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Modernize packaging and update to support pymc > v4 #127

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Mar 6, 2024
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731b2ab
require dev version of twobody
adrn Jan 12, 2024
e667453
fix build
adrn Jan 14, 2024
da06f90
update versions
adrn Jan 14, 2024
6441c02
update packaging
adrn Jan 15, 2024
a1ac12d
restrict python version
adrn Jan 15, 2024
c6d103e
remove 3.11
adrn Jan 15, 2024
7fbf20e
oops - oldest numpy issue
adrn Jan 16, 2024
cc7cf6a
oof - pinning versions
adrn Jan 16, 2024
94fd200
ditch python 3.10 and scipy path
adrn Jan 16, 2024
f1f46bb
change random_state to rng and some reformat
adrn Mar 3, 2024
102ae34
wowowow got it working with pymc v5
adrn Mar 3, 2024
5228c99
Remove old setup_package files
adrn Mar 3, 2024
97970a2
pymc version req
adrn Mar 3, 2024
2b5f9b7
formatting and getting tests to at least run (but fail)
adrn Mar 3, 2024
762ed6d
working on getting tests to pass again
adrn Mar 3, 2024
0135c12
tests passing again
adrn Mar 4, 2024
67c2f82
remove some old packaging stuff
adrn Mar 4, 2024
b43f203
redo ci and cd
adrn Mar 4, 2024
b4ac621
try getting run notebooks working
adrn Mar 5, 2024
d1221b8
remove circleci stuff
adrn Mar 5, 2024
b763953
remove python 3.12
adrn Mar 5, 2024
e65ce4a
old nb setup
adrn Mar 5, 2024
992b8d7
tutorials install flag
adrn Mar 5, 2024
a870eae
fix mcmc sampling
adrn Mar 5, 2024
8a82c22
use more of keplerianorbit and deprecate phase_fold argument
adrn Mar 5, 2024
c968733
update examples in docs and make sure they run
adrn Mar 5, 2024
ef5560d
corner py
adrn Mar 6, 2024
f7548f4
what why
adrn Mar 6, 2024
54543d9
skip mcmc test on macos ci
adrn Mar 6, 2024
e9c4574
oops update docs config and run notebooks
adrn Mar 6, 2024
23410b9
REVERT THIS - testing if multipool is the issue
adrn Mar 6, 2024
c907380
fix make-data notebook
adrn Mar 6, 2024
852ec0a
skip multipool test on mac
adrn Mar 6, 2024
0829c56
fix notebook 1
adrn Mar 6, 2024
07ee421
exit early if nb fails
adrn Mar 6, 2024
76873d2
note about exoplanet
adrn Mar 6, 2024
11f42dd
docs tweaks
adrn Mar 6, 2024
a098fcf
import os
adrn Mar 6, 2024
20d3557
fix various sphinx things
adrn Mar 6, 2024
ca6d17f
ignore docs build dir
adrn Mar 6, 2024
6322061
trying to figure out what is failing on CI
adrn Mar 6, 2024
e5c07a0
add nbsphinx, duh
adrn Mar 6, 2024
e5aeee4
changelog entry
adrn Mar 6, 2024
940d4f4
formatting
adrn Mar 6, 2024
7f42d95
theme options
adrn Mar 6, 2024
a8656b1
change theme and redo index page
adrn Mar 6, 2024
644f887
use rng when sampling from prior and add regression test
adrn Mar 6, 2024
d65fc94
disable test on macos CI
adrn Mar 6, 2024
ebb2030
tight layout
adrn Mar 6, 2024
3516c31
try pinning pytables
adrn Mar 6, 2024
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12 changes: 0 additions & 12 deletions .circleci/branch_name_check.sh

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7 changes: 0 additions & 7 deletions .circleci/ci_skip_check.sh

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95 changes: 0 additions & 95 deletions .circleci/config.yml

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25 changes: 0 additions & 25 deletions .circleci/execute_notebooks.sh

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2 changes: 0 additions & 2 deletions .gitattributes

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73 changes: 73 additions & 0 deletions .github/workflows/cd.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
name: Continuous Deployment

on:
workflow_dispatch:
pull_request:
push:
branches:
- main
release:
types:
- published

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

env:
FORCE_COLOR: 3

jobs:
dist:
name: Distribution build
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0

- uses: hynek/build-and-inspect-python-package@v2

# Upload to Test PyPI on every commit on main.
test-publish:
needs: [dist]
name: Test Publish to TestPyPI
environment: pypi
permissions:
id-token: write
runs-on: ubuntu-latest
if:
github.repository_owner == 'adrn' && github.event_name == 'push' &&
github.ref == 'refs/heads/main'

steps:
- name: Download packages built by build-and-inspect-python-package
uses: actions/download-artifact@v4
with:
name: Packages
path: dist

- name: Upload package to Test PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
repository-url: https://test.pypi.org/legacy/

publish:
needs: [dist]
name: Publish to PyPI
environment: pypi
permissions:
id-token: write
runs-on: ubuntu-latest
if: github.event_name == 'release' && github.event.action == 'published'

steps:
- name: Download packages built by build-and-inspect-python-package
uses: actions/download-artifact@v4
with:
name: Packages
path: dist

- uses: pypa/gh-action-pypi-publish@release/v1
if: github.event_name == 'release' && github.event.action == 'published'
42 changes: 42 additions & 0 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
name: Tests

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

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

env:
FORCE_COLOR: 3

jobs:
test:
runs-on: ${{ matrix.os }}
strategy:
matrix:
python-version: ["3.9", "3.10", "3.11"]
os: ["ubuntu-latest", "macos-latest"]
steps:

- uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install -e .[test]

- name: Test package
run: >-
python -m pytest -ra --cov --cov-report=xml --cov-report=term --durations=20

- name: Upload coverage report
uses: codecov/[email protected]
84 changes: 0 additions & 84 deletions .github/workflows/packaging.yml

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