Gseapy

bug fixed version

* improved the output file in ``ssgsea``:
- samples.raw.es.txt: enrichment score for all samples
- samples.normalized.es.txt: normalized enrichment score (nes) for all samples
- subfolders of each sample: nes, fdr, p-values are calculated by original GSEA method.
- **note**: enrichment plot only shows es

* ssgsea: scaled ES, add ``sample_norm_type`` argument to specify rank method. 36, rank method including:
- rank
- log_rank
- log
how these methods rank genes, see [ssGSEAprojection](http://rowley.mit.edu/caw_web/ssGSEAProjection/ssGSEAProjection.Library.R) , line 86.
* improved gct file input for ssgsea, gsea
- reset_index for pandas series index after sorting values (gct input)
* enrichr: fixed bug in single column input of dataframe
* docs improvement: new links, and more examples, see http://gseapy.rtfd.io/

Since 0.8.0, **multiprocessing** have been added to speed up calculation.
However, when multiprocessing mode is on, null distribution generated from random permutation are the same if each gene set has same gene member. This will affect a few users when input subsets only differ in enrich terms inside gene_set.gmt file. But from 0.8.5 and later, the broken null distribution are not issues any more.

**Users should use 0.8.5 and later to get most accurate results.**

For detail bugs:

* critical: fixed broken null distribution when permutation type is phenotype 28, thanks for iseekwonderful
* critical: now, fixed random permutation bug in Prerank and ssGSEA module. see 32.

And now, data input improvment
* ssGSEA:
- Accept a Series with gene names as index and return a dataframe 27
- Accept gene expression matrix in gct format 27
- Accept dataframe with only one column but gene names as index.
* Prerank:
- supports datafame with only one column but gene names as index
- supports Seires input
- dataframe with only two column, first col is gene name.
* Replot:
- fixed attribute no found bugs

bug fixed version

* add retry logic when query Enrichr database (fixed timeout error)
* fixed bugs in enrichr API when using latest Enrichr libraries(2017)
* fixed bugs in log file output
* handle ``NA`` or duplicated gene names in prerank module
* handle ``fdr q-value`` when fdr q-value > 1, thanks for Matteo Zhang.

New Features:
---------------------------------

* Add new **Single Sample GSEA** function to gseapy. Either Use it in command line or interactive python console. Please see documentations for more details
* **Parallel Computing** support for GSEApy. Now, you could use ``-p`` parameter to specify cpu numbers you would like to use.
* The time cost for ``phenotype``permutation (in gsea procedure) is much decreased.
* The source code for GSEApy has been re-build and re-designed. It become more extendable and easier to maintain

**API changes:**
-----------------------------

* ``call`` module have been renamed to ``gsea`` for better usage, previous ``call()`` is been deprecated, and you should use ``gsea()`` instead.
* The option ``-p`` for ``permutation_type`` has changed to ``-t``. ``-p`` is used to specify processor number now.
see details in documents.

Bugs fixes
------------------------------

* fixed some minor bugs when using ``Enrichr`` and ``Replot`` module
* fixed a potential bug in preprocessing step(in ``gsea`` mode, prerank or ssgsea is not affected). GSEApy filtered out genes when ``standard deviation`` of samples equal to zero.
* fixed column and row orders in ``gsea`` heatmap output.
* optimized the report output and naming rules.