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Jim dev #167

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merged 291 commits into from
Oct 17, 2024
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94e5dfa
Updated runManager.py
xuyuon Jul 25, 2024
4267d97
Changed corner plot default setting
xuyuon Jul 25, 2024
8ab92a4
Removing inverse.
kazewong Jul 25, 2024
d8b2d1f
Add transformation function
kazewong Jul 25, 2024
ca1d6b6
Combine should be working now
kazewong Jul 25, 2024
2f3f412
Sine is an illegal transform since its Jacobian could be negative
kazewong Jul 25, 2024
4978cb1
Modify Uniform and add UniformSphere
thomasckng Jul 25, 2024
c1115bd
Add Sine and Cosine Prior
thomasckng Jul 26, 2024
01a6c1e
Revert "Modify Uniform and add UniformSphere"
thomasckng Jul 26, 2024
7ee4133
Add standard normal distribution
thomasckng Jul 26, 2024
6a35792
Add periodic uniform prior
thomasckng Jul 26, 2024
1bcf32c
Reformat
thomasckng Jul 26, 2024
17450be
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Jul 26, 2024
5d98aeb
Revert "Merge branch '98-moving-naming-tracking-into-jim-class-from-p…
thomasckng Jul 26, 2024
87ee212
Minor text change
thomasckng Jul 26, 2024
cc1448e
Remove PeriodicUniform
thomasckng Jul 26, 2024
6070f13
Use self.sample_base
thomasckng Jul 26, 2024
8a301f2
Update prior.py
thomasckng Jul 26, 2024
d761f6b
Update prior.py to include powerLaw
xuyuon Jul 26, 2024
b9a7255
Update transforms.py
xuyuon Jul 26, 2024
2f6e12a
format and updating typing hint
kazewong Jul 25, 2024
194c565
Revert "Update transforms.py"
thomasckng Jul 26, 2024
5807f3c
Revert "Update prior.py to include powerLaw"
thomasckng Jul 26, 2024
98625c3
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Jul 26, 2024
8256d0e
Comment out old prior
thomasckng Jul 26, 2024
b42b0f4
Reformat
thomasckng Jul 26, 2024
ba7dabb
Merge pull request #111 from thomasckng/sphere_prior
thomasckng Jul 26, 2024
a9629b2
Update Prior naming
kazewong Jul 26, 2024
fbba5af
Standize Transform naming
kazewong Jul 26, 2024
93b6dc9
Merge pull request #107 from xuyuon/run-manager
kazewong Jul 26, 2024
dd27330
Updated Test files
xuyuon Jul 26, 2024
a46af6b
Merge pull request #88 from xuyuon/add-spin-transform
kazewong Jul 26, 2024
4a5d932
Fixing naming problem and add base_distribution tracer
kazewong Jul 26, 2024
3497b6d
Merge pull request #2 from kazewong/98-moving-naming-tracking-into-ji…
thomasckng Jul 26, 2024
27dc870
Updated powerlaw
xuyuon Jul 26, 2024
f7b883d
Updated powerlaw
xuyuon Jul 26, 2024
1665b1c
Updated powerlaw
xuyuon Jul 26, 2024
f51847d
Updated powerlaw
xuyuon Jul 26, 2024
f7876e6
Updated prior.py to include UniformComponenChirpMassPrior
xuyuon Jul 26, 2024
0b2c7cf
Fix priors
thomasckng Jul 27, 2024
d917f96
Add prior tests
thomasckng Jul 27, 2024
9390495
Merge branch 'prior-test' into 98-moving-naming-tracking-into-jim-cla…
thomasckng Jul 27, 2024
142fe54
Set constraint on powerlaw prior input
xuyuon Jul 29, 2024
fa6a6e2
Added test_power_law
xuyuon Jul 29, 2024
a8c0673
Updated ParetoTransform to avoid divide by zero
xuyuon Jul 29, 2024
6ce5b36
Revert update on ParetoTransform
xuyuon Jul 29, 2024
e9511b9
Updated test_prior.py
xuyuon Jul 29, 2024
54082ea
Updated test_prior.py
xuyuon Jul 29, 2024
9ad64a1
Updated test_prior.py
xuyuon Jul 29, 2024
ce437c4
Updated test_prior.py
xuyuon Jul 29, 2024
18d5184
Updated test_prior.py
xuyuon Jul 29, 2024
7c05d14
Updated test_prior.py
xuyuon Jul 29, 2024
f647bf0
Remove unnecessary test
thomasckng Jul 29, 2024
6171ce5
Reformat
thomasckng Jul 29, 2024
ab7447b
Change naming
thomasckng Jul 29, 2024
1b67056
Removed bilby
xuyuon Jul 29, 2024
b2dd606
Merge pull request #113 from xuyuon/98-moving-naming-tracking-into-ji…
kazewong Jul 29, 2024
9d59c4d
Move unit test to unit directory
kazewong Jul 29, 2024
b3110df
Update priors naming issue
kazewong Jul 29, 2024
024c5c3
base parameter names seem working
kazewong Jul 29, 2024
ac43d54
fix cosine naming error
kazewong Jul 29, 2024
151c37d
prior test now all pass
kazewong Jul 29, 2024
576ce7c
Fix likelihood sampling issue due to parameter name transformation
kazewong Jul 29, 2024
7625dbe
Instead of defining univariate and multivariate,
kazewong Jul 30, 2024
9ac722f
Adding some transform, should be working
kazewong Jul 30, 2024
935b314
Refactor into NtoN and NtoM transform
kazewong Jul 30, 2024
685670a
Fix bugs in ArcSine
kazewong Jul 30, 2024
39126f5
Add inverse mass transform
thomasckng Jul 30, 2024
46bd044
Update sequential prior class and test_GW15014.py.
kazewong Jul 31, 2024
a0161ee
Merge pull request #5 from kazewong/98-moving-naming-tracking-into-ji…
thomasckng Jul 31, 2024
8e1441b
correct sign errors and minior bugs
kazewong Jul 31, 2024
dfdfffa
Add mass transform
thomasckng Jul 31, 2024
dd03bf6
Fixed powerLaw
xuyuon Jul 31, 2024
735415e
Fixed powerLaw
xuyuon Jul 31, 2024
cec7447
Fixed powerLaw
xuyuon Jul 31, 2024
74e553d
Fixed powerLaw
xuyuon Jul 31, 2024
9d87e58
Add simplex transform
thomasckng Jul 31, 2024
5f33346
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Jul 31, 2024
52fa0eb
Change transform to take dictionary as input for transform_func
kazewong Jul 31, 2024
2aef04b
Updated test_prior.py
xuyuon Jul 31, 2024
1e389bb
Add UniformComponentMassPrior
thomasckng Jul 31, 2024
0252392
prior system should work with dictionary function now
kazewong Jul 31, 2024
cb75bb9
update transform
kazewong Jul 31, 2024
fd32f20
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Jul 31, 2024
561e628
Move subclassing structure
kazewong Jul 31, 2024
1aaf5ea
Remove transformation
thomasckng Jul 31, 2024
5bfdda1
Remove prior
thomasckng Jul 31, 2024
77a6ad1
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Jul 31, 2024
2401df8
Add mass transform
thomasckng Jul 31, 2024
f932c77
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Jul 31, 2024
ff35a82
Add Bound transforming transform
kazewong Jul 31, 2024
47af9cf
no nans now, but the code can be consolidate
kazewong Aug 1, 2024
1c45acb
Merge branch 'kazewong:98-moving-naming-tracking-into-jim-class-from-…
xuyuon Aug 1, 2024
b5e06a6
Solve conflict
thomasckng Aug 1, 2024
b7d08d3
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Aug 1, 2024
255fad3
Fixed powerLaw
xuyuon Aug 1, 2024
fcdc120
Fixed powerLaw
xuyuon Aug 1, 2024
06eb3ad
Reformatted
xuyuon Aug 1, 2024
8e5b326
Add sky position transform
thomasckng Aug 1, 2024
10d51b2
Modify sky position transform
thomasckng Aug 1, 2024
8368d00
Change util func name
thomasckng Aug 1, 2024
b4f6052
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
thomasckng Aug 1, 2024
1cb0d11
Revert "Merge branch '98-moving-naming-tracking-into-jim-class-from-p…
thomasckng Aug 1, 2024
78e93c5
Merge
thomasckng Aug 1, 2024
080bd8b
Modify integration test
thomasckng Aug 1, 2024
4058d32
Reformat
thomasckng Aug 1, 2024
cdf771d
Add typecheck
thomasckng Aug 1, 2024
02c5650
minor typo
thomasckng Aug 1, 2024
ce7ac34
Rename sampler
thomasckng Aug 1, 2024
7d44aa4
Fix test
thomasckng Aug 1, 2024
7826122
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
xuyuon Aug 1, 2024
aab31ff
Merge pull request #1 from kazewong/98-moving-naming-tracking-into-ji…
xuyuon Aug 1, 2024
45be9ae
Revert "Fixed PowerLaw prior"
xuyuon Aug 1, 2024
0acb87c
Merge pull request #120 from kazewong/revert-115-98-moving-naming-tra…
xuyuon Aug 1, 2024
e9288c8
Fix BoundToUnbound transform
thomasckng Aug 1, 2024
114178f
Merge branch 'kazewong:98-moving-naming-tracking-into-jim-class-from-…
xuyuon Aug 1, 2024
d5a34f2
Updated prior.py and transforms.py
xuyuon Aug 1, 2024
34f3d26
Updated test_prior.py
xuyuon Aug 1, 2024
fe500a7
Use ifos list
thomasckng Aug 1, 2024
0d28520
Fix jim summary and get_samples
thomasckng Aug 1, 2024
f7e3fe8
Fix jim output functions
thomasckng Aug 1, 2024
68bef54
Modify Transform
thomasckng Aug 1, 2024
87593e1
Fix jim output
thomasckng Aug 1, 2024
730fe31
Add comment
thomasckng Aug 1, 2024
ed727af
Updated test_prior.py
xuyuon Aug 2, 2024
9d191da
Updated test_prior.py
xuyuon Aug 2, 2024
957335e
Merge pull request #121 from xuyuon/98-moving-naming-tracking-into-ji…
kazewong Aug 2, 2024
5a5ff2f
Add sky position transform
thomasckng Aug 2, 2024
277e893
Merge branch '98-moving-naming-tracking-into-jim-class-from-prior-cla…
kazewong Aug 2, 2024
bd915ef
Add powerlaw transform back
kazewong Aug 2, 2024
ba86a65
Move single_event prior and transform
thomasckng Aug 2, 2024
3e1ea71
Tidy up test
thomasckng Aug 2, 2024
6ad882a
Add utils.py
thomasckng Aug 2, 2024
ede2b99
Move log_i0
thomasckng Aug 2, 2024
e764696
Fixing check
thomasckng Aug 2, 2024
9d9c833
Merge pull request #118 from thomasckng/transform
kazewong Aug 2, 2024
093dd09
Updated jim.py
xuyuon Aug 2, 2024
ceb0b7f
Added spin transform
xuyuon Aug 2, 2024
b972aea
Updated transform.py
xuyuon Aug 2, 2024
d4a4386
Updated test_GW150914_pv2.py
xuyuon Aug 2, 2024
0d6a5e5
Updated transform.py
xuyuon Aug 2, 2024
91f2f89
Updated test_GW150914_pv2.py
xuyuon Aug 2, 2024
6fc8887
Updated utils.py
xuyuon Aug 2, 2024
49d604d
Fix mass transform test
thomasckng Aug 2, 2024
3b7f9e8
Reformated
xuyuon Aug 2, 2024
ac0b1f5
Use PowerLaw for distance
thomasckng Aug 2, 2024
e0a61fa
Reformated
xuyuon Aug 2, 2024
6374772
Rename test_GW150914_pv2.py to test_GW150914_PV2.py
xuyuon Aug 2, 2024
fa134f9
Add heterodyne test
thomasckng Aug 2, 2024
2c9c6a6
Fix typecheck
thomasckng Aug 2, 2024
15e4074
Shorten test runtime
thomasckng Aug 2, 2024
87440db
Merge pull request #122 from xuyuon/98-moving-naming-tracking-into-ji…
kazewong Aug 2, 2024
e1800da
Merge pull request #123 from thomasckng/transform
kazewong Aug 2, 2024
174d43a
Fix jim output functions
thomasckng Aug 3, 2024
14121d7
Delete test_GW150914_PV2.py
thomasckng Aug 3, 2024
0a9f58f
Create test_GW150914_Pv2.py
thomasckng Aug 3, 2024
1b79a3a
Merge pull request #127 from thomasckng/transform
kazewong Aug 4, 2024
f33a782
Adding transform from geocentric arrival time to detector arrival time
tsunhopang Aug 12, 2024
3505394
Adding transform from distance to SNR weighted distance
tsunhopang Aug 12, 2024
df75ceb
updating the typing for object attributes
tsunhopang Aug 13, 2024
9f2f52b
Adding geocentric phase to detector phase
tsunhopang Aug 13, 2024
b62970f
Adding ZeroLikelihood for testing purpose
tsunhopang Aug 13, 2024
4ea3322
Adding the missing mode 2pi for phasing transform
tsunhopang Aug 13, 2024
7a4bae0
Test wip
tsunhopang Aug 13, 2024
d5f86e5
Phase renaming
tsunhopang Aug 13, 2024
0a2e68c
wip
Aug 13, 2024
b96512c
Push conditional bijective transform
kazewong Aug 14, 2024
526e33c
Switch to using conditional transform
Aug 14, 2024
dbf3f30
Switch to using conditional transform
Aug 14, 2024
a375361
Fixing jacobian handling
Aug 14, 2024
d79af97
Both arrival phase and time transform are fully vectorized
Aug 16, 2024
bcbcbe2
Shifting distance transform to conditional
Aug 16, 2024
8dab27b
update example
Aug 16, 2024
fd33882
Fixing the single sided unbound transform
Aug 16, 2024
450772f
Added code to create and reverse transforms for more flexibility
ThibeauWouters Aug 17, 2024
03e76dc
Update extrinsic test
Aug 17, 2024
83b0d14
Make sure 1d transforms are created correctly
ThibeauWouters Aug 18, 2024
8fe4b5f
bugfix for single sided transform
tsunhopang Aug 19, 2024
a19b556
Update test
Aug 19, 2024
6d2cd97
update distance transform
tsunhopang Aug 19, 2024
6993dd9
Update test
Aug 19, 2024
ff65fcf
Update arrival time transform
tsunhopang Aug 19, 2024
b98d783
Update test
Aug 19, 2024
e399a5e
Fix typo
tsunhopang Aug 19, 2024
583b759
Fix typo
tsunhopang Aug 19, 2024
e803823
Merge pull request #6 from kazewong/98-moving-naming-tracking-into-ji…
xuyuon Aug 21, 2024
c6605f6
Update transforms.py
xuyuon Aug 21, 2024
59dd222
Update runManager.py
xuyuon Aug 21, 2024
702ee20
Update runManager.py
xuyuon Aug 21, 2024
7910785
Merge pull request #137 from xuyuon/fix-jacobian
kazewong Aug 22, 2024
b621dc9
Making the tests lightweight again
ThibeauWouters Aug 22, 2024
c66c65c
Reverted some src code and updated tests accordingly
ThibeauWouters Aug 22, 2024
f0bca2f
Formatting
ThibeauWouters Aug 22, 2024
1d4bb21
Updated the tests to the new transforms
ThibeauWouters Aug 27, 2024
95bc462
New transforms
ThibeauWouters Aug 27, 2024
b3898e1
precommit
ThibeauWouters Aug 27, 2024
45ebe76
Delete test/integration/corner.jpeg
ThibeauWouters Aug 28, 2024
6f31acd
Delete test/integration/diagnostic.jpeg
ThibeauWouters Aug 28, 2024
98e9c0b
Delete test/integration/single_event_runrun_manager_summary.txt
ThibeauWouters Aug 28, 2024
ad90d09
Further consolidation as requested
ThibeauWouters Sep 2, 2024
0e96439
Merge pull request #132 from ThibeauWouters/98-moving-naming-tracking…
kazewong Sep 2, 2024
b003785
Merge branch 'jim-dev' of github.com:kazewong/JaxGW into 98-moving-na…
kazewong Sep 2, 2024
7ed4c54
Move transform test into unit. Note that the current one will fail be…
kazewong Sep 2, 2024
93ea485
Putting transform test in backburner
kazewong Sep 2, 2024
d2c0416
Merge pull request #108 from kazewong/98-moving-naming-tracking-into-…
kazewong Sep 2, 2024
71ceb88
Merge pull request #151 from kazewong/jim-dev
kazewong Sep 10, 2024
93b6483
Updating initial position sampling. Also changing GW150914_IMRPhenomD.py
kazewong Sep 10, 2024
24235c2
Merge pull request #152 from kazewong/150-slow-initialize-point-gener…
kazewong Sep 10, 2024
ff12e0b
Update transforms.py
thomasckng Sep 16, 2024
aef6124
minor bug fix on initial sample noon_finite_guess
kazewong Sep 16, 2024
3d3b20a
Merge pull request #155 from thomasckng/transform-fix
thomasckng Sep 17, 2024
5cf1668
Update jim.py
thomasckng Sep 17, 2024
d25ae42
Merge branch 'jim-dev' into extrinsic_parameter_sampling_improvement_…
tsunhopang Sep 18, 2024
3a5cbf7
remove duplicated SpinToCartesianSpinTransform
tsunhopang Sep 18, 2024
c25048f
Minor fix
tsunhopang Sep 18, 2024
4822962
replace vectorize with vmap
kazewong Sep 20, 2024
617f3e7
Try fixing github precommit
kazewong Sep 20, 2024
766c36e
Try fixing github precommit
kazewong Sep 20, 2024
b993358
Merge pull request #161 from tsunhopang/extrinsic_parameter_sampling_…
kazewong Sep 20, 2024
f391bd7
Merge pull request #160 from thomasckng/remove-legacy-likelihood-maxi…
kazewong Sep 20, 2024
646e159
black formatting for GW150914_IMRPhenomD
kazewong Sep 20, 2024
de6ab60
Rename IMRPhenomPv2
kazewong Sep 20, 2024
41abe69
Delete redundant spin function
kazewong Sep 20, 2024
84ff0b7
update PV2 example
kazewong Sep 20, 2024
c666bcb
update Pv2 example
kazewong Sep 20, 2024
799ffc9
update PV2
kazewong Sep 20, 2024
a94586e
Update parameters from theta to tilt in accordence to Lalsuite
kazewong Sep 20, 2024
9507310
update Pv2
kazewong Sep 20, 2024
7dd5145
update pv2
kazewong Sep 20, 2024
4cf6b27
update transform name
kazewong Oct 5, 2024
66027c3
fix Pv2 prior and transform
kazewong Oct 7, 2024
d69c05a
move prior functions to the right place. Also add magnitude options t…
kazewong Oct 13, 2024
d062ee1
format
kazewong Oct 13, 2024
c5957b4
Add GW170817 example
kazewong Oct 13, 2024
d0554fa
Merge pull request #163 from kazewong/Fix-spin-reparameterization
kazewong Oct 13, 2024
f9080a2
Use uv for package management
kazewong Oct 16, 2024
6d89b18
update docs
kazewong Oct 16, 2024
efb1fe1
Nuke outdated examples
kazewong Oct 16, 2024
7d757f9
update pyproject dependency
kazewong Oct 16, 2024
87e0824
Fixing GW150914 Pv2 test
tsunhopang Oct 16, 2024
54cb2e1
Update GW150914 PhenomD example
tsunhopang Oct 16, 2024
5849660
update python requirement
kazewong Oct 16, 2024
ae9204a
Update GW170817 PhenomD
tsunhopang Oct 16, 2024
cfde5e3
update package workflow
kazewong Oct 16, 2024
5082e1b
update workflow
kazewong Oct 16, 2024
38de2ac
Fixing the Pv2 test again
tsunhopang Oct 16, 2024
6feea3d
Merge pull request #166 from tsunhopang/example_and_test_fixing
kazewong Oct 17, 2024
4055acb
update build system
kazewong Oct 17, 2024
c9e2cf0
Merge pull request #165 from kazewong/PackagingUpdate
kazewong Oct 17, 2024
7205c56
Update python-publish.yml
kazewong Oct 17, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/pre-commit.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,4 +25,4 @@ jobs:
python -m pip install pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
python -m pip install .
- uses: pre-commit/[email protected].0
- uses: pre-commit/[email protected].1
38 changes: 19 additions & 19 deletions .github/workflows/python-package.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,7 @@

name: Python package

on:
push:
branches: [ "main" ]
pull_request:
branches: [ "main" ]
on: [push]

jobs:
build:
Expand All @@ -18,18 +14,22 @@ jobs:
matrix:
python-version: ["3.10", "3.11"]


steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
python -m pip install .
- name: Test with pytest
run: |
pytest
- uses: actions/checkout@v4

- name: Install uv
uses: astral-sh/setup-uv@v3

- name: Set up Python ${{ matrix.python-version }}
run: uv python install ${{ matrix.python-version }}

- name: Install the project
run: uv sync --all-extras --dev

- name: Run tests
# For example, using `pytest`
run: uv run pytest

- name: Run build
run: uv build
36 changes: 20 additions & 16 deletions .github/workflows/python-publish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,20 +20,24 @@ jobs:

runs-on: ubuntu-latest


steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: '3.x'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install build
- name: Build package
run: python -m build
- name: Publish package
uses: pypa/[email protected]
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
- uses: actions/checkout@v4

- name: Install uv
uses: astral-sh/setup-uv@v3

- name: Set up Python ${{ matrix.python-version }}
run: uv python install ${{ matrix.python-version }}

- name: Install the project
run: uv sync --all-extras --dev

- name: Run build
run: uv build

- name: Publish package
uses: pypa/[email protected]
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
Empty file added docs/tutorials/naming_system.md
Empty file.
138 changes: 0 additions & 138 deletions example/GW150914.py

This file was deleted.

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