Merge branch 'base-software-updates' into 'master'

Base software updates

Closes #57

See merge request bob/bob.conda!423

conda/beat-devel/meta.yaml

@@ -2,7 +2,7 @@
 {% set nopin = ['ca-certificates', 'certifi', 'openssl', 'libstdcxx-ng', 'libgcc-ng', 'libcxx', 'libcxxabi'] %}
 package:
   name: beat-devel
-  version: 2019.08.08
+  version: 2019.08.09
 
 build:
   # the build number must be zero all the time.
@@ -15,7 +15,7 @@ build:
 requirements:
   host:
     - python {{ python }}
-    - bob-devel 2019.08.08
+    - bob-devel 2019.08.09
     - docker-py 4.0.2
     - flask 1.0.2
     - flask-cors 3.0.7
@@ -26,7 +26,7 @@ requirements:
     - python-graphviz 0.8.4
     - pyzmq 17.1.2
     - simplejson 3.16.0
-    - sphinxcontrib-programoutput 0.11
+    - sphinxcontrib-programoutput 0.14
     - sphinxcontrib-httpdomain 1.7.0
     - psycopg2 2.7.6.1
   run:

conda/bob-devel/meta.yaml

@@ -2,9 +2,9 @@
 {% set nopin = ['ca-certificates', 'certifi', 'openssl', 'libstdcxx-ng', 'libgcc-ng', 'libcxx', 'libcxxabi'] %}
 package:
   name: bob-devel
-  # please update the version of beat-devel and update bob-devel's version there
-  # as well in the same merge request.
-  version: 2019.08.08
+  # please update the version of beat-devel and update bob-devel's version
+  # there as well in the same merge request.
+  version: 2019.08.09
 
 build:
   # the build number must be zero all the time.
@@ -17,9 +17,9 @@ build:
 requirements:
   host:
     - python {{ python }}
-    # IMPORTANT: To update this list, create a conda environment with all the below
-    # packages without any pinning. Once the environment is resolved, observe those
-    # versions and put them here.
+    # IMPORTANT: To update this list, create a conda environment with all the
+    # below packages without any pinning. Once the environment is resolved,
+    # observe those versions and put them here.
 
     # Dependency list of bob packages. Everything is pinned to allow for better
     # reproducibility.
@@ -29,7 +29,7 @@ requirements:
     - click-plugins 1.1.1
     - cmake 3.14.0
     - coverage 4.5.3
-    - cyvlfeat 0.4.6
+    - cyvlfeat 0.5.1
     - docopt 0.6.2
     # to make sure we get ffmpeg from our own channel which has more codecs
     - ffmpeg 4.0 hadceb68_1  # [linux]
@@ -47,22 +47,22 @@ requirements:
     - libsvm 3.22
     - libtiff 4.0.10
     - matplotlib 3.1.0
-    - menpo 0.8.1
-    - menpofit 0.5.0
+    - menpo 0.9.1
+    - menpofit 0.6.1
     - mkl 2019.4
-    - mne 0.15.2
-    - mr.developer 1.38
+    - mne 0.18.1
+    - mr.developer 2.0.0
     - nose 1.3.7
     - numpy 1.16.4
     - opencv 3.4.2
     - pillow 6.1.0
     - pkg-config 0.29.2
-    - pyedflib 0.1.11
+    - pyedflib 0.1.14
     - cudatoolkit 9.0  # [linux]
     - pytorch 1.1.0  # [linux]
     - pyyaml 5.1.1
     - requests 2.22.0
-    - schema 0.6.8
+    - schema 0.7.0
     - scikit-image 0.15.0
     - scikit-learn 0.21.2
     - scipy 1.2.1
@@ -76,9 +76,10 @@ requirements:
     - tensorflow 1.14.0
     - torchvision 0.3.0  # [linux]
     - vlfeat 0.9.21
-    - zc.buildout 2.12.2
+    - zc.buildout 2.13.2
     - zc.recipe.egg 2.0.7
-    # beat-devel direct dependencies that leak to bob-devel as indirect dependencies:
+    # beat-devel direct dependencies that leak to bob-devel as indirect
+    # dependencies:
     - termcolor 1.1.0
     # semi-supported dependencies (drop them if they conflict):
     - dlib 19.7

conda/cyvlfeat/meta.yaml

 {% set name = "cyvlfeat" %}
-{% set version = "0.4.6" %}
-{% set sha256 = "5bc5de3c2e40240b8cb6ff06d744fe92911635d7b61c3a034ba93f6297df4732" %}
+{% set version = "0.5.1" %}
+{% set sha256 = "816d0609c5f5a1b4e4a620a9cb204abe26c8cd6a166d077923242f6cf15c2c09" %}
 
 package:
   name: {{ name }}
@@ -12,7 +12,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 0
 
 requirements:
   build:
@@ -25,7 +25,6 @@ requirements:
     - cython {{ cython }}
     - numpy {{ numpy }}
     - vlfeat {{ vlfeat }}
-    # - msinttypes r26  # [win]
 
   run:
     - python

conda/ipdb/meta.yaml

-{% set version = "0.11" %}
+{% set version = "0.12.2" %}
 
 package:
   name: ipdb
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/i/ipdb/ipdb-{{ version }}.tar.gz
-  sha256: 7081c65ed7bfe7737f83fa4213ca8afd9617b42ff6b3f1daf9a3419839a2a00a
+  sha256: 473fdd798a099765f093231a8b1fabfa95b0b682fce12de0c74b61a4b4d8ee57
 
 build:
   number: 0
@@ -16,12 +16,12 @@ build:
 requirements:
   build:
     - python
-    - ipython >=5.0.0
+    - ipython >=5.1.0
     - setuptools
 
   run:
     - python
-    - ipython >=5.0.0
+    - ipython >=5.1.0
 
 test:
   requires:

conda/menpo/meta.yaml

 {% set name = "menpo" %}
-{% set version = "0.8.1" %}
-{% set sha256 = "3b74f1e598bb8ee561f3f48714be007ba7d4dc4a326a35125e436fa570e7e73f" %}
+{% set version = "0.9.1" %}
+{% set sha256 = "691f74ec6544bc56753b17a9f72d368f2928eaab5c2bf19673482552631683e9" %}
 
 package:
   name: {{ name }}
@@ -10,14 +10,9 @@ source:
   fn: {{ name }}-v{{ version }}.tar.gz
   url: https://github.com/menpo/menpo/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
-  patches:
-    # removes the pinning for scipy<1
-    # removes the pinning for matplotlib<2
-    # relaxes the pathlib pinning for python 2.x
-    - relax-pins.patch
 
 build:
-  number: 8
+  number: 0
   script: python setup.py install --single-version-externally-managed --record=record.txt
   run_exports:
     - {{ pin_subpackage(name, max_pin='x.x') }}
@@ -30,7 +25,6 @@ requirements:
   host:
     - python
     - setuptools
-    - pathlib 1.0
     - numpy {{ numpy }}
     - cython {{ cython }}
     - ffmpeg {{ ffmpeg }}
@@ -41,19 +35,20 @@ requirements:
     - {{ pin_compatible('numpy') }}
 
     # Scientific Python Stack
-    - scipy <1.3
-    - pillow >=3.0
+    - scipy >=1.0
+    - pillow >=4.0
 
     # Features
-    - cyvlfeat >=0.4.3,<0.5
+    - cyvlfeat >=0.5,<0.6
 
     # Visualization
-    - matplotlib
+    - matplotlib >=3.0
 
 test:
   requires:
     - mock
     - nose
+    - pytest
     - coverage
 
   files:
@@ -63,7 +58,7 @@ test:
     - {{ name }}
 
   commands:
-    - nosetests {{ name }} -v --with-coverage --cover-package={{ name }} --exclude=".*test_rasterize_matplotlib_basic_line.*" --exclude=".*homogeneous_test.*" --exclude=".*test_importing_v1_ljson_null_values.*"
+    - nosetests -v --exclude=".*test_labels.*" {{ name }}
     - conda inspect linkages -p $PREFIX {{ name }}  # [not win]
     - conda inspect objects -p $PREFIX {{ name }}  # [osx]
 
@@ -75,4 +70,3 @@ about:
 extra:
   recipe-maintainers:
     - anjos
-

conda/menpofit/meta.yaml

-{% set version = "0.5.0" %}
+{% set version = "0.6.1" %}
 
 package:
   name: menpofit
@@ -19,19 +19,20 @@ requirements:
 
   run:
     - python
-    - menpo >=0.8,<0.9
+    - menpo >=0.9,<0.10
     - scikit-learn >=0.16
 
 test:
   requires:
     - nose
+    - pytest
     - mock
 
   imports:
     - menpofit
 
   commands:
-    - nosetests menpofit
+    - nosetests -v menpofit
 
 about:
   home: https://github.com/menpo/menpofit/

conda/mne/meta.yaml

-{% set version = "0.15.2" %}
+{% set version = "0.18.1" %}
 
 package:
   name: mne
@@ -19,102 +19,19 @@ requirements:
 
   run:
     - python
-    - numpy >=1.8
-    - scipy >=0.12
-    - matplotlib >=1.3
+    - numpy >=1.11.3
+    - scipy >=0.17.1
+    - matplotlib >=1.5
     - scikit-learn >=0.18
-    - pandas >=0.12
+    - pandas >=0.18
 
 test:
 
-  requires:
-    - nose
-
-  source_files:
-    - mne/io/brainvision/tests/data/*
-    - mne/io/bti/tests/data/*
-    - mne/io/edf/tests/data/*
-    - mne/io/egi/tests/data/*
-    - mne/io/kit/tests/data/*
-    - mne/io/nicolet/tests/data/*
-    - mne/io/tests/data/*
-    - mne/preprocessing/tests/data/*
-
   imports:
     - mne
-    - mne.beamformer
-    - mne.beamformer.tests
-    - mne.channels
-    - mne.channels.tests
-    - mne.commands
-    - mne.commands.tests
-    - mne.connectivity
-    - mne.connectivity.tests
-    - mne.data
-    - mne.datasets
-    - mne.datasets._fake
-    - mne.datasets.brainstorm
-    - mne.datasets.eegbci
-    - mne.datasets.megsim
-    - mne.datasets.misc
-    - mne.datasets.multimodal
-    - mne.datasets.sample
-    - mne.datasets.somato
-    - mne.datasets.spm_face
-    - mne.datasets.testing
-    - mne.datasets.tests
-    - mne.decoding
-    - mne.decoding.tests
-    - mne.externals
-    - mne.externals.h5io
-    - mne.externals.tempita
-    - mne.forward
-    - mne.forward.tests
-    - mne.gui
-    - mne.gui.tests
-    - mne.inverse_sparse
-    - mne.inverse_sparse.tests
-    - mne.io
-    - mne.io.array
-    - mne.io.array.tests
-    - mne.io.brainvision
-    - mne.io.brainvision.tests
-    - mne.io.bti
-    - mne.io.bti.tests
-    - mne.io.cnt
-    - mne.io.cnt.tests
-    - mne.io.ctf
-    - mne.io.ctf.tests
-    - mne.io.edf
-    - mne.io.edf.tests
-    - mne.io.eeglab
-    - mne.io.egi
-    - mne.io.egi.tests
-    - mne.io.fiff
-    - mne.io.fiff.tests
-    - mne.io.kit
-    - mne.io.kit.tests
-    - mne.io.nicolet
-    - mne.io.nicolet.tests
-    - mne.io.tests
-    - mne.minimum_norm
-    - mne.minimum_norm.tests
-    - mne.preprocessing
-    - mne.preprocessing.tests
-    - mne.realtime
-    - mne.realtime.tests
-    - mne.simulation
-    - mne.simulation.tests
-    - mne.stats
-    - mne.stats.tests
-    - mne.tests
-    - mne.time_frequency
-    - mne.time_frequency.tests
-    - mne.viz
-    - mne.viz.tests
 
   commands:
-    - nosetests -sv mne
+    - mne
 
 about:
   home: https://github.com/mne-tools/mne-python/

conda/mr.developer/meta.yaml

-{% set version = "1.38" %}
+{% set version = "2.0.0" %}
 
 package:
   name: mr.developer
@@ -7,7 +7,7 @@ package:
 source:
   fn: mr.developer-{{ version }}.tar.gz
   url: https://pypi.io/packages/source/m/mr.developer/mr.developer-{{ version }}.tar.gz
-  md5: bffc800578cb5c75cfd8b17b4403368f
+  sha256: 76e5db1b7d8a4a324049d7529c02312dc2b6b267b5113ab326d112bdd71cf445
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   run:
     - python
     - setuptools
+    - six
     - zc.buildout >=1.2.0
 
 test:

conda/pyedflib/meta.yaml

 {% set name = "pyedflib" %}
-{% set version = "0.1.11" %}
+{% set version = "0.1.14" %}
 
 package:
   name: {{ name }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://pypi.io/packages/source/p/pyEDFlib/pyEDFlib-{{ version }}.tar.gz
-  md5: 28c88693ec65ae0bd950f0a8002f4104
+  sha256: cd4a0747df1557d9d724f4cf91c8ea76a9a26c6d2280bb2696bb05334fc61bc6
 
 build:
-  number: 1
+  number: 0
   script: python setup.py install --single-version-externally-managed --record=record.txt
 
 requirements:

conda/schema/meta.yaml

-{% set version = "0.6.8" %}
+{% set version = "0.7.0" %}
 
 package:
   name: schema
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/s/schema/schema-{{ version }}.tar.gz
-  sha256: fa1a53fe5f3b6929725a4e81688c250f46838e25d8c1885a10a590c8c01a7b74
+  sha256: 44add3ef9016c85ac4b0291b45286a657d0df309b31528ca8d0a9c6d0aa68186
 
 build:
   number: 0
@@ -23,6 +23,7 @@ requirements:
 
 test:
   requires:
+    - mock
     - pytest
 
   source_files:

conda/sphinxcontrib-programoutput/meta.yaml

 {% set name = "sphinxcontrib-programoutput" %}
-{% set version = "0.11" %}
-{% set sha256 = "cbec3ee1c3abd09e105115ab69cb5ade8ca1be9811565a844f973e93e0314837" %}
+{% set version = "0.14" %}
+{% set sha256 = "75b182e9e8cf7efe828cac2c351bb737b00a76bc3aa60fd1a9b2b7096e99c383" %}
 
 package:
   name: {{ name|lower }}

conda/zc.buildout/meta.yaml

-{% set version = "2.12.2" %}
+{% set version = "2.13.2" %}
 
 package:
   name: zc.buildout