Package libspatialindex, rtree #32000

DRKWang · 2021-06-17T23:33:37Z

Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial indexing features for the spatially curious Python user. These features include:

Nearest neighbor search

Intersection search

Multi-dimensional indexes

Clustered indexes (store Python pickles directly with index entries)

Bulk loading

Deletion

Disk serialization

Custom storage implementation (to implement spatial indexing in ZODB, for example).

Although it is named as Rtree, it also provides options for its variants in terms of splitting. There are 3 ways for it, that is, linear, quadratic, and R* tree splitting. The difference of them can be found here https://en.wikipedia.org/wiki/R-tree.

We create a normal package for Rtree.

PyPI package: https://pypi.org/project/Rtree/
points to... https://github.com/Toblerity/Rtree
latest documentation: https://rtree.readthedocs.io/en/latest/
libspatialindex library: https://libspatialindex.org/en/latest/

In addition,
CGAL also provides an implementation called "Intersecting Sequences of dD Iso-oriented Boxes" for the R tree, https://doc.cgal.org/latest/Box_intersection_d/index.html#Chapter_Intersecting_Sequences_of_dD_Iso-oriented_Boxes.

CC: @mkoeppe

Component: packages: optional

Keywords: Rtree, spatial index

Author: Binshuai Wang, Matthias Koeppe

Branch/Commit: public/32000 @ dfc5410

Issue created by migration from https://trac.sagemath.org/ticket/32000

The text was updated successfully, but these errors were encountered:

DRKWang · 2021-06-18T16:21:06Z

Branch: public/32000

mkoeppe · 2021-06-18T17:47:18Z

comment:4

The branch does not exist - did you push it?

sagetrac-git · 2021-06-23T18:05:47Z

Commit: a60179a

sagetrac-git · 2021-06-23T18:05:47Z

Branch pushed to git repo; I updated commit sha1. New commits:

mkoeppe · 2021-06-23T18:16:17Z

comment:6

This branch does not have your new files.

sagetrac-git · 2021-06-25T01:30:07Z

Changed commit from a60179a to eb62e8a

sagetrac-git · 2021-06-25T01:30:07Z

Branch pushed to git repo; I updated commit sha1. New commits:

`c18ed02`	`add new package rtree and libspatialindex`
`eb62e8a`	`For updating public/32000`

mkoeppe · 2021-06-25T17:28:22Z

comment:8

the .txt files - the file names should all be lowercase. See the files for the existing packages. You can see the names that we use by typing grep SYSTEM= tox.ini
We do not distinguish the various Debian variants (there should be no separate file for ubuntu, devuan, etc.)

First line of SPKG.rst should have a brief description, see format for other packages

mkoeppe · 2021-06-25T17:29:52Z

comment:9

checksums.ini - please add a line upstream_url as explained here https://doc.sagemath.org/html/en/developer/packaging.html#upstream-urls

mkoeppe · 2021-06-25T17:31:11Z

comment:10

build/pkgs/rtree/SPKG.rst is referring to "AABBTree", that's probably a copy-paste error

sagetrac-git · 2021-06-25T17:43:17Z

Changed commit from eb62e8a to c552a1e

sagetrac-git · 2021-06-25T17:43:17Z

Branch pushed to git repo; I updated commit sha1. New commits:

`c552a1e`	`build/pkgs/libspatialindex: Make it a normal package`

mkoeppe · 2021-06-25T17:44:10Z

comment:12

I've added full packaging as a normal package to libspatialindex because homebrew does not provide a package for it

mkoeppe · 2021-06-25T17:44:10Z

Author: Binshuai Wang, Matthias Koeppe

mkoeppe · 2021-06-25T17:46:31Z

comment:13

The file build/pkgs/rtree/requirements.txt needs to be removed because it makes the package a "pip package", so checksums.ini is being ignored

mkoeppe · 2021-06-25T17:55:19Z

comment:14

Does rtree use the executables mvrtree from libspatialindex, or does it link to library? In the latter case, the spkg-configure.m4 should be changed to use AC_LINK_IFELSE. You can see a usage example in build/pkgs/ntl/spkg-configure.m4

sagetrac-git · 2021-06-25T18:13:51Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`2330ca9`	`add new package rtree and libspatialindex`
`5902e3c`	`build/pkgs/libspatialindex: Make it a normal package`

sagetrac-git · 2021-06-25T18:13:51Z

Changed commit from c552a1e to 5902e3c

DRKWang · 2021-06-30T01:22:05Z

comment:16

Replying to @mkoeppe:

I've added full packaging as a normal package to libspatialindex because homebrew does not provide a package for it

I just found that homebrew provides a package for libspatialindex but it is in a different name: spatialindex, which is why I did not add it in .distros. You may check it from here https://repology.org/project/spatialindex/versions#homebrew

sagetrac-git · 2021-06-30T17:31:42Z

Branch pushed to git repo; I updated commit sha1. New commits:

`791aafd`	`update SPKG.rst, correct distros, add url in checksums.ini, revise spkg-configure`

sagetrac-git · 2021-06-30T17:31:42Z

Changed commit from 5902e3c to 791aafd

DRKWang · 2021-06-30T17:34:35Z

comment:18

Replying to @mkoeppe:

The file build/pkgs/rtree/requirements.txt needs to be removed because it makes the package a "pip package", so checksums.ini is being ignored

I have deleted it.

DRKWang · 2021-06-30T17:37:23Z

comment:19

Replying to @mkoeppe:

the .txt files - the file names should all be lowercase. See the files for the existing packages. You can see the names that we use by typing grep SYSTEM= tox.ini
We do not distinguish the various Debian variants (there should be no separate file for ubuntu, devuan, etc.)

First line of SPKG.rst should have a brief description, see format for other packages

The names of those files in .distros have been changed following this format.

mkoeppe · 2021-07-01T05:09:40Z

comment:27

Thanks for fixing this - that was a tricky one.

DRKWang · 2021-07-01T14:44:08Z

comment:28

Replying to @mkoeppe:

Thanks for fixing this - that was a tricky one.

No problem, thanks for your encouragement.

sagetrac-git · 2021-09-11T18:28:44Z

Changed commit from 720ff79 to 674d982

sagetrac-git · 2021-09-11T18:28:44Z

Branch pushed to git repo; I updated commit sha1. New commits:

`594bb26`	`make a whole change for RealSet class with using 'self.__class__' and '@classmethod', as well as adding a new subclass RealSet_rtree.`
`dfc5410`	`Merge branch 'public/32000' of trac.sagemath.org:sage into realset_rtree`
`674d982`	`"Fixed 2 bugs:`

DRKWang · 2021-09-11T18:34:50Z

comment:31

I just made a wrong commit, which is 674d982, for this ticket. Is there any way to retract it?

mkoeppe · 2021-09-11T19:46:30Z

comment:32

git reset --hard HEAD~ takes away the top commit on your branch.

Using git push --force you can send the updated branch to the remote.

sagetrac-git · 2021-09-11T19:55:28Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

sagetrac-git · 2021-09-11T19:55:28Z

Changed commit from 674d982 to dfc5410

DRKWang · 2021-09-11T19:57:12Z

comment:34

Replying to @mkoeppe:

git reset --hard HEAD~ takes away the top commit on your branch.

Using git push --force you can send the updated branch to the remote.

I see. Thanks!

mkoeppe · 2022-02-01T16:03:40Z

comment:37

Docbuild fails

OSError: /sage/local/var/lib/sage/venv-python3.10.2/lib/python3.10/site-packages/sage/geometry/cone.py:docstring of sage.geometry.cone.ConvexRationalPolyhedralCone.polar:6: WARNING: Bullet list ends without a blank line; unexpected unindent.

mkoeppe · 2022-02-01T16:06:33Z

comment:38

actually #32170

mkoeppe · 2023-02-12T03:34:17Z

Branch has merge conflicts

DRKWang added this to the sage-9.4 milestone Jun 17, 2021

DRKWang added c: packages: optional labels Jun 17, 2021

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DRKWang changed the title ~~Package Rtree~~ Package R tree Jun 17, 2021

DRKWang added the t: enhancement label Jun 18, 2021

mkoeppe changed the title ~~Package R tree~~ Package libspatialindex, rtree Jun 25, 2021

mkoeppe modified the milestones: sage-9.4, sage-9.5 Jul 19, 2021

mkoeppe added the s: needs review label Dec 3, 2021

mkoeppe modified the milestones: sage-9.5, sage-9.6 Dec 18, 2021

mkoeppe added s: needs work and removed s: needs review labels Feb 1, 2022

mkoeppe added s: needs review and removed s: needs work labels Feb 1, 2022

mkoeppe modified the milestones: sage-9.6, sage-9.7 Apr 2, 2022

mkoeppe modified the milestones: sage-9.7, sage-9.8 Aug 6, 2022

mkoeppe modified the milestones: sage-9.8, sage-9.9 Jan 7, 2023

mkoeppe added s: needs work and removed s: needs review labels Feb 12, 2023

mkoeppe removed this from the sage-10.0 milestone Mar 16, 2023

Package libspatialindex, rtree #32000

Package libspatialindex, rtree #32000

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