Merge pull request #186 from astrofrog/update-infrastructure

Update package infrastructure

.github/workflows/main.yml

@@ -0,0 +1,19 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      envs: |
+        - linux: codestyle
+          pytest: false
+        - linux: py37-test-oldestdeps
+        - macos: py38-test
+        - windows: py39-test
+        - linux: py310-test
+        - linux: py310-test-devdeps
+      coverage: 'codecov'

.gitignore

@@ -1,7 +1,67 @@
+# Compiled files
+*.py[cod]
+*.a
+*.o
+*.so
+__pycache__
+
+# Ignore .c files by default to avoid including generated code. If you want to
+# add a non-generated .c extension, use `git add -f filename.c`.
+*.c
+
+# Other generated files
+*/version.py
+*/cython_version.py
+htmlcov
+.coverage
+MANIFEST
+.ipynb_checkpoints
+
+# Sphinx
+docs/api
+docs/_build
+
+# Eclipse editor project files
+.project
+.pydevproject
+.settings
+
+# Pycharm editor project files
+.idea
+
+# Floobits project files
+.floo
+.flooignore
+
+# Visual Studio Code project files
+.vscode
+
+# Packages/installer info
+*.egg
+*.egg-info
+dist
 build
-*.egg-info/
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+
+# Other
+.cache
+.tox
+.*.sw[op]
+*~
 .project
 .pydevproject
-*.pyc
-.settings/
+.settings
+pip-wheel-metadata/
+
+# Mac OSX
+.DS_Store
 
+.tmp

.readthedocs.yml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: '3.7'
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+formats: []

CHANGES

@@ -1,7 +1,7 @@
 0.3.0 (unreleased)
 ------------------
 
-- No changes yet
+- Updated package infrastructure. [#186]
 
 0.2.0 (2016-09-29)
 ------------------

MANIFEST.in

@@ -1,6 +1,16 @@
-include LICENSE
-include CHANGES
-include runtests.py
-recursive-include astrodendro/tests *.npz
-recursive-include astrodendro/tests/benchmark_data *.fits
+include README.rst
+include CHANGES.rst
+include setup.cfg
+include LICENSE.rst
+include pyproject.toml
+
+recursive-include astrodendro *.pyx *.c *.pxd
 recursive-include docs *
+recursive-include licenses *
+recursive-include scripts *
+
+prune build
+prune docs/_build
+prune docs/api
+
+global-exclude *.pyc *.o

astrodendro/__init__.py

@@ -1,9 +1,9 @@
 # Licensed under an MIT open source license - see LICENSE
 
-from .dendrogram import Dendrogram, periodic_neighbours
-from .structure import Structure
-from .analysis import ppv_catalog, pp_catalog
-from .plot import DendrogramPlotter
-from .viewer import BasicDendrogramViewer
+from .dendrogram import Dendrogram, periodic_neighbours  # noqa
+from .structure import Structure  # noqa
+from .analysis import ppv_catalog, pp_catalog  # noqa
+from .plot import DendrogramPlotter  # noqa
+from .viewer import BasicDendrogramViewer  # noqa
 
-__version__ = '0.3.0.dev'
+from .version import version as __version__  # noqa

astrodendro/analysis.py

@@ -12,12 +12,11 @@
 from astropy import units as u
 from astropy.wcs import WCS
 
-from . import six
 from .structure import Structure
 from .flux import UnitMetadataWarning
 from .progressbar import AnimatedProgressBar
 
-__all__ = ['ppv_catalog', 'pp_catalog']
+__all__ = ['ppv_catalog', 'pp_catalog', 'PPStatistic', 'PPVStatistic', 'PPPStatistic', 'SpatialBase']
 
 
 def memoize(func):
@@ -77,7 +76,7 @@ def __init__(self, values, indices):
             Location of each element of values. The i-th array in the tuple
             describes the ith positional dimension
         """
-        self.values = values.astype(np.float)
+        self.values = values.astype(float)
         self.indices = indices
 
     @memoize
@@ -126,13 +125,13 @@ def mom2_along(self, direction):
             The variance (or co-variance matrix) of the data along the
             specified direction(s).
         """
-        w = np.atleast_2d(direction).astype(np.float)
+        w = np.atleast_2d(direction).astype(float)
         for row in w:
             row /= np.linalg.norm(row)
 
         result = np.dot(np.dot(w, self.mom2()), w.T)
         if result.size == 1:
-            result = np.asscalar(result)
+            result = result.item()
         return result
 
     @memoize
@@ -233,7 +232,7 @@ def __init__(self, key, description, default=None, strict=False):
                If True, raise KeyError if metadata not provided.
                This overrides default
         """
-        if not isinstance(key, six.string_types):
+        if not isinstance(key, str):
             raise TypeError("Key is", key, type(key))
         self.key = key
         self.description = description or 'no description'
@@ -684,15 +683,13 @@ def _make_catalog(structures, fields, metadata, statistic, verbose=False):
             progress_bar + 1
             progress_bar.show_progress()
 
-
     result.sort('_idx')
 
     if verbose:
         progress_bar.progress = 100  # Done
         progress_bar.show_progress()
         print("")  # newline
 
-
     return result
 
 
@@ -724,7 +721,7 @@ def ppv_catalog(structures, metadata, fields=None, verbose=True):
 
     with warnings.catch_warnings():
         warnings.simplefilter("once" if verbose else 'ignore', category=MissingMetadataWarning)
-        warnings.simplefilter("once" if verbose else 'ignore', category=UnitMetadataWarning)        
+        warnings.simplefilter("once" if verbose else 'ignore', category=UnitMetadataWarning)
         return _make_catalog(structures, fields, metadata, PPVStatistic, verbose)