Merge pull request #245 from Rungetf/testing

Testing

.gitignore

@@ -39,3 +39,7 @@ nosetests.xml
 # Ignore all emacs backup files
 *~
 .Rproj.user
+
+# pytest
+.pytest_cache/
+.cache

.travis.yml

@@ -10,25 +10,7 @@ os:
 stages:
   - lint
   - test
-jobs:
-  include:
-    - stage: lint
-      env:
-        - LINT=1
-        - TRAVIS_PYTHON_VERSION=2.7
-      before_install:
-        - curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -o miniconda.sh
-        - bash miniconda.sh -b -p $HOME/miniconda
-        - PATH_WITHOUT_CONDA="$PATH"
-        - export PATH="$HOME/miniconda/bin:$PATH"
-        - hash -r
-        - conda config --set always_yes yes --set changeps1 no
-        - conda update -q conda
-      install:
-        - conda install --yes python=2.7 flake8
-      script:
-        - if [[ "$LINT" == "1" ]]; then flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712 ; fi
-
+
 # Setup anaconda
 before_install:
   - export HIC_TEST_DATA_DIR="`pwd`/hicexplorer/test/test_data/"
@@ -45,14 +27,111 @@ before_install:
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
-
 # Install packages
 install:
   - conda install --yes -c conda-forge -c bioconda python=$TRAVIS_PYTHON_VERSION --file requirements.txt
   - conda install --yes -c conda-forge -c bioconda pytest
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then conda install --yes -c defaults -c conda-forge -c bioconda configparser ; fi
   - python setup.py install
-
 # command to run tests
 script:
-  - py.test hicexplorer --doctest-modules
+  - py.test hicexplorer/test/test_pytest_collected_items.py --doctest-modules --capture=sys
+  - py.test hicexplorer/test/general/ --doctest-modules --capture=sys
+  - py.test hicexplorer --doctest-modules --ignore=hicexplorer/test/
+jobs:
+  include:
+    - stage: lint
+      env:
+        - LINT=1
+      before_install:
+        - curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -o miniconda.sh
+        - bash miniconda.sh -b -p $HOME/miniconda
+        - PATH_WITHOUT_CONDA="$PATH"
+        - export PATH="$HOME/miniconda/bin:$PATH"
+        - hash -r
+        - conda config --set always_yes yes --set changeps1 no
+        - conda update -q conda
+      install:
+        - conda install --yes python=2.7 flake8
+      script:
+        - if [[ "$LINT" == "1" ]]; then flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712 ; fi
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_build_matrix_trivial_runs.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_build_matrix_trivial_runs.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_build_matrix_trivial_runs.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_build_matrix_trivial_runs.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_buildMatrix.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_buildMatrix.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_buildMatrix.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_buildMatrix.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_two.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_two.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_two.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_two.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_three.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=2.7
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_three.py
+    - stage: test
+      os: linux
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_three.py
+    - stage: test
+      os: osx
+      env: TRAVIS_PYTHON_VERSION=3.6
+      script: py.test hicexplorer/test/long_run/test_hicAggregateContacts_trivial_runs_three.py

hicexplorer/test/test_hicAggregateContacts.py → hicexplorer/test/general/test_hicAggregateContacts.py

@@ -18,7 +18,7 @@
 # DIFF = 60
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 tolerance = 13  # default matplotlib pixed difference tolerance
 
 

hicexplorer/test/test_hicCorrectMatrix.py → hicexplorer/test/general/test_hicCorrectMatrix.py

@@ -6,7 +6,7 @@
 from matplotlib.testing.compare import compare_images
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 
 def test_correct_matrix():

hicexplorer/test/test_hicCorrelate.py → hicexplorer/test/general/test_hicCorrelate.py

@@ -4,7 +4,7 @@
 from matplotlib.testing.compare import compare_images
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 
 def test_correlate():

hicexplorer/test/test_hicExport.py → hicexplorer/test/general/test_hicExport.py

@@ -5,7 +5,7 @@
 import os
 import numpy.testing as nt
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/hicExport/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/hicExport/"
 
 NPZ_MATRIX = ROOT + "matrix.npz"
 COOL_MATRIX = ROOT + "matrix.cool"

hicexplorer/test/general/test_hicFindEnrichedContacts.py

@@ -0,0 +1,67 @@
+""" Testsuite for hicFindEnrichedContacts """
+from hicexplorer import hicFindEnrichedContacts as hicfec
+from hicexplorer import HiCMatrix as hm
+import os
+import numpy as np
+import numpy.testing as nt
+from scipy.sparse import csr_matrix
+
+# ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+# original_matrix = ROOT + "small_test_matrix_50kb_res"
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
+sam_R1 = ROOT + "small_test_R1_unsorted.bam"
+sam_R2 = ROOT + "small_test_R2_unsorted.bam"
+dpnii_file = ROOT + "DpnII.bed"
+
+from psutil import virtual_memory
+mem = virtual_memory()
+memory = mem.total / 2**30
+
+
+# memory in GB the test computer needs to have to run the test case
+LOW_MEMORY = 2
+MID_MEMORY = 7
+HIGH_MEMORY = 200
+
+
+def test_getPearson():
+    cut_intervals = [('a', 0, 10, 1), ('a', 10, 20, 1),
+                     ('a', 20, 30, 1), ('a', 30, 40, 1), ('b', 40, 50, 1)]
+    hic = hm.hiCMatrix()
+    hic.nan_bins = []
+    matrix = np.array([[1, 8, 5, 3, 0],
+                       [0, 4, 15, 5, 1],
+                       [0, 0, 0, 0, 2],
+                       [0, 0, 0, 0, 1],
+                       [0, 0, 0, 0, 0]])
+
+    hic.matrix = csr_matrix(matrix)
+    hic.setMatrix(hic.matrix, cut_intervals)
+
+    pearson = hicfec.getPearson(hic.matrix)
+
+    nt.assert_equal(pearson.shape, (5, 5))
+    for row in pearson:
+        for value in row:
+            assert -1 <= value.all() <= 1
+
+    hic = hm.hiCMatrix()
+    hic.nan_bins = []
+    matrix = np.array([[2, 2, 3, 4, 5],
+                       [1, 2, 3, 4, 5],
+                       [1, 2, 2, 4, 5],
+                       [1, 2, 3, 2, 5],
+                       [1, 2, 3, 4, 2]
+                       ])
+
+    hic.matrix = csr_matrix(matrix)
+    hic.setMatrix(hic.matrix, cut_intervals)
+
+    pearson = hicfec.getPearson(hic.matrix)
+
+    nt.assert_equal(pearson.shape, (5, 5))
+    nt.assert_equal(pearson, np.zeros(shape=pearson.shape))
+    for row in pearson:
+        for value in row:
+            assert -1 <= value.all() <= 1

hicexplorer/test/test_hicFindTADs.py → hicexplorer/test/general/test_hicFindTADs.py

@@ -6,7 +6,7 @@
 import numpy.testing as nt
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 
 def are_files_equal(file1, file2, pDifference=10):

hicexplorer/test/test_hicMergeMatrixBins.py → hicexplorer/test/general/test_hicMergeMatrixBins.py

@@ -5,7 +5,7 @@
 import numpy.testing as nt
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 
 def test_correct_matrix():

hicexplorer/test/test_hicPCA.py → hicexplorer/test/general/test_hicPCA.py

@@ -5,7 +5,7 @@
 import numpy.testing as nt
 import numpy as np
 import pyBigWig
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 import logging
 log = logging.getLogger(__name__)

hicexplorer/test/test_hicPlotDistVsCounts.py → hicexplorer/test/general/test_hicPlotDistVsCounts.py

@@ -7,7 +7,7 @@
 import os.path
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 
 def test_plot():

hicexplorer/test/test_hicPlotMatrix.py → hicexplorer/test/general/test_hicPlotMatrix.py

@@ -9,8 +9,8 @@
 mem = virtual_memory()
 memory = mem.total / 2 ** 30
 import hicexplorer.hicPlotMatrix
-tolerance = 20  # default matplotlib pixed difference tolerance
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+tolerance = 60  # default matplotlib pixed difference tolerance
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 # memory in GB the test computer needs to have to run the test case
 LOW_MEMORY = 2

hicexplorer/test/test_hicPlotTADs.py → hicexplorer/test/general/test_hicPlotTADs.py

@@ -5,7 +5,7 @@
 import pytest
 import sys
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 h5_browser_track = """
 

hicexplorer/test/test_hicPlotViewpoint.py → hicexplorer/test/general/test_hicPlotViewpoint.py

@@ -8,7 +8,7 @@
 import os.path
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 
 
 def are_files_equal(file1, file2):

hicexplorer/test/test_hicTransform.py → hicexplorer/test/general/test_hicTransform.py

@@ -8,7 +8,7 @@
 from os.path import basename, dirname
 
 
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/../test_data/"
 original_matrix = ROOT + "small_test_matrix_50kb_res.h5"