PySAL Change Log Statistics

In [1]:

    

import gitreleases


    

In [3]:

    

from __future__ import print_function
import os
import json
import re
import sys
import pandas

from datetime import datetime, timedelta
from time import sleep
from subprocess import check_output
try:
    from urllib import urlopen
except:
    from urllib.request import urlopen

import ssl
#import yaml

context = ssl._create_unverified_context()


    

In [4]:

    

with open('package_versions.txt', 'r') as package_list:
    packages = dict([line.strip().split() for line in package_list.readlines()])


    

In [5]:

    

packages


    

    
Out[5]:





{'libpysal': '4.2.1',
 'esda': '2.2.0',
 'giddy': '2.3.0',
 'inequality': '1.0.0',
 'pointpats': '2.1.0',
 'segregation': '1.1.1',
 'spaghetti': '1.4.0',
 'mgwr': '2.1.1',
 'spglm': '1.0.7',
 'spint': '1.0.6',
 'spreg': '1.0.4',
 'spvcm': '0.2.1.post1',
 'tobler': '0.2.0',
 'mapclassify': '2.2.0',
 'splot': '1.1.2'}

In [6]:

    

release_date = '2020-01-31'
start_date = '2019-07-31'


    

In [7]:

    

since_date = '--since="{start}"'.format(start=start_date)
since_date
since = datetime.strptime(start_date+" 0:0:0", "%Y-%m-%d %H:%M:%S")
since


    

    
Out[7]:





datetime.datetime(2019, 7, 31, 0, 0)

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In [8]:

    

cmd = ['git', 'log', '--format=* %aN', since_date]


    

In [9]:

    

CWD = os.path.abspath(os.path.curdir)


    

In [10]:

    

CWD


    

    
Out[10]:





'/home/serge/Dropbox/p/pysal/src/pysal/tools'

In [11]:

    

os.chdir('tmp/esda')
os.getcwd()


    

    
Out[11]:





'/home/serge/Dropbox/p/pysal/src/pysal/tools/tmp/esda'

In [12]:

    

ncommits = len(check_output(cmd).splitlines())


    

In [13]:

    

ncommits


    

    
Out[13]:





17

In [14]:

    

identities = {'Levi John Wolf': ('ljwolf', 'Levi John Wolf'),
              'Serge Rey': ('Serge Rey', 'Sergio Rey', 'sjsrey', 'serge'),
              'Wei Kang': ('Wei Kang', 'weikang9009'),
              'Dani Arribas-Bel': ('Dani Arribas-Bel', 'darribas')
}

def regularize_identity(string):
    string = string.decode()
    for name, aliases in identities.items():
        for alias in aliases:
            if alias in string:
                string = string.replace(alias, name)
    if len(string.split(' '))>1:
        string = string.title()
    return string.lstrip('* ')


    

In [15]:

    

from collections import Counter
author_cmd = ['git', 'log', '--format=* %aN', since_date]


    

In [16]:

    

ncommits = len(check_output(cmd).splitlines())
all_authors = check_output(author_cmd).splitlines()
counter = Counter([regularize_identity(author) for author in all_authors])
#        global_counter += counter
#        counters.update({'.'.join((package,subpackage)): counter})
unique_authors = sorted(set(all_authors))


    

In [17]:

    

unique_authors


    

    
Out[17]:





[b'* James Gaboardi',
 b'* Serge Rey',
 b'* Sergio Rey',
 b'* Wei Kang',
 b'* ljwolf']

In [18]:

    

counter.keys()


    

    
Out[18]:





dict_keys(['Serge Rey', 'Levi John Wolf', 'James Gaboardi', 'Wei Kang'])

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In [19]:

    

from datetime import datetime, timedelta
ISO8601 = "%Y-%m-%dT%H:%M:%SZ"
PER_PAGE = 100
element_pat = re.compile(r'<(.+?)>')
rel_pat = re.compile(r'rel=[\'"](\w+)[\'"]')


    

In [20]:

    

def parse_link_header(headers):
    link_s = headers.get('link', '')
    urls = element_pat.findall(link_s)
    rels = rel_pat.findall(link_s)
    d = {}
    for rel,url in zip(rels, urls):
        d[rel] = url
    return d

def get_paged_request(url):
    """get a full list, handling APIv3's paging"""
    results = []
    while url:
        #print("fetching %s" % url, file=sys.stderr)
        f = urlopen(url)
        results.extend(json.load(f))
        links = parse_link_header(f.headers)
        url = links.get('next')
    return results

def get_issues(project="pysal/pysal", state="closed", pulls=False):
    """Get a list of the issues from the Github API."""
    which = 'pulls' if pulls else 'issues'
    url = "https://api.github.com/repos/%s/%s?state=%s&per_page=%i" % (project, which, state, PER_PAGE)
    return get_paged_request(url)


def _parse_datetime(s):
    """Parse dates in the format returned by the Github API."""
    if s:
        return datetime.strptime(s, ISO8601)
    else:
        return datetime.fromtimestamp(0)


def issues2dict(issues):
    """Convert a list of issues to a dict, keyed by issue number."""
    idict = {}
    for i in issues:
        idict[i['number']] = i
    return idict


def is_pull_request(issue):
    """Return True if the given issue is a pull request."""
    return 'pull_request_url' in issue


def issues_closed_since(period=timedelta(days=365), project="pysal/pysal", pulls=False):
    """Get all issues closed since a particular point in time. period
can either be a datetime object, or a timedelta object. In the
latter case, it is used as a time before the present."""

    which = 'pulls' if pulls else 'issues'

    if isinstance(period, timedelta):
        period = datetime.now() - period
    url = "https://api.github.com/repos/%s/%s?state=closed&sort=updated&since=%s&per_page=%i" % (project, which, period.strftime(ISO8601), PER_PAGE)
    allclosed = get_paged_request(url)
    # allclosed = get_issues(project=project, state='closed', pulls=pulls, since=period)
    filtered = [i for i in allclosed if _parse_datetime(i['closed_at']) > period]

    # exclude rejected PRs
    if pulls:
        filtered = [ pr for pr in filtered if pr['merged_at'] ]

    return filtered


def sorted_by_field(issues, field='closed_at', reverse=False):
    """Return a list of issues sorted by closing date date."""
    return sorted(issues, key = lambda i:i[field], reverse=reverse)


def report(issues, show_urls=False):
    """Summary report about a list of issues, printing number and title.
    """
    # titles may have unicode in them, so we must encode everything below
    if show_urls:
        for i in issues:
            role = 'ghpull' if 'merged_at' in i else 'ghissue'
            print('* :%s:`%d`: %s' % (role, i['number'],
                                        i['title'].encode('utf-8')))
    else:
        for i in issues:
            print('* %d: %s' % (i['number'], i['title'].encode('utf-8')))


    

In [23]:

    

since


    

    
Out[23]:





datetime.datetime(2019, 7, 31, 0, 0)

In [24]:

    

all_issues = {}
all_pulls = {}
total_commits = 0
issue_details = {}
pull_details = {}
for package in packages:
    subpackage = package
    subpackages = packages[package].split()
    print(package)
    prj = 'pysal/{subpackage}'.format(subpackage=package)
    os.chdir(CWD)
    os.chdir('tmp/{subpackage}'.format(subpackage=package))
    issues = issues_closed_since(since, project=prj,pulls=False)
    pulls = issues_closed_since(since, project=prj,pulls=True)
    issues = sorted_by_field(issues, reverse=True)
    pulls = sorted_by_field(pulls, reverse=True)
    issue_details[subpackage] = issues
    pull_details[subpackage] = pulls
    n_issues, n_pulls = map(len, (issues, pulls))
    n_total = n_issues + n_pulls
    all_issues[subpackage] = n_total, n_pulls
   
os.chdir(CWD)


    

    




libpysal
esda
giddy
inequality
pointpats
segregation
spaghetti
mgwr
spglm
spint
spreg
spvcm
tobler
mapclassify
splot

In [25]:

    

issue_details


    

    
Out[25]:





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   'html_url': 'https://github.com/pysal/libpysal/pull/230',
   'id': 545322537,
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   'number': 230,
   'title': 'raise warning when islands are used in to_adjlist',
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   'created_at': '2020-01-04T19:25:12Z',
   'updated_at': '2020-01-04T20:29:26Z',
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   'body': 'This addresses issue #218 '},
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   'author_association': 'MEMBER',
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   'body': "Hello,\r\n\r\nI was using libpysal to conduct esda. I was doing the spatial weights using continuity weights but it pops up the following errors:\r\n\r\n---------------------------------------------------------------------------\r\nAttributeError                            Traceback (most recent call last)\r\n<ipython-input-189-9a78d6d6df16> in <module>\r\n     13             break\r\n     14         c_type = crime_type[i*2+j]\r\n---> 15         li_bg = esda.moran.Moran_Local(blgp_crime[c_type], qW_blgp)\r\n     16         mi_bg = esda.moran.Moran(blgp_crime[c_type], qW_blgp)\r\n     17         sig = 1 * (li_bg.p_sim < 0.05)\r\n\r\nE:\\Anaconda\\envs\\incenTrip\\lib\\site-packages\\pysal\\explore\\esda\\moran.py in __init__(self, y, w, transformation, permutations, geoda_quads)\r\n    870         np.seterr(**orig_settings)\r\n    871         self.z = z\r\n--> 872         w.transform = transformation\r\n    873         self.w = w\r\n    874         self.permutations = permutations\r\n\r\nE:\\Anaconda\\envs\\incenTrip\\lib\\site-packages\\libpysal\\weights\\weights.py in set_transform(self, value)\r\n    943                     row_sum = sum(wijs) * 1.0\r\n    944                     if row_sum == 0.0:\r\n--> 945                         if not self.silent_island_warning:\r\n    946                             print(('WARNING: ', i, ' is an island (no neighbors)'))\r\n    947                     weights[i] = [wij / row_sum for wij in wijs]\r\n\r\nAttributeError: 'Queen' object has no attribute 'silent_island_warning'\r\n\r\nI check the raw code and can't find things about silent_island_warning.\r\n\r\nThank you.\r\n\r\nBest,\r\n"},
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    'updated_at': '2020-01-04T19:33:41Z',
    'due_on': '2019-12-31T08:00:00Z',
    'closed_at': None},
   'comments': 2,
   'created_at': '2019-12-29T21:11:11Z',
   'updated_at': '2020-01-04T15:28:48Z',
   'closed_at': '2020-01-04T15:28:47Z',
   'author_association': 'CONTRIBUTOR',
   'body': 'Hi, since the latest release libpysal will not import on windows due to encoding error. It raises `UnicodeDecodeError: \'charmap\' codec can\'t decode byte 0x9d in position 503: character maps to <undefined>`. \r\n\r\nDetails: https://ci.appveyor.com/project/martinfleis/momepy/builds/29802733\r\n\r\nHighly likely caused by #176. I assume that adding `encoding="utf8"` to `open()` on lines 50 and 56 will fix the issue. I am unable to try that locally as I do not have windows machine until 6th of January.'},
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   'number': 215,
   'title': 'libpysal 4.2.0 Windows import issue',
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    'title': 'Next Release',
    'description': 'This is the todo list for the Dec. 2019 release of libpysal, the core of the PySAL metapackage. ',
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    'open_issues': 13,
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    'created_at': '2019-06-25T13:18:11Z',
    'updated_at': '2020-01-04T19:33:41Z',
    'due_on': '2019-12-31T08:00:00Z',
    'closed_at': None},
   'comments': 6,
   'created_at': '2019-12-30T00:50:12Z',
   'updated_at': '2020-01-04T15:28:09Z',
   'closed_at': '2020-01-04T15:28:09Z',
   'author_association': 'MEMBER',
   'pull_request': {'url': 'https://api.github.com/repos/pysal/libpysal/pulls/215',
    'html_url': 'https://github.com/pysal/libpysal/pull/215',
    'diff_url': 'https://github.com/pysal/libpysal/pull/215.diff',
    'patch_url': 'https://github.com/pysal/libpysal/pull/215.patch'},
   'body': 'This PR addresses:\r\n  * pysal/libpysal#214\r\n\r\nWith the following machine `libpysal` can be read in:\r\n```python\r\nIn [1]: %load_ext watermark \r\nIn [2]: %watermark\r\n2019-12-29T19:35:00-05:00\r\n\r\nCPython 3.7.5\r\nIPython 7.10.2\r\n\r\ncompiler   : MSC v.1916 64 bit (AMD64)\r\nsystem     : Windows\r\nrelease    : 10\r\nmachine    : AMD64\r\nprocessor  : Intel64 Family 6 Model 61 Stepping 4, GenuineIntel\r\nCPU cores  : 1\r\ninterpreter: 64bit\r\n```\r\n\r\n**However**, the following errors/failures occur ***in windows*** during local `nosetests` (three of which also occur ***in macOS***[see bottom]):\r\n\r\n```\r\n\r\n======================================================================\r\nERROR: test_casting (libpysal.io.iohandlers.tests.test_csvWrapper.test_csvWrapper)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\tests\\test_csvWrapper.py", line 47, in test_casting\r\n    self.obj.cast(\'WKT\', WKTParser())\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\fileio.py", line 230, in cast\r\n    raise KeyError("%s" % key)\r\nKeyError: \'WKT\'\r\n\r\n======================================================================\r\nERROR: test_deserialize (libpysal.io.iohandlers.tests.test_db.Test_sqlite_reader)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\tests\\test_db.py", line 54, in tearDown\r\n    os.remove(\'test.db\')\r\nPermissionError: [WinError 32] The process cannot access the file because it is being used by another process: \'test.db\'\r\n\r\n======================================================================\r\nERROR: test_writeNones (libpysal.io.iohandlers.tests.test_pyDbfIO.test_DBF)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\tests\\test_pyDbfIO.py", line 115, in test_writeNones\r\n    os.remove(fname)\r\nPermissionError: [WinError 32] The process cannot access the file because it is being used by another process: \'C:\\\\Users\\\\200059~1\\\\AppData\\\\Local\\\\Temp\\\\tmpzax2d812.dbf\'\r\n\r\n======================================================================\r\nERROR: test_true_rook2 (libpysal.weights.tests.test__contW_lists.TestContiguityWeights)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\weights\\tests\\test__contW_lists.py", line 75, in test_true_rook2\r\n    \'stl_hom.shp\'), ROOK, \'POLY_ID_OG\')\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\weights\\tests\\test__contW_lists.py", line 120, in build_W\r\n    ids = db.by_col[idVariable]\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\tables.py", line 21, in __getitem__\r\n    return self.p._get_col(key)\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\pyDbfIO.py", line 110, in _get_col\r\n    raise AttributeError(\'Field: % s does not exist in header\' % key)\r\nAttributeError: Field: POLY_ID_OG does not exist in header\r\n\r\n======================================================================\r\nFAIL: Doctest: libpysal.cg.shapely_ext.buffer\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\doctest.py", line 2196, in runTest\r\n    raise self.failureException(self.format_failure(new.getvalue()))\r\nAssertionError: Failed doctest test for libpysal.cg.shapely_ext.buffer\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\shapely_ext.py", line unknown line number, in buffer\r\n\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\shapely_ext.py", line ?, in libpysal.cg.shapely_ext.buffer\r\nFailed example:\r\n    g.buffer(1.0).area        # 16-gon approx of a unit radius circle\r\nExpected:\r\n    3.1365484905459389\r\nGot:\r\n    3.1365484905459384\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\shapely_ext.py", line ?, in libpysal.cg.shapely_ext.buffer\r\nFailed example:\r\n    g.buffer(1.0, 128).area   # 128-gon approximation\r\nExpected:\r\n    3.1415138011443009\r\nGot:\r\n    3.141513801144299\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\shapely_ext.py", line ?, in libpysal.cg.shapely_ext.buffer\r\nFailed example:\r\n    list(g.buffer(1.0, cap_style=\'square\').exterior.coords)\r\nException raised:\r\n    Traceback (most recent call last):\r\n      File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\doctest.py", line 1329, in __run\r\n        compileflags, 1), test.globs)\r\n      File "<doctest libpysal.cg.shapely_ext.buffer[5]>", line 1, in <module>\r\n        list(g.buffer(1.0, cap_style=\'square\').exterior.coords)\r\n      File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\site-packages\\shapely\\geometry\\base.py", line 593, in buffer\r\n        mitre_limit))\r\n      File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\site-packages\\shapely\\topology.py", line 78, in __call__\r\n        return self.fn(this._geom, *args)\r\n    ctypes.ArgumentError: argument 5: <class \'TypeError\'>: wrong type\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\shapely_ext.py", line ?, in libpysal.cg.shapely_ext.buffer\r\nFailed example:\r\n    g.buffer(1.0, cap_style=\'square\').area\r\nException raised:\r\n    Traceback (most recent call last):\r\n      File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\doctest.py", line 1329, in __run\r\n        compileflags, 1), test.globs)\r\n      File "<doctest libpysal.cg.shapely_ext.buffer[6]>", line 1, in <module>\r\n        g.buffer(1.0, cap_style=\'square\').area\r\n      File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\site-packages\\shapely\\geometry\\base.py", line 593, in buffer\r\n        mitre_limit))\r\n      File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\site-packages\\shapely\\topology.py", line 78, in __call__\r\n        return self.fn(this._geom, *args)\r\n    ctypes.ArgumentError: argument 5: <class \'TypeError\'>: wrong type\r\n\r\n\r\n======================================================================\r\nFAIL: Doctest: libpysal.cg.sphere.geogrid\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\doctest.py", line 2196, in runTest\r\n    raise self.failureException(self.format_failure(new.getvalue()))\r\nAssertionError: Failed doctest test for libpysal.cg.sphere.geogrid\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\sphere.py", line 438, in geogrid\r\n\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\cg\\sphere.py", line 461, in libpysal.cg.sphere.geogrid\r\nFailed example:\r\n    geogrid(pup,pdown,3,lonx=False)\r\nExpected:\r\n    [(42.023768, -87.946389), (42.02393997819538, -87.80562679358316), (42.02393997819538, -87.66486420641684), (42.023768, -87.524102), (41.897317, -87.94638900000001), (41.8974888973743, -87.80562679296166), (41.8974888973743, -87.66486420703835), (41.897317, -87.524102), (41.770866000000005, -87.94638900000001), (41.77103781320412, -87.80562679234043), (41.77103781320412, -87.66486420765956), (41.770866000000005, -87.524102), (41.644415, -87.946389), (41.64458672568646, -87.80562679171955), (41.64458672568646, -87.66486420828045), (41.644415, -87.524102)]\r\nGot:\r\n    [(42.023768, -87.946389), (42.02393997819538, -87.80562679358316), (42.02393997819538, -87.66486420641684), (42.023768, -87.524102), (41.897317, -87.94638900000001), (41.8974888973743, -87.80562679296166), (41.8974888973743, -87.66486420703835), (41.897317, -87.524102), (41.770866000000005, -87.94638900000001), (41.77103781320412, -87.80562679234043), (41.77103781320412, -87.66486420765956), (41.770866000000005, -87.524102), (41.644415, -87.946389), (41.64458672568647, -87.80562679171955), (41.64458672568647, -87.66486420828045), (41.644415, -87.524102)]\r\n\r\n\r\n======================================================================\r\nFAIL: Doctest: libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "C:\\Users\\200059719\\AppData\\Local\\conda\\conda\\envs\\test_momepy\\lib\\doctest.py", line 2196, in runTest\r\n    raise self.failureException(self.format_failure(new.getvalue()))\r\nAssertionError: Failed doctest test for libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\n  File "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\csvWrapper.py", line 15, in __init__\r\n\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\csvWrapper.py", line 24, in libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\nFailed example:\r\n    f.header\r\nExpected:\r\n    [\'WKT\', \'NAME\', \'STATE_NAME\', \'STATE_FIPS\', \'CNTY_FIPS\', \'FIPS\', \'FIPSNO\', \'HR7984\', \'HR8488\', \'HR8893\', \'HC7984\', \'HC8488\', \'HC8893\', \'PO7984\', \'PO8488\', \'PO8893\', \'PE77\', \'PE82\', \'PE87\', \'RDAC80\', \'RDAC85\', \'RDAC90\']\r\nGot:\r\n    [\'FIPSNO\', \'NAME\', \'STATE_NAME\', \'STATE_FIPS\', \'CNTY_FIPS\', \'FIPS\', \'HC7984\', \'HC8488\', \'HC8893\', \'PO7984\', \'PO8488\', \'PO8893\']\r\n----------------------------------------------------------------------\r\nFile "C:\\Users\\200059719\\libpysal\\libpysal\\io\\iohandlers\\csvWrapper.py", line 26, in libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\nFailed example:\r\n    f._spec\r\nExpected:\r\n    [<class \'str\'>, <class \'str\'>, <class \'str\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>]\r\nGot:\r\n    [<class \'int\'>, <class \'str\'>, <class \'str\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>]\r\n\r\n\r\nName                                      Stmts   Miss  Cover\r\n-------------------------------------------------------------\r\nlibpysal\\__init__.py                          5      0   100%\r\nlibpysal\\cg\\__init__.py                       8      0   100%\r\nlibpysal\\cg\\alpha_shapes.py                 142     55    61%\r\nlibpysal\\cg\\kdtree.py                        84     11    87%\r\nlibpysal\\cg\\locators.py                     218     12    94%\r\nlibpysal\\cg\\ops\\__init__.py                   2      0   100%\r\nlibpysal\\cg\\ops\\_accessors.py                15      3    80%\r\nlibpysal\\cg\\ops\\_shapely.py                  59     32    46%\r\nlibpysal\\cg\\ops\\atomic.py                     7      0   100%\r\nlibpysal\\cg\\ops\\tabular.py                   47     21    55%\r\nlibpysal\\cg\\polygonQuadTreeStructure.py     553     80    86%\r\nlibpysal\\cg\\rtree.py                        416     35    92%\r\nlibpysal\\cg\\segmentLocator.py               258    131    49%\r\nlibpysal\\cg\\shapely_ext.py                  209    159    24%\r\nlibpysal\\cg\\shapes.py                       473     46    90%\r\nlibpysal\\cg\\sphere.py                       154     42    73%\r\nlibpysal\\cg\\standalone.py                   310     19    94%\r\nlibpysal\\cg\\voronoi.py                       98     21    79%\r\nlibpysal\\common.py                           51     19    63%\r\nlibpysal\\examples\\__init__.py                21      2    90%\r\nlibpysal\\examples\\base.py                   145     68    53%\r\nlibpysal\\examples\\builtin.py                 39      4    90%\r\nlibpysal\\examples\\remotes.py                 65      9    86%\r\nlibpysal\\io\\__init__.py                       5      0   100%\r\nlibpysal\\io\\fileio.py                       210     75    64%\r\nlibpysal\\io\\geotable\\__init__.py              1      0   100%\r\nlibpysal\\io\\geotable\\dbf.py                  46     30    35%\r\nlibpysal\\io\\geotable\\file.py                 42     24    43%\r\nlibpysal\\io\\geotable\\shp.py                  13      5    62%\r\nlibpysal\\io\\geotable\\utils.py                30     12    60%\r\nlibpysal\\io\\geotable\\wrappers.py             30     19    37%\r\nlibpysal\\io\\iohandlers\\__init__.py           23      2    91%\r\nlibpysal\\io\\iohandlers\\arcgis_dbf.py         78      6    92%\r\nlibpysal\\io\\iohandlers\\arcgis_swm.py        110      4    96%\r\nlibpysal\\io\\iohandlers\\arcgis_txt.py         60     14    77%\r\nlibpysal\\io\\iohandlers\\csvWrapper.py         61      5    92%\r\nlibpysal\\io\\iohandlers\\dat.py                19      1    95%\r\nlibpysal\\io\\iohandlers\\db.py                 58      9    84%\r\nlibpysal\\io\\iohandlers\\gal.py                99      5    95%\r\nlibpysal\\io\\iohandlers\\geobugs_txt.py        84      1    99%\r\nlibpysal\\io\\iohandlers\\geoda_txt.py          59     11    81%\r\nlibpysal\\io\\iohandlers\\gwt.py               137     25    82%\r\nlibpysal\\io\\iohandlers\\mat.py                47      6    87%\r\nlibpysal\\io\\iohandlers\\mtx.py                40      1    98%\r\nlibpysal\\io\\iohandlers\\pyDbfIO.py           237     49    79%\r\nlibpysal\\io\\iohandlers\\pyShpIO.py           116     28    76%\r\nlibpysal\\io\\iohandlers\\stata_txt.py          74      1    99%\r\nlibpysal\\io\\iohandlers\\template.py           77     57    26%\r\nlibpysal\\io\\iohandlers\\wk1.py                91      8    91%\r\nlibpysal\\io\\iohandlers\\wkt.py                46      8    83%\r\nlibpysal\\io\\tables.py                        89     16    82%\r\nlibpysal\\io\\util\\__init__.py                  3      0   100%\r\nlibpysal\\io\\util\\shapefile.py               380     18    95%\r\nlibpysal\\io\\util\\weight_converter.py         48     13    73%\r\nlibpysal\\io\\util\\wkb.py                      78     66    15%\r\nlibpysal\\io\\util\\wkt.py                      42      5    88%\r\nlibpysal\\weights\\__init__.py                  8      0   100%\r\nlibpysal\\weights\\_contW_lists.py             77      6    92%\r\nlibpysal\\weights\\adjtools.py                 89     15    83%\r\nlibpysal\\weights\\contiguity.py              146     34    77%\r\nlibpysal\\weights\\distance.py                250     36    86%\r\nlibpysal\\weights\\set_operations.py          103     34    67%\r\nlibpysal\\weights\\spatial_lag.py              43      3    93%\r\nlibpysal\\weights\\spintW.py                   67      6    91%\r\nlibpysal\\weights\\user.py                     44      7    84%\r\nlibpysal\\weights\\util.py                    465     58    88%\r\nlibpysal\\weights\\weights.py                 510     87    83%\r\n-------------------------------------------------------------\r\nTOTAL                                      7714   1579    80%\r\n----------------------------------------------------------------------\r\nRan 728 tests in 178.610s\r\n\r\nFAILED (SKIP=41, errors=4, failures=3)\r\n```\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n```\r\n======================================================================\r\nERROR: test_casting (libpysal.io.iohandlers.tests.test_csvWrapper.test_csvWrapper)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "/Users/user/libpysal/libpysal/io/iohandlers/tests/test_csvWrapper.py", line 47, in test_casting\r\n    self.obj.cast(\'WKT\', WKTParser())\r\n  File "/Users/user/libpysal/libpysal/io/fileio.py", line 230, in cast\r\n    raise KeyError("%s" % key)\r\nKeyError: \'WKT\'\r\n\r\n======================================================================\r\nERROR: test_true_rook2 (libpysal.weights.tests.test__contW_lists.TestContiguityWeights)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "/Users/user/libpysal/libpysal/weights/tests/test__contW_lists.py", line 75, in test_true_rook2\r\n    \'stl_hom.shp\'), ROOK, \'POLY_ID_OG\')\r\n  File "/Users/user/libpysal/libpysal/weights/tests/test__contW_lists.py", line 120, in build_W\r\n    ids = db.by_col[idVariable]\r\n  File "/Users/user/libpysal/libpysal/io/tables.py", line 21, in __getitem__\r\n    return self.p._get_col(key)\r\n  File "/Users/user/libpysal/libpysal/io/iohandlers/pyDbfIO.py", line 110, in _get_col\r\n    raise AttributeError(\'Field: % s does not exist in header\' % key)\r\nAttributeError: Field: POLY_ID_OG does not exist in header\r\n\r\n======================================================================\r\nFAIL: Doctest: libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File "/Users/user/miniconda3/envs/py3_lps_dev/lib/python3.6/doctest.py", line 2199, in runTest\r\n    raise self.failureException(self.format_failure(new.getvalue()))\r\nAssertionError: Failed doctest test for libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\n  File "/Users/user/libpysal/libpysal/io/iohandlers/csvWrapper.py", line 15, in __init__\r\n\r\n----------------------------------------------------------------------\r\nFile "/Users/user/libpysal/libpysal/io/iohandlers/csvWrapper.py", line 24, in libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\nFailed example:\r\n    f.header\r\nExpected:\r\n    [\'WKT\', \'NAME\', \'STATE_NAME\', \'STATE_FIPS\', \'CNTY_FIPS\', \'FIPS\', \'FIPSNO\', \'HR7984\', \'HR8488\', \'HR8893\', \'HC7984\', \'HC8488\', \'HC8893\', \'PO7984\', \'PO8488\', \'PO8893\', \'PE77\', \'PE82\', \'PE87\', \'RDAC80\', \'RDAC85\', \'RDAC90\']\r\nGot:\r\n    [\'FIPSNO\', \'NAME\', \'STATE_NAME\', \'STATE_FIPS\', \'CNTY_FIPS\', \'FIPS\', \'HC7984\', \'HC8488\', \'HC8893\', \'PO7984\', \'PO8488\', \'PO8893\']\r\n----------------------------------------------------------------------\r\nFile "/Users/user/libpysal/libpysal/io/iohandlers/csvWrapper.py", line 26, in libpysal.io.iohandlers.csvWrapper.csvWrapper.__init__\r\nFailed example:\r\n    f._spec\r\nExpected:\r\n    [<class \'str\'>, <class \'str\'>, <class \'str\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>, <class \'float\'>]\r\nGot:\r\n    [<class \'int\'>, <class \'str\'>, <class \'str\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>, <class \'int\'>]\r\n\r\n\r\nName                                      Stmts   Miss  Cover\r\n-------------------------------------------------------------\r\nlibpysal/__init__.py                          5      0   100%\r\nlibpysal/cg/__init__.py                       8      0   100%\r\nlibpysal/cg/alpha_shapes.py                 142     46    68%\r\nlibpysal/cg/kdtree.py                        84     11    87%\r\nlibpysal/cg/locators.py                     218     12    94%\r\nlibpysal/cg/ops/__init__.py                   2      0   100%\r\nlibpysal/cg/ops/_accessors.py                15      3    80%\r\nlibpysal/cg/ops/_shapely.py                  59     32    46%\r\nlibpysal/cg/ops/atomic.py                     7      0   100%\r\nlibpysal/cg/ops/tabular.py                   47     21    55%\r\nlibpysal/cg/polygonQuadTreeStructure.py     553     80    86%\r\nlibpysal/cg/rtree.py                        416     35    92%\r\nlibpysal/cg/segmentLocator.py               258    131    49%\r\nlibpysal/cg/shapely_ext.py                  209    159    24%\r\nlibpysal/cg/shapes.py                       473     46    90%\r\nlibpysal/cg/sphere.py                       154     34    78%\r\nlibpysal/cg/standalone.py                   310     18    94%\r\nlibpysal/cg/voronoi.py                       98     16    84%\r\nlibpysal/common.py                           51      4    92%\r\nlibpysal/examples/__init__.py                21      1    95%\r\nlibpysal/examples/base.py                   145     58    60%\r\nlibpysal/examples/builtin.py                 39      4    90%\r\nlibpysal/examples/remotes.py                 65      9    86%\r\nlibpysal/io/__init__.py                       5      0   100%\r\nlibpysal/io/fileio.py                       210     75    64%\r\nlibpysal/io/geotable/__init__.py              1      0   100%\r\nlibpysal/io/geotable/dbf.py                  46     30    35%\r\nlibpysal/io/geotable/file.py                 42     24    43%\r\nlibpysal/io/geotable/shp.py                  13      5    62%\r\nlibpysal/io/geotable/utils.py                30     12    60%\r\nlibpysal/io/geotable/wrappers.py             30     19    37%\r\nlibpysal/io/iohandlers/__init__.py           23      2    91%\r\nlibpysal/io/iohandlers/arcgis_dbf.py         78      6    92%\r\nlibpysal/io/iohandlers/arcgis_swm.py        110      4    96%\r\nlibpysal/io/iohandlers/arcgis_txt.py         60     14    77%\r\nlibpysal/io/iohandlers/csvWrapper.py         61      0   100%\r\nlibpysal/io/iohandlers/dat.py                19      1    95%\r\nlibpysal/io/iohandlers/db.py                 58      9    84%\r\nlibpysal/io/iohandlers/gal.py                99      5    95%\r\nlibpysal/io/iohandlers/geobugs_txt.py        84      1    99%\r\nlibpysal/io/iohandlers/geoda_txt.py          59     11    81%\r\nlibpysal/io/iohandlers/gwt.py               137     25    82%\r\nlibpysal/io/iohandlers/mat.py                47      6    87%\r\nlibpysal/io/iohandlers/mtx.py                40      1    98%\r\nlibpysal/io/iohandlers/pyDbfIO.py           237     49    79%\r\nlibpysal/io/iohandlers/pyShpIO.py           116     28    76%\r\nlibpysal/io/iohandlers/stata_txt.py          74      1    99%\r\nlibpysal/io/iohandlers/template.py           77     57    26%\r\nlibpysal/io/iohandlers/wk1.py                91      8    91%\r\nlibpysal/io/iohandlers/wkt.py                46      8    83%\r\nlibpysal/io/tables.py                        89     16    82%\r\nlibpysal/io/util/__init__.py                  3      0   100%\r\nlibpysal/io/util/shapefile.py               380     18    95%\r\nlibpysal/io/util/weight_converter.py         48     13    73%\r\nlibpysal/io/util/wkb.py                      78     66    15%\r\nlibpysal/io/util/wkt.py                      42      5    88%\r\nlibpysal/weights/__init__.py                  8      0   100%\r\nlibpysal/weights/_contW_lists.py             77      6    92%\r\nlibpysal/weights/adjtools.py                 89     14    84%\r\nlibpysal/weights/contiguity.py              146     21    86%\r\nlibpysal/weights/distance.py                250     18    93%\r\nlibpysal/weights/set_operations.py          103     23    78%\r\nlibpysal/weights/spatial_lag.py              43      3    93%\r\nlibpysal/weights/spintW.py                   67      5    93%\r\nlibpysal/weights/user.py                     44      7    84%\r\nlibpysal/weights/util.py                    465     40    91%\r\nlibpysal/weights/weights.py                 510     43    92%\r\n-------------------------------------------------------------\r\nTOTAL                                      7714   1419    82%\r\n----------------------------------------------------------------------\r\nRan 727 tests in 68.534s\r\n\r\nFAILED (SKIP=41, errors=2, failures=1)\r\n```\r\n'},
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   'title': 'Constructing contiguity spatial weights using from_dataframe and from_shapefile could give different results',
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     'name': 'bug',
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     'default': True,
     'description': "functionality that: returns invalid, erroneous, or meaningless results; or doesn't work at all."}],
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   'created_at': '2019-12-17T00:55:34Z',
   'updated_at': '2020-01-04T15:23:11Z',
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   'author_association': 'MEMBER',
   'body': 'Constructing contiguity spatial weights using `from_dataframe` and `from_shapefile` could give different results. An example notebook with the Baltimore example data set is given [here](https://github.com/weikang9009/libpysal/blob/weight/notebooks/weight_issue.ipynb).\r\n\r\nBased on the Baltimore example data set, constructing a Queen or Rook contiguity weight directly from the shapefile will give a (210,210) weight matrix (with `from_shapefile`), while constructing that from the GeoDataFrame will produce a (211,211) weight matrix (with `from_shapefile`).\r\n\r\nIn contrast, KNN constructor gives identical spatial weight matrices (both are (211,211)).\r\n'},
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   'number': 213,
   'title': 'fix bug 212',
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   'created_at': '2019-12-26T22:48:38Z',
   'updated_at': '2020-01-04T15:22:21Z',
   'closed_at': '2020-01-04T15:22:21Z',
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   'body': "Sorry I didn't see #212 earlier. This fixes the described bug by ensuring that the `try/except` block of `libpysal.weights.util.get_points_array()` is safe for lazy input. Before, the [linked explanation succinctly describes the source of the bug.](https://github.com/pysal/libpysal/issues/212#issuecomment-569144720)."},
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   'number': 216,
   'title': 'alpha_shapes docs not rendering',
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   'body': "```\r\nfrom libpysal.weights import Voronoi\r\nimport numpy as np\r\n\r\nnp.random.seed(12345)\r\npoints= np.random.random((500,2))*10 + 10\r\nw_test = Voronoi(points)\r\nassert len(w_test.neighbors) == len(points)\r\n```\r\n\r\nThis fails and I believe it should not. \r\n\r\n- Platform information:\r\n```\r\nposix darwin\r\nposix.uname_result(sysname='Darwin', nodename='xxxx', release='18.6.0', version='Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64', machine='x86_64')\r\n```\r\n- Python version: \r\n```\r\n3.6.5 (default, Mar 30 2018, 06:41:53)\r\n[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.39.2)]\r\n```\r\n- SciPy version:\r\n```\r\n1.0.1\r\n```\r\n- NumPy version:\r\n```\r\n1.14.2\r\n```\r\n"},
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   'body': 'It is possible that we run into non-ergodic Markov chains, e.g. it might be impossible to migrate from one Markov state to another. Right now, the [`steady_state`](https://github.com/pysal/giddy/blob/master/giddy/ergodic.py#L12)  function for calculating the limiting distribution and the [`fmpt`](https://github.com/pysal/giddy/blob/master/giddy/ergodic.py#L62) function calculating first mean passage times can only deal with non-ergodic Markov chains. It will be useful to extend these functions to deal with non-ergodic Markov chains.\r\n'},
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   'body': 'This PR is to extend functions for Markov classes to deal with non-ergodic Markov chains. \r\n\r\nInstead of changing the behavior of existing functions like `giddy.ergodic.steady_state` and `giddy.ergodic.fmpt` which explicitly claim that they are only suitable for regular Markov chain, I added two functions: \r\n* [`giddy.ergodic.steady_state_general`](https://github.com/weikang9009/giddy/blob/limiting/giddy/ergodic.py#L64) \r\n* [`giddy.ergodic.fmpt_general`](https://github.com/weikang9009/giddy/blob/limiting/giddy/ergodic.py#L187)\r\n\r\nwhich could deal with reducible Markov chains. For instance, if the Markov chain has two communicating classes, `giddy.ergodic.steady_state_general` will return an array of two vectors (see [here](https://github.com/weikang9009/giddy/blob/limiting/giddy/ergodic.py#L105) for an example in the inline docstring.), and [`giddy.ergodic.fmpt_general`](https://github.com/weikang9009/giddy/blob/limiting/giddy/ergodic.py#L228) will return an array which contains `np.inf` since it is impossible to get a state in class 1 if the system starts at a state in class 2 (see [here] for an example in the inline docstring.).\r\n\r\nThese two functions replace`giddy.ergodic.steady_state` and `giddy.ergodic.fmpt` in classes `Markov`, `Spatial_Markov`, `FullRank_Markov` and `GeoRank_Markov` for estimating the steady state distributions and first mean passage times (spatially conditional or not).\r\n\r\nAnother enhancement is adding an optional parameter [`fill_diag `](https://github.com/weikang9009/giddy/blob/limiting/giddy/markov.py#L68) to each of these Markov related classes to allow users to determine whether a stochastic transition probability matrix (each row summing to 1) is desired.\r\n\r\n\r\n'},
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   'body': 'When running segregation indexes, I get a non-corresponding output legend (Out).  It repeats the same output line: "segregation.spatial.spatial_indexes.SpatialDissim" regardless if the index has change...  here an example of two different indexes, same Out legend:\r\n<img width="1123" alt="Screen Shot 2019-08-22 at 7 20 42 PM" src="https://user-images.githubusercontent.com/30789214/63562496-adf35780-c512-11e9-9bce-6f1e01986708.png">\r\n\r\n\r\nThis seems to be the default Output line in my local results... in every index...but this is not the case in the examples from the notebook.  \r\n\r\nAny ideas as to what can be the problem in my local version?  Thanks!!!\r\n\r\n'},
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   'body': 'Currently, we are point to https://github.com/spatialucr/geosnap/tree/master/geosnap/data, but we need to update this.'},
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   'body': "the following will result in a np.nan value for the `statistic` because `n_nonhsip_black_persons` has NaN values. \r\n\r\n```python\r\ndc = Community(source='ltdb', cbsafips='47900')\r\ndc = dc.tracts.merge(dc.census,left_on='geoid', right_index=True)\r\ndc_sd = SpatialDissim(dc, group_pop_var='n_nonhisp_black_persons', total_pop_var='n_total_pop')\r\n```\r\nWe should either move to more robust numpy operators that handle nans, or check whether there are any present in `group_pop_var` or `total_pop_var` and raise accordingly"},
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   'body': "Segregation on PySAL started to fail on travis https://travis-ci.org/pysal/pysal/jobs/566597373#L2405\r\n\r\nThis is due to indexes that rely on simulations and, therefore, numpy seeds. Travis now is building using numpy 1.17.0 (released 6 days ago). Some features were changed in the generating process of the seeds as you can read in https://github.com/numpy/numpy/releases.\r\n\r\n![image](https://user-images.githubusercontent.com/22593188/62322131-34a79e00-b459-11e9-9c19-27c6ee572ca3.png)\r\n\r\nI upgraded locally my numpy to 1.17.0 (previously it was 1.16.0) and, now, my seed generates the values that match the new tests (7 digit precision).\r\n\r\nSince I don't think it is a good thing the rely on the numpy version for the simulation-based tests... I think I'll increase the degree of tolerance of all tests and rewrite the tests (inference based also will change since they also rely on numpy seeds)."},
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   'body': '#### wrap up work\r\n* [x] close all issues/PRs related to `v1.4` or move to +1/`v2.0` release\r\n    * [x] TSP notebook #330 (#342)/ #110 / #100 \r\n      * [x] Use_case-tsp.ipynb\r\n      * punt to `v2.0`\r\n    * [x] figure out sphinx issue or punt to next release #339, #342 \r\n* [x] review/rename/rerun notebooks\r\n  * [x] remove/assimilate [Snapping_Demonstration.ipynb](https://github.com/pysal/spaghetti/blob/master/notebooks/Snapping_Demonstration.ipynb)\r\n   * [x] rename ~~[Spaghetti_Pointpatterns_Empirical.ipynb](https://github.com/pysal/spaghetti/blob/master/notebooks/Spaghetti_Pointpatterns_Empirical.ipynb)~~ --> Basic_spaghetti_tutorial.ipynb\r\n   * [x] rename ~~[Network_Usage.ipynb](https://github.com/pysal/spaghetti/blob/master/notebooks/Network_Usage.ipynb)~~ --> Advanced_spaghetti_tutorial.ipynb\r\n  * [x] rename ~~[Facility_Location.ipynb](https://github.com/pysal/spaghetti/blob/master/notebooks/Facility_Location.ipynb)~~ --> Use_case-facility_location.ipynb\r\n  * [x] uniform notebook layout\r\n      * [x] standardize font\r\n      * [x] disclaimer/citation\r\n      * [x] Title/subtitle/author\r\n      * [x] explanation/structure\r\n      * [x] load watermark / system watermark\r\n      * [x] notebook requirements\r\n      * [x] (uniform) import structure\r\n      * [x] watermark -iv\r\n      * [x] nb_black formatting for cells\r\n   * [x] update notebook links in `README.md`\r\n   * [x] binderize notebooks in docs (see [`giddy`](https://giddy.readthedocs.io/en/latest/tutorial.html) for example)(also #78)\r\n* [x] review `README.md` for references to version\r\n  * [x] ~~python~~ --> Python\r\n\r\n---------------------------------------------------------------\r\n#### release `v1.4.0`\r\n* [x] bump version in `__init__`\r\n* [x] rerun `docsrc`\r\n* [x] update CHANGELOG (automatic) **if needed**\r\n* [x] release on `github`\r\n* [x] release on `pypi`\r\n* [x] release on `conda-forge`\r\n   * [x] set [`sha256`](https://github.com/conda-forge/spaghetti-feedstock/blob/9839400d2564d17c404e6aff626388c881aa6a13/recipe/meta.yaml#L10) as a variable in the feedstock recipe (as is done in [`watermark-feedstock`](https://github.com/conda-forge/watermark-feedstock/blob/047b3788fb3076b63700cead651525ca226d5511/recipe/meta.yaml#L3)).\r\n   * [x] update [`doc_url`](https://github.com/conda-forge/spaghetti-feedstock/blob/9839400d2564d17c404e6aff626388c881aa6a13/recipe/meta.yaml#L46) in the feedstock recipe\r\n  * [x] update [`home`](https://github.com/conda-forge/spaghetti-feedstock/blob/9839400d2564d17c404e6aff626388c881aa6a13/recipe/meta.yaml#L34) in the feedstock recipe\r\n  * [x] update [`description`](https://github.com/conda-forge/spaghetti-feedstock/blob/9839400d2564d17c404e6aff626388c881aa6a13/recipe/meta.yaml#L39) in the feedstock recipe\r\n* [ ] ~~update CHANGELOG (manual)~~\r\n---------------------------------------------------------------\r\n#### ~~announce `v1.4.0`~~ save announcement for `v1.4.1` #365 \r\n* [ ] ~~announce on `pysal/pysal.github.io`~~\r\n* [ ] ~~announce on Twitter/LinkedIn/etc.~~'},
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   'body': 'Following #336 & #337, a review of the docs are needed for stale/broken links. Examples include:\r\n  *  [`libpysal.weights.weights.W`](https://libpysal.readthedocs.io/en/latest/generated/libpysal.weights.W.html#libpysal.weights.W) in [`spaghetti.Network.extract_components`](https://pysal.org/spaghetti/generated/spaghetti.Network.extract_components.html#spaghetti.Network.extract_components)\r\n\r\nSpecifically check for links to other packages link `geopandas`. Be sure to check check the generated locally for format and link functionality.'},
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   'created_at': '2019-12-22T22:49:20Z',
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   'body': 'While working on #339, I came across a parameter, which is present in several methods, that needs review.\r\n 1. `n_proccess` is spelled incorrectly in `Network.distancbandweights()` --> `n_processes`.\r\n 2. The default value of `n_processes` is `None`, which then defaults to `1` if the user does not specify either `"all"` for all cores of the CPU or request a specific number of cores, `2` for example. This should probably by explicitly set as a default of `n_processes =1` because there could never actually be `None` processes...\r\n\r\n\r\n * [x] [`Network.distancbandweights()`](https://github.com/pysal/spaghetti/blob/d4930d62c9073791b9f08dac6f4ee698808050e2/spaghetti/network.py#L827)\r\n* [x] [`Network.full_distance_matrix()`](https://github.com/pysal/spaghetti/blob/d4930d62c9073791b9f08dac6f4ee698808050e2/spaghetti/network.py#L1381)\r\n* [x] [`Network.allneighbordistances()`](https://github.com/pysal/spaghetti/blob/d4930d62c9073791b9f08dac6f4ee698808050e2/spaghetti/network.py#L1469)\r\n* [x]  [`Network.nearestneighbordistances()`](https://github.com/pysal/spaghetti/blob/d4930d62c9073791b9f08dac6f4ee698808050e2/spaghetti/network.py#L1746)'},
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   'body': '**Describe the bug**\r\n`descartes` now required for plotting polygons:\r\n\r\n`ImportError: The descartes package is required for plotting polygons in geopandas.`\r\n\r\n--> [Facility_Location.ipynb](https://github.com/pysal/spaghetti/blob/master/notebooks/Facility_Location.ipynb)\r\n\r\n\r\n\r\n```\r\n---------------------------------------------------------------------------\r\nModuleNotFoundError                       Traceback (most recent call last)\r\n~/miniconda3/envs/py3_spgh_dev/lib/python3.6/site-packages/geopandas/plotting.py in plot_polygon_collection(ax, geoms, values, color, cmap, vmin, vmax, **kwargs)\r\n     84     try:\r\n---> 85         from descartes.patch import PolygonPatch\r\n     86     except ImportError:\r\n\r\nModuleNotFoundError: No module named \'descartes\'\r\n\r\nDuring handling of the above exception, another exception occurred:\r\n\r\nImportError                               Traceback (most recent call last)\r\n<ipython-input-25-3ccffdf37b5a> in <module>\r\n      1 add_to_plot = {\'streets\':streets,\r\n      2                \'buffer\':streets_buffer}\r\n----> 3 plotter(plot_aux=add_to_plot, buffered=buff, title=title)\r\n\r\n<ipython-input-8-a2109470473d> in plotter(fig, base, plot_aux, buffered, model, pt1_size, pt2_size, plot_res, save_fig, title, figsize)\r\n     55                 df.plot(ax=base, lw=2, color=\'k\', zorder=1)\r\n     56             if k == \'buffer\':\r\n---> 57                 df.plot(ax=base, color=\'y\', lw=.25, alpha=.25, zorder=1)\r\n     58             if k == \'cli_tru\':\r\n     59                 if plot_res:\r\n\r\n~/miniconda3/envs/py3_spgh_dev/lib/python3.6/site-packages/geopandas/geodataframe.py in plot(self, *args, **kwargs)\r\n    548         from there.\r\n    549         """\r\n--> 550         return plot_dataframe(self, *args, **kwargs)\r\n    551 \r\n    552     plot.__doc__ = plot_dataframe.__doc__\r\n\r\n~/miniconda3/envs/py3_spgh_dev/lib/python3.6/site-packages/geopandas/plotting.py in plot_dataframe(df, column, cmap, color, ax, cax, categorical, legend, scheme, k, vmin, vmax, markersize, figsize, legend_kwds, classification_kwds, **style_kwds)\r\n    425         return plot_series(df.geometry, cmap=cmap, color=color, ax=ax,\r\n    426                            figsize=figsize, markersize=markersize,\r\n--> 427                            **style_kwds)\r\n    428 \r\n    429     # To accept pd.Series and np.arrays as column\r\n\r\n~/miniconda3/envs/py3_spgh_dev/lib/python3.6/site-packages/geopandas/plotting.py in plot_series(s, cmap, color, ax, figsize, **style_kwds)\r\n    295         values_ = values[poly_idx] if cmap else None\r\n    296         plot_polygon_collection(ax, polys, values_, facecolor=facecolor,\r\n--> 297                                 cmap=cmap, **style_kwds)\r\n    298 \r\n    299     # plot all LineStrings and MultiLineString components in same collection\r\n\r\n~/miniconda3/envs/py3_spgh_dev/lib/python3.6/site-packages/geopandas/plotting.py in plot_polygon_collection(ax, geoms, values, color, cmap, vmin, vmax, **kwargs)\r\n     85         from descartes.patch import PolygonPatch\r\n     86     except ImportError:\r\n---> 87         raise ImportError("The descartes package is required"\r\n     88                           " for plotting polygons in geopandas.")\r\n     89     from matplotlib.collections import PatchCollection\r\n\r\nImportError: The descartes package is required for plotting polygons in geopandas.\r\n```'},
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   'body': "**Describe the bug**\r\nmodule 'pysal.explore.spaghetti' has no attribute 'element_as_gdf'\r\n\r\n**To Reproduce**\r\nRunning the example Spaghetti_Pointpatterns_Empirical.ipynb\r\n"},
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   'body': 'The current implementation on [`spaghetti.util.compute_length()` performs a raw euclidean distance calculation using `numpy`](https://github.com/pysal/spaghetti/blob/e9d31e0c2fa937583fab225c8093955c757cd27c/spaghetti/util.py#L47). However, this same result can be obtained through [`libpysal.cg.standalone.get_points_dist()`](https://github.com/pysal/libpysal/blob/ed098ea900bde6a9913b96e162d64a72a9615e11/libpysal/cg/standalone.py#L467-L488). Switching from the current implementation to using the `libpysal.cg` implementation will be beneficial in two ways:\r\n1. improves DRY programming\r\n2. improves performance by approx. 5x, as shown below\r\n\r\n```python\r\n>>> import math\r\n>>> import numpy\r\n>>> pt1 = (0,0)\r\n>>> pt2 = (3,4)\r\n\r\n# spaghetti.util.compute_length\r\n>>> %timeit numpy.sqrt((pt1[0] - pt2[0]) ** 2 + (pt1[1] - pt2[1]) ** 2)\r\n# 1.6 µs ± 29.1 ns per loop (mean ± std. dev. of 7 runs, 1000000 loops each)\r\n\r\n# libpysal.cg.standalone.get_points_dist\r\n>>> %timeit math.hypot(pt1[0] - pt2[0], pt1[1] - pt2[1])\r\n# 277 ns ± 4.21 ns per loop (mean ± std. dev. of 7 runs, 1000000 loops each)\r\n```\r\n\r\n**This is a part of [Refactor: `spaghetti v2.0`](https://github.com/pysal/spaghetti/wiki/Refactor:-spaghetti-v2.0#keys)**'},
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   'body': 'After following our [installation instructions](https://github.com/pysal/tobler/blob/master/README.md#installation), we are getting breakage:\r\n\r\n\r\n```\r\n~/Dropbox/t/tobler/github/tobler/tobler/data.py in <module>\r\n      1 from urllib.parse import unquote, urlparse\r\n      2 \r\n----> 3 import quilt3\r\n      4 \r\n      5 \r\n\r\n~/anaconda3/envs/tobler/lib/python3.7/site-packages/quilt3-3.1.5-py3.7.egg/quilt3/__init__.py in <module>\r\n      5 warnings.filterwarnings("ignore", message="numpy.dtype size changed")\r\n      6 \r\n----> 7 from .api import (\r\n      8     copy,\r\n      9     put,\r\n\r\n~/anaconda3/envs/tobler/lib/python3.7/site-packages/quilt3-3.1.5-py3.7.egg/quilt3/api.py in <module>\r\n      2 from urllib.parse import quote, urlparse, unquote\r\n      3 \r\n----> 4 from .data_transfer import copy_file, get_bytes, delete_url, put_bytes, list_url\r\n      5 from .formats import FormatRegistry\r\n      6 from .search_util import search_api\r\n\r\n~/anaconda3/envs/tobler/lib/python3.7/site-packages/quilt3-3.1.5-py3.7.egg/quilt3/data_transfer.py in <module>\r\n     20 from tqdm import tqdm\r\n     21 \r\n---> 22 from .session import create_botocore_session\r\n     23 from .util import QuiltException, make_s3_url, parse_file_url, parse_s3_url\r\n     24 from . import xattr\r\n\r\n~/anaconda3/envs/tobler/lib/python3.7/site-packages/quilt3-3.1.5-py3.7.egg/quilt3/session.py in <module>\r\n     20 AUTH_PATH = BASE_PATH / \'auth.json\'\r\n     21 CREDENTIALS_PATH = BASE_PATH / \'credentials.json\'\r\n---> 22 VERSION = pkg_resources.require(\'quilt3\')[0].version\r\n     23 \r\n     24 def _load_auth():\r\n\r\n~/anaconda3/envs/tobler/lib/python3.7/site-packages/pkg_resources/__init__.py in require(self, *requirements)\r\n    898         included, even if they were already activated in this working set.\r\n    899         """\r\n--> 900         needed = self.resolve(parse_requirements(requirements))\r\n    901 \r\n    902         for dist in needed:\r\n\r\n~/anaconda3/envs/tobler/lib/python3.7/site-packages/pkg_resources/__init__.py in resolve(self, requirements, env, installer, replace_conflicting, extras)\r\n    789                 # Oops, the "best" so far conflicts with a dependency\r\n    790                 dependent_req = required_by[req]\r\n--> 791                 raise VersionConflict(dist, req).with_context(dependent_req)\r\n    792 \r\n    793             # push the new requirements onto the stack\r\n\r\nContextualVersionConflict: (python-dateutil 2.8.1 (/home/serge/anaconda3/envs/tobler/lib/python3.7/site-packages), Requirement.parse(\'python-dateutil<=2.8.0\'), {\'quilt3\'})\r\n```'},
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   'body': "Hi,\r\n\r\nfor some reason, if I want to install mapclassify with python3.7 on windows from conda-forge, I'll get UnsatisfiableError (https://ci.appveyor.com/project/martinfleis/momepy/builds/28862313). In the environment is nothing else:\r\n\r\n```\r\nname: test\r\nchannels:\r\n  - conda-forge\r\ndependencies:\r\n  - python=3.7\r\n  - mapclassify\r\n```\r\n \r\nIf I unpin python, I get python3.8 but mapclassify 2.0.1. So I sense the issue with scikit-learn, but I have no clue why this happens. The same situation is with pysal.\r\n\r\nEdit: If I keep mapclassify only, you get 2.0.1, if I pin mapclassify to 2.1.1 I get the error."},
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   'body': 'Updating the currently supported Python versions in `setup.py` from `3.5` & `3.6` to `3.6` & `3.7`, as tested in [`.travis.yml`](https://github.com/pysal/mapclassify/blob/master/.travis.yml).'},
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   'title': 'BUG: HeadTailBreaks raise RecursionError',
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   'body': 'HeadTailBreaks raises RecursionError if the maximum value within data is there twice (or more). Then it simply locks itself in the loop in `values[values >= mean]` - mean will be always the same and both values will always returned.\r\n\r\nSteps to reproduce:\r\n```\r\ndata = np.random.pareto(2, 1000)\r\ndata = np.append(data, data.max())\r\n\r\nmc.HeadTailBreaks(data)\r\n```\r\n\r\nI assume that once there are only the same values within remaining values, `head_tail_breaks` should stop:\r\n\r\n```\r\ndef head_tail_breaks(values, cuts):\r\n    """\r\n    head tail breaks helper function\r\n    """\r\n    values = np.array(values)\r\n    mean = np.mean(values)\r\n    cuts.append(mean)\r\n    if len(values) > 1:\r\n        if len(set(values)) > 1:  #this seems to fix the issue\r\n            return head_tail_breaks(values[values >= mean], cuts)\r\n    return cuts\r\n```\r\n\r\nHowever, I am not sure if it is the intended behaviour to stop and keep multiple values in the last bin as it does not reflect the definition of HeadTailBreaks algorithm (but I cannot see another solution). Happy to do a PR if this is how you want to fix that.'},
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   'body': "UserDefined attempts to add max value of given array to bins if that is not covered by given bins. However, it expects that bins are a list (`bins.append(max(y))`), while it could be any array-like. Even mapclassify's own `self.bins` gives array. I have changed this behaviour using np.append to cover all possibilities. \r\n\r\nSteps to replicate the issue:\r\n\r\n```py\r\nx = list(range(1, 1000))\r\ny = list(range(1, 500))\r\nnb = mc.NaturalBreaks(y)\r\nuserdefined = mc.UserDefined(x, nb.bins)\r\n```\r\n\r\n_(That's all from me today, I just happened to work with mapclassify a lot today and found these simple issues. Thank you for this great package!)_"},
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   'title': 'BUG: avoid deprecation warning in HeadTailBreaks',
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   'body': "After recent changes of classifiers' names, HeadTailBreaks returns DeprecationWarning even if a new name if used, because it uses the old one in the function itself. That is changed to use the new name.\r\n\r\nTo reproduce call HeadTailBreaks on any data.\r\n\r\n```\r\ndata = [1, 1, 1, 4, 5, 10]\r\nmc.HeadTailBreaks(data)\r\n```\r\n```\r\n/Users/martin/anaconda3/envs/geo_dev/lib/python3.7/site-packages/mapclassify/classifiers.py:86: DeprecationWarning: Call to deprecated function (or staticmethod) headTail_breaks. (use head_tail_breaks)\r\n  return headTail_breaks(values[values >= mean], cuts)\r\n```"},
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   'body': "Hi,\r\n\r\nas part of https://github.com/openjournals/joss-reviews/issues/1882 I am trying to simply follow your installation docs and initially I did not succeed. (under macOS 10.15)\r\n\r\n```\r\nconda create -n splot python\r\nconda activate splot\r\npip install splot\r\n```\r\n\r\n```\r\n...\r\nCollecting pyproj\r\n  Downloading https://files.pythonhosted.org/packages/8c/7e/c34acb5abca1916ba0a294df4a90935d6d1cfc446ad1c076986bbf0118d3/pyproj-2.4.1.tar.gz (462kB)\r\n     |████████████████████████████████| 471kB 2.8MB/s \r\n  Installing build dependencies ... done\r\n  Getting requirements to build wheel ... error\r\n  ERROR: Command errored out with exit status 1:\r\n   command: /Users/martin/anaconda3/envs/splot/bin/python /Users/martin/anaconda3/envs/splot/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /var/folders/d0/qyf0yvzd0n9ctn2wr3r4l1vw0000gn/T/tmp889iudeu\r\n       cwd: /private/var/folders/d0/qyf0yvzd0n9ctn2wr3r4l1vw0000gn/T/pip-install-4pkixl3a/pyproj\r\n  Complete output (1 lines):\r\n  ERROR: Minimum supported proj version is 6.2.0, installed version is 5.2.0.\r\n  ----------------------------------------\r\nERROR: Command errored out with exit status 1: /Users/martin/anaconda3/envs/splot/bin/python /Users/martin/anaconda3/envs/splot/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /var/folders/d0/qyf0yvzd0n9ctn2wr3r4l1vw0000gn/T/tmp889iudeu Check the logs for full command output.\r\n```\r\n\r\nI am aware that you are saying that it is compatible with 3.5 and 3.6 only (why? because of this issue?). Using `conda create -n splot python=3.6` it goes well. But it can be confusing.\r\n\r\nI am perfectly aware that this is not `splot` issue, but `pyproj`, being dependency of GeoPandas. As installation of `geopandas` from `pip` is notoriously problematic (http://geopandas.org/install.html), I would welcome a bit more information in your docs what to do. I can install `geopandas` from `conda-forge` and then `splot` from `pip`, which works perfectly, but this information could be in the documentation.\r\n\r\nI see that splot is on conda-forge in the same version as on PyPI, why you don't mention this option as well? `conda install -c conda-forge splot` works smoothly.\r\n\r\nI would recommend adding `conda-forge` option to documentation and link to` geopandas` docs for `pip` troubleshooting (as the issue is caused by `geopandas`).\r\n\r\nAlso, I do not understand '_splot supports python 3.5 and 3.6 only_' note as from conda-forge it comes with 3.8."},
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   'updated_at': '2020-01-18T20:24:09Z',
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   'body': 'Hi,\r\n\r\nthis is a very minor thing, but Usage section in the readme is a strange fragment only. \r\n\r\n> splot supports many different https://github.com/pysal/splot/blob/master/notebooks/mapping_vba.ipynb\r\n\r\nI would assume that it points me to https://github.com/pysal/splot/tree/master/notebooks, or that is not the intention with examples?\r\n\r\ncc openjournals/joss-reviews#1882'},
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   'title': 'JOSS: missing figure captions',
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   'body': 'Hi,\r\nI believe this is the last issue I am opening as a part of https://github.com/openjournals/joss-reviews/issues/1882. \r\n\r\nFigures in you paper are missing captions. I see that they are in the `paper.md`, but they did not show up in pdf. I guess it is an issue with markdown syntax. Can you check that?'},
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   'created_at': '2020-01-08T01:21:30Z',
   'updated_at': '2020-01-18T19:41:14Z',
   'closed_at': '2020-01-18T19:41:14Z',
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   'body': 'Update of installation instructions in documentation\r\n\r\n* adding information about dependencies\r\n* informing users of ways of trouble shooting\r\n* including conda-forge installation instructions\r\n\r\naddresses #88 \r\n\r\n'},
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   'created_at': '2020-01-16T23:56:03Z',
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   'body': 'This PR builds on top of #96 and addresses #90 and #92 \r\n\r\n* add figure captions in `paper.md` through markdown italics formatting\r\n* add links of notebook examples and other material to `README.md` under `Usage` section\r\n* add script lightning talk as documentation under introduction in `README.md`'},
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   'title': '[BUG] vba_choropleth failure',
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   'created_at': '2019-10-03T21:48:52Z',
   'updated_at': '2020-01-17T20:38:21Z',
   'closed_at': '2020-01-17T20:38:20Z',
   'author_association': 'MEMBER',
   'body': 'standard run of VBA_choropleth currently failing:\r\n\r\n```---------------------------------------------------------------------------\r\nValueError                                Traceback (most recent call last)\r\n<ipython-input-5-e2e864f55e9b> in <module>\r\n      8 vba_choropleth(x, y, gdf, rgb_mapclassify=dict(classifier=\'quantiles\'),\r\n      9                alpha_mapclassify=dict(classifier=\'quantiles\'),\r\n---> 10                cmap=\'RdBu\', ax=axs[1])\r\n     11 \r\n     12 # set figure style\r\n\r\n~/code/splot/splot/_viz_value_by_alpha_mpl.py in vba_choropleth(x_var, y_var, gdf, cmap, divergent, revert_alpha, alpha_mapclassify, rgb_mapclassify, ax, legend)\r\n    285                                          divergent=divergent,\r\n    286                                          revert_alpha=revert_alpha)\r\n--> 287     gdf.plot(color=rgba, ax=ax)\r\n    288     ax.set_axis_off()\r\n    289     ax.set_aspect(\'equal\')\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/geopandas/geodataframe.py in plot(self, *args, **kwargs)\r\n    604         from there.\r\n    605         """\r\n--> 606         return plot_dataframe(self, *args, **kwargs)\r\n    607 \r\n    608     plot.__doc__ = plot_dataframe.__doc__\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/geopandas/plotting.py in plot_dataframe(df, column, cmap, color, ax, cax, categorical, legend, scheme, k, vmin, vmax, markersize, figsize, legend_kwds, classification_kwds, **style_kwds)\r\n    500             figsize=figsize,\r\n    501             markersize=markersize,\r\n--> 502             **style_kwds\r\n    503         )\r\n    504 \r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/geopandas/plotting.py in plot_series(s, cmap, color, ax, figsize, **style_kwds)\r\n    339         values_ = values[poly_idx] if cmap else None\r\n    340         plot_polygon_collection(\r\n--> 341             ax, polys, values_, facecolor=facecolor, cmap=cmap, **style_kwds\r\n    342         )\r\n    343 \r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/geopandas/plotting.py in plot_polygon_collection(ax, geoms, values, color, cmap, vmin, vmax, **kwargs)\r\n    111                     kwargs[att] = np.take(kwargs[att], multiindex)\r\n    112 \r\n--> 113     collection = PatchCollection([PolygonPatch(poly) for poly in geoms], **kwargs)\r\n    114 \r\n    115     if values is not None:\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/collections.py in __init__(self, patches, match_original, **kwargs)\r\n   1803             kwargs[\'antialiaseds\'] = [p.get_antialiased() for p in patches]\r\n   1804 \r\n-> 1805         Collection.__init__(self, **kwargs)\r\n   1806 \r\n   1807         self.set_paths(patches)\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/collections.py in __init__(self, edgecolors, facecolors, linewidths, linestyles, capstyle, joinstyle, antialiaseds, offsets, transOffset, norm, cmap, pickradius, hatch, urls, offset_position, zorder, **kwargs)\r\n    160 \r\n    161         self._path_effects = None\r\n--> 162         self.update(kwargs)\r\n    163         self._paths = None\r\n    164 \r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/artist.py in update(self, props)\r\n    972 \r\n    973         with cbook._setattr_cm(self, eventson=False):\r\n--> 974             ret = [_update_property(self, k, v) for k, v in props.items()]\r\n    975 \r\n    976         if len(ret):\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/artist.py in <listcomp>(.0)\r\n    972 \r\n    973         with cbook._setattr_cm(self, eventson=False):\r\n--> 974             ret = [_update_property(self, k, v) for k, v in props.items()]\r\n    975 \r\n    976         if len(ret):\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/artist.py in _update_property(self, k, v)\r\n    969                     raise AttributeError(\'{!r} object has no property {!r}\'\r\n    970                                          .format(type(self).__name__, k))\r\n--> 971                 return func(v)\r\n    972 \r\n    973         with cbook._setattr_cm(self, eventson=False):\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/collections.py in set_facecolor(self, c)\r\n    676         """\r\n    677         self._original_facecolor = c\r\n--> 678         self._set_facecolor(c)\r\n    679 \r\n    680     def get_facecolor(self):\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/collections.py in _set_facecolor(self, c)\r\n    659         except AttributeError:\r\n    660             pass\r\n--> 661         self._facecolors = mcolors.to_rgba_array(c, self._alpha)\r\n    662         self.stale = True\r\n    663 \r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/colors.py in to_rgba_array(c, alpha)\r\n    292     result = np.empty((len(c), 4), float)\r\n    293     for i, cc in enumerate(c):\r\n--> 294         result[i] = to_rgba(cc, alpha)\r\n    295     return result\r\n    296 \r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/colors.py in to_rgba(c, alpha)\r\n    175         rgba = None\r\n    176     if rgba is None:  # Suppress exception chaining of cache lookup failure.\r\n--> 177         rgba = _to_rgba_no_colorcycle(c, alpha)\r\n    178         try:\r\n    179             _colors_full_map.cache[c, alpha] = rgba\r\n\r\n~/miniconda3/envs/dev/lib/python3.7/site-packages/matplotlib/colors.py in _to_rgba_no_colorcycle(c, alpha)\r\n    238         # float)` and `np.array(...).astype(float)` all convert "0.5" to 0.5.\r\n    239         # Test dimensionality to reject single floats.\r\n--> 240         raise ValueError("Invalid RGBA argument: {!r}".format(orig_c))\r\n    241     # Return a tuple to prevent the cached value from being modified.\r\n    242     c = tuple(c.astype(float))\r\n\r\nValueError: Invalid RGBA argument: 0.0196078431372549```'},
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   'body': "@sjsrey and I are planning on submitting `splot` as a [JOSS paper](http://joss.theoj.org)\r\n\r\nI would like to invite you to join in on this project and publication. I leave it up to you to decide wether you think your contribution has been substantial enough to be listed as a co-author. Additionally, there are a couple more tasks to implement before submission in case you would like to up your contribution. Feel free to note down your name to whichever task you are most likely to be able to contribute to. Include your-self and your affiliation in the list of authors.\r\n\r\nDeadline for submission in July 1st.\r\n\r\nAn example submissions can be found [here](https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography) and I am also happy to help out with more questions. \r\n\r\n***To-Do's***\r\n\r\n**Package**: (due date June 10)\r\n- [x] test all lines of code not tested, see #57  (@slumnitz)\r\n~- [ ] choropleth option in splot.mapping, see #50~ (integration with mapclassify first)\r\n- [x] Moran scatterplot equal bounds, see #51 (@ljwolf, @slumnitz)\r\n- [ ] (optional?) environment.yml for easy install\r\n- [x] check notebooks (@slumnitz)\r\n- [ ] esda local tests plotting function providing an option for selecting correction procedue for multiple testing (FDR-based (related to https://github.com/pysal/esda/pull/52), Bonferroni correction, etc)? (@weikang9009) \r\n- [x] docs building: readthedocs configuration file migrates from v1 to v2 as suggested in readthedocs that v1 should not be used (similar to [giddy](https://github.com/pysal/giddy/pull/92)) (@weikang9009 https://github.com/pysal/splot/pull/64 )\r\n- [x] move from supporting python 3.5 and 3.6 to python 3.6 and 3.7 as suggested in the last pysal dev meeting? (@weikang9009 @jGaboardi https://github.com/pysal/splot/pull/63)\r\n- [x] set up dual travis tests againist pysal dependencies (pip and github version) (@weikang9009 https://github.com/pysal/splot/pull/69)\r\n(- [ ] mapclassify natural breaks maintenance #65 (@weikang9009 ))\r\n\r\nOnce everything is done: (due date June 12)\r\n- [x] release splot 1.1.0 on pipy (@slumnitz)\r\n- [x] release splot 1.1.0 on Conda-forge (@slumnitz)\r\n\r\n[**`paper.md`**](https://github.com/pysal/splot/tree/master/paper): (due date June 19)\r\n- [x] list of authors and affiliations (@slumnitz, @sjsrey )\r\n- [x] summary for non-specialist audience (@slumnitz)\r\n    - [x] statement of need: target audience, problems the software can solve (I could use help here, @ljwolf can help)\r\n    - [x] installation instructions\r\n    - [ ] example usage for real world analysis problems or reference\r\n- [x] outlook/ roadmap (@slumnitz)\r\n- [x] key references (I could use help here) (@weikang9009)\r\n- [ ] statement of commit history ()\r\n- [x] Acknowledgements (@slumnitz)\r\n\r\nOnce draft is out:\r\n- [x] happy to review (@jGaboardi, )\r\n\r\n**`README.md`**: (due date June 10)\r\n- [x] link to CoC, (@slumnitz)\r\n- [x] description on how to contribute (@slumnitz)\r\n- [x] guidlines for reporting issues and participation (@slumnitz)\r\n- [x] update dependencies (@slumnitz)\r\n- [x] include Conda-forge installation (@slumnitz)\r\n- [x] refer to examples (@slumnitz)\r\n- [x] update installation instructions once release is out\r\n- [x] include DOI once release is out (https://zenodo.org/)\r\n\r\nLooking forward to getting this ready with you! Please feel free to add ideas and other tasks if you see fit :)"},
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   'body': 'Multiple citations are separated with a `;` instead of `,` which was\r\ncausing the paper to not render properly. Also fixes the missing\r\ncitation of `Arribas-Bel2017` to `arribas-bel2017looking` which I assume\r\nis what was intended (feel free to change if this is wrong).\r\n\r\nRelated to openjournals/joss-reviews#1838\r\n\r\nHello! Please make sure to check all these boxes before submitting a Pull Request\r\n(PR). Once you have checked the boxes, feel free to remove all text except the\r\njustification in point 5. \r\n\r\n1. [x] You have run tests on this submission, either by using [Travis Continuous Integration testing](https://github.com/pysal/pysal/wiki/GitHub-Standard-Operating-Procedures#automated-testing-w-travis-ci) testing or running `nosetests` on your changes?\r\n2. [ ] This pull request is directed to the `pysal/dev` branch.\r\n3. [ ] This pull introduces new functionality covered by\r\n   [docstrings](https://en.wikipedia.org/wiki/Docstring#Python) and\r\n   [unittests](https://docs.python.org/2/library/unittest.html)? \r\n4. [ ] You have [assigned a\r\n   reviewer](https://help.github.com/articles/assigning-issues-and-pull-requests-to-other-github-users/) and added relevant [labels](https://help.github.com/articles/applying-labels-to-issues-and-pull-requests/)\r\n5. [ ] The justification for this PR is: Fixes JOSS reference formatting issues.\r\n'},
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In [26]:

    

import pickle 

pickle.dump( issue_details, open( "issue_details.p", "wb" ) )

pickle.dump( pull_details, open("pull_details.p", "wb"))


    

In [ ]: