simplified travis build and introduced single VERSION file (NeuralEns…

…emble#222)

* simplified travis build

* added requirements min version test

* refactored setup.py

* [SPADE] fim as an extra module

* test_spade.py: print if fim.so is found during the test

* always install neo by pip

* inlcude test/*.txt in a pypi tarball

* Revert "[SPADE] fim as an extra module"

* test conda 3.5 -> pip 3.5

* download fim.so at 'pip install .'

* fix travis

* moved downloading fim.so from setup.py to spade

* pep 8 fix

* added test_download_spade_fim

.gitignore

@@ -71,3 +71,5 @@ Thumbs.db
 
 # Things specific to this project #
 ###################################
+# ignored folder for fast prototyping
+ignored/

.travis.yml

@@ -1,44 +1,84 @@
-dist: precise
+dist: xenial
 language: python
 sudo: false
 
 addons:
    apt:
-      packages:
-      - libatlas3gf-base
-      - libatlas-dev
-      - libatlas-base-dev
-      - liblapack-dev
-      - gfortran
-      - python-scipy
-
-python:
-  - 2.7.13     
-
-env:
-  matrix:
-    # This environment tests the newest supported anaconda env
-    - DISTRIB="conda" PYTHON_VERSION="2.7" INSTALL_MKL="true"
-      NUMPY_VERSION="1.15.1" SCIPY_VERSION="1.1.0" PANDAS_VERSION="0.23.4"
-      SIX_VERSION="1.10.0" COVERAGE="true"
-    - DISTRIB="conda" PYTHON_VERSION="3.5" INSTALL_MKL="true"
-      NUMPY_VERSION="1.15.1" SCIPY_VERSION="1.1.0" PANDAS_VERSION="0.23.4"
-      SIX_VERSION="1.10.0" COVERAGE="true"
-    # This environment tests minimal dependency versions
-    - DISTRIB="conda_min" PYTHON_VERSION="2.7" INSTALL_MKL="false"
-      SIX_VERSION="1.10.0" NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.14.0" COVERAGE="true"
-    - DISTRIB="conda_min" PYTHON_VERSION="3.4" INSTALL_MKL="false"
-      SIX_VERSION="1.10.0" NUMPY_VERSION="1.8.2" SCIPY_VERSION="0.14.0" COVERAGE="true"
-    # basic Ubuntu build environment
-    - DISTRIB="ubuntu" PYTHON_VERSION="2.7" INSTALL_ATLAS="true"
-      COVERAGE="true"
-    # This environment tests for mpi
-    - DISTRIB="mpi" PYTHON_VERSION="3.5" INSTALL_MKL="false"
-      NUMPY_VERSION="1.15.1" SCIPY_VERSION="1.1.0" SIX_VERSION="1.10.0"
-      MPI_VERSION="2.0.0" COVERAGE="true" MPI="true"
-
-install: source continuous_integration/install.sh
-script: bash continuous_integration/test_script.sh
+     update: true
+
+
+matrix:
+  include:
+    - name: "conda 2.7"
+      python: 2.7
+      env: DISTRIB="conda"
+
+    - name: "pip 2.7"
+      python: 2.7
+      env: DISTRIB="pip"
+
+    - name: "pip 3.5"
+      python: 3.5
+      env: DISTRIB="pip"
+
+    - name: "conda 3.6"
+      python: 3.6
+      env: DISTRIB="conda"
+
+    - name: "pip 3.6"
+      python: 3.6
+      env: DISTRIB="pip"
+
+    - name: "pip 3.6 requirements-extras"
+      python: 3.6
+      env: DISTRIB="pip"
+      before_install: sudo apt install -y libopenmpi-dev openmpi-bin
+      before_script: pip install -r requirements-extras.txt
+      script: mpiexec -n 1 nosetests --with-coverage --cover-package=elephant
+
+    - name: "conda 3.7"
+      python: 3.7
+      env: DISTRIB="conda"
+
+  exclude:
+    - name: "pip 3.6 requirements min version"
+      # excluded due to unmet dependencies in neo, quantities, and scipy
+      python: 3.6
+      env: DISTRIB="pip"
+      before_install:
+        - sudo apt install libblas-dev liblapack-dev libatlas-base-dev gfortran
+        - sed -i 's/>=/==/g' requirements.txt
+
+
+install:
+  - if [[ "${DISTRIB}" == "conda" ]];
+    then
+      export MINICONDA_PATH=${HOME}/miniconda;
+      export PATH=${MINICONDA_PATH}/bin:${PATH};
+      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      bash miniconda.sh -b -p ${MINICONDA_PATH};
+      conda config --set always_yes yes;
+      conda update conda;
+      conda create --name elephant_env python=${TRAVIS_PYTHON_VERSION};
+      source activate elephant_env;
+      conda install mkl;
+      conda config --append channels conda-forge;
+      sed '/^neo/d' requirements.txt > requirements-conda.txt;
+      conda install --file requirements-conda.txt;
+      echo "'neo' will be installed by pip from requirements.txt later on";
+      pip list;
+    else
+      pip install -r requirements.txt;
+    fi
+
+  - pip -V
+  - pip install coverage coveralls nose
+  - pip install .
+  - pip list
+  - python --version
+
+script:
+  nosetests --with-coverage --cover-package=elephant
+
 after_success:
-    - if [[ "$COVERAGE" == "true" ]]; then coveralls || echo "failed"; fi
-cache: apt
+  coveralls || echo "coveralls failed"

MANIFEST.in

@@ -1,8 +1,12 @@
-# Include requirements
-include requirement*.txt
 include README.rst
 include LICENSE.txt
 include AUTHORS.txt
-include elephant/test/spike_extraction_test_data.npz
+include elephant/VERSION
+include elephant/current_source_density_src/README.md
+include elephant/current_source_density_src/test_data.mat
+include elephant/spade_src/LICENCE
+include elephant/test/spike_extraction_test_data.txt
 recursive-include doc *
-prune doc/build
+
+# special care for the files, used in setup.py
+include elephant/spade_src/fim_manager.py

doc/conf.py

@@ -56,10 +56,14 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
+
+root_dir = os.path.dirname(os.path.dirname(__file__))
+with open(os.path.join(root_dir, 'elephant', 'VERSION')) as version_file:
+    # The full version, including alpha/beta/rc tags.
+    release = version_file.read().strip()
+
 # The short X.Y version.
-version = '0.6'
-# The full version, including alpha/beta/rc tags.
-release = '0.6.2'
+version = '.'.join(release.split('.')[:-1])
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/developers_guide.rst

@@ -174,19 +174,18 @@ All code should conform as much as possible to `PEP 8`_, and should run with
 Python 2.7 and 3.2-3.5.
 
 
-Making a release
+Making a release (maintainers only)
 ----------------
 
 .. TODO: discuss branching/tagging policy.
 
 .. Add a section in /doc/releases/<version>.rst for the release.
 
-First, check that the version string (in :file:`elephant/__init__.py`, :file:`setup.py`,
-:file:`doc/conf.py`, and :file:`doc/install.rst`) is correct.
+1. Increment the Elephant package version in :file:`elephant/VERSION`, if necessary.
 
-Second, check that the copyright statement (in :file:`LICENCE.txt`, :file:`README.md`, and :file:`doc/conf.py`) is correct.
+2. Check that the copyright statement (in :file:`LICENCE.txt`, :file:`README.md`, and :file:`doc/conf.py`) is correct.
 
-Third, if there is a new module do not forget to add the modulename to the :file:`doc/module.rst` and make a file with a short description in :file:`doc/reference/<modulename>.rst`. 
+3. If there is a new module do not forget to add the modulename to the :file:`doc/module.rst` and make a file with a short description in :file:`doc/reference/<modulename>.rst`.
 
 To build a source package::
 

elephant/VERSION

@@ -0,0 +1 @@
+0.6.2

elephant/__init__.py

@@ -6,29 +6,13 @@
 :license: Modified BSD, see LICENSE.txt for details.
 """
 
-from . import (statistics,
-               spike_train_generation,
-               spike_train_correlation,
-               unitary_event_analysis,
-               cubic,
-               spectral,
-               kernels,
-               spike_train_dissimilarity,
-               spike_train_surrogates,
-               signal_processing,
-               current_source_density,
-               change_point_detection,
-               phase_analysis,
-               sta,
-               conversion,
-               neo_tools,
-               spade,
-               cell_assembly_detection)
 
-try:
-    from . import pandas_bridge
-    from . import asset
-except ImportError:
-    pass
+def _get_version():
+    import os
+    elephant_dir = os.path.dirname(__file__)
+    with open(os.path.join(elephant_dir, 'VERSION')) as version_file:
+        version = version_file.read().strip()
+    return version
 
-__version__ = "0.6.2"
+
+__version__ = _get_version()

elephant/current_source_density_src/utility_functions.py

@@ -44,7 +44,7 @@ def check_for_duplicated_electrodes(elec_pos):
     -------
     has_duplicated_elec : Boolean
     """
-    unique_elec_pos = np.vstack({tuple(row) for row in elec_pos})
+    unique_elec_pos = np.unique(elec_pos, axis=0)
     has_duplicated_elec = unique_elec_pos.shape == elec_pos.shape
     return has_duplicated_elec