- feat(cicd): updated ci-cd.yml
BREAKING CHANGE: release standard version. (0392a4a)
- fix(version): release standard version with publication
BREAKING CHANGE: first standard version. (
26c4230)
- doc(readme): updated readme
BREAKING CHANGE: releasing first version with publication (3cd49bb)
- fix(numCPUs): replaced cpu_count() by sched_getaffinity() (
a3cfcf2)
- perf(maxBoxLenCPU): modified formula for nested parallelisation (
79dfda7)
- feat(voxel): renamed exePath as fastbcPath (
3d7662f)
- doc(readme): rephrased sentences related to .exe files to emphasise platform agnosticity (
abb73a6)
- build(deps): bump pillow from 10.0.1 to 10.2.0 (#16)
Bumps pillow from 10.0.1 to 10.2.0.
updated-dependencies:
- dependency-name: pillow dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (4729e86)
- feat(findNN): capped the maximum indices for neighbour searching (
db8a5e0)
- perf(mkdir): avoid creating unnecessary directories (
19139bf)
- build(deps-dev): bump gitpython from 3.1.37 to 3.1.41 (#14)
Bumps gitpython from 3.1.37 to 3.1.41.
updated-dependencies:
- dependency-name: gitpython dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (200bd2f)
- build(deps-dev): bump jinja2 from 3.1.2 to 3.1.3 (#15)
Bumps jinja2 from 3.1.2 to 3.1.3.
updated-dependencies:
- dependency-name: jinja2 dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (b2ea74d)
- build(deps): bump fonttools from 4.40.0 to 4.43.0 (#13)
Bumps fonttools from 4.40.0 to 4.43.0.
updated-dependencies:
- dependency-name: fonttools dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (00c8d10)
- build(deps-dev): bump jupyter-server from 2.7.2 to 2.11.2 (#12)
Bumps jupyter-server from 2.7.2 to 2.11.2.
updated-dependencies:
- dependency-name: jupyter-server dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (f4f3304)
-
feat(boxCnt): reverted back to version without the additional argument (
620ed70) -
feat(returnCoordsRange): fixed conflicts between new and old commits (
b9b8b71) -
feat(runBoxCnt): added optional argument to return atomic coordinates (
a230b08)
- build(deps-dev): bump cryptography from 41.0.4 to 41.0.6 (#11)
Bumps cryptography from 41.0.4 to 41.0.6.
updated-dependencies:
- dependency-name: cryptography dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (7c2d342)
- build(ray): removed from package requirement (
7c04dd6)
- feat(Pool): reverted back to concurrent.futures (
4a6ea8b)
-
build(ray): added to dependency (
3cc42c0) -
build(mpi4py): added package to installation requirement (
0ca6a56) -
build(deps-dev): bump urllib3 from 2.0.6 to 2.0.7 (#10)
Bumps urllib3 from 2.0.6 to 2.0.7.
updated-dependencies:
- dependency-name: urllib3 dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (d77afa2)
-
feat(ray): used Pool from ray (
c07487f) -
feat(Pool): replace concurrent.futures with mpi4py.futures (
3276631)
- build(deps-dev): bump gitpython from 3.1.35 to 3.1.37 (#9)
Bumps gitpython from 3.1.35 to 3.1.37.
updated-dependencies:
- dependency-name: gitpython dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (8aaa6af)
-
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
809c1f4) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
87b16b7)
- feat(findNN): removed ceil() from stepSize definition (
aac4f34)
- build(deps): bump pillow from 9.5.0 to 10.0.1 (#8)
Bumps pillow from 9.5.0 to 10.0.1.
updated-dependencies:
- dependency-name: pillow dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (d83e100)
- build(deps-dev): bump urllib3 from 2.0.3 to 2.0.6 (#7)
Bumps urllib3 from 2.0.3 to 2.0.6.
updated-dependencies:
- dependency-name: urllib3 dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (820e10d)
- build(deps-dev): bump gitpython from 3.1.32 to 3.1.35 (#5)
Bumps gitpython from 3.1.32 to 3.1.35.
updated-dependencies:
- dependency-name: gitpython dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (a679ded)
- build(deps-dev): bump cryptography from 41.0.3 to 41.0.4 (#6)
Bumps cryptography from 41.0.3 to 41.0.4.
updated-dependencies:
- dependency-name: cryptography dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (92c2846)
- build: merge branch 'main' of github.com:Jon-Ting/sphractal into main (
71bbb6e)
-
refactor(utils.py): added default value to findNN() radMult (
f6d823e) -
refactor(utils): removed redundant comment (
136ce36)
- build: merge branch 'main' of github.com:Jon-Ting/sphractal into main (
273e956)
- fix(findSlope): synchronised printing outputs with actual box-counting results when previous values are returned (
7a9b15e)
- fix(findNN): enlarged stepSize to identify neighbours on surface with {100} packings (
4f51e17)
- test(findNN): updated related test function (
7618001)
-
feat(runBoxCnt): added bulkCN as optional argument (
ddc8b7a) -
feat(runBoxCnt): added radMult as an optional argument (
2464081)
- build(deps-dev): bump jupyter-server from 2.7.0 to 2.7.2 (#3)
Bumps jupyter-server from 2.7.0 to 2.7.2.
updated-dependencies:
- dependency-name: jupyter-server dependency-type: indirect ...
Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (75625ef)
- build(poetry.lock): resolved tornado dependabot alert (
918e49d)
-
feat(findAtomsWithSurfNeighs): renamed findTargetAtoms() (
e4ff459) -
feat(runBoxCnt): modified default value for minSample (
866d551)
- fix(tests): updated test functions related to findTargetAtoms() (
e0a2557)
- perf(scanBox): removed redundant steps for inclusion of inner surface box counts (
94da738)
- build(ci-cd.yml): reverted back to usual publishing pipeline (
bc1539a)
-
build(ci-cd.yml): resolved conflicts (
5bc16c7) -
build(ci-cd.yml): added retrieve distribution step to publishing job (
22b696b)
- build(dist): ignored dist/ (
2f9a9c5)
- fix(build): added dist/ (
5f04a0d)
- fix(build): added dist/ (
078c188)
- build(.gitignore): stopped ignoring dist/ (
fdcab07)
- fix(ci-cd.yml): separate out a new pipeline for publishing
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (f7a9989)
- fix(ci-cd.yml): added permission lines to specify trusted publishing flow
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (589468b)
- build(ci-cd.yml): removed usernames and API tokens from file
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (136659b)
- build(ci-cd.yml): dealt with repository_url deprecation issue
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (af9b5a7)
- build(ci-cd.yml): uncommented documentation building step
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (5df24cc)
- build(setup.py): made description on PyPI consistent with GitHub repo (
d88a90e)
-
docs(example): made sure all codes are visible in notebook (
bc6db5c) -
docs(readme): fixed pypi readme rendering issue (
d6cf985)
-
docs(readme): attempt to fix pypi readme rendering issue (
ac8099a) -
docs(example): updated example notebook (
753e0f8) -
docs: improved consistency of the docstrings for all functions (
bbb613d) -
docs(readme): made readme statements more concise (
f1ef8ce)
- refactor(findSlope): made sure estimation results are reported after all plots are shown (
b490982)
- docs(readme): fixed position of first image
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (fbfb2f5)
- build: merge branch 'main' of github.com:Jon-Ting/sphractal into main (
60a51ef)
- docs(findNN): added docstring for the function (
7b22a4c)
-
feat(findSlope): modified while loop condition to better reflect the minSample specified (
2805b74) -
feat(findSlope): modified while loop condition to better reflect the minSample specified (
a7b7270)
- fix(tests): removed redundant test combinations (
374c5f1)
- perf(findSlope): added assertion for minSample to make sure it's integer (
ba6698d)
- build(gitpython) : resolved dependency issue (
fa8994f)
-
fix(tests): corrected the function called to test getCaseStudyPaths() (
8dcf30c) -
fix(test): corrected the number of case study coordinate files to be retrieved (
84afd20) -
fix(data): included the rhombic dodecahedron atomic coordinates as data (
84edfb7)
- refactor: merge branch 'main' of github.com:Jon-Ting/sphractal into main (
90d40f9)
- docs(init): made documentations in init.py more concise (
49dc087)
- fix(readthedocs): fixed the rendering errors on Sphinx documentations (
850613a)
- refactor(outDir): set default variable string to 'outputs' (
da0e7b2)
- build(ci-cd): commented out documentation re-rendering step from ci-cd.yml
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (e7bcaa3)
- fix(findSlope): fixed calling variable before assignment issue (
6426881)
- fix(findSlope): fixed calling variable before assignment issue (
c5a94a4)
- build(gitignore): removed redundancies in .gitignore (
be426cd)
- docs(example): updated usage of findSlope() in example notebook (
17f5b6f)
- feat(findSlope): returned final range of box lengths (
a955fd4)
- fix(test): fixed test function related to findSlope() (
8a95cb3)
-
build(poetry.lock): resolved dependencies vulnerability (
216b0d3) -
build(dist): removed dist/ directory (
043389f) -
build(fastbc): ignored fastbc/ (
3e0933a) -
build(poetry.lock): updated crytography package version (
6962299) -
build(fastbc): updated commits from fastbc/ repo (
d32f9d3) -
build(condaforge): removed staged-recipes (
e262310) -
build: allowed PSR to bump package version in setup.py as well (
823f80b) -
build(condaforge): added staged-recipes for publication to conda-forge (
0c09dab) -
build(setup): included setup.py in pyproject.toml (
4412644) -
build: ignored dist/ (
d3b183a) -
build: added information to be displayed for pip show in pyproject.toml (
ef9a3c1) -
build(setup): added setup.py (
7c58f40) -
build(dist): stopped ignoring dist/ (
43f1264) -
build: preparing for releasev0.3.0 (
25ee6ba) -
build: updated poetry.lock (
1e1d824) -
build: updated all dependencies (
3af9a9e) -
build: added dependencies (
442a6ca)
-
docs(boxCnt): improved conciseness of the docstring for runBoxCnt() (
083f977) -
docs(example): explained the choice of numPoints in example.ipynb (
8f45bd2) -
docs(example): updated example.ipynb with recoloured and reoriented figures (
9c17801) -
docs(surfVoxel): simplified docstring for voxelBoxCnts() (
4d7a395) -
docs(surfVoxel): updated recommendations of resource allocations for voxelBoxCnts() (
e0eedb0) -
docs(example): updated example.ipynb (
578d85d) -
docs(readme): fixed paragraphing problems
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (a637259)
- docs(readme): fixed fastbc repo link
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (c43c213)
- docs(readme): added figures to readme
Signed-off-by: Jonathan Yik Chang Ting <[email protected]> (813de14)
-
docs(readme): removed dollar signs from readme (
c6fc475) -
docs(example): updated example notebook (
76ecff9) -
docs(readme): updated variable name change on readme (
ff81621) -
docs(readme): added background section to readme (
bcfbb62) -
docs(readme): omitted features under development (
b9af10a) -
docs(example): fixed a typo in example.ipynb (
157adc3) -
docs(readme): fixed typo in readme (
92b38b8) -
docs(findSlope): added in-line comments for findSlope() (
573a20c) -
docs(example): updated example.ipynb with new figures (
8341718) -
docs(example): deleted .virtual_documents from docs/ (
78dbe38) -
docs(example): updated example.ipynb to make sure fastBC executable could be detected (
42cd8a6) -
docs(readme): updated readme to specify the delay in point cloud functionalities (
4d73e24) -
docs(readme): updated readme (
a5e3aa0) -
docs(readme): updated readme (
3ab9697) -
docs(mult): added recommendations for radMult and alphaMult to constants.py (
90f31b4) -
docs(example): completed example.ipynb (
4b60535) -
docs(findSurf): tidied up docstring for findSurf() (
8bb5fb9) -
docs(help): elaborated docstring to be returned from help() (
543925b) -
docs: updated readme for C++ file and docstrings for surfPointClouds.py functions (
a30fff9) -
docs: updated readme and example (
c142036) -
docs: updated readme and example (
47c4e72) -
docs: updated readme and example (
476ff31)
-
feat(datasets): added functions to access the case study atomic data (
126b444) -
feat(data): added atomic coordinates used for case studies (
8111d48) -
feat(data): added validation data (
7161b6e) -
feat(boxCnt): changed 'lenRange' into 'trimLen' (
8c9eeaf) -
feat(surfVoxel): implemented parallelisation functionalities for generation of point cloud representation of surface (#1)
-
docs(boxCnt): updated docstrings of runBoxCnt()
-
refactor(surfExact): renamed variables related to multiprocessings in surfExact.py
-
docs(exactSurf): modified docstring for the 'exactSurf' parameter of runBoxCnt()
-
feat(surfVoxel): initialised parallelisation implementation for voxel representation
-
build(fastbc): updated fastbc repo
-
perf(surfVoxel): first stable version with parallelisation for surfVoxel functionalities
-
build(fastbc): updated fastbc commits
-
fix(surfVoxel): corrected the equation to get minAtomCPU
Co-authored-by: Jonathan Ting <[email protected]>
Co-authored-by: github-actions <[email protected]> (1a576ed)
-
feat(data): updated example xyz files for scaling tests (
2e65389) -
feat(boxLenConc): optimised resource allocations for more general cases (
b107c07) -
feat(data): unified and included more example data (
c4cbe5e) -
feat(data): added more example data and updated functionalities to get them (
d65c3d2) -
feat(findSlope): added notebook option to findSlope() plots (
f6c6123) -
feat(boxCnt): moved box-counting functions for each representation to respective modules (
e8bbe38) -
feat: renamed modules, functions, variables to more concise names (
0119301) -
feat(minValFromBound): added the input argument to related functionalities for exact surface representation (
0ad3a49) -
feat(figType): renamed options for figType based on seaborn style (
f1a8fb1) -
feat(boxLenConc): implemented automatic parallelisation functionalities (
b4f6c36) -
feat(findSlope): added functionalities to generate publication-ready figures (
5653519) -
feat(pointcloud): implemented and provided clear instructions to use point cloud surface representation related functionalities (
62d247c) -
feat: added CI/CD workflow (
8a78e22) -
feat(init): added imports for more functions (
f655fef) -
feat(findNN): allowed calcBL to be specified (
b5c123c) -
feat(datasets): added example.xyz and new module to get its path (
89f20dd) -
feat: add example data and datasets module (
83e9473) -
feat: added all source codes (
f73f23c)
-
fix(readme): fixed readme broken links (
dabe6e4) -
fix(tests): added test function for getCaseStudyDataPaths() (
d324685) -
fix(surfVoxel): imported cpu_count() from multiprocessing (
640025f) -
fix(test): updated ted test function for validation data (
dcc47b9) -
fix(findTargetAtoms): enabled the function to handle single atom case (
2650e06) -
fix: enabled findNN() and findSurf() to handle single atom input (
8cfdae4) -
fix(test): updated test functions related to example data (
d40e923) -
fix(datasets): fixed a typo in getWeakScalingDataPaths() (
533b5c7) -
fix(datasets): added functions to get example data to package namespace (
1302cdc) -
fix(datasets): updated functions to get the xyz files used for scaling tests (
05f61fb) -
fix(maxWorkers): fix zero cpu for parallelisation error (
af00b98) -
fix(boxLenScanMaxWorkers): fixed formula for resource allocations (
165ec58) -
fix(fastbc): updated fastbc submodule name (
43a9976) -
fix(findTargetAtoms): fixed the function for rmInSurf=False (
c21fd67) -
fix(test): updated test functions (
894d223) -
fix(readme): fixed broken links in readme (
3e68a87) -
fix(findSlope): reverted to producing figures with png format (
a6ed73e) -
fix(version): fixed PSR not bumping pyproject.toml version mistake (
e2e01bb) -
fix(version): updated pyproject.toml for PSR to bump version in it as well (
2ce1374) -
fix(setup): turned tuple for classifiers in setup.py into list (
5fa7910) -
fix(test): commented out tests for functionalities related to point cloud representation temporarily (
86c5192) -
fix(test): fixed missing directory error when running pytest from package root (
062c4db) -
fix(mkdir): made sure that directories are generated before files are (
c529767) -
fix(cicd): updated ci-cd workflow (
24b253c) -
fix(findSurf): fixed 'numNeigh' option in findSurf() (
796d14c) -
fix(scanAllAtoms): scanAllAtoms() now prints 1/eps instead of magnFac (
2c3b4a3) -
fix(datasets): getExampleDataPath() returns str instead of PosixPath (
6989942)
-
perf(findSurf): sped up alpha shape algorithm (
427536d) -
perf(boxLenConc): reduced the number of times of calling cpu_counts() (
c0911cf)
-
refactor(datasets): added getCaseStudyDataPaths() to package namespace (
47508f6) -
refactor(numPoints): made the variable name consistent across the package (
4d419b9) -
refactor(boxCnt): made box count outputs printed more concise (
47aacc3) -
refactor(fastbc): updated fastbc submodule name (
26a2f8d) -
refactor(findNN): removed unnecessary space and repeated codes (
2dc8afd) -
refactor(boxCnt): renamed PC to VX and ES to EX (
ec9f93c) -
refactor(surfPointClouds): renamed surfPointClouds.py to surfVoxel.py (
1be2ab5) -
refactor: renamed alphaMult in findNN() to radMult (
ba452d0) -
refactor(import): reordered import sequences following best practices (
feeed14) -
refactor: reformatted the files to follow pep8 (
8b54722) -
refactor(gitignore): ignored and removed files under development (
312761a) -
refactor: added sphractal-feedstock to .gitmodules (
efa0361) -
refactor(radType): changed default radType to 'atomic' (
d272ea9) -
refactor(bin): added compiled C++ GPU code (
b6e6fb6)
-
style(exactBoxCnts): removed a print statement from the function (
139b046) -
style: included more information in printing statements of getSphereBoxCnts() (
e6bfcee) -
style: added space in print statements for better visibility (
1584c60)
-
test(trimLen): updated change in variable name (
e442aa6) -
test(example): updated test functions for functions related to example data (
fb1c8f0) -
test: updated test functions and fixtures for findTargetAtoms() (
35c7a55) -
test(example): added test function for new example function (
d07b85e) -
test: uncommented a test function for findSlope() (
6d6b75b) -
test: updated docstrings in test functions that are commented out (
ed69a98) -
test: added unit tests for higher level functions (
f1269a5) -
test: added tests for some functions (
1350d4c)
-
Merge branch 'main' of github.com:Jon-Ting/sphractal (
3de0d64) -
Merge branch 'main' of github.com:Jon-Ting/sphractal (
ff4fe90) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
2830ed3) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
dacfae8) -
feat(nexactBoxCnts: added numCPUs as input argument to the function (
f1e01c9) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
428347a) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
d0577b6) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
be2f0ea) -
Merge branch 'main' of github.com:Jon-Ting/sphractal into main (
7af5410) -
Update ci-cd.yml (
fcd19ca) -
initial package setup (
268b378)