Tests and travis

.travis.yml

@@ -0,0 +1,13 @@
+language: python
+
+python:
+  - "3.5"
+
+install:
+  # pyflakes for general syntax check
+  - pip install pyflakes
+  - pip install .
+
+script:
+  - pyflakes disteval
+  - python setup.py test

disteval/__init__.py

@@ -3,28 +3,24 @@
 from logging import getLogger
 
 import numpy as np
-from tqdm import tqdm
-
 
 from sklearn.model_selection import StratifiedKFold
-from sklearn.metrics import roc_curve, auc
 
 from .scripts.classifier_characteristics import ClassifierCharacteristics
 from .scripts.recursive_selection_parallel import get_all_auc_scores
 
-from .scripts.preparation import prepare_data
 
 logger = getLogger('disteval')
 
 __author__ = "Mathis Börner and Jens Buß"
 
 
 def cv_test_ref_classification(clf,
-                 X,
-                 y,
-                 sample_weight=None,
-                 cv_steps=10,
-                 return_all_models=False):
+                               X,
+                               y,
+                               sample_weight=None,
+                               cv_steps=10,
+                               return_all_models=False):
     """Runs a classification betwenn the test data and the reference data.
     This classification is run in a cross-validation with a provided
     classifier. The classifier needs a fit function to start the model
@@ -89,18 +85,15 @@ def cv_test_ref_classification(clf,
         cv_step = np.zeros_like(y, dtype=int)
         if return_all_models:
             from copy import deepcopy
-            trained_clfs= []
+            trained_clfs = []
         for i, [train_idx, test_idx] in enumerate(cv_iterator):
             X_train = X[train_idx]
             X_test = X[test_idx]
             y_train = y[train_idx]
-            y_test = y[test_idx]
             if sample_weight is None:
                 sample_weight_train = None
-                sample_weight_test = None
             else:
                 sample_weight_train = sample_weight[train_idx]
-                sample_weight_test = sample_weight[test_idx]
             clf = clf.fit(X=X_train,
                           y=y_train,
                           sample_weight=sample_weight_train)
@@ -202,8 +195,8 @@ def recursive_feature_selection_roc_auc(clf,
         'Classifier sanity check failed!'
 
     if n_features > X.shape[1]:
-        log.info(' \'n_features\' higher than total number of features.'
-                 ' \'n_features\' reduced!')
+        logger.info(' \'n_features\' higher than total number of features.'
+                    ' \'n_features\' reduced!')
         n_features = X.shape[1]
     auc_scores = np.zeros((X.shape[1], n_features))
     selected_features = []
@@ -227,11 +220,11 @@ def recursive_feature_selection_roc_auc(clf,
                 index_best = idx
             if matching_features:
                 if forward:
-                    if np.abs(auc-0.5) < np.abs(value_best-0.5):
+                    if np.abs(auc - 0.5) < np.abs(value_best - 0.5):
                         value_best = auc
                         index_best = idx
                 else:
-                    if np.abs(auc-0.5) > np.abs(value_best-0.5):
+                    if np.abs(auc - 0.5) > np.abs(value_best - 0.5):
                         value_best = auc
                         index_best = idx
             else:
@@ -246,10 +239,3 @@ def recursive_feature_selection_roc_auc(clf,
         auc_scores[:, len(selected_features)] = auc_scores_i
         selected_features.append(index_best)
     return selected_features, auc_scores
-
-
-
-
-
-
-

disteval/scripts/__init__.py

@@ -2,4 +2,10 @@
 from __future__ import absolute_import, print_function, division
 
 from .classifier_characteristics import ClassifierCharacteristics
-from .preparation import prepare_data, shrink_data, convert_and_remove_non_finites
+from .preparation import prepare_data, shrink_data
+from .preparation import convert_and_remove_non_finites
+
+__all__ = ['ClassifierCharacteristics',
+           'prepare_data',
+           'shrink_data',
+           'convert_and_remove_non_finites']

disteval/scripts/recursive_selection_parallel.py

@@ -4,9 +4,8 @@
 
 import numpy as np
 
-
-from sklearn.model_selection import StratifiedKFold
 from sklearn.metrics import roc_auc_score
+from sklearn.model_selection import StratifiedKFold
 
 
 def __single_auc_score__(feature_i,
@@ -117,8 +116,8 @@ def get_all_auc_scores(clf,
     if cv_steps < 2:
         raise ValueError('\'cv_steps\' must be 2 or higher')
     else:
-        cv_iterator = strat_kfold.split(X, y)
-        cv_indices = [[train, test] for train, test in cv_iterator]
+        cv_iterator = StratifiedKFold.split(n_splits=cv_steps)
+        cv_indices = [[train, test] for train, test in cv_iterator.split(X, y)]
     test_features = np.array([int(i) for i in range(X.shape[1])
                               if i not in selected_features], dtype=int)
 
@@ -167,10 +166,10 @@ def get_all_auc_scores(clf,
         auc_scores = []
         for feature_i, test_set in test_sets.items():
             _, auc = __single_auc_score__(feature_i=feature_i,
-                                                  clf=clf,
-                                                  cv_indices=cv_indices,
-                                                  X=X[:, test_set],
-                                                  y=y,
-                                                  sample_weight=sample_weight)
+                                          clf=clf,
+                                          cv_indices=cv_indices,
+                                          X=X[:, test_set],
+                                          y=y,
+                                          sample_weight=sample_weight)
             auc_scores[feature_i] = auc
     return auc_scores

docs/Makefile

@@ -0,0 +1,225 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  epub3      to make an epub3"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  dummy      to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pydisteval.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pydisteval.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/pydisteval"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pydisteval"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."