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Branch: master
Commits on Oct 23, 2018
  1. Strip all Jupyter style tags (including those that specify scope)

    stefanv committed Oct 23, 2018
  2. Require jupytercontrib that works with latest Jupyter

    stefanv committed Oct 23, 2018
  3. Use latest pypi packages in Docker & wercker builds

    stefanv committed Oct 23, 2018
  4. Merge pull request #341 from stefanv/errata-japanese-translation

    jni committed Oct 23, 2018
    Fix errors reported during Japanese translation
  5. Fix errors reported during Japanese translation

    stefanv committed Oct 23, 2018
Commits on Oct 18, 2018
  1. Correct import for urllib in html_image_unpacker

    stefanv committed Oct 18, 2018
  2. Fix Docker image locales

    stefanv committed Oct 18, 2018
  3. Merge branch 'stefanv/docker-build'

    stefanv committed Oct 18, 2018
  4. Fix building via Docker image (based on PR #339 by @CNOCycle)

    stefanv committed Oct 18, 2018
    - Move image to Debian stable
    - Use OS-provided version of Python
    - Remove Python and nodejs binary links (no longer required)
    - Import urllib submodules correctly
    - Install Python dependencies in docker compose
Commits on Oct 7, 2018
  1. Update README.md

    jni committed Oct 7, 2018
Commits on Sep 24, 2018
  1. Merge pull request #336 from jni/fix-terminator

    jni committed Sep 24, 2018
    Fix terminator vision image link
  2. Print image source if html error encountered in embedder

    jni committed Sep 24, 2018
Commits on May 16, 2018
  1. Merge pull request #326 from jni/pandas-index-fix

    stefanv committed May 16, 2018
    Select genes by name instead of numerical index
Commits on Apr 14, 2018
  1. Merge pull request #327 from jni/10-9

    stefanv committed Apr 14, 2018
    Bug fixes for 32-bit NumPy
Commits on Apr 10, 2018
  1. Address @stefanv's comments

    jni committed Apr 10, 2018
Commits on Mar 31, 2018
  1. Add a callout box explaining number precision

    jni committed Mar 31, 2018
  2. We multiply by 10^6 so numbers don’t get too small

    jni committed Mar 31, 2018
    … Not “too big” as in current version.
  3. Fix RPKM computation to work with int32 counts

    jni committed Mar 31, 2018
    `1e9 * C` results in overflow when C is of type int32, as happens by
    default in many windows installs of NumPy.
    
    Code demonstrating the problem:
    
    ```python
    In [21]: 1e9 * np.array([2**32-1], dtype=np.float32)
    Out[21]: array([  4.29496730e+18], dtype=float32)
    
    In [22]: 1e9 * np.array([2**32-1], dtype=np.int32)
    Out[22]: array([ -1.00000000e+09])
    ```
Commits on Mar 28, 2018
  1. Select genes by name instead of numerical index

    jni committed Mar 28, 2018
    It turns out that in version 0.20, pandas changed the way that index
    merging happens [1]_, and now preserves the order of the *left* index,
    rather than the right one. We could change the order of index merging,
    but then people with pandas 0.19 would have issues. Better to make
    ourselves independent of index sort order, and grab the exact genes
    we want independently.
    
    .. [1]: https://pandas.pydata.org/pandas-docs/version/0.20/whatsnew.html#index-intersection-and-inner-join-now-preserve-the-order-of-the-left-index
Commits on Feb 13, 2018
  1. Add quick link to binder notebooks

    stefanv committed Feb 13, 2018
Commits on Sep 15, 2017
  1. Merge pull request #320 from jni/fix-makefile-paths

    stefanv committed Sep 15, 2017
    Link data and style dirs from nb dir
  2. Make sure html and nb are dependent on build dirs

    jni committed Sep 15, 2017
  3. Use relative instead of abspath for linking

    jni committed Sep 15, 2017
    This way if they move the entire elegant scipy directory tree, the
    symlink will still work.
  4. Fix linking and make more robust to existing files

    jni committed Sep 15, 2017
  5. Link data and style dirs from nb dir

    jni committed Sep 15, 2017
Commits on Sep 13, 2017
  1. Merge pull request #317 from jni/editor

    stefanv committed Sep 13, 2017
    Update Ch1 with editorial changes
  2. Update chapter 2 with editorial changes (#318)

    jni authored and stefanv committed Sep 13, 2017
Commits on Sep 12, 2017
  1. Remove another caption from another informal figure

    jni committed Sep 12, 2017
  2. Change arr.sum() use to np.sum(arr)

    jni committed Sep 12, 2017
Commits on Sep 8, 2017
  1. Finish ch1 ed additions

    jni committed Sep 8, 2017
Commits on Sep 6, 2017
  1. Update caption casing

    jni committed Sep 6, 2017