back out naming changes

hail-is · Oct 5, 2020 · 6f861a9 · 6f861a9
1 parent 164fce5
commit 6f861a9
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Showing 8 changed files with 43 additions and 40 deletions.
diff --git a/.gitignore b/.gitignore
@@ -20,3 +20,4 @@ hs_err_pid*.log
 *hail/python/hail/docs/tutorials/data*
 *hail/python/hailtop/pipeline/docs/output*
 .mypy_cache/
+*.out
diff --git a/hail/python/hail/docs/api.rst b/hail/python/hail/docs/api.rst
@@ -17,10 +17,10 @@ Classes
     :toctree: ./
     :template: class.rst
 
-    ~hail.table.Table
-    ~hail.table.GroupedTable
-    ~hail.matrixtable.MatrixTable
-    ~hail.matrixtable.GroupedMatrixTable
+    hail.Table
+    hail.GroupedTable
+    hail.MatrixTable
+    hail.GroupedMatrixTable
 
 Modules
 ~~~~~~~

diff --git a/hail/python/hail/docs/experimental/index.rst b/hail/python/hail/docs/experimental/index.rst
@@ -38,14 +38,14 @@ Genetics Methods
     load_dataset
     ld_score
     ld_score_regression
-    ~expressions.write_expression
-    ~expressions.read_expression
+    write_expression
+    read_expression
     filtering_allele_frequency
     hail_metadata
     plot_roc_curve
-    ~phase_by_transmission.phase_by_transmission
-    ~phase_by_transmission.phase_trio_matrix_by_transmission
-    ~phase_by_transmission.explode_trio_matrix
+    phase_by_transmission
+    phase_trio_matrix_by_transmission
+    explode_trio_matrix
     import_gtf
     get_gene_intervals
     export_entries_by_col

diff --git a/hail/python/hail/docs/expressions.rst b/hail/python/hail/docs/expressions.rst
@@ -4,36 +4,36 @@ Expressions
 .. toctree::
     :maxdepth: 2
 
-.. currentmodule:: hail.expr.expressions
+.. currentmodule:: hail.expr
 
 .. autosummary::
 
-   ~eval
+   eval
 
 .. autosummary::
     :nosignatures:
     :toctree:
     :template: class2.rst
 
-    ~base_expression.Expression
-    ~typed_expressions.ArrayExpression
-    ~typed_expressions.ArrayNumericExpression
-    ~typed_expressions.BooleanExpression
-    ~typed_expressions.CallExpression
-    ~typed_expressions.CollectionExpression
-    ~typed_expressions.DictExpression
-    ~typed_expressions.IntervalExpression
-    ~typed_expressions.LocusExpression
-    ~typed_expressions.NumericExpression
-    ~typed_expressions.Int32Expression
-    ~typed_expressions.Int64Expression
-    ~typed_expressions.Float32Expression
-    ~typed_expressions.Float64Expression
-    ~typed_expressions.SetExpression
-    ~typed_expressions.StringExpression
-    ~typed_expressions.StructExpression
-    ~typed_expressions.TupleExpression
-    ~typed_expressions.NDArrayExpression
-    ~typed_expressions.NDArrayNumericExpression
+    Expression
+    ArrayExpression
+    ArrayNumericExpression
+    BooleanExpression
+    CallExpression
+    CollectionExpression
+    DictExpression
+    IntervalExpression
+    LocusExpression
+    NumericExpression
+    Int32Expression
+    Int64Expression
+    Float32Expression
+    Float64Expression
+    SetExpression
+    StringExpression
+    StructExpression
+    TupleExpression
+    NDArrayExpression
+    NDArrayNumericExpression
 
 .. autofunction:: eval
diff --git a/hail/python/hail/docs/genetics/index.rst b/hail/python/hail/docs/genetics/index.rst
@@ -14,8 +14,8 @@ genetics
     :toctree: ./
     :template: class.rst
 
-    ~call.Call
-    ~locus.Locus
-    ~pedigree.Pedigree
-    ~reference_genome.ReferenceGenome
-    ~pedigree.Trio
+    Call
+    Locus
+    Pedigree
+    ReferenceGenome
+    Trio
diff --git a/hail/python/hail/docs/methods/genetics.rst b/hail/python/hail/docs/methods/genetics.rst
@@ -1,6 +1,8 @@
 Genetics
 --------
 
+.. _methods_genetics:
+
 .. currentmodule:: hail.methods
 
 .. toctree::
@@ -29,7 +31,7 @@ Genetics
     split_multi_hts
     summarize_variants
     transmission_disequilibrium_test
-    ~family_methods.trio_matrix
+    trio_matrix
     variant_qc
     vep
 

diff --git a/hail/python/hail/docs/methods/index.rst b/hail/python/hail/docs/methods/index.rst
@@ -74,7 +74,7 @@ Methods
     split_multi
     split_multi_hts
     transmission_disequilibrium_test
-    ~family_methods.trio_matrix
+    trio_matrix
     variant_qc
     vep
 

diff --git a/hail/python/hail/docs/utils/index.rst b/hail/python/hail/docs/utils/index.rst
@@ -5,8 +5,8 @@ utils
 
 .. autosummary::
 
-    ~interval.Interval
-    ~struct.Struct
+    Interval
+    Struct
     hadoop_open
     hadoop_copy
     hadoop_exists