Merge pull request #9 from sage-home/dev

Pulling in latest dev branch
sage-home · Aug 10, 2020 · dd0adda · dd0adda
2 parents 594e2dc + 39b1b6c
commit dd0adda
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Showing 51 changed files with 5,359 additions and 2,426 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,20 @@ __pycache__
 *egg-info*
 build/
 dist/
+.DS_store
 
 # Documentation with Sphinx #
 docs/build
 docs/make.bat
+
+# Test data
+sage_analysis/tests/test_data/generated_plots/
+sage_analysis/tests/test_data/*_0
+sage_analysis/tests/test_data/*.hdf5
+sage_analysis/tests/test_data/*.tar
+sage_analysis/tests/test_data/*.par
+sage_analysis/tests/test_data/*.a_list
+.hypothesis/
+
+.mypy_cache
+.coverage*
diff --git a/docs/source/api/galaxy_analysis.rst b/docs/source/api/galaxy_analysis.rst
@@ -0,0 +1,5 @@
+sage_analysis.GalaxyAnalysis
+============================
+
+.. autoclass:: sage_analysis.GalaxyAnalysis
+    :members:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -50,8 +50,10 @@
                        'h5py': ('https://h5py.readthedocs.io/en/stable', None)}
 
 # Autodoc configuration
-autodoc_default_options = {'members': None,
-                           'private-members': None}
+autodoc_default_options = {
+    'members': None,
+    "special-members": "__init__",
+}
 autodoc_member_order = 'groupwise'
 autodoc_inherit_docstrings = False
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -36,18 +36,18 @@ Maintainers
 
    introduction
    user/setting_up_sage
-   user/analysing_sage
-   user/history
-   user/multiple_models
-   user/custom_calculations
-   user/custom_data_classes
+   user/analyzing_sage
+   user/defining_custom_properties
+   user/analyzing_custom_properties
+   user/analyzing_custom_data
 
 .. _api-docs:
 
 .. toctree::
    :maxdepth: 2
    :caption: API Reference
 
+   api/galaxy_analysis
    api/model
    api/sage_hdf5
    api/sage_binary

diff --git a/docs/source/user/analysing_sage.rst b/docs/source/user/analysing_sage.rst
diff --git a/docs/source/user/analyzing_custom_data.rst b/docs/source/user/analyzing_custom_data.rst
@@ -0,0 +1,2 @@
+Analyzing Custom Data
+=====================