packingcubes 0.2.3__tar.gz → 0.3.1__tar.gz

{packingcubes-0.2.3 → packingcubes-0.3.1}/.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
       - name: Install pixi and run tests
-        uses: prefix-dev/setup-pixi@v0.9.4
+        uses: prefix-dev/setup-pixi@v0.9.5
         with:
           pixi-version: v0.66.0
           cache: true

packingcubes-0.3.1/.github/workflows/docs.yml

@@ -0,0 +1,29 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - master
+      - main
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/configure-pages@v5
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: pip install zensical
+      - run: zensical build --clean
+      - uses: actions/upload-pages-artifact@v4
+        with:
+          path: site
+      - uses: actions/deploy-pages@v4
+        id: deployment

{packingcubes-0.2.3 → packingcubes-0.3.1}/.github/workflows/pypi-publish.yml

@@ -22,7 +22,7 @@ jobs:
         with:
             python-version: "3.x"
       - name: Install pixi
-        uses: prefix-dev/setup-pixi@v0.9.4
+        uses: prefix-dev/setup-pixi@v0.9.5
         with:
           pixi-version: v0.66.0
           cache: true

packingcubes-0.3.1/.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+ build:
+   os: ubuntu-24.04
+   tools:
+     python: latest
+   jobs:
+     create_environment:
+         - asdf plugin add pixi
+         - asdf install pixi latest
+         - asdf global pixi latest
+     install:
+       - pixi install -e docs
+     build:
+       html:
+         - zensical build
+     post_build:
+       - mkdir -p $READTHEDOCS_OUTPUT/html/
+       - cp --recursive site/* $READTHEDOCS_OUTPUT/html/

{packingcubes-0.2.3 → packingcubes-0.3.1}/CHANGELOG.md

@@ -1,3 +1,126 @@
+## [0.3.1] - 2026-04-15
+
+### 🚀 Features
+
+- Expose benchmarking scripts on install ([d9a53e2](https://github.com/astrosocket/packingcubes/commit/d9a53e2a65e627902e42fee8976af4ff336284cc))
+
+### 🐛 Bug Fixes
+
+- Forgot to update exposed cube script path ([fe91cd6](https://github.com/astrosocket/packingcubes/commit/fe91cd665eca9a4a3782fca1459f65815a025f1b))
+- Nthreads should be set inside function ([785dd10](https://github.com/astrosocket/packingcubes/commit/785dd10e0a29dd17fd996e470d831ca967d6613f))
+
+### 🚜 Refactor
+
+- Remove old Benchmarking code ([11d1a7b](https://github.com/astrosocket/packingcubes/commit/11d1a7b1bb41ba56d0d8a74a99c777c6781a5879))
+- No longer need search object bounding boxes ([5c3fdc5](https://github.com/astrosocket/packingcubes/commit/5c3fdc581047f107461bc8c8a7ca605856eeb36e))
+- Adding new cubes module files ([4d071ec](https://github.com/astrosocket/packingcubes/commit/4d071ec3e09f226d12f3e54b5fa7022f4f90b859))
+- Removing old cubes module ([629b134](https://github.com/astrosocket/packingcubes/commit/629b1340e911ce3706b47753dfe410de8d95660e))
+
+### 📚 Documentation
+
+- Minor updates to packed_format for better rendering ([a0bd3f3](https://github.com/astrosocket/packingcubes/commit/a0bd3f311baa3ee725e6aa9a5ddf9c9b4f25acb0))
+- Add basic readthedocs and zensical setup ([e7a8765](https://github.com/astrosocket/packingcubes/commit/e7a87655900c898f76f4c4d20839c2d4d01bf96a))
+- Move from doc folder to docs folder ([7fef852](https://github.com/astrosocket/packingcubes/commit/7fef852672bf7e04f1a7070a325112e5dc66619c))
+
+### 🧪 Testing
+
+- Increasing test deadline ([b2c148c](https://github.com/astrosocket/packingcubes/commit/b2c148c10f9328c7083aa601298fd735ce45946c))
+- Major benchmarking overhaul ([d857c86](https://github.com/astrosocket/packingcubes/commit/d857c86e74f84b7d1beeeeaf91c1098f77b8abc4))
+- Handle ints that are bigger than unit64, vectors ([16c081a](https://github.com/astrosocket/packingcubes/commit/16c081a999143e3256fead54766460d3ca477f5f))
+- Add additional large integer test ([f504380](https://github.com/astrosocket/packingcubes/commit/f50438094591cc2aa418f4b42faad40650396d46))
+- Fix floating point error in test ([f207ce6](https://github.com/astrosocket/packingcubes/commit/f207ce69e7632339eee2bf96f5f7a33b58cc7829))
+
+### ⚙️ Miscellaneous Tasks
+
+- *(release)* Update Changelog ([da51d42](https://github.com/astrosocket/packingcubes/commit/da51d429a33a4b4b59f19baa67b9c0f688dffdf5))
+## [0.3.0] - 2026-04-07
+
+### 🚀 Features
+
+- Switch to custom heap implementation ([0cabc92](https://github.com/astrosocket/packingcubes/commit/0cabc92a97eebd31b3d0172122f3f50dbcdbb850))
+- Update Cubes API for get_closest_particles ([8f8627c](https://github.com/astrosocket/packingcubes/commit/8f8627c73d3b7bbab53f92839558996a7b91f884))
+- Add get_closest_particles for Cubes ([234c1d7](https://github.com/astrosocket/packingcubes/commit/234c1d7984b36caaaa824bac3d24cb7f4f62e31b))
+- Add clip_to_box method ([261933b](https://github.com/astrosocket/packingcubes/commit/261933b1fe3ca34d7a720b512714154c8bdb1092))
+- Change slice handling to use slice lists ([85e8aa2](https://github.com/astrosocket/packingcubes/commit/85e8aa213d4aa483028c97f0555d55ecb3585e17))
+- Expose save_dataset if Dataset passed to KDtree ([dcb735f](https://github.com/astrosocket/packingcubes/commit/dcb735fec2b989feb1e0335362a76a27fbabe5d6))
+- Updated default workers argument and warning ([79c1d49](https://github.com/astrosocket/packingcubes/commit/79c1d49fdc4b350f3841084a845de5b1444c5cc5))
+- Switch to using ParticleCubes as the backing search object ([9368f3f](https://github.com/astrosocket/packingcubes/commit/9368f3ffec410e27ccdebb18cff4524d41e31165))
+- Add stubs for closest particle queries and index lists for cubes ([de36637](https://github.com/astrosocket/packingcubes/commit/de366370eac8a72a0d3dceea6191ae9abcfb5fe8))
+- Add methods to get particle_index_lists ([6442a16](https://github.com/astrosocket/packingcubes/commit/6442a16e20486323ba23a43ba6fd12810de99c49))
+- Add method to save ParticleCubes to file ([e2298ab](https://github.com/astrosocket/packingcubes/commit/e2298ab7ce3abd732ada9cb2294b99ee952094d4))
+- Add method to get single ParticleCubes instance ([8eecee6](https://github.com/astrosocket/packingcubes/commit/8eecee65f72b0a8c81d92393641ecac5a5ebaeb7))
+- Add _get_indices_in_shape, replace in _sphere, _box ([7f79f2b](https://github.com/astrosocket/packingcubes/commit/7f79f2b4fbaf182f2c04554196010c3f3c734a1f))
+- Allow single string particle types when making cubes ([7b7bb19](https://github.com/astrosocket/packingcubes/commit/7b7bb1944aa9de10c304b3acd5aefc0f9594ebbe))
+- Add a pass to remove empty cubes ([c1e2c2b](https://github.com/astrosocket/packingcubes/commit/c1e2c2b3a4ebab75aa98012c89d170607caca164))
+- Add PackedTree __len__ as number of particles ([34c2c87](https://github.com/astrosocket/packingcubes/commit/34c2c87d2cf9f865baea0728a716318f39556f83))
+
+### 🐛 Bug Fixes
+
+- Forgot to increase scale ([8c5bb15](https://github.com/astrosocket/packingcubes/commit/8c5bb150c2a6c9e98236b45392b2617cb8afdffc))
+- Nodes were changing the tree box ([202cd07](https://github.com/astrosocket/packingcubes/commit/202cd07a5a2eab5e5ecebe426b9e3d749dd5523d))
+- Handle passing None to particle_threshold ([3bd6629](https://github.com/astrosocket/packingcubes/commit/3bd6629bbf18689d61f0c8bb35bd7bbdf1b30b50))
+- Some keys not populated yet in incremental saving ([b1ca1a5](https://github.com/astrosocket/packingcubes/commit/b1ca1a581b4ad70a2b6272a6b51675a6ed33e0d6))
+- Add default value for number_balls ([22410d8](https://github.com/astrosocket/packingcubes/commit/22410d83eba5de2dd983135d8e10659b88c17f19))
+- Bounding_box setup after position loading ([202e658](https://github.com/astrosocket/packingcubes/commit/202e6585b34d55ab3b41ea35588de34c18f9164c))
+- Explicit type conversion, move objmode out of loop ([0f6fea0](https://github.com/astrosocket/packingcubes/commit/0f6fea057eaa6ed8d3643aabdeb755fc100bc991))
+- ParticleCubes don't have particle_type, clean up warning ([cc3b6d8](https://github.com/astrosocket/packingcubes/commit/cc3b6d8bf434ff0db68994fd6c278ab9283bc198))
+- Incorrect box sizes passed to tree construction ([520000f](https://github.com/astrosocket/packingcubes/commit/520000f14472ddc7b167d7c6c4d4b8a841111f90))
+- More off-by-one errors ([1f74205](https://github.com/astrosocket/packingcubes/commit/1f742055978885617d03f2a3491f0cca4b045ad0))
+- Actually sort in place ([0837807](https://github.com/astrosocket/packingcubes/commit/0837807541424b52c67725ac6625d80d5a125505))
+- Leaf root nodes should still check partiality ([f08e3db](https://github.com/astrosocket/packingcubes/commit/f08e3dbd7899935fe61300d4be04748fac4dbc4d))
+- Off-by-one error on node length ([c1af9e2](https://github.com/astrosocket/packingcubes/commit/c1af9e2432c89581f8182089c66648281ff1d407))
+- Dumb off-by-one error ([870315f](https://github.com/astrosocket/packingcubes/commit/870315f78c65e43c5112a2833fbde35d3f3c36af))
+
+### 💼 Other
+
+- Fix another parallel list index casting ([ed3f038](https://github.com/astrosocket/packingcubes/commit/ed3f0386cbc3883ec7e2b257dcfabf00654b8f0e))
+
+### 🚜 Refactor
+
+- Move boxsize processing to separate function ([b32fd92](https://github.com/astrosocket/packingcubes/commit/b32fd92f54e8033579897b41b748e9026c913352))
+- Make variable names more consistent ([5531354](https://github.com/astrosocket/packingcubes/commit/553135414765df435a84387862f060cd79d17930))
+- Change Cubes class to MultiCubes, add factory functions ([01bc347](https://github.com/astrosocket/packingcubes/commit/01bc347f4644689f5d91f2d60873ad5a6740d8d8))
+- Use self._get_indices_in_shape instead _get_indices_in_shape ([7cb35ba](https://github.com/astrosocket/packingcubes/commit/7cb35ba39329351bee1b3a42d6cfb3cf9484bccc))
+- Remove _big_index_tuple type ([849cf90](https://github.com/astrosocket/packingcubes/commit/849cf9025b5b95b738eb08d11f6d875403c1bb3c))
+- Change order of methods in file ([efe7069](https://github.com/astrosocket/packingcubes/commit/efe7069fce39337fcf56094ce253f3278f46d0e8))
+- Change output from list to array ([cd7fd50](https://github.com/astrosocket/packingcubes/commit/cd7fd50ded41a942a47736754dba299e499b1df2))
+- Remove unnecessary bounding_box ([6ac9a7c](https://github.com/astrosocket/packingcubes/commit/6ac9a7c780d18a936e57a66d4ba4a57ece8e0ab4))
+
+### 📚 Documentation
+
+- Add query performance timings ([0201e7d](https://github.com/astrosocket/packingcubes/commit/0201e7dca67bbe898c84486a8cdcae85da9f081f))
+- Formatting, update timings, switch to creation, improve scale plot ([3c5f347](https://github.com/astrosocket/packingcubes/commit/3c5f347fab42a2ad27cf11d1db30d04a9f0fe9b4))
+- Fix description of workers in qbp ([732a599](https://github.com/astrosocket/packingcubes/commit/732a5994aa0674e965d0ea70f602e1e5b05bd121))
+- Clean up _get_indices_in_shape ([083fafb](https://github.com/astrosocket/packingcubes/commit/083fafb13529e48b92e930f01df51e0adb843896))
+- Add missed changelog addition ([c19cdc4](https://github.com/astrosocket/packingcubes/commit/c19cdc4a09f669c41725ad0a32c724bc739dcaa7))
+
+### ⚡ Performance
+
+- Rework get_closest_particles to use min-heap ([54afcdd](https://github.com/astrosocket/packingcubes/commit/54afcddcb6937e649e5c74ec7061f3bc588e0dd5))
+- Updated timings showing strong scaling ([1dcd768](https://github.com/astrosocket/packingcubes/commit/1dcd7686a8e66ffa5718bb8510c811eb22a5a2f8))
+- Change query_ball_point defaults to performant values ([45b7521](https://github.com/astrosocket/packingcubes/commit/45b75214df4287a6e88fdcaba4ce2aa9bba45fc0))
+- Subboxes should probably be safe ([0bb1aee](https://github.com/astrosocket/packingcubes/commit/0bb1aee130ae7038269fd673d330380b77b54e32))
+- Skip extraneous function call ([723bf13](https://github.com/astrosocket/packingcubes/commit/723bf13103f88889135566669ff3d8aace32cac7))
+
+### 🎨 Styling
+
+- Supress additional enumeration warning ([efac873](https://github.com/astrosocket/packingcubes/commit/efac8735d6e026b29b0f41cbee98169a00b997fd))
+- Suppress complaint about enumerating for loops ([fef8c84](https://github.com/astrosocket/packingcubes/commit/fef8c842ef2cdf321eb6c3112293a3d81ce32c2f))
+
+### 🧪 Testing
+
+- Update query test to use config k, return sorted ([7942f96](https://github.com/astrosocket/packingcubes/commit/7942f966ab3f7359156ebc94e88580cbfe6f1483))
+- Add performance options for query timing ([e8831ee](https://github.com/astrosocket/packingcubes/commit/e8831ee6b17570be58212a69aec2b7c136248fca))
+- Kdtree query tests are working again ([d4359e6](https://github.com/astrosocket/packingcubes/commit/d4359e603d294be4d954251c6bf1d6a4d6d489e0))
+- Stop saving dataset changes, API updates, cube profile update ([eec90ae](https://github.com/astrosocket/packingcubes/commit/eec90ae616c7033fc00f3a2b21e14df49527b3b7))
+- Switch to custom timer for search objects ([7a039b2](https://github.com/astrosocket/packingcubes/commit/7a039b287d54f7ee44c7b31ae539a67ffa9410f0))
+- Update profiling notebook ([cfe673f](https://github.com/astrosocket/packingcubes/commit/cfe673ffb8636223781519b828c0a1544302e837))
+- Update benchmarking data ([c5a47dd](https://github.com/astrosocket/packingcubes/commit/c5a47dd2c2ac77adbd8b635f0bea8323f1a9383f))
+- Save output on every loop iteration for incremental results ([10571af](https://github.com/astrosocket/packingcubes/commit/10571aff35786399ba7a02b8f561c80a7be99904))
+- Add extra debug information ([eee95a0](https://github.com/astrosocket/packingcubes/commit/eee95a0777908605eec6de387817d2aa0737526c))
+- Use new slice lists to load chunks of dataset instead of striding ([a1be6db](https://github.com/astrosocket/packingcubes/commit/a1be6db72e50161608afd8a0f5946a7529fafb7e))
+- Add test for just the numba search portion ([eb9f60e](https://github.com/astrosocket/packingcubes/commit/eb9f60e1b33c3676e99907d709420b2b96925b4b))
+- Add custom scaling to tests ([e5c45d8](https://github.com/astrosocket/packingcubes/commit/e5c45d82929580f02ef67ec8f7cce6c607de9cb3))
 ## [0.2.3] - 2026-03-25
 
 ### 🚀 Features
@@ -46,6 +169,7 @@
 
 ### 🚀 Features
 
+- Enhancements derived from updating the README ([#12](https://github.com/astrosocket/packingcubes/issues/12)) ([256877c](https://github.com/astrosocket/packingcubes/commit/256877c79eb08fcc1dc6ee54d138c1ad67687a45))
 - Flesh out the readme ([e757b45](https://github.com/astrosocket/packingcubes/commit/e757b4586b2c79fe11e2152f70019a567f367d01))
 - Support passing a regular array to Cubes constructor ([c59097b](https://github.com/astrosocket/packingcubes/commit/c59097b8eb844dda5be5510125b7b4c487e7c54c))
 - Allow loading cubes data from file ([d45b5d7](https://github.com/astrosocket/packingcubes/commit/d45b5d70ee30975a870f75ee6ee348e745fafa37))

{packingcubes-0.2.3 → packingcubes-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: packingcubes
-Version: 0.2.3
+Version: 0.3.1
 Summary: PackingCubes octree implementation for astro data
 Author: Michael Ryan
 Author-email: Josh Borrow <josh@joshborrow.com>

packingcubes-0.3.1/docs/index.md

@@ -0,0 +1,6 @@
+---
+icon: lucide/box
+---
+
+--8<-- "README.md"
+

packingcubes-0.3.1/docs/javascripts/mathjax.js

@@ -0,0 +1,24 @@
+window.MathJax = {
+  tex: {
+    inlineMath: [["\\(", "\\)"]],
+    displayMath: [["\\[", "\\]"]],
+    processEscapes: true,
+    processEnvironments: true
+  },
+  options: {
+    ignoreHtmlClass: ".*|",
+    processHtmlClass: "arithmatex"
+  }
+};
+
+document$.subscribe(() => { 
+  MathJax.startup.output.clearCache()
+  MathJax.typesetClear()
+  MathJax.texReset()
+  MathJax.typesetPromise()
+})
+
+component$.subscribe(({ ref }) => {
+  if (ref.classList.contains("md-annotation"))
+    MathJax.typesetPromise([ref])
+})

{packingcubes-0.2.3/doc → packingcubes-0.3.1/docs}/packed_format.md

@@ -1,6 +1,6 @@
 # Packed Format Design Specification
 
-Version 1.0.0
+Version 1.0.1
 
 This file documents the format used to describe a PackedTree data structure.
 
@@ -13,7 +13,7 @@ The basic unit of the packed format is the `field`, currently defined as a
 and internally is stored as a numpy array of such.
 
 
-# Tree Metadata
+## Tree Metadata
 
 | Field | Bytes   | Description                                                                                                                                            |
 | ----- | ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------ |
@@ -32,6 +32,7 @@ and internally is stored as a numpy array of such.
 | 35    | 140-143 | Particle threshold                                                                                                                                     |
 
 Timestamp is currently computed via
+
 ```python
 # conversion to timestamp
 t = np.float64(datetime.datetime.now(tz=datetime.UTC).timestamp())
@@ -40,6 +41,7 @@ datetime.datetime.fromtimestamp(t, tz=datetime.UTC)
 ```
 
 For the checksum, use [xxhash's xxh3](https://pypi.org/project/xxhash/) (not part of the standard library):
+
 ```python
 from xxhash import xxh3_64_intdigest 
 
@@ -47,9 +49,23 @@ checksum = xxh3_64_intdigest(packed_tree)
 ```
 This creates a uint64 checksum.
 
-# Tree Data Structure
+## Tree Data Structure
+
+Essentially we can think of the tree structure as the equivalent of `numpy`'s
+structured array, except in an octree structure as opposed to the linear array
+structure. Thus, the bytes are organized such that all information for a node
+(*including it's children!*) are together in sequential order. 
+
+The intent is to mimic the in-memory structure of a simple tree from a language
+like C, where every child node pointer has been replaced by the actual bytes
+of the child node.
+
+Thus, the first few bytes correspond to data attached to the root node, the
+next few bytes are the first child's data, followed by the first grandchild,
+etc., in a pre-order depth-first traversal of the tree.
 
-## Internal Node:
+
+### Internal Node:
 
 | skip_length | node_start | node_end | child_flag  | my_index | level | unused | C0  | C1  | C5  | C6  | C7  | parent_offset |
 | ----------- | ---------- | -------- | ----------- | -------- | ----- | ------ | --- | --- | --- | --- | --- | ------------- |
@@ -58,13 +74,38 @@ This creates a uint64 checksum.
 | field 0      | field 1     | field 2   | field 3      |          |       |        | *   | *   | *   | *   | *   | field 4        |
 
 For the present case, `child_flag` would be 227 ($=2^0 + 2^1 + 2^5 + 2^6 + 2^7$). If all 5 nodes were leaves, then `skip_length`=30.
-## Leaf Node:
+
+### Leaf Node:
 Size = 5 fields = 20 bytes
 
 | skip_length=20 | node_start | node_end | child_flag=0 | my_index | level | unused | parent_offset |
 | -------------- | ---------- | -------- | ------------ | -------- | ----- | ------ | ------------- |
 | uint32         | uint32     | uint32   | uint8        | uint8    | uint8 | uint8  | uint32        |
 
-## Example:
+### Example:
 ![Example packed array implementation](example_packed.jpg)
 Here, $x_{s}$, $x_{e}$, and $x_{m}$ are the node_start, node_end, and metadata (child_flag, my_index, level, and empty) fields for node $x$. The starred nodes in the tree are the last sibling for each group of children.
+
+
+<script id="MathJax-script" src="https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js"></script>
+<script>
+  window.MathJax = {
+    tex: {
+      inlineMath: [["\\(", "\\)"]],
+      displayMath: [["\\[", "\\]"]],
+      processEscapes: true,
+      processEnvironments: true
+    },
+    options: {
+      ignoreHtmlClass: ".*|",
+      processHtmlClass: "arithmatex"
+    }
+  };
+
+  document$.subscribe(() => {
+    MathJax.startup.output.clearCache()
+    MathJax.typesetClear()
+    MathJax.texReset()
+    MathJax.typesetPromise()
+  })
+</script>

{packingcubes-0.2.3 → packingcubes-0.3.1}/examples/Profiling.py

@@ -33,6 +33,7 @@
 
 # %%
 # %load_ext profila
+# %load_ext pyinstrument
 
 from time import time  # noqa: E402
 
@@ -73,12 +74,11 @@ tree.get_particle_indices_in_sphere(center=center, radius=radius)
 cubes = Cubes(
     dataset=ds,
     particle_types=["PartType0"],
+    save_dataset=False,
 )
 
 # %%
-cubes.get_particle_indices_in_sphere(
-    particle_types="PartType0", center=center, radius=radius
-)
+cubes.get_particle_indices_in_sphere(center=center, radius=radius)
 
 # %%
 kdtree = KDTree(
@@ -127,10 +127,13 @@ while (time() - start) < 30:
 # %%
 # %%profila
 
-cubes = Cubes(
-    dataset=ds,
-    particle_types="PartType0",
-)
+start = time()
+while (time() - start) < 30:
+    cubes = Cubes(
+        dataset=ds,
+        particle_types=["PartType0"],
+        save_dataset=False,
+    )
 
 # %% [markdown] jp-MarkdownHeadingCollapsed=true
 # ## Profile cubes search
@@ -190,11 +193,8 @@ while (time() - start) < 30:
 # %% [markdown]
 # # Python profiling
 
-# %%
-# %load_ext pyinstrument
-
 # %% [markdown]
-# ##
+# ## KDTree (python)
 
 # %%
 kdtree = KDTree(
@@ -214,7 +214,47 @@ sph_box = sph.bounding_box
 
 start = time()
 while (time() - start) < 30:
-    sph_inds = kdtree.query_ball_point(x=centers[0], r=radius)
+    sph_inds = kdtree.query_ball_point(
+        x=centers[0], r=radius, return_data_indices=True, return_lists=False
+    )
+
+# %% [markdown]
+# ## Packed (python)
+
+# %%
+tree = Optree(dataset=ds)
+center = np.array([15000, 15000, 15000])
+radius = 1000
+
+# %% [markdown]
+# ### Packed search
+
+# %%
+# %%pyinstrument
+
+start = time()
+while (time() - start) < 30:
+    sph_inds = tree.get_particle_indices_in_sphere(center=center, radius=radius)
+
+# %% [markdown]
+# ## Cubes
+
+# %% [markdown]
+# ### Cubes creation
+
+# %%
+# %%pyinstrument
+
+start = time()
+while (time() - start) < 30:
+    cubes = Cubes(
+        dataset=ds,
+        particle_types=["PartType0"],
+        save_dataset=False,
+    )
+
+# %% [markdown]
+# ### Cubes search
 
 # %%
 

{packingcubes-0.2.3 → packingcubes-0.3.1}/packingcubes/__init__.py

@@ -1,8 +1,19 @@
 import logging
 from importlib.metadata import PackageNotFoundError, version
 
-from packingcubes.cubes import Cubes as Cubes
+from packingcubes.cubes import (
+    Cubes as Cubes,
+)
+from packingcubes.cubes import (
+    MultiCubes as MultiCubes,
+)
+from packingcubes.cubes import (
+    ParticleCubes as ParticleCubes,
+)
 from packingcubes.cubes import make_cubes as make_cubes
+from packingcubes.cubes import (
+    make_ParticleCubes as make_ParticleCubes,
+)
 from packingcubes.data_objects import (
     GadgetishHDF5Dataset as HDF5Dataset,
 )
@@ -24,6 +35,9 @@ __all__ = [
     "KDTree",
     "make_cubes",
     "Cubes",
+    "ParticleCubes",
+    "MultiCubes",
+    "make_ParticleCubes",
     "__version__",
 ]
 

{packingcubes-0.2.3 → packingcubes-0.3.1}/packingcubes/bounding_box.py

@@ -462,7 +462,7 @@ class BoundingBox(BoundingVolume):
         in_box = np.empty((xyz.shape[0],), dtype=np.bool_)
         bx, by, bz, dx, dy, dz = self.box
         for i in range(xyz.shape[0]):
-            x, y, z = xyz[i, 0:2]
+            x, y, z = xyz[i, 0:3]
             in_box[i] = (
                 ((bx <= x) & (x <= bx + dx))
                 & ((by <= y) & (y <= by + dy))
@@ -493,7 +493,7 @@ class BoundingBox(BoundingVolume):
         in_box = 0
         bx, by, bz, dx, dy, dz = self.box
         for i in range(xyz.shape[0]):
-            x, y, z = xyz[i, 0:2]
+            x, y, z = xyz[i, 0:3]
             in_box += (
                 ((bx <= x) & (x <= bx + dx))
                 & ((by <= y) & (y <= by + dy))
@@ -592,6 +592,45 @@ class BoundingBox(BoundingVolume):
         cz = min(max(z, bz + jz), bz + dz - jz)
         return cx, cy, cz
 
+    def clip_to_box(self, obox: BoundingBox) -> int:
+        """
+        Clip this box so it entirely fits within obox
+
+        Note: this action is potentiall unsafe! We do no checking that the new
+        box is correct in terms of floating point precision.
+
+        Args:
+            obox: BoundingBox
+            The box to clip to
+
+        Returns:
+            Returns 0 if any of the dx terms are 0, 1 otherwise
+        """
+        # The algorithm is similar to project_point_on_box
+        x, y, z, dx, dy, dz = self.box
+        ox, oy, oz, odx, ody, odz = obox.box
+
+        x = min(max(x, ox), ox + odx)
+        y = min(max(y, oy), oy + ody)
+        z = min(max(z, oz), oz + odz)
+        xfar = min(max(x + dx, ox), ox + odx)
+        yfar = min(max(y + dy, oy), oy + ody)
+        zfar = min(max(z + dz, oz), oz + odz)
+
+        new_dx = xfar - x
+        new_dy = yfar - y
+        new_dz = zfar - z
+
+        if new_dx <= 0 or new_dy <= 0 or new_dz <= 0:
+            return 0
+        self.box[0] = x
+        self.box[3] = new_dx
+        self.box[1] = y
+        self.box[4] = new_dy
+        self.box[2] = z
+        self.box[5] = new_dz
+        return 1
+
     def check_box_overlap(self, obox: BoundingBox) -> int:
         """
         Return the "overlap" between this box and obox
@@ -614,13 +653,13 @@ class BoundingBox(BoundingVolume):
         # check if any overlap at all
         # pxyz = obox.project_point_on_box( our center)
         # overlap = self.contains(pxyz)
-        x, y, z, odx, ody, odz = obox.box
+        ox, oy, oz, odx, ody, odz = obox.box
         mx, my, mz = self.midplane()
         bx, by, bz, dx, dy, dz = self.box
 
-        cx = min(max(mx, x), x + odx)
-        cy = min(max(my, y), y + ody)
-        cz = min(max(mz, z), z + odz)
+        cx = min(max(mx, ox), ox + odx)
+        cy = min(max(my, oy), oy + ody)
+        cz = min(max(mz, oz), oz + odz)
 
         overlap = (
             ((bx <= cx) & (cx <= bx + dx))
@@ -632,12 +671,12 @@ class BoundingBox(BoundingVolume):
             return 0
 
         # check how many vertices are contained
-        x0 = x
-        x1 = x + odx
-        y0 = y
-        y1 = y + ody
-        z0 = z
-        z1 = z + odz
+        x0 = ox
+        x1 = ox + odx
+        y0 = oy
+        y1 = oy + ody
+        z0 = oz
+        z1 = oz + odz
 
         overlap = (
             ((bx <= x0) & (x0 <= bx + dx))
@@ -789,7 +828,7 @@ class BoundingSphere(BoundingVolume):
         cx, cy, cz = self.center
         in_sph = np.empty((xyz.shape[0],), dtype=np.bool_)
         for i in range(xyz.shape[0]):
-            x, y, z = xyz[i, 0:2]
+            x, y, z = xyz[i, 0:3]
             in_sph[i] = (cx - x) ** 2 + (cy - y) ** 2 + (cz - z) ** 2 <= r2
         return in_sph
 
@@ -817,7 +856,7 @@ class BoundingSphere(BoundingVolume):
         r2 = self.radius * self.radius
         cx, cy, cz = self.center
         for i in range(xyz.shape[0]):
-            x, y, z = xyz[i, 0:2]
+            x, y, z = xyz[i, 0:3]
             in_sph += (cx - x) ** 2 + (cy - y) ** 2 + (cz - z) ** 2 <= r2
         return in_sph
 
@@ -843,13 +882,13 @@ class BoundingSphere(BoundingVolume):
         # check if any overlap at all
         # pxyz = obox.project_point_on_box( our center)
         # overlap = self.contains(pxyz)
-        x, y, z, odx, ody, odz = obox.box
+        ox, oy, oz, odx, ody, odz = obox.box
         cx, cy, cz = self.center
         r2 = self.radius * self.radius
 
-        px = min(max(cx, x), x + odx)
-        py = min(max(cy, y), y + ody)
-        pz = min(max(cz, z), z + odz)
+        px = min(max(cx, ox), ox + odx)
+        py = min(max(cy, oy), oy + ody)
+        pz = min(max(cz, oz), oz + odz)
 
         overlap = (cx - px) ** 2 + (cy - py) ** 2 + (cz - pz) ** 2 <= r2
 
@@ -857,12 +896,12 @@ class BoundingSphere(BoundingVolume):
             return 0
 
         # check how many vertices are contained
-        x0 = x
-        x1 = x + odx
-        y0 = y
-        y1 = y + ody
-        z0 = z
-        z1 = z + odz
+        x0 = ox
+        x1 = ox + odx
+        y0 = oy
+        y1 = oy + ody
+        z0 = oz
+        z1 = oz + odz
 
         overlap = (cx - x0) ** 2 + (cy - y0) ** 2 + (cz - z0) ** 2 <= r2
 

packingcubes-0.3.1/packingcubes/cubes/__init__.py

@@ -0,0 +1,23 @@
+from packingcubes.cubes.cubes_creation import (
+    Cubes as Cubes,
+)
+from packingcubes.cubes.cubes_creation import (
+    CubesError as CubesError,
+)
+from packingcubes.cubes.cubes_creation import (
+    make_cubes as make_cubes,
+)
+from packingcubes.cubes.cubes_creation import (
+    make_ParticleCubes as make_ParticleCubes,
+)
+from packingcubes.cubes.multi_cubes import MultiCubes as MultiCubes
+from packingcubes.cubes.particle_cubes import ParticleCubes as ParticleCubes
+
+__all__ = [
+    "Cubes",
+    "CubesError",
+    "make_cubes",
+    "make_ParticleCubes",
+    "MultiCubes",
+    "ParticleCubes",
+]