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Python Extension#71

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stevengj merged 38 commits intoNanoComp:masterfrom
Luochenghuang:master
Nov 29, 2024
Merged

Python Extension#71
stevengj merged 38 commits intoNanoComp:masterfrom
Luochenghuang:master

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@Luochenghuang
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@Luochenghuang Luochenghuang commented Nov 15, 2024 •
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Closes #70

  • Adds swig interface libctlgeom.i file.
  • Adds the python wrapper on top of the SWIG wrapper for more pythonic user experience.
  • Adds query vectorization.
  • Adds tests for the python wrapper.
  • Adds build script that automatically generate Python bindings using SWIG, compile the extension module, and Install the package using pip.
  • Adds the setup.py file for pip installation.
  • Adds the extension readme.
  • Adds a demo Jupyter Notebook.

@Luochenghuang
add swig
5da23c7
@Luochenghuang
Add python wrapper for swig generated python API
694d915 
This is to simplify the creation and manipulation of swig objects.
@Luochenghuang
fix bug where when query the material in tree the second time causes …
3a98fae 
…a crash.

improve memory management of the MATERIAL_TYPE
@Luochenghuang
Add Prism and SlatedPrism
34edeb5
@Luochenghuang
extend the bounding of the group object from float("-inf") to float("…
4b83858 
…inf")
@Luochenghuang
When material_type is NULL, constitutes a None in python.
01ecc24
@Luochenghuang
clean up the code a little bit
51065c6
@Luochenghuang
add jupyter notebook to showcase the interface
84715d7
@Luochenghuang
add 1000 sphere case
072f95d
@Luochenghuang
Add benchmark
8b1d2dd
@Luochenghuang
Modify the build script to include relative directories for header fi…
c9c3134 
…les.

Previously usr/local/include was used, which is undesirable.
@Luochenghuang
Add new macros for when compiling for swig; get rid of manual include…
41be3cd 
…s in the .i
@Luochenghuang
Add readme, minor edits
9076e6a
@Luochenghuang
Change dir name to python
7919184
@Luochenghuang
Update the bulid script to add autogen.sh
ce3b93e
@Luochenghuang
Get rid of Guile dependency for when building python extension
742cf41
@Luochenghuang
update gitignore to exclude python extension generated files
896274e
@Luochenghuang
Make bounding_box return actual coordinates; Get rid of Material obje…
9ed3791 
…ct; get_volume() -> volume();
@Luochenghuang
Improve docs, make things more pythonic.
2d5008d
@Luochenghuang
Add vector3 arrays and enable creation of Prisms and SlantedPrisms
b3a4743
@Luochenghuang
Clean up .i file
3a7cdce
@Luochenghuang
Add tests to the ctlgeom module
1c4a78e
@Luochenghuang
Add tests for ObjectGroup
4b35188
@Luochenghuang
Add readme for python extension
db2df0a
@Luochenghuang
Add loop in c in material_of_numpy_points_in_tree for x10 speed up
bfe89e2
@Luochenghuang
update notebook
1ad3961
@Luochenghuang
Add python wrappers for vecterized queries of materials in group.
1c80504 
Add tests as well.
@Luochenghuang
update readme
cc12467
@Luochenghuang
rename test.ipynb to demo.ipynb
82c54e8
@Luochenghuang Luochenghuang marked this pull request as ready for review November 15, 2024 22:37
oskooi
oskooi reviewed Nov 17, 2024
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Comment thread python/ctlgeom.py Outdated
Comment thread python/setup.py Outdated
@stevengj
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stevengj commented Nov 18, 2024

See #70 (comment), which I meant to post on this PR.

@stevengj stevengj mentioned this pull request Nov 18, 2024
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Luochenghuang commented Nov 20, 2024 •
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See #70 (comment), which I meant to post on this PR.

Great, thank you! I pulled your automake build into this PR. I also made some tweaks. Let me know if they make sense to you.

stevengj
stevengj reviewed Nov 21, 2024
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Comment thread configure.ac Outdated
stevengj
stevengj reviewed Nov 21, 2024
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Comment thread utils/python/__init__.py Outdated
stevengj
stevengj reviewed Nov 21, 2024
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Comment thread doc/docs/Installation.md Outdated
stevengj
stevengj reviewed Nov 21, 2024
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Comment thread doc/docs/Installation.md Outdated
@Luochenghuang
Automatically grab python 3
04fac59
@Luochenghuang
Keep namespace cleaner
020c2a3 
Import libctlgeom as a module instead of import all names from
libctlgeom
@Luochenghuang
Make python install instruction canonical
65b919b
stevengj
stevengj reviewed Nov 29, 2024
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Comment thread doc/docs/Installation.md
make
make install
```
Please follow the [instructions here](../../utils/python/README.md) to install the python extension.
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@stevengj stevengj Nov 29, 2024

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this needs to be an http to github … I don't think readthedocs will let you link outside the docs directory?

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let's merge this and then you can do a PR to make a proper link once it is merged and appears on github.

@stevengj stevengj merged commit 88e4254 into NanoComp:master Nov 29, 2024
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Python API for libctlgeom?

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@Luochenghuang @stevengj @oskooi