Skip to content

Commit 8adc92d

Browse files
michaelraczyckimichaelraczycki
committed
Merge branch 'main' into adding_icdf_functions
rebase of main .
2 parents 4d63656 + 047141c commit 8adc92d

File tree

155 files changed

+2551
-1272
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

155 files changed

+2551
-1272
lines changed

‎.github/workflows/devcontainer-docker-image.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@ jobs:
2222
uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b
2323

2424
- name: Setup Docker buildx
25-
uses: docker/setup-buildx-action@v2.4.0
25+
uses: docker/setup-buildx-action@v2.4.1
2626

2727
- name: Prepare metadata
2828
id: meta
@@ -42,7 +42,7 @@ jobs:
4242

4343
- name: Build and push Docker image
4444
id: docker_build
45-
uses: docker/build-push-action@e551b19e49efd4e98792db7592c17c09b89db8d8
45+
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
4646
with:
4747
context: .
4848
file: scripts/dev.Dockerfile

‎.github/workflows/docker-image.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ jobs:
3434
type=semver,pattern={{major}}.{{minor}}
3535
3636
- name: Build and load image
37-
uses: docker/build-push-action@v3
37+
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
3838
with:
3939
context: .
4040
file: scripts/Dockerfile
@@ -46,7 +46,7 @@ jobs:
4646
docker run --rm ${{ env.CONTAINER_NAME }} conda run -n pymc-dev python -c 'import pymc;print(pymc.__version__)'
4747
4848
- name: Build and push
49-
uses: docker/build-push-action@v3
49+
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
5050
with:
5151
context: .
5252
push: true

‎.github/workflows/tests.yml

Lines changed: 66 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -38,65 +38,67 @@ jobs:
3838
python-version: ["3.10"]
3939
test-subset:
4040
- |
41-
pymc/tests/test_util.py
42-
pymc/tests/test_pytensorf.py
43-
pymc/tests/test_math.py
44-
pymc/tests/backends/test_base.py
45-
pymc/tests/backends/test_ndarray.py
46-
pymc/tests/step_methods/hmc/test_hmc.py
47-
pymc/tests/test_func_utils.py
48-
pymc/tests/distributions/test_shape_utils.py
49-
pymc/tests/distributions/test_mixture.py
41+
tests/test_util.py
42+
tests/test_pytensorf.py
43+
tests/test_math.py
44+
tests/backends/test_base.py
45+
tests/backends/test_ndarray.py
46+
tests/step_methods/hmc/test_hmc.py
47+
tests/test_func_utils.py
48+
tests/distributions/test_shape_utils.py
49+
tests/distributions/test_mixture.py
50+
tests/test_testing.py
5051
5152
- |
52-
pymc/tests/distributions/test_continuous.py
53-
pymc/tests/distributions/test_multivariate.py
53+
tests/distributions/test_continuous.py
54+
tests/distributions/test_multivariate.py
5455
5556
- |
56-
pymc/tests/distributions/test_bound.py
57-
pymc/tests/distributions/test_censored.py
58-
pymc/tests/distributions/test_simulator.py
59-
pymc/tests/sampling/test_forward.py
60-
pymc/tests/sampling/test_population.py
61-
pymc/tests/stats/test_convergence.py
62-
pymc/tests/stats/test_log_likelihood.py
63-
pymc/tests/distributions/test_distribution.py
64-
pymc/tests/distributions/test_discrete.py
57+
tests/distributions/test_bound.py
58+
tests/distributions/test_censored.py
59+
tests/distributions/test_simulator.py
60+
tests/sampling/test_forward.py
61+
tests/sampling/test_population.py
62+
tests/stats/test_convergence.py
63+
tests/stats/test_log_likelihood.py
64+
tests/distributions/test_distribution.py
65+
tests/distributions/test_discrete.py
6566
6667
- |
67-
pymc/tests/tuning/test_scaling.py
68-
pymc/tests/tuning/test_starting.py
69-
pymc/tests/distributions/test_dist_math.py
70-
pymc/tests/distributions/test_transform.py
71-
pymc/tests/sampling/test_mcmc.py
72-
pymc/tests/sampling/test_parallel.py
73-
pymc/tests/test_printing.py
68+
tests/tuning/test_scaling.py
69+
tests/tuning/test_starting.py
70+
tests/distributions/test_dist_math.py
71+
tests/distributions/test_transform.py
72+
tests/sampling/test_mcmc.py
73+
tests/sampling/test_parallel.py
74+
tests/test_printing.py
7475
7576
- |
76-
pymc/tests/distributions/test_timeseries.py
77-
pymc/tests/gp/test_cov.py
78-
pymc/tests/gp/test_gp.py
79-
pymc/tests/gp/test_mean.py
80-
pymc/tests/gp/test_util.py
81-
pymc/tests/test_model.py
82-
pymc/tests/test_model_graph.py
83-
pymc/tests/ode/test_ode.py
84-
pymc/tests/ode/test_utils.py
85-
pymc/tests/step_methods/hmc/test_quadpotential.py
77+
tests/distributions/test_timeseries.py
78+
tests/gp/test_cov.py
79+
tests/gp/test_gp.py
80+
tests/gp/test_mean.py
81+
tests/gp/test_util.py
82+
tests/test_model.py
83+
tests/test_model_graph.py
84+
tests/ode/test_ode.py
85+
tests/ode/test_utils.py
86+
tests/step_methods/hmc/test_quadpotential.py
8687
8788
- |
88-
pymc/tests/distributions/test_truncated.py
89-
pymc/tests/logprob/test_abstract.py
90-
pymc/tests/logprob/test_censoring.py
91-
pymc/tests/logprob/test_composite_logprob.py
92-
pymc/tests/logprob/test_cumsum.py
93-
pymc/tests/logprob/test_joint_logprob.py
94-
pymc/tests/logprob/test_mixture.py
95-
pymc/tests/logprob/test_rewriting.py
96-
pymc/tests/logprob/test_scan.py
97-
pymc/tests/logprob/test_tensor.py
98-
pymc/tests/logprob/test_transforms.py
99-
pymc/tests/logprob/test_utils.py
89+
tests/backends/test_mcbackend.py
90+
tests/distributions/test_truncated.py
91+
tests/logprob/test_abstract.py
92+
tests/logprob/test_censoring.py
93+
tests/logprob/test_composite_logprob.py
94+
tests/logprob/test_cumsum.py
95+
tests/logprob/test_joint_logprob.py
96+
tests/logprob/test_mixture.py
97+
tests/logprob/test_rewriting.py
98+
tests/logprob/test_scan.py
99+
tests/logprob/test_tensor.py
100+
tests/logprob/test_transforms.py
101+
tests/logprob/test_utils.py
100102
101103
fail-fast: false
102104
runs-on: ${{ matrix.os }}
@@ -164,10 +166,10 @@ jobs:
164166
floatx: [float64]
165167
python-version: ["3.8"]
166168
test-subset:
167-
- pymc/tests/variational/test_approximations.py pymc/tests/variational/test_callbacks.py pymc/tests/variational/test_inference.py pymc/tests/variational/test_opvi.py pymc/tests/test_initial_point.py
168-
- pymc/tests/test_model.py pymc/tests/sampling/test_mcmc.py
169-
- pymc/tests/gp/test_cov.py pymc/tests/gp/test_gp.py pymc/tests/gp/test_mean.py pymc/tests/gp/test_util.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py pymc/tests/smc/test_smc.py pymc/tests/sampling/test_parallel.py
170-
- pymc/tests/step_methods/test_metropolis.py pymc/tests/step_methods/test_slicer.py pymc/tests/step_methods/hmc/test_nuts.py pymc/tests/step_methods/test_compound.py pymc/tests/step_methods/hmc/test_hmc.py
169+
- tests/variational/test_approximations.py tests/variational/test_callbacks.py tests/variational/test_inference.py tests/variational/test_opvi.py tests/test_initial_point.py
170+
- tests/test_model.py tests/sampling/test_mcmc.py
171+
- tests/gp/test_cov.py tests/gp/test_gp.py tests/gp/test_mean.py tests/gp/test_util.py tests/ode/test_ode.py tests/ode/test_utils.py tests/smc/test_smc.py tests/sampling/test_parallel.py
172+
- tests/step_methods/test_metropolis.py tests/step_methods/test_slicer.py tests/step_methods/hmc/test_nuts.py tests/step_methods/test_compound.py tests/step_methods/hmc/test_hmc.py
171173

172174
fail-fast: false
173175
runs-on: ${{ matrix.os }}
@@ -238,16 +240,17 @@ jobs:
238240
python-version: ["3.9"]
239241
test-subset:
240242
- |
241-
pymc/tests/sampling/test_parallel.py
242-
pymc/tests/test_data.py
243-
pymc/tests/test_model.py
243+
tests/sampling/test_parallel.py
244+
tests/test_data.py
245+
tests/variational/test_minibatch_rv.py
246+
tests/test_model.py
244247
245248
- |
246-
pymc/tests/sampling/test_mcmc.py
249+
tests/sampling/test_mcmc.py
247250
248251
- |
249-
pymc/tests/backends/test_arviz.py
250-
pymc/tests/variational/test_updates.py
252+
tests/backends/test_arviz.py
253+
tests/variational/test_updates.py
251254
fail-fast: false
252255
runs-on: ${{ matrix.os }}
253256
env:
@@ -305,14 +308,14 @@ jobs:
305308
env_vars: TEST_SUBSET
306309
name: ${{ matrix.os }} ${{ matrix.floatx }}
307310
fail_ci_if_error: false
308-
jax:
311+
external_samplers:
309312
strategy:
310313
matrix:
311314
os: [ubuntu-20.04]
312315
floatx: [float64]
313316
python-version: ["3.9"]
314317
test-subset:
315-
- pymc/tests/sampling/test_jax.py
318+
- tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
316319
fail-fast: false
317320
runs-on: ${{ matrix.os }}
318321
env:
@@ -360,7 +363,7 @@ jobs:
360363
conda activate pymc-test
361364
pip install -e .
362365
python --version
363-
- name: Install jax specific dependencies
366+
- name: Install external samplers
364367
run: |
365368
conda activate pymc-test
366369
pip install "numpyro>=0.8.0"
@@ -382,7 +385,7 @@ jobs:
382385
floatx: [float32]
383386
python-version: ["3.10"]
384387
test-subset:
385-
- pymc/tests/sampling/test_mcmc.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py
388+
- tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py
386389
fail-fast: false
387390
runs-on: ${{ matrix.os }}
388391
env:

‎.pre-commit-config.yaml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ repos:
99
- id: debug-statements
1010
- id: end-of-file-fixer
1111
- id: no-commit-to-branch
12-
args: [--branch, master]
12+
args: [--branch, main]
1313
- id: requirements-txt-fixer
1414
exclude: ^requirements-dev\.txt$
1515
- id: trailing-whitespace
@@ -39,7 +39,7 @@ repos:
3939
- id: black
4040
- id: black-jupyter
4141
- repo: https://github.com/PyCQA/pylint
42-
rev: v2.16.1
42+
rev: v2.16.3
4343
hooks:
4444
- id: pylint
4545
args: [--rcfile=.pylintrc]

‎.readthedocs.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ python:
99
path: .
1010

1111
conda:
12-
environment: "conda-envs/environment-dev.yml"
12+
environment: "conda-envs/environment-docs.yml"
1313

1414
build:
1515
os: "ubuntu-20.04"

‎MANIFEST.in

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,3 @@
1-
recursive-include pymc/tests/data *
2-
recursive-include source *
3-
# because of an upload-size limit by PyPI, we're temporarily removing docs from the tarball:
4-
recursive-exclude docs *
51
include requirements.txt
62
include *.md *.rst
73
include scripts/*.sh

‎Makefile

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -55,9 +55,6 @@ clean:
5555
rm -rf $(SOURCEDIR)/api/generated
5656
rm -rf $(SOURCEDIR)/api/**/generated
5757
rm -rf $(SOURCEDIR)/api/**/classmethods
58-
rm -rf $(SOURCEDIR)/contributing/private_api/generated
59-
rm -rf $(SOURCEDIR)/contributing/private_api/**/generated
60-
rm -rf $(SOURCEDIR)/contributing/private_api/**/classmethods
6158
rm -rf docs/jupyter_execute
6259

6360
html:

‎codecov.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ coverage:
2020
base: auto
2121

2222
ignore:
23-
- "pymc/tests/*"
23+
- "tests/*"
2424
- "pymc/_version.py"
2525

2626
comment:

‎conda-envs/environment-dev.yml

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ dependencies:
1414
- numpy>=1.15.0
1515
- pandas>=0.24.0
1616
- pip
17-
- pytensor=2.9.1
17+
- pytensor=2.10.1
1818
- python-graphviz
1919
- networkx
2020
- scipy>=1.4.1
@@ -41,3 +41,4 @@ dependencies:
4141
- pip:
4242
- git+https://github.com/pymc-devs/pymc-sphinx-theme
4343
- numdifftools>=0.9.40
44+
- mcbackend>=0.4.0

‎conda-envs/environment-docs.yml

Lines changed: 35 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
# "dev" conda envs are to be used by devs in setting their local environments
2+
name: pymc-docs
3+
channels:
4+
- conda-forge
5+
- defaults
6+
dependencies:
7+
# Base dependencies
8+
- arviz>=0.13.0
9+
- cachetools>=4.2.1
10+
- cloudpickle
11+
- fastprogress>=0.2.0
12+
- numpy>=1.15.0
13+
- pandas>=0.24.0
14+
- pip
15+
- pytensor=2.9.1
16+
- python-graphviz
17+
- scipy>=1.4.1
18+
- typing-extensions>=3.7.4
19+
# Extra dependencies for docs build
20+
- ipython>=7.16
21+
- jax
22+
- jupyter-sphinx
23+
- myst-nb
24+
- numpydoc
25+
- pre-commit>=2.8.0
26+
- sphinx-copybutton
27+
- sphinx-design
28+
- sphinx-notfound-page
29+
- sphinx>=1.5
30+
- sphinxext-rediraffe
31+
- watermark
32+
- sphinx-remove-toctrees
33+
- pip:
34+
- git+https://github.com/pymc-devs/pymc-sphinx-theme
35+
- numdifftools>=0.9.40

‎conda-envs/environment-test.yml

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ dependencies:
1717
- numpy>=1.15.0
1818
- pandas>=0.24.0
1919
- pip
20-
- pytensor=2.9.1
20+
- pytensor=2.10.1
2121
- python-graphviz
2222
- networkx
2323
- scipy>=1.4.1
@@ -31,3 +31,4 @@ dependencies:
3131
- types-cachetools
3232
- pip:
3333
- numdifftools>=0.9.40
34+
- mcbackend>=0.4.0

‎conda-envs/windows-environment-dev.yml

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ dependencies:
1414
- numpy>=1.15.0
1515
- pandas>=0.24.0
1616
- pip
17-
- pytensor=2.9.1
17+
- pytensor=2.10.1
1818
- python-graphviz
1919
- networkx
2020
- scipy>=1.4.1
@@ -38,3 +38,4 @@ dependencies:
3838
- pip:
3939
- git+https://github.com/pymc-devs/pymc-sphinx-theme
4040
- numdifftools>=0.9.40
41+
- mcbackend>=0.4.0

‎conda-envs/windows-environment-test.yml

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ dependencies:
1717
- numpy>=1.15.0
1818
- pandas>=0.24.0
1919
- pip
20-
- pytensor=2.9.1
20+
- pytensor=2.10.1
2121
- python-graphviz
2222
- networkx
2323
- scipy>=1.4.1
@@ -31,3 +31,4 @@ dependencies:
3131
- types-cachetools
3232
- pip:
3333
- numdifftools>=0.9.40
34+
- mcbackend>=0.4.0

‎docs/source/api/backends.rst

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,5 @@ Internal structures
1818
:toctree: generated/
1919

2020
NDArray
21-
point_list_to_multitrace
2221
base.BaseTrace
2322
base.MultiTrace

‎docs/source/api/data.rst

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,4 +12,3 @@ Data
1212
Data
1313
GeneratorAdapter
1414
Minibatch
15-
align_minibatches

‎docs/source/api/distributions/simulator.rst

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,4 @@ Simulator
66
.. autosummary::
77
:toctree: generated
88

9-
SimulatorRV
109
Simulator
11-
KullbackLiebler

‎docs/source/api/distributions/timeseries.rst

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,6 @@ Timeseries
66
.. autosummary::
77
:toctree: generated
88

9-
AR1
109
AR
1110
GaussianRandomWalk
1211
GARCH11

0 commit comments

Comments
 (0)