .. [HDLTL10] *B. Huang, Y. Dai, R. Li, D. Tang and W. Li*, **Finger-vein authentication based on wide line detector and pattern normalization**, Proceedings on 20th International Conference on Pattern Recognition (ICPR), 2010.
 
-.. [MD13] *L. Mirmohamadsadeghi and A. Drygajlo*, **Palm vein recognition using local texture patterns**, IET Biometrics, pp. 1-9, 2013.
+.. #not used [MD13] *L. Mirmohamadsadeghi and A. Drygajlo*, **Palm vein recognition using local texture patterns**, IET Biometrics, pp. 1-9, 2013.
 
 .. [TVM14] *Pedro Tome, Matthias Vanoni and Sébastien Marcel*, **On the Vulnerability of Finger Vein Recognition to Spoofing**, in: IEEE International Conference of the Biometrics Special Interest Group (BIOSIG), Darmstadt, Germay, pages 1 - 10, IEEE, 2014