Merge pull request #43 from deeptools/azure-pipelines

Set up CI with Azure Pipelines

azure-pipelines.yml

@@ -0,0 +1,80 @@
+pr:
+  autoCancel: true
+
+jobs:
+
+- job: 'Linux'
+  timeoutInMinutes: 0
+  pool:
+    vmImage: 'ubuntu-latest'
+  strategy:
+    matrix:
+      Python36:
+        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
+      Python38:
+        python.version: '3.8'
+
+  steps:
+  - bash: |
+      echo "##vso[task.prependpath]$CONDA/bin"
+      hash -r
+    displayName: Add conda to PATH
+  - bash: |
+      conda config --set always_yes yes --set changeps1 no
+      conda info -a
+      conda create -n hicmatrix --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
+      source activate hicmatrix
+      conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
+      conda install --yes -c conda-forge -c bioconda nose
+      conda install --yes pathlib
+      conda install --yes -c defaults -c conda-forge -c bioconda configparser
+      python setup.py install
+    displayName: installing dependencies
+  - script: |
+      source activate hicmatrix
+      flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F401,F403,E402,F999,F405,E712
+    displayName: linting
+  - script: |
+      source activate hicmatrix
+      py.test hicmatrix/test/ --capture=sys
+    displayName: pytest
+
+- job: 'OSX'
+  timeoutInMinutes: 0
+  pool:
+    vmImage: 'macOS-10.14'
+  strategy:
+    matrix:
+      Python36:
+        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
+      Python38:
+        python.version: '3.8'
+
+  steps:
+  - bash: |
+      echo "##vso[task.prependpath]$CONDA/bin"
+      hash -r
+    displayName: Add conda to PATH
+  - bash: |
+      conda config --set always_yes yes --set changeps1 no
+      conda info -a
+      conda create -n hicmatrix --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
+      source activate hicmatrix
+      conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
+      conda install --yes -c conda-forge -c bioconda nose
+      conda install --yes pathlib
+      conda install --yes -c defaults -c conda-forge -c bioconda configparser
+      python setup.py install
+    displayName: installing dependencies
+  - script: |
+      source activate hicmatrix
+      flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F401,F403,E402,F999,F405,E712
+    displayName: linting
+  - script: |
+      source activate hicmatrix
+      py.test hicmatrix/test/ --capture=sys
+    displayName: pytest

hicmatrix/HiCMatrix.py

@@ -13,7 +13,6 @@
 from intervaltree import IntervalTree, Interval
 import cooler
 import time
-from collections import Counter
 
 from .utilities import toBytes
 from .utilities import toString
@@ -170,7 +169,7 @@ def getBinSize(self):
                 return self.bin_size
             # If there are more bins, the diff will be compared
             # to the median of the differences between starts
-            median = int(np.median(np.concatenate([np.diff([start for chro, start, end, extra in self.cut_intervals if chro == cur_chrom]) for cur_chrom, nb in Counter(chrom).items() if nb > 1])))
+            median = int(np.median(np.diff(start)))
 
             # check if the bin size is
             # homogeneous
@@ -335,7 +334,7 @@ def fit_cut_intervals(cut_intervals):
             return cut_intervals
         chrom, start, end, extra = zip(*cut_intervals)
 
-        median = int(np.median(np.concatenate([np.diff([start for chro, start, end, extra in cut_intervals if chro == cur_chrom]) for cur_chrom, nb in Counter(chrom).items() if nb > 1])))
+        median = int(np.median(np.diff(start)))
         diff = np.array(end) - np.array(start)
         # check if the bin size is homogeneous
         if len(np.flatnonzero(diff != median)) > (len(diff) * 0.01):