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Ripley numpy #54

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Jul 4, 2020
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3ac35c6
start ripley in numpy-oriented style
ljwolf May 4, 2020
47d9580
add start of rosetta stone
ljwolf May 4, 2020
9dea068
fix printing for j function
ljwolf May 10, 2020
5b39a8e
actually compute two-sided p-values for tests
ljwolf May 10, 2020
04da4a7
support keep replication option
ljwolf May 10, 2020
cce6346
force the unimplemented dispatch to error
ljwolf May 10, 2020
4ad5ece
fix shapely dispatching for multipolygons
ljwolf May 10, 2020
93a42c3
code hygene and force arrays where needed
ljwolf May 10, 2020
b433b3d
move to k_neighbors where possible
ljwolf May 10, 2020
371369a
force integer n_observations
ljwolf May 10, 2020
bd7a135
fix bugs in simulate and argpassing
ljwolf May 10, 2020
c40fd04
finalize internal logic/changes for ripley_test
ljwolf May 10, 2020
1723bae
add further update of notebook
ljwolf May 10, 2020
489bd33
move to using volume for scipy convex hulls
ljwolf Jun 1, 2020
a2b34b9
fix docs & add __all__
ljwolf Jun 1, 2020
e650ad0
since _k_neighbors removes self-neighbors, we need to use k=1 for the…
ljwolf Jun 1, 2020
2e8273d
code hygene and correctness changes
ljwolf Jun 1, 2020
a7e68e0
move the bbox comparison around to catch the array and avoid warnings
ljwolf Jun 2, 2020
bfbeab8
fix linearization in the l function
ljwolf Jun 2, 2020
5834930
move to replications instead of reference_distribution
ljwolf Jun 2, 2020
f11e881
fix empty space distribution with inputted distances
ljwolf Jun 2, 2020
650a252
shape replications better & use truncation in supports
ljwolf Jun 2, 2020
2ae1357
fix geometry typedispatching
ljwolf Jun 5, 2020
5882077
flip linearized
ljwolf Jun 5, 2020
02e7b59
update work in progress notebooks
ljwolf Jun 5, 2020
989efc7
move to using "simulations" instead of "replications"
ljwolf Jun 8, 2020
75e75a4
rework types again for shapely
ljwolf Jun 8, 2020
bfb00e8
[WIP] improve the notebook
ljwolf Jun 8, 2020
b3427fb
fixup simulate_from vs simulate options
ljwolf Jun 10, 2020
2656033
finalize the notebook
ljwolf Jun 10, 2020
77b3e7b
split distance statistics into random, geometry, and keep distance st…
ljwolf Jun 11, 2020
b9fd24d
move ripley in
ljwolf Jun 11, 2020
bf18813
move deprecated classes to deprecated_distance_statistics module
ljwolf Jun 11, 2020
991e0c4
use different defaults for the normal simulators given their structure
ljwolf Jun 11, 2020
3782ac5
use more numerically-stable normal simulator
ljwolf Jun 11, 2020
b482fa9
hull is infact not idempotent
ljwolf Jun 11, 2020
71c0242
fix contains check zip
ljwolf Jun 11, 2020
fd7bca8
flesh out docstrings in random.py
ljwolf Jun 11, 2020
7b48ef8
add docs to geometry
ljwolf Jun 11, 2020
0e48cb2
finalize docstrings in new distance_statistics module
ljwolf Jun 11, 2020
96aa8d2
add deprecation warnings
ljwolf Jun 11, 2020
5b1fa0d
update process.py with deprecation warning in init
ljwolf Jun 11, 2020
5e313ac
add shapely as a testing dependency
ljwolf Jun 11, 2020
4e02e4c
fix missing imports
ljwolf Jun 11, 2020
aef808a
move imports into * using __all__
ljwolf Jun 11, 2020
fce2c8b
fix stat_function break and hull computation
ljwolf Jun 11, 2020
7c1bc2f
use hull since simulate_from is deprecated
ljwolf Jun 11, 2020
a4006c5
missing warnings in geometry
ljwolf Jun 11, 2020
b3f0f55
add fallback for non-area to treat the object like an array
ljwolf Jun 11, 2020
234dea6
blacken tests of deprecated functions and change imports
ljwolf Jun 11, 2020
c840b7f
change tests to accommodate refactor
ljwolf Jun 11, 2020
69694f6
add pygeos to testing requirements
ljwolf Jun 11, 2020
18b99fd
add pytest to testing requirements
ljwolf Jun 11, 2020
766c437
move spatial testing requirements to travis because of pypi issues
ljwolf Jun 11, 2020
090b06b
mised one test migrating to geometry
ljwolf Jun 11, 2020
be997f1
add scikit to the testing requirements
ljwolf Jun 11, 2020
7cfe458
add geopandas to testing dependcies
ljwolf Jun 11, 2020
f8a2036
try having sklearn in the pip install
ljwolf Jun 11, 2020
b7b9193
TEST: move to pytest off of nosetest
sjsrey Jun 28, 2020
38a1c54
TEST: move from nosetests to pytest
sjsrey Jun 28, 2020
7fab7e2
TEST: debugging travis max recursion issue
sjsrey Jun 28, 2020
0557a1b
TESTS: bumping miniconda
sjsrey Jun 28, 2020
f4aa4ec
TEST: fixing conditional testing logic in Jacquez
sjsrey Jun 28, 2020
0dcf9c5
TEST: travis debugging
sjsrey Jun 28, 2020
53b4227
TEST: add 3.8 testing
sjsrey Jun 28, 2020
89ee205
TEST: allow 3.6 failures due to recursion limits on pytest
sjsrey Jun 28, 2020
1928d58
update docstring for plain bbox
ljwolf Jul 4, 2020
4f4f4d6
Merge pull request #1 from sjsrey/ripley-numpy
ljwolf Jul 4, 2020
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11 changes: 7 additions & 4 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ branches:
python:
- 3.6
- 3.7
- 3.8

env:
- PYSAL_PYPI=true MPLBACKEND='pdf'
Expand All @@ -16,11 +17,11 @@ matrix:
allow_failures: #allow travis tests to fail if using the github version of libpysal
- python: 3.6
env: PYSAL_PYPI=false MPLBACKEND='pdf'
- python: 3.7
env: PYSAL_PYPI=false MPLBACKEND='pdf'
- python: 3.6
env: PYSAL_PYPI=true MPLBACKEND='pdf'

before_install:
- wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- chmod +x miniconda.sh
- ./miniconda.sh -b -p ./miniconda
- export PATH=`pwd`/miniconda/bin:$PATH
Expand All @@ -33,6 +34,7 @@ install:
- conda install --yes pip
- pip install -r requirements.txt
- pip install -r requirements_tests.txt
- conda install --yes -c conda-forge pygeos shapely geopandas
# configure dual tests (for dependency libpysal)
- if "$PYSAL_PYPI"; then
echo 'testing pypi libpysal' && pip install libpysal;
Expand All @@ -45,7 +47,8 @@ install:
script:
- python setup.py sdist >/dev/null
- python setup.py install
- nosetests --verbose --with-coverage --cover-package=pointpats;
# - nosetests --verbose --with-coverage --cover-package=pointpats;
- pytest pointpats

notifications:
email:
Expand Down
827 changes: 827 additions & 0 deletions notebooks/distance_statistics-numpy-oriented.ipynb

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