Merge pull request #36 from biocore/fix_arrow_scaling

Adding tests, documentation, arrow scaling issue

.coveragerc

@@ -11,6 +11,7 @@ branch = True
 include = */deicode/*
 
 [report]
+show_missing = True
 exclude_lines =
     pragma: no cover
     raise NotImplementedError

CHANGELOG.md

@@ -1,5 +1,34 @@
 # DEICODE changelog
 
+## Version 0.2.3 (2019-6-18)
+
+### Backward-incompatible changes [stable]
+
+* The following option names have changed when running DEICODE:
+  (this is true for both QIIME2, python, and the standalone interfaces)
+
+| Original Name        | New Name             |
+| -------------------- | -------------------- |
+| `--rank`             | `--n_components`     |
+| `--iterations`       | `--max_iterations`   |
+
+* `deicode.optspace` has been replaced by `deicode.matrix_completion`.
+  * `deicode.optspace.OptSapce` has been replaced by `deicode.matrix_completion.MatrixCompletion`.
+* `deicode._optspace` has been replaced by `deicode.optspace`.
+  * `deicode._optspace.optspace` has been replaced by `deicode.optspace.OptSpace`.
+
+### Performance enhancements
+
+* Updated `deicode.optspace.OptSpace.svd_sort` to be readable and included
+  comments to make the code easier to follow
+* Added several tests that were missing for ValueError(s) to get better code coverage
+
+### Bug fixes
+
+* Arrow scaling issues [first raised here](https://forum.qiime2.org/t/deicode-rpca-biplot-are-the-vectors-distorting-the-plot/9497).
+  * this was caused by some bit of code that was borrowed from sklearn in
+    `deicode.optspace.OptSpace.svd_sort`. Just deleting a few lines fixed it.
+
 ## Version 0.2.2 (2019-4-22)
 
 ### Features

README.md

@@ -26,13 +26,13 @@ Usage: deicode [OPTIONS]
 Options:
   --in-biom TEXT               Input table in biom format.  [required]
   --output-dir TEXT            Location of output files.  [required]
-  --rank INTEGER               The underlying low-rank structure (suggested: 1
+  --n_components INTEGER       The underlying low-rank structure (suggested: 1
                                < rank < 10) [minimum 2]  [default: 3]
   --min-sample-count INTEGER   Minimum sum cutoff of sample across all
                                features  [default: 500]
   --min-feature-count INTEGER  Minimum sum cutoff of features across all
                                samples  [default: 10]
-  --iterations INTEGER         The number of iterations to optimize the
+  --max_iterations INTEGER         The number of iterations to optimize the
                                solution (suggested to be below 100; beware of
                                overfitting) [minimum 1]  [default: 5]
   --help                       Show this message and exit.

deicode/__init__.py

@@ -8,4 +8,4 @@
 #
 # ----------------------------------------------------------------------------
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"

deicode/base.py

@@ -16,20 +16,3 @@ def transform(self):
         """ Apply imputation to X_sparse
         """
         return self.sample_weights
-
-
-class _BaseTransform(object):
-
-    """Base class for transformation/norm methods.
-    Warning: This class should not be used directly.
-    Use derived classes instead.
-    """
-    @abstractmethod
-    def fit(self):
-        """ Placeholder for fit this
-        should be implemented by sub-method"""
-
-    def transform(self):
-        """ Apply imputation to X_sparse
-        """
-        return self.X_sp