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pysal / segregation

Segregation Measurement, Inferential Statistics, and Decomposition Analysis
https://pysal.org/segregation/
BSD 3-Clause "New" or "Revised" License
112 stars 26 forks source link

api docs not rendering fully #58

Closed sjsrey closed 5 years ago

sjsrey commented 5 years ago

Compare segregation with giddy.

renanxcortes commented 5 years ago

hm... I still didn't find a way to fix this, but I have a strong feeling that it broke because we changed the api of the segregation module recently. So, instead of for example segregation.non_spatial_indexes.Dissim now it is segregation.aspatial.Dissim.

The current doc that it is generated is with the old API: image

How can I create a new set of files @knaaptime ?

renanxcortes commented 5 years ago

Do I need to run conf.py?

sjsrey commented 5 years ago

Do I need to run conf.py?

If you update the api.rst file, and then run make html it should regenerate those rst files.

renanxcortes commented 5 years ago

After fixing locally the html that sphinx generated locally and everything is fixed and pushed. However, I'm facing many other issues in the sphinx internal building. After figuring out that I needed to add sphinx_bootstrap_theme also in the requirements.txt (https://github.com/pysal/segregation/pull/66/commits/6a535096087e149ebadfb9f83be90e3293004191) I'm running now in this issue:

Running Sphinx v1.8.5

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/checkouts/latest/doc/conf.py", line 25, in <module>
    import segregation
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/__init__.py", line 8, in <module>
    from . import spatial
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/spatial/__init__.py", line 1, in <module>
    from .spatial_indexes import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/spatial/spatial_indexes.py", line 10, in <module>
    import libpysal
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/__init__.py", line 28, in <module>
    from . import io
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/__init__.py", line 3, in <module>
    from .iohandlers import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/iohandlers/__init__.py", line 4, in <module>
    from . import gwt
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/iohandlers/gwt.py", line 3, in <module>
    from ...weights.weights import W
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/__init__.py", line 2, in <module>
    from .distance import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/distance.py", line 7, in <module>
    from .util import isKDTree, get_ids, get_points_array_from_shapefile,\
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/util.py", line 17, in <module>
    import geopandas as gpd
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/__init__.py", line 1, in <module>
    from geopandas.geoseries import GeoSeries
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/geoseries.py", line 13, in <module>
    from geopandas.base import GeoPandasBase, _unary_op, _CoordinateIndexer
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/base.py", line 17, in <module>
    from rtree.core import RTreeError
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/__init__.py", line 1, in <module>
    from .index import Rtree
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/index.py", line 5, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/core.py", line 125, in <module>
    raise OSError("Could not find libspatialindex_c library file")
OSError: Could not find libspatialindex_c library file

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 203, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 380, in eval_config_file
    raise ConfigError(msg % traceback.format_exc())
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/checkouts/latest/doc/conf.py", line 25, in <module>
    import segregation
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/__init__.py", line 8, in <module>
    from . import spatial
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/spatial/__init__.py", line 1, in <module>
    from .spatial_indexes import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/spatial/spatial_indexes.py", line 10, in <module>
    import libpysal
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/__init__.py", line 28, in <module>
    from . import io
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/__init__.py", line 3, in <module>
    from .iohandlers import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/iohandlers/__init__.py", line 4, in <module>
    from . import gwt
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/iohandlers/gwt.py", line 3, in <module>
    from ...weights.weights import W
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/__init__.py", line 2, in <module>
    from .distance import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/distance.py", line 7, in <module>
    from .util import isKDTree, get_ids, get_points_array_from_shapefile,\
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/util.py", line 17, in <module>
    import geopandas as gpd
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/__init__.py", line 1, in <module>
    from geopandas.geoseries import GeoSeries
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/geoseries.py", line 13, in <module>
    from geopandas.base import GeoPandasBase, _unary_op, _CoordinateIndexer
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/base.py", line 17, in <module>
    from rtree.core import RTreeError
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/__init__.py", line 1, in <module>
    from .index import Rtree
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/index.py", line 5, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/core.py", line 125, in <module>
    raise OSError("Could not find libspatialindex_c library file")
OSError: Could not find libspatialindex_c library file

Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/checkouts/latest/doc/conf.py", line 25, in <module>
    import segregation
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/__init__.py", line 8, in <module>
    from . import spatial
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/spatial/__init__.py", line 1, in <module>
    from .spatial_indexes import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/segregation/spatial/spatial_indexes.py", line 10, in <module>
    import libpysal
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/__init__.py", line 28, in <module>
    from . import io
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/__init__.py", line 3, in <module>
    from .iohandlers import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/iohandlers/__init__.py", line 4, in <module>
    from . import gwt
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/io/iohandlers/gwt.py", line 3, in <module>
    from ...weights.weights import W
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/__init__.py", line 2, in <module>
    from .distance import *
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/distance.py", line 7, in <module>
    from .util import isKDTree, get_ids, get_points_array_from_shapefile,\
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/libpysal/weights/util.py", line 17, in <module>
    import geopandas as gpd
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/__init__.py", line 1, in <module>
    from geopandas.geoseries import GeoSeries
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/geoseries.py", line 13, in <module>
    from geopandas.base import GeoPandasBase, _unary_op, _CoordinateIndexer
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/geopandas/base.py", line 17, in <module>
    from rtree.core import RTreeError
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/__init__.py", line 1, in <module>
    from .index import Rtree
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/index.py", line 5, in <module>
    from . import core
  File "/home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/envs/latest/lib/python3.7/site-packages/rtree/core.py", line 125, in <module>
    raise OSError("Could not find libspatialindex_c library file")
OSError: Could not find libspatialindex_c library file

which I believe is similar to one discussed in https://github.com/pysal/spaghetti/issues/268. I'm still trying to debug this. If you have any clue how to do this @weikang9009 and @jGaboardi I appreciate it! Thanks!

renanxcortes commented 5 years ago

After following https://github.com/pysal/spaghetti/pull/272/commits/4d73cf536e04d3114594e41470329c0b3874acdb#diff-0112b253036ac23d3e0ac498694769d7 and adding conda in readthedocs.yml

The new error is

Processing /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/checkouts/latest
  WARNING: segregation 1.0.6 does not provide the extra 'docs'
  WARNING: segregation 1.0.6 does not provide the extra 'tests'
Requirement already up-to-date: pandas in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (0.24.2)
Collecting geopandas (from segregation==1.0.6)
  Using cached https://files.pythonhosted.org/packages/74/42/f4b147fc7920998a42046d0c2e65e61000bc5d104f1f8aec719612cb2fc8/geopandas-0.5.0-py2.py3-none-any.whl
Requirement already up-to-date: matplotlib in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (3.1.0)
Requirement already up-to-date: scikit-learn in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (0.21.2)
Requirement already up-to-date: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (0.9.0)
Requirement already up-to-date: numpy in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (1.16.4)
Collecting scipy (from segregation==1.0.6)
  Downloading https://files.pythonhosted.org/packages/72/4c/5f81e7264b0a7a8bd570810f48cd346ba36faedbd2ba255c873ad556de76/scipy-1.3.0-cp36-cp36m-manylinux1_x86_64.whl (25.2MB)
Requirement already up-to-date: libpysal in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (4.1.0)
Requirement already up-to-date: osmnx in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (0.10)
Requirement already up-to-date: pandana in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (0.4.1)
Requirement already up-to-date: urbanaccess in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from segregation==1.0.6) (0.2.0)
Collecting sphinx_bootstrap_theme (from segregation==1.0.6)
  Using cached https://files.pythonhosted.org/packages/a9/b8/ebcd1a7c579eb85929bbfd54617c5c484ba8cd78e4d3499d749e64b5ad3b/sphinx-bootstrap-theme-0.7.1.tar.gz
Requirement already up-to-date: python-dateutil>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from pandas->segregation==1.0.6) (2.8.0)
Requirement already up-to-date: pytz>=2011k in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from pandas->segregation==1.0.6) (2019.1)
Collecting fiona (from geopandas->segregation==1.0.6)
  Downloading https://files.pythonhosted.org/packages/89/4a/193cd6a75e51062c85f4e1cd6f312b3bbda6e26ba7510f152ef5016f0b16/Fiona-1.8.6-cp36-cp36m-manylinux1_x86_64.whl (17.9MB)
Collecting shapely (from geopandas->segregation==1.0.6)
  Downloading https://files.pythonhosted.org/packages/38/b6/b53f19062afd49bb5abd049aeed36f13bf8d57ef8f3fa07a5203531a0252/Shapely-1.6.4.post2-cp36-cp36m-manylinux1_x86_64.whl (1.5MB)
Collecting pyproj (from geopandas->segregation==1.0.6)
  Downloading https://files.pythonhosted.org/packages/ac/1a/81ef33d97354eb7d1765a921ecaf2ece41fd7927937b7c74124b6a2a0d99/pyproj-2.2.0-cp36-cp36m-manylinux1_x86_64.whl (11.2MB)
Requirement already up-to-date: cycler>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from matplotlib->segregation==1.0.6) (0.10.0)
Requirement already up-to-date: kiwisolver>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from matplotlib->segregation==1.0.6) (1.1.0)
Requirement already up-to-date: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from matplotlib->segregation==1.0.6) (2.4.0)
Requirement already up-to-date: joblib>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from scikit-learn->segregation==1.0.6) (0.13.2)
Requirement already up-to-date: Rtree>=0.8.3 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from osmnx->segregation==1.0.6) (0.8.3)
Requirement already up-to-date: networkx>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from osmnx->segregation==1.0.6) (2.3)
Requirement already up-to-date: descartes>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from osmnx->segregation==1.0.6) (1.1.0)
Requirement already up-to-date: requests>=2.21 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from osmnx->segregation==1.0.6) (2.22.0)
Requirement already up-to-date: tables>=3.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from pandana->segregation==1.0.6) (3.5.2)
Collecting osmnet>=0.1.2 (from pandana->segregation==1.0.6)
  Using cached https://files.pythonhosted.org/packages/68/64/ec9b88e7cb694b33a1adf9822e40e513d6676a122121769d8ccdd773596f/osmnet-0.1.5-py2.py3-none-any.whl
Requirement already up-to-date: cython>=0.25.2 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from pandana->segregation==1.0.6) (0.29.10)
Requirement already up-to-date: six>=1.11 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from urbanaccess->segregation==1.0.6) (1.12.0)
Requirement already up-to-date: geopy>=1.11.0 in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from urbanaccess->segregation==1.0.6) (1.20.0)
Collecting pyyaml>=3.11 (from urbanaccess->segregation==1.0.6)
  Using cached https://files.pythonhosted.org/packages/a3/65/837fefac7475963d1eccf4aa684c23b95aa6c1d033a2c5965ccb11e22623/PyYAML-5.1.1.tar.gz
Requirement already up-to-date: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/segregation-renan/conda/latest/lib/python3.6/site-packages (from sphinx_bootstrap_theme->segregation==1.0.6) (41.0.1)
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  Stored in directory: /tmp/pip-ephem-wheel-cache-vnox4udc/wheels/e2/21/dd/56e76a047f4a942b82d67fbb6dd62c07a9fb86225d253d532d
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Successfully built segregation sphinx-bootstrap-theme pyyaml
Installing collected packages: fiona, shapely, pyproj, geopandas, scipy, sphinx-bootstrap-theme, segregation, osmnet, pyyaml, urllib3, certifi
  Found existing installation: Fiona 1.8.4
    Uninstalling Fiona-1.8.4:
      Successfully uninstalled Fiona-1.8.4
  Found existing installation: Shapely 1.6.4.post1
    Uninstalling Shapely-1.6.4.post1:
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  Found existing installation: pyproj 1.9.6
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  Found existing installation: scipy 1.2.1
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  Found existing installation: PyYAML 5.1
ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

I think that perhaps adding a --ignore-installed somewhere would do the trick (at least for this part).

I'm still trying to debug (I've been doing other stuffs in other of my local branches but unsuccessfully) the current built is being performed in https://github.com/renanxcortes/segregation/tree/rtd_test_from_pysal_master.

renanxcortes commented 5 years ago

Just wanted to flag that the same issue happens sometimes with certifi.

renanxcortes commented 5 years ago

Eureka! So, after spending some time debugging sphinx I figure out that I could go with the classical pip channel instead of the conda option.

In summary, the problem was when I use the pip channel I run into OSError: Could not find libspatialindex_c library file, on the other hand when I go with the conda channel I run into ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

It ended that the pip was the one I solved by adding some libraries that depended on C as mock in the beginning of conf.py (such as rtree) such as explained in https://docs.readthedocs.io/en/stable/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules. The built ran smoothly! :)

I think that this could be an alternative to https://github.com/pysal/spaghetti/issues/268.

weikang9009 commented 5 years ago

@renanxcortes the citations and references are not properly rendered or showing up. image image

renanxcortes commented 5 years ago

Ow, indeed! I didn't see that! Thanks, @weikang9009 ! I'll take a look at this! It's probably something with the sphinx bibtex library!

renanxcortes commented 5 years ago

Fixed now with https://github.com/pysal/segregation/pull/68! :) (I also moved numpydoc from outside of the mock in https://github.com/pysal/segregation/pull/69)