Sampling Potentials Architecture

.github/workflows/ci_tests.yml

@@ -5,15 +5,14 @@ name: CI
 
 on:
   push:
-    # only build on select branches
-    branches:
+    tags:
+    branches:  # only build on select branches
       - main
       - master  # TODO delete when transition
       - release/*
 
   pull_request:
-    # only build on PRs against main
-    branches:
+    branches:  # only build on PRs against main
       - main
       - master  # TODO delete when transition
 
@@ -56,13 +55,12 @@ jobs:
             python: 3.8
             toxenv: py38-test-cov
 
-          # Done with pre-commit
-          # - name: code style
+          # - name: code style.  # Done with pre-commit
           #   os: ubuntu-latest
           #   python: 3.x
           #   toxenv: codestyle
 
-          # - name: Documentation Build  # Done with RTD
+          # - name: Documentation Build  # Done with RTD on public repos.
           #   os: ubuntu-latest
           #   python: 3.x
           #   toxenv: build_docs
@@ -147,10 +145,10 @@ jobs:
             python: 3.8
             toxenv: py38-test-alldeps
 
-          - name: py3.8 - all deps (Windows)
+          - name: py3.8 - min deps (Windows)
             os: windows-latest
             python: 3.8
-            toxenv: py38-test-alldeps
+            toxenv: py38-test
 
     steps:
     - name: Checkout code
@@ -177,6 +175,7 @@ jobs:
 
   # ---------------------------------------------
   # Many Versions
+  # Comment out for private repos
 
   versions:
     needs: further

.gitignore

@@ -4,13 +4,16 @@
 ###############################################################################
 # Project-Specific
 
+# Big Data Files
+/discO/data/sim_CC_100
+
 # scratch folder
 scratch/
+notes/
 
 # _old
 **/_old
 
-
 # scripts
 scripts/**/output
 
@@ -77,6 +80,7 @@ sdist
 develop-eggs
 .installed.cfg
 distribute-*.tar.gz
+*.dev*
 
 # Other
 .cache
@@ -109,9 +113,3 @@ pip-wheel-metadata/
 *.sublime-project
 /sftp-config-alt.json
 /sftp-config.json
-
-# R stuff
-.Rproj.use
-/.Rproj.user
-/.Rhistory
-/.RData

.mailmap

@@ -0,0 +1,3 @@
+Nathaniel Starkman <nstarman@users.noreply.github.com> Nathaniel Starkman <nstarkman@protonmail.com>
+Nathaniel Starkman <nstarman@users.noreply.github.com> Nathaniel Starkman (@nstarman) <nstarkman@protonmail.com>
+Nathaniel Starkman <nstarman@users.noreply.github.com> nstarman <nstarman@users.noreply.github.com>

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v3.4.0
     hooks:
     - id: check-added-large-files
     - id: check-case-conflict
@@ -9,11 +9,64 @@ repos:
     - id: check-toml
     - id: check-yaml
     - id: debug-statements
+    - id: destroyed-symlinks
     - id: detect-private-key
     - id: end-of-file-fixer
     - id: fix-encoding-pragma
     - id: requirements-txt-fixer
     - id: trailing-whitespace
+
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.7.0
+    hooks:
+    - id: python-check-blanket-noqa
+    - id: python-check-mock-methods
+    - id: python-no-eval
+    - id: python-no-log-warn
+    - id: python-use-type-annotations
+    - id: rst-backticks
+    - id: rst-directive-colons
+    - id: rst-inline-touching-normal
+    - id: text-unicode-replacement-char
+
+-   repo: https://github.com/asottile/add-trailing-comma
+    rev: v2.0.2
+    hooks:
+    -   id: add-trailing-comma
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hooks
+    rev: master
+    hooks:
+    - id: check-mailmap
+    - id: forbid-binary
+    - id: script-must-have-extension
+    - id: script-must-not-have-extension
+    - id: shellcheck
+    - id: shfmt
+
+-   repo: https://github.com/mgedmin/check-manifest
+    rev: master
+    hooks:
+    - id: check-manifest
+
+-   repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: master
+    hooks:
+    - id: autopep8
+
+-   repo: https://github.com/asottile/seed-isort-config
+    rev: v2.2.0
+    hooks:
+    - id: seed-isort-config
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.7.0
+    hooks:
+    - id: isort
+      additional_dependencies: ["toml"]
+
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
     - id: flake8
       args: # arguments to configure flake8
         # making isort line length compatible with black
@@ -26,17 +79,29 @@ repos:
         # https://flake8.pycqa.org/en/latest/user/error-codes.html
         - "--ignore=F405,W503"
         - "--exclude=*/_astropy_init.py docs/conf.py"
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v1.9.3
-    hooks:
-        - id: seed-isort-config
--   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v4.3.21
-    hooks:
-        - id: isort
-          additional_dependencies: ["toml"]
+
 -   repo: https://github.com/psf/black
-    rev: stable
+    rev: 20.8b1
+    hooks:
+    - id: black
+      additional_dependencies: ["toml"]
+-   repo: https://github.com/asottile/blacken-docs
+    rev: v1.9.1
     hooks:
-        - id: black
-          additional_dependencies: ["toml"]
+    -   id: blacken-docs
+        additional_dependencies: [black==20.8b1]
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 0.5.6
+  hooks:
+    - id: nbqa-black
+      additional_dependencies: [black==20.8b1]
+      args: [--nbqa-mutate]
+    - id: nbqa-flake8
+      additional_dependencies: [flake8==3.8.4]
+      args: [--nbqa-mutate]
+    - id: nbqa-pyupgrade
+      additional_dependencies: [pyupgrade==2.7.3]
+      args: [--nbqa-mutate, --py36-plus]
+    - id: nbqa-isort
+      additional_dependencies: [isort==5.6.4]
+      args: [--nbqa-mutate]

CHANGES.rst

@@ -7,12 +7,119 @@ Adopt Project-template from @nstarman
 New Features
 ------------
 
+discO.common
+^^^^^^^^^^^^
+
+Code that can be used all over the package. It's not core, it's common.
+
+- Add types for type hinting: [#17]
+
+    + EllipsisType : ``type(Ellipsis)`` b/c ellipsis fails.
+    + UnitType : the type of astropy's ``UnitBase`` and ``FunctionUnitBasse``
+    + QuantityType : the type of astropy's ``Quantity``
+    + FrameType : the type of astropy's ``BaseCoordinateFrame``
+    + SkyCoordType : the type of astropy's ``SkyCoord``
+    + CoordinateType : the union of FrameType & SkyCoordType
+    + FrameLikeType : the union of CoordinateType & str
+
+        * anything that can be used in ``frame=`` in  ``Skycoord(...,frame=)``
+
+
+discO.config
+^^^^^^^^^^^^
+
+- Add configuration for default frame. Defaults to "icrs". [#17]
+
+
+discO.core
+^^^^^^^^^^
+
+Where the unified architecture is defined.
+
+Modules:
+
+- ``core`` : the base class. [#17]
+- ``sample`` : for sampling from a Potential. [#17]
+- ``measurement`` : for resampling, given observational errors. [#17]
+
+
+**discO.core.core**
+
+The base class samplers, fitters, and most everything else.
+If a ``package`` is defined as a class argument, it parses the package and
+stores it in the class. This is used for registering classes into registry
+classes.
+
+subclasses must override the ``_registry`` and ``__call__`` methods.
+
+
+**discO.core.sample**
+
+PotentialSampler : base class for sampling potentials [#17]
+
+    + registers subclasses. Each subclass is for sampling from potentials from
+      a different package. Eg. ``GalpyPotentialSampler`` for sampling ``galpy``
+      potentials.
+    + PotentialSampler can be used to initialize & wrap any of its subclasses.
+      This is controlled by the argument ``return_specific_class``. If False,
+      it returns the subclass itself.
+    + Takes a ``potential`` and a ``frame`` (astropy CoordinateFrame). The
+      potential is used for sampling, but the resultant points are not located
+      in any reference frame, which we assign with ``frame``.
+    + ``__call__`` and ``sample`` are used to sample the potential
+    + ``resample`` (and ``resampler``) sample the potential many times. This can
+      be done for many iterations and different sample number points.
+
+
+**discO.core.measurement**
+
+- MeasurementErrorSampler : abstract base class for resampling a potential given measurement errors [#17]
+
+    + registers subclasses. Each subclass is for resampling in a different way.
+    + MeasurementErrorSampler can be used to wrap any of its subclasses.
+
+- GaussianMeasurementErrorSampler : apply uncorrelated Gaussian errors [#17]
+
+
 discO.data
 ^^^^^^^^^^
 
 - Add Milky_Way_Sim_100 data [#10]
 
 
+discO.extern
+^^^^^^^^^^^^
+
+Where classes for external packages are held.
+
+
+discO.extern.agama
+^^^^^^^^^^^^^^^^^^
+
+- AGAMAPotentialSampler [#17]
+
+    + Sample from ``agama`` potentials.
+    + stores the mass and potential as attributes on the returned ``SkyCoord``
+
+
+discO.extern.galpy
+^^^^^^^^^^^^^^^^^^
+
+- GalpyPotentialSampler [#17]
+
+    + Sample from ``galpy`` potentials with a corresponding distribution function.
+    + stores the mass and potential as attributes on the returned ``SkyCoord``
+
+
+discO.utils
+^^^^^^^^^^^
+
+- resolve_framelike [#17]
+
+    Determine the frame and return a blank instance for anything that can be
+    used in ``frame=`` in  ``Skycoord(...,frame=)``
+
+
 API Changes
 -----------
 
@@ -25,6 +132,17 @@ Bug Fixes
 N/A
 
 
+Docs
+----
+
+- Added glossary [#17]
+
+    + 'frame-like'
+    + 'coord-like'
+    + 'coord scalar' and 'coord-like scalar'
+    + 'coord array' and 'coord-like array'
+
+
 Other Changes and Additions
 ---------------------------
 
@@ -36,12 +154,16 @@ Other Changes and Additions
 
 - Use GitHub for CI [#12]
 
+    + On tag [#17]
+
 - Dependabot yml [#13]
 
 - Issues Templates [#14]
 
 - Update from project template [#18]
 
+- Add ``.mailmap`` [#17]
+
 
 Actions
 ^^^^^^^
@@ -50,6 +172,7 @@ Actions
 
 - Pre-commit [#18]
 
-    (`isort <https://pypi.org/project/isort/>`_
-    -> `black <https://pypi.org/project/black/>`_
-    -> `flake8 <https://pypi.org/project/flake8/>`_)
+    - `isort <https://pypi.org/project/isort/>`_
+    - `black <https://pypi.org/project/black/>`_
+    - `flake8 <https://pypi.org/project/flake8/>`_
+    - many others from `precommit <https://pre-commit.com/hooks.html>`__ [#17]