fix typo in docs

uio-bmi · Jun 24, 2021 · c8402fc · c8402fc
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Showing 5 changed files with 7 additions and 7 deletions.
diff --git a/docs/source/developer_docs/dev_docs_util.rst b/docs/source/developer_docs/dev_docs_util.rst
@@ -1,5 +1,5 @@
 .. note::
 
-  When adding new features to immuneML, some utility classes are already available. For instance, to construct a path, you can use :code:`PathBuilder.build_from_objects()` function.
+  When adding new features to immuneML, some utility classes are already available. For instance, to construct a path, you can use :code:`PathBuilder.build()` function.
   If you need to validate some parameters when constructing an object in :code:`build_object()` functions, for example, you can use :code:`ParameterValidator` class.
   For the full list of such classes, see the `util` package.
diff --git a/docs/source/developer_docs/how_to_add_new_ML_method.rst b/docs/source/developer_docs/how_to_add_new_ML_method.rst
@@ -219,7 +219,7 @@ An example of the unit test TestNewSVM is given below.
           svm.fit(EncodedData(x, y), 'default')
 
           path = EnvironmentSettings.tmp_test_path / "my_svm_load/"
-          PathBuilder.build_from_objects(path)
+          PathBuilder.build(path)
 
           with open(path / "svm.pickle", "wb") as file:
               pickle.dump(svm.get_model(), file)

diff --git a/docs/source/developer_docs/how_to_add_new_encoding.rst b/docs/source/developer_docs/how_to_add_new_encoding.rst
@@ -131,7 +131,7 @@ An example of the implementation of :code:`NewKmerFrequencyEncoder` for the :py:
             if params.learn_model:
                 vectorizer = DictVectorizer(sparse=False, dtype=float)
                 vectorized_examples = vectorizer.fit_transform(examples)
-                PathBuilder.build_from_objects(params.result_path)
+                PathBuilder.build(params.result_path)
                 with self.vectorizer_path.open('wb') as file:
                     pickle.dump(vectorizer, file)
             else:
@@ -210,7 +210,7 @@ An example of the unit test TestNewKmerFrequencyEncoder is given below.
         def test_encode(self):
             path = EnvironmentSettings.tmp_test_path / "new_kmer_encoding/"
 
-            PathBuilder.build_from_objects(path)
+            PathBuilder.build(path)
 
             # create a dataset
             repertoires, metadata = RepertoireBuilder.build_from_objects([["AAAT"], ["TAAA"]], path, {'l1': [1, 0]})

diff --git a/docs/source/developer_docs/how_to_add_new_preprocessing.rst b/docs/source/developer_docs/how_to_add_new_preprocessing.rst
@@ -135,7 +135,7 @@ An example of the unit test TestNewClonesPerRepertoireFilter is given below.
 
         def test_process(self):
             path = EnvironmentSettings.tmp_test_path / "clones_per_repertoire_filter"
-            PathBuilder.build_from_objects(path)
+            PathBuilder.build(path)
             dataset = RepertoireDataset(repertoires=RepertoireBuilder.build_from_objects([["ACF", "ACF", "ACF"],
                                                                            ["ACF", "ACF"],
                                                                            ["ACF", "ACF", "ACF", "ACF"]], path)[0])

diff --git a/docs/source/developer_docs/how_to_add_new_report.rst b/docs/source/developer_docs/how_to_add_new_report.rst
@@ -95,7 +95,7 @@ An example implementation is shown below. It includes implementations of abstrac
             figure.update_layout(xaxis=dict(tickmode='array', tickvals=df["sequence_lengths"]), yaxis=dict(tickmode='array', tickvals=df["counts"]),
                                  title="Sequence length distribution", template="plotly_white")
             figure.update_traces(marker_color=px.colors.diverging.Tealrose[0])
-            PathBuilder.build_from_objects(self.result_path)
+            PathBuilder.build(self.result_path)
 
             file_path = self.result_path / "sequence_length_distribution.html"
             figure.write_html(str(file_path))
@@ -141,7 +141,7 @@ An example of the unit test TestNewSequenceLengthDistribution is given below.
 
         def test_generate_report(self):
             path = EnvironmentSettings.tmp_test_path / "datareports"
-            PathBuilder.build_from_objects(path)
+            PathBuilder.build(path)
 
             rep1 = Repertoire.build_from_sequence_objects(sequence_objects=[ReceptorSequence(amino_acid_sequence="AAA", identifier="1"),
                                                                             ReceptorSequence(amino_acid_sequence="AAAA", identifier="2"),