Publication-ready v2: GitHub Actions CI, Sphinx docs, PyPI publishing; drop Docker/Binder - #44

Merged

brmather merged 196 commits into

tanaka-probabilistic

Jul 24, 2026

Commits on May 18, 2018

Add files via upload
rdelhaye
authored
cd5d8d2
Add files via upload
rdelhaye
authored
cfcf273
Create readme.txt
rdelhaye
authored
7f7cfef
Add files via upload
rdelhaye
authored
9db2a2c

Commits on Jun 25, 2018

Re-organise folder structure
Ben Mather
committed
ccb4373
Defragmented some of the legacy code and new Notebooks
Ben Mather
committed
8395d53
Random fractal model
Ben Mather
committed
3606daa

Commits on Jul 7, 2018

Updated jupyter notebooks
Ben Mather
committed
5bdee39

Commits on Jul 8, 2018

Ex4 Notebook improvements
Ben Mather
committed
23642c3

Commits on Jul 9, 2018

Reduce int -> float operations
Ben Mather
committed
a586ec6
Updated examples for Bouligand approach
Ben Mather
committed
1e70fc7

Commits on Jul 10, 2018

New mapping function to export GeoTIFFs
Ben Mather
committed
17913e5
Merge branch 'Testing' of https://github.com/brmather/pycurious into Testing
Ben Mather
committed
c9a01b8

Commits on Jul 12, 2018

Updated Jupyter notebooks.
Robert Delhaye
committed
82eb33d
Updated Jupyter notebooks. Ex2a essentially complete. Ex4 in progress.
Robert Delhaye
committed
27f4232

Commits on Jul 17, 2018

Updated Ex4 Notebook with importing/exporting data
Ben Mather
committed
177e435

Commits on Jul 26, 2018

export / import geotiff now working correctly
Ben Mather
committed
f4d095e

Commits on Jul 27, 2018

Ex2a Notebook updated
Robert Delhaye
committed
0a34e01
Ex2a Notebook updated
Robert Delhaye
committed
5d25446
Ex3, Tanaka tests added
Robert Delhaye
committed
14f3396
BM added new method Compute Tanaka
Robert Delhaye
committed
2583ca7
Tanaka method split to access Zt, Zo constituents
Robert Delhaye
committed
46ccca0
Merge branch 'Testing' of https://github.com/brmather/pycurious into Testing
Robert Delhaye
committed
18661d2

Commits on Aug 26, 2018

Changes to include sigma2 in misfit
Ben Mather
committed
b5384a5
Merge branch 'Testing' of https://github.com/brmather/pycurious into Testing
Ben Mather
committed
22676c6
Moving Notebooks to resemble some form of structure
Ben Mather
committed
c392f1d
More moving...
Ben Mather
committed
d8c2a2b

Commits on Aug 28, 2018

Notebooks complete!
Ben Mather
committed
a1b0449
Forgot Ex1 from Tanaka
Ben Mather
committed
4d74468
Merge pull request #1 from brmather/Testing
Ben Mather
authored
1d09b7e
Directory restructuring
Ben Mather
committed
fe5b6f9

Commits on Aug 29, 2018

Added the GNU Lesser General Public License
Ben Mather
committed
b0b8881
Set theme jekyll-theme-cayman
Ben Mather
committed
8818d72
Final bugs before v0.1
Ben Mather
committed
56954c5
Merge branch 'master' of https://github.com/brmather/pycurious
Ben Mather
committed
cfef878
version 0.1 release
Ben Mather
committed
b677b82

Commits on Aug 30, 2018

You always forget a few things...
Ben Mather
committed
b9f6d41

Commits on Sep 3, 2018

Simple parallelism using OpenMP
Ben Mather
committed
53ca62f
Only instantiate the available processors
Ben Mather
committed
b0bec71

Commits on Sep 28, 2018

No need to evaluate probability twice
Ben Mather
committed
cd112b3

Commits on Oct 2, 2018

Initial commit of thermal solver
Ben Mather
committed
22377f7
Updated documentation for thermal solver
Ben Mather
committed
4f15ba5

Commits on Oct 3, 2018

Stupid mistake in metropolis_hastings routine
Ben Mather
committed
5e1ad77

Commits on Oct 9, 2018

Bug fix to the standard deviation of Phi
Ben Mather
committed
8d4166b

Commits on Oct 23, 2018

Include the uncertainty on the power spectrum
Ben Mather
committed
90297d6
Slight efficiency improvement
Ben Mather
committed
e2b9a6b
Merge branch multiprocessing
Ben Mather
committed
82a7efd

Commits on Oct 25, 2018

Change back the weighting of the spectrum
Ben Mather
committed
60c2ecc

Commits on Jan 2, 2019

Merge pull request #2 from brmather/multiprocessing
Ben Mather
authored
b331acc

Commits on Jan 10, 2019

Add Dockerfile and update version
Ben Mather
committed
db6ba97
Convert Notebooks to Python 3
Ben Mather
committed
7f29178
build off base image
Ben Mather
committed
efbe3c2
Move dockerfile to top level directory
Ben Mather
committed
4f3bc2c

Commits on Mar 19, 2019

Reorganising directory structure
Ben Mather
committed
99fb6bc

Commits on Mar 20, 2019

Updated README.md and directory structure for docker
Ben Mather
committed
6cdc13f

Commits on Jun 3, 2019

Restructure directory
Ben Mather
committed
74c1837
Forgot a few files...
Ben Mather
committed
ccc75c2
Deleted lots of broken tests and fixed docstrings
Ben Mather
committed
9b42487
Added HtML documentation
Ben Mather
committed
24704c9

Commits on Jun 4, 2019

Committing TravisCI configuration
Ben Mather
committed
ea3276e
updated travisCI script
Ben Mather
committed
5de863c
Merge pull request #4 from brmather/restructure
Ben Mather
authored
9e24435
Properly generate the docs
Ben Mather
committed
4820344
Forgot scipy dependency
Ben Mather
committed
b5781a9
Authentification works now, but 'file exists' error
Ben Mather
committed
a85d77d
set verbose to see what is going on
Ben Mather
committed
e556955
Try again specifying docs folder
Ben Mather
committed
fac2cdb
Hooray! Now I can delete the docs folder
Ben Mather
committed
9228fac
We have to create docs folder to put the docs in...
Ben Mather
committed
5271a66

Commits on Jun 6, 2019

try testing on diffferent o/s
Ben Mather
committed
0acb6df
More elaborate travis build system
Ben Mather
committed
433ee9c
Multiple python nestings do not work
Ben Mather
committed
3e4f95f
update osx to python3.7
Ben Mather
committed
f0d528a
OSX doesn't come with python installed
Ben Mather
committed
bf2d9b9
Try making osx language generic
Ben Mather
committed
4749717
I think I got it this time
Ben Mather
committed
cc25ecd
First iteration of JOSS paper
Ben Mather
committed
3cae9cc
updated Dockerfile
Ben Mather
committed
63aa7af
Merge pull request #6 from brmather/master
Ben Mather
authored
ff31d45

Commits on Jun 15, 2019

Add download functionality
Ben Mather
committed
bed4551
Updated README.md with link to docs
Ben Mather
committed
b63a5b3

Commits on Jun 17, 2019

Updated Ex5 with download scripts
Ben Mather
committed
f1d8518
Updated manifest and added contribution guide
Ben Mather
committed
9e1e6ca

Commits on Jun 18, 2019

Add PyPI deployment
Ben Mather
committed
f5138be
First lot of tests
Ben Mather
committed
c0aa7b9
Updated with some more tests
Ben Mather
committed
5a9d1fc
Merge branch 'dev' of github.com:brmather/pycurious into dev
Ben Mather
committed
61b0891
Remove matplotlib dependency from Bouligand_forward.py
Ben Mather
committed
a5654ce
Now running tests with Travis-CI
Ben Mather
committed
123ffad
Run tests in Dockerfile
Ben Mather
committed
6655328
Merge pull request #8 from brmather/dev
Ben Mather
authored
16615ff

Commits on Jun 20, 2019

Updated a lot of docstrings
Ben Mather
committed
790d4dd
Adding PyCurious logo
Ben Mather
committed
17489a8
Updated README and StartHere.ipynb
Ben Mather
committed
207a3b3
Getting ready for 0.3.2
Ben Mather
committed
ccff214
Prevent EMAG2 from being packaged on my computer
Ben Mather
committed
340f903

Commits on Jun 21, 2019

Better logo!
Ben Mather
committed
e7a2b9b

Commits on Jun 24, 2019

Merge branch 'master' into paper
Ben Mather
committed
0f25055
Final edits to paper.md before submission to JOSS
Ben Mather
committed
883d2da
Merge pull request #9 from brmather/paper
Ben Mather
authored
3d059d3
Getting ready for 0.4 release
Ben Mather
committed
5c3b7e4
Remove Rob's phoney ORCID
Ben Mather
committed
3bc83bc

Commits on Jul 1, 2019

Slight improvements to documentation
Ben Mather
committed
380728f

Commits on Jul 8, 2019

JOSS edits
jessepisel
committed
d03795a

Commits on Jul 9, 2019

Updated contribution guide
Ben Mather
committed
ad77ccd
Merge pull request #12 from jessepisel/JOSS_review
Ben Mather
authored
fcc6bac

Commits on Jul 10, 2019

Commits on Jul 11, 2019

Add environment.yml
santisoler
committed
73ac9c3
Add eggs and .so files to .gitignore
santisoler
committed
dd7c497
Add conda instructions to README.md
santisoler
committed
30a5c78

Commits on Jul 12, 2019

Merge pull request #24 from santisoler/styling
Ben Mather
authored
2f04089
Merge pull request #25 from santisoler/environment
Ben Mather
authored
7bfb424
Check equal node spacing
Ben Mather
committed
2a285f3
Updatd docstring for CurieGrid
Ben Mather
committed
f238ebe
raise error if window is too big
Ben Mather
committed
1dd73b3
Refactoring code for computing power spectrum
Ben Mather
committed
2ea5bab
Changed pdoc to latex_math branch
Ben Mather
committed
53b70fa
Come on Travis...
Ben Mather
committed
3f84d65

Commits on Jul 13, 2019

Commits on Jul 14, 2019

Rework remove_trend_linear
Ben Mather
committed
c273e3d

Commits on Jul 15, 2019

Improve docstrings for CurieGrid and CurieOptimise
Ben Mather
committed
b6fb432
Remove scale argument from power spectrum
Ben Mather
committed
4ac6d01
Remove `CurieGrid.radial_spectrum_log`
Ben Mather
committed
1ae9986
Update rdelhaye ORCID
Ben Mather
committed
c838a4a
Add jupyter as dependency
santisoler
committed
248358d
Merge pull request #26 from brmather/power_spectrum
Ben Mather
authored
692ca6e

Commits on Jul 16, 2019

Fix #29
Ben Mather
committed
12a4cd3
Merge pull request #28 from santisoler/jupyter
Ben Mather
authored
bf0e384

Commits on Jul 17, 2019

Improved testing suite using pytest
Ben Mather
committed
07fb3ca
Updated logo (slightly)
Ben Mather
committed
36adcb5
Merge branch 'master' of github.com:brmather/pycurious
Ben Mather
committed
1ce5b91

Commits on Jul 18, 2019

Include `pytest.fixture` within testing suite
Ben Mather
committed
bb6c1c8
Add pytest to environment.yml
santisoler
committed
eee9752

Commits on Jul 19, 2019

Merge pull request #30 from santisoler/pytest-conda
Ben Mather
authored
553d640
Reformatting to PEP8 standard
Ben Mather
committed
90098de
Merge branch 'master' of github.com:brmather/pycurious
Ben Mather
committed
bbaf611

Commits on Jul 24, 2019

Update paper.md (#31)

lheagy
authored and
Ben Mather
committed
7f94ffc
Bump to version 1.0
Ben Mather
committed
13b7f36
Zenodo failed so lets try 1.0.1
Ben Mather
committed
2b77244
Update to version 1.0.2 to match Zenodo (hopefully!)
Ben Mather
committed
2c05022

Commits on Jul 25, 2019

Update paper.md
kyleniemeyer
authored
e3a968f

Commits on Jul 26, 2019

Merge pull request #33 from kyleniemeyer/patch-1
Ben Mather
authored
1af5de5

Commits on Jul 29, 2019

Add citation
Ben Mather
committed
98e5c6e

Commits on Oct 17, 2019

Updated docker instructions
Ben Mather
authored
a4d896d

Commits on Jan 15, 2020

Skip OpenMP cruft for nprocs=1
Ben Mather
committed
ef59a55
Merge branch 'master' of github.com:brmather/pycurious
Ben Mather
committed
9b962e0
version bump to 1.0.3
Ben Mather
committed
7ad34c6

Commits on Jan 18, 2020

New mapping function `ungrid`
Ben Mather
committed
5c9bdf4
Merge branch 'master' of github.com:brmather/pycurious
Ben Mather
committed
d5f9ca7

Commits on Jan 31, 2020

Add export to netCDF4 function
Ben Mather
committed
232b02a

Commits on Feb 25, 2020

Slightly more efficient handling of large masks
Ben Mather
committed
9fe4c56
Getting ready for 1.1 release
Ben Mather
committed
6a7cc9c
import netcdf4 function
Ben Mather
committed
565dccd

Commits on Mar 1, 2020

bugfix for older windows builds
Ben Mather
committed
b969920

Commits on Nov 16, 2020

pyproj syntax has changed in v6
Ben Mather
committed
16610b5

Commits on May 30, 2022

restructure repo and bring setup.py up to date
Ben Mather
committed
85c7dc3

Commits on May 31, 2022

Split CurieOptimise into CurieOptimiseBouligand and CurieOptimiseTanaka
Ben Mather
committed
13949f0

Commits on Jun 1, 2022

some bug fixes
Ben Mather
committed
6fd2d7b
remove azimuthal spectrum
Ben Mather
committed
d87fb1f
new and updated Tanaka notebooks
Ben Mather
committed
7e9a633
oops - don't want to include modified centroid method notebook
Ben Mather
committed
4f0c05f
Use amplitude spectrum instead of the square root of the amplitude spectrum
jonnyford
committed
6bb691f
Update notebooks to use amplitude spectrum
jonnyford
committed
7862cbe

Commits on Jun 6, 2022

Merge pull request #37 from jonnyford/tanaka2-fix
Ben Mather
authored
5431621

Commits on Jul 20, 2026

Modernise packaging and drop the Cython extension

Ben Mather
and
claude
committed
63bd709
Update code and tests for the CurieOptimise split

Ben Mather
and
claude
committed
9515958
Update README and notebooks for the restructured Examples directory

Ben Mather
and
claude
committed
9424381
Stop parallelise_routine deadlocking when a worker dies

Ben Mather
and
claude
committed
ebd1f04
Correct the wavenumber grid and expose radial bin counts

Ben Mather
and
claude
committed
a6373e8
Record Bouligand findings for the separate workstream

Ben Mather
and
claude
committed
73610ce
Add synthetics with a known Curie depth, and recovery tests

Ben Mather
and
claude
committed
1ed895b
Finish CurieOptimiseTanaka: correct weighting, real uncertainties

Ben Mather
and
claude
committed
f349484
Stop check_bands reporting every problem twice

Ben Mather
and
claude
committed
0ef953d
Update Tanaka notebooks for the rewritten class

Ben Mather
and
claude
committed
b75e055
Ignore downloaded datasets and notebook-generated rasters

Ben Mather
and
claude
committed
2036298
Fix Ex5, and declare GDAL as an optional dependency

Ben Mather
and
claude
committed
2bf1869

Commits on Jul 21, 2026

Give CurieOptimiseBouligand real uncertainties

Ben Mather
and
claude
committed
7cdb987
Share the generator, fix the sampler, calibrate the Tanaka error bars

Ben Mather
and
claude
committed
030c42b
Rewrite the Bouligand notebooks around a known answer

Ben Mather
and
claude
committed
5ae801a
Re-run every notebook, and commit them without outputs

Ben Mather
and
claude
committed
1ec338a
Simplify: share the GLS solve, drop dead options, cut test time

Ben Mather
and
claude
committed
035cf17
Bound dz below the cosh overflow, not at the physical limit

Ben Mather
and
claude
committed
0f71945
Add CLAUDE.md

Ben Mather
and
claude
committed
eb99dff
Honour max_processors in CurieOptimiseBouligand

Ben Mather
and
claude
committed
95cffbc
List the notebooks in MANIFEST.in instead of globbing them

Ben Mather
and
claude
committed
e4b7e34

Commits on Jul 22, 2026

Bin the radial spectrum with bincount instead of a mask per bin

Ben Mather
and
claude
committed
460342f

Commits on Jul 23, 2026

remove_trend_linear: separable plane fit instead of an SVD

brmather
and
claude
committed
ea2a624
Guard the separable detrend against a singleton axis

Ben Mather
and
claude
committed
fd0c681

Commits on Jul 24, 2026

radial_spectrum: rfft2 with Hermitian weighting instead of fft2

Ben Mather
and
claude
committed
24de644
Overhaul packaging and docs for the v2 release

Ben Mather
and
claude
committed
e10749a
Merge the v1 master line into the v2 rewrite; keep the v2 tree

Ben Mather
and
claude
committed
ab4b4d5