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Branch: master
Commits on Nov 28, 2019
  1. Merge pull request #350 from rossbar/dep/sync

    jni committed Nov 28, 2019
    Update and sync dependencies in `requirements.txt` and `environment.yml`
Commits on Mar 18, 2019
  1. Remove counts.txt from Makefile

    jni committed Mar 18, 2019
  2. Use bz2 to open counts file

    jni committed Mar 18, 2019
  3. Depend on bz2 instead of txt

    jni committed Mar 18, 2019
Commits on Oct 23, 2018
  1. Merge pull request #341 from stefanv/errata-japanese-translation

    jni committed Oct 23, 2018
    Fix errors reported during Japanese translation
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 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 Sep 15, 2017
  1. Make sure html and nb are dependent on build dirs

    jni committed Sep 15, 2017
  2. 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.
  3. Fix linking and make more robust to existing files

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

    jni committed Sep 15, 2017
Commits on Sep 13, 2017
  1. 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
Commits on Aug 12, 2017
  1. Add link to the notebook repo

    jni committed Aug 12, 2017
  2. Change book link to elegant-scipy.com

    jni committed Aug 12, 2017
    This allows us to change it to our preferred sales channel for the
    book. Currently, this points to the DRM-free epub and pdf books at
    ebooks.com.
Commits on Jul 13, 2017
  1. Move call for code to notes folder

    jni committed Jul 13, 2017
  2. Add Arnet parser example to tools

    jni committed May 27, 2017
  3. Ignore node_modules directory

    jni committed May 27, 2017
Commits on Jun 3, 2017
  1. Add fixed URL for bonkersworld comic

    jni committed Jun 3, 2017
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