Move py2bit to a requirement and indicate changing #438

.travis.yml

@@ -26,8 +26,7 @@ before_install:
 # Install packages
 install:
   - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib=1.5.0 nose flake8
-  - conda install --yes -c https://conda.anaconda.org/bioconda pysam pyBigWig
-  - pip install git+https://github.com/dpryan79/py2bit
+  - conda install --yes -c https://conda.anaconda.org/bioconda pysam pyBigWig py2bit
   - python setup.py install
 
 # command to run tests

CHANGES.txt

@@ -12,6 +12,7 @@
  * `computeMatrix --sortRegions` has a new `keep` option, which is the default. This mimics the behavior in deepTools prior to 2.3.0 where the output order matched the input order. This is, of course, a bit slower, so if the order doesn't matter then use `no`.
  * Fixed issue #435, where `plotHeatmap --sortRegions region_length` would crash with an error.
  * Output bedGraph files are now sorted (#439).
+ * Values stored in bedGraph files (and therefore placed into bigWig files) now use python's "general" format with 6 digits of precision. This tends to produce slightly larger files, but with less loss for values near 0 (see #438).
 
 2.3.6
 

requirements.txt

@@ -2,6 +2,6 @@ numpy>=1.9.0
 scipy>=0.17.0
 matplotlib>=1.4.0
 pysam>=0.8.2
-py2bit>=0.1.0
+py2bit>=0.2.0
 numpydoc>=0.5
 pyBigWig>=0.2.1

setup.py

@@ -150,7 +150,8 @@ def openREADME():
         "matplotlib >= 1.4.0",
         "pysam >= 0.8.2",
         "numpydoc >=0.5",
-        "pyBigWig >=0.2.1"
+        "pyBigWig >=0.2.1",
+        "py2bit >= 0.2.0"
     ],
     zip_safe=False,
     ext_modules=[module1],