Gdsctools

* BUG:

- add missing CSS in the distribution

* CHANGES:

- SPEEDUP:
- tissue specific analysis computational time decreased by 50%
by dropping the creation of dataframe and using a simple numpy array
inside ANOVA.anova_one_drug_one_feature
- Creation of volcano plots uses pure javascript for the data packages
and the creation of the volcano plots was dramatically sped up by a
factor between 10 and 100e. One can still create volcano plot manually
in pure matplotlib.
- Similarly, boxplots for tissue, MSI and all associations are now
created using JS.
- Data packages have been refactored. The major difference concerns
the HTML layout (most HTML files are now in the sub-directory
called associations) so that is it cleaner at the top level. The volcano
plots are not in PNG format anymore but pure HTML/JS, which can be
exported manually. The consequences is that the creation of data
packages is 10 times faster.
- The standalone application had 2 options removed: --feature (alone)
and --fast options
- Drug Identifier are now handled as pure integer. For back
compatibility, old files that mix up IC50 and Genomic Features (e.g. v17
data) are still interpreted; the DRUG ID in that case are written as
Drug_ID_IC50 and are transformed as just <ID> everywhere.
- associations output were named 1.html, 2.html... and are now named
a1.html, a2.html...
- Because DRUG_ID are now integer and all HTML stored in the same directory
the naming of the HTML files have been altered (e.g., associations starts
- Report now accepts only one argument (the anova isntance). Second
argument (results) is now optional. If not provided, ANOVA are computed on
the fly
- Multicore module removed but ANOVA.anova_all has multicore option. This
seems to work on Linux systems. Not tested on windows or MacOsX
- IC50 may have duplicated drug ids (at different concentrations). Not good
practice but that the format of e.g. v18, v19 IC50 files. A class
IC50Cluster was created to interepret those files. ANOVA will switch to
IC50Cluster automatically if there are duplicated files.
- Settings: low_memory option has been removed

* CHANGES:

- The parameter **pvalue_threshold** in the general settings was changed
from infinite to 10e-3. This has an effect on the numlber of significant
hits reported in the HTML reports and volvano plots. This should not have
a strong impact on the number of hits but guarantees a reasonably low
pvalue before multiple testing
- If an input file named with .csv extension but the content is tabulated,
there was no immediate error but lead to errors later (e.g. in ANOVA), which
is difficult to debug. Now, in such cases, an error will occur immediately
when reading the file.
- The warnings about MEDIA factor is removed since most of the files do not
contain that column.

* BUG

- The data packages were stored in the "ALL" directory, which may be a TCGA
tissue by itself. This has been renamed into "tissue_packages".

* BUG:

- add missing file in the setup.py

* BUG:

- Fixes the missing data package in the setup for pip installation

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