Merge pull request #62 from brittonsmith/hcnew

HaloCatalog refactor and improvements

.circleci/config.yml

@@ -102,16 +102,18 @@ commands:
       - run:
           name: "Build yt_astro_analysis and run tests."
           command: |
+            # tag the tip so we can get back there
+            git tag tip
             source $BASH_ENV
             source $HOME/venv/bin/activate
             # generate answers if not cached
-            if [ ! -f $TEST_DIR/$TEST_NAME/$TEST_NAME ]; then
+            if [ ! -d $TEST_DIR/$TEST_NAME ]; then
               git checkout $GOLD_STANDARD
               pip install -e .
               nosetests $TEST_FLAGS --answer-store
             fi
             # return to tip and run comparison tests
-            git checkout -
+            git checkout tip
             pip install -e .
             coverage run `which nosetests` $TEST_FLAGS
             # code coverage report

.gitignore

@@ -3,8 +3,8 @@ yt_astro_analysis.egg-info
 __config__.py
 freetype.cfg
 rockstar.cfg
-yt_astro_analysis/halo_finding/rockstar/rockstar_groupies.c
-yt_astro_analysis/halo_finding/rockstar/rockstar_interface.c
+yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar_groupies.c
+yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar_interface.c
 yt_astro_analysis/ppv_cube/ppv_utils.c
 syntax: glob
 *~

doc/source/api_reference.rst

@@ -14,40 +14,37 @@ on cosmological halos.  It is also the primary interface for halo finding.
 .. autosummary::
    :toctree: generated/
 
-   ~yt_astro_analysis.halo_analysis.halo_catalog.HaloCatalog
-   ~yt_astro_analysis.halo_analysis.halo_finding_methods.HaloFindingMethod
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.HaloCallback
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.delete_attribute
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.halo_sphere
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.iterative_center_of_mass
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.load_profiles
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.phase_plot
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.profile
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.save_profiles
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.sphere_bulk_velocity
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.sphere_field_max_recenter
-   ~yt_astro_analysis.halo_analysis.halo_callbacks.virial_quantities
-   ~yt_astro_analysis.halo_analysis.halo_filters.HaloFilter
-   ~yt_astro_analysis.halo_analysis.halo_filters.not_subhalo
-   ~yt_astro_analysis.halo_analysis.halo_filters.quantity_value
-   ~yt_astro_analysis.halo_analysis.halo_quantities.HaloQuantity
-   ~yt_astro_analysis.halo_analysis.halo_quantities.bulk_velocity
-   ~yt_astro_analysis.halo_analysis.halo_quantities.center_of_mass
-   ~yt_astro_analysis.halo_analysis.halo_recipes.HaloRecipe
-   ~yt_astro_analysis.halo_analysis.halo_recipes.calculate_virial_quantities
-
-Halo Finding
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_catalog.HaloCatalog
+   ~yt_astro_analysis.halo_analysis.halo_catalog.analysis_operators.add_callback
+   ~yt_astro_analysis.halo_analysis.halo_catalog.analysis_operators.add_filter
+   ~yt_astro_analysis.halo_analysis.halo_catalog.analysis_operators.add_quantity
+   ~yt_astro_analysis.halo_analysis.halo_catalog.analysis_operators.add_recipe
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.delete_attribute
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.halo_sphere
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.iterative_center_of_mass
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.load_profiles
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.phase_plot
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.profile
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.save_profiles
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.sphere_bulk_velocity
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.sphere_field_max_recenter
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_callbacks.virial_quantities
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_filters.not_subhalo
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_filters.quantity_value
+   ~yt_astro_analysis.halo_analysis.halo_catalog.halo_recipes.calculate_virial_quantities
+
+Halo Finders
 ------------
 
-These provide direct access to the halo finders.  However, it is strongly
-recommended to use the ``HaloCatalog``.
+The halo finders should only be run from the ``HaloCatalog``, but the links below
+display the various settings available for each.
 
 .. autosummary::
    :toctree: generated/
 
-   ~yt_astro_analysis.halo_finding.halo_objects.FOFHaloFinder
-   ~yt_astro_analysis.halo_finding.halo_objects.HOPHaloFinder
-   ~yt_astro_analysis.halo_finding.rockstar.rockstar.RockstarHaloFinder
+   ~yt_astro_analysis.halo_analysis.halo_finding.halo_objects.FOFHaloFinder
+   ~yt_astro_analysis.halo_analysis.halo_finding.halo_objects.HOPHaloFinder
+   ~yt_astro_analysis.halo_analysis.halo_finding.rockstar.rockstar.RockstarHaloFinder
 
 Cosmology Observation
 ---------------------

doc/source/conf.py

@@ -77,9 +77,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.1.0.dev1'
+version = '1.1.0.dev2'
 # The full version, including alpha/beta/rc tags.
-release = '1.1.0.dev1'
+release = '1.1.0.dev2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.