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merged 3 commits into from
Jun 20, 2022
Merged

Get rid of python-version specific conda environments #5911

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b0adade
Get rid of python-version specific conda test environments
ricardoV94 Jun 20, 2022
f60808a
Get rid of python-version specific conda dev environments
ricardoV94 Jun 20, 2022
96b2bd7
Install sphinx-design via conda
ricardoV94 Jun 20, 2022
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78 changes: 44 additions & 34 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@ jobs:
matrix:
os: [ubuntu-20.04]
floatx: [float64]
python-version: ["3.7"]
test-subset:
- |
pymc/tests/test_util.py
Expand Down Expand Up @@ -88,12 +89,12 @@ jobs:
- name: Cache conda
uses: actions/cache@v3
env:
# Increase this value to reset cache if environment-test-py37.yml has not changed
# Increase this value to reset cache if environment-test.yml has not changed
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/environment-test-py37.yml') }}
key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/environment-test.yml') }}
- name: Cache multiple paths
uses: actions/cache@v3
env:
Expand All @@ -111,20 +112,21 @@ jobs:
miniforge-variant: Mambaforge
miniforge-version: latest
mamba-version: "*"
activate-environment: pymc-test-py37
activate-environment: pymc-test
channel-priority: strict
environment-file: conda-envs/environment-test-py37.yml
environment-file: conda-envs/environment-test.yml
python-version: ${{matrix.python-version}}
use-mamba: true
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install-pymc
run: |
conda activate pymc-test-py37
conda activate pymc-test
pip install -e .
pip install --pre -U polyagamma
python --version
- name: Run tests
run: |
conda activate pymc-test-py37
conda activate pymc-test
python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v2
Expand All @@ -137,6 +139,7 @@ jobs:
matrix:
os: [windows-latest]
floatx: [float64]
python-version: ["3.8"]
test-subset:
- pymc/tests/test_variational_inference.py pymc/tests/test_initial_point.py
- pymc/tests/test_pickling.py pymc/tests/test_profile.py pymc/tests/test_step.py
Expand All @@ -156,12 +159,12 @@ jobs:
- name: Cache conda
uses: actions/cache@v3
env:
# Increase this value to reset cache if conda-envs/environment-test-py38.yml has not changed
# Increase this value to reset cache if conda-envs/windows-environment-test.yml has not changed
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/windows-environment-test-py38.yml') }}
key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/windows-environment-test.yml') }}
- name: Cache multiple paths
uses: actions/cache@v3
env:
Expand All @@ -179,22 +182,23 @@ jobs:
miniforge-variant: Mambaforge
miniforge-version: latest
mamba-version: "*"
activate-environment: pymc-test-py38
activate-environment: pymc-test
channel-priority: strict
environment-file: conda-envs/windows-environment-test-py38.yml
environment-file: conda-envs/windows-environment-test.yml
python-version: ${{matrix.python-version}}
use-mamba: true
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install-pymc
run: |
conda activate pymc-test-py38
conda activate pymc-test
pip install -e .
pip install --pre -U polyagamma
python --version
- name: Run tests
# This job uses a cmd shell, therefore the environment variable syntax is different!
# The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
run: >-
conda activate pymc-test-py38 &&
conda activate pymc-test &&
python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v2
Expand All @@ -207,6 +211,7 @@ jobs:
matrix:
os: [macos-latest]
floatx: [float64]
python-version: ["3.9"]
test-subset:
- |
pymc/tests/test_parallel_sampling.py
Expand All @@ -232,12 +237,12 @@ jobs:
- name: Cache conda
uses: actions/cache@v3
env:
# Increase this value to reset cache if environment-test-py39.yml has not changed
# Increase this value to reset cache if environment-test.yml has not changed
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/environment-test-py39.yml') }}
key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/environment-test.yml') }}
- name: Cache multiple paths
uses: actions/cache@v3
env:
Expand All @@ -255,14 +260,15 @@ jobs:
miniforge-variant: Mambaforge
miniforge-version: latest
mamba-version: "*"
activate-environment: pymc-test-py39
activate-environment: pymc-test
channel-priority: strict
environment-file: conda-envs/environment-test-py39.yml
environment-file: conda-envs/environment-test.yml
python-version: ${{matrix.python-version}}
use-mamba: true
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install pymc
run: |
conda activate pymc-test-py39
conda activate pymc-test
pip install -e .
python --version
- name: Run tests
Expand All @@ -279,6 +285,7 @@ jobs:
matrix:
os: [ubuntu-20.04]
floatx: [float64]
python-version: ["3.9"]
test-subset:
- pymc/tests/test_sampling_jax.py
fail-fast: false
Expand All @@ -294,12 +301,12 @@ jobs:
- name: Cache conda
uses: actions/cache@v3
env:
# Increase this value to reset cache if environment-test-py39.yml has not changed
# Increase this value to reset cache if environment-test.yml has not changed
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/environment-test-py39.yml') }}
key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/environment-test.yml') }}
- name: Cache multiple paths
uses: actions/cache@v3
env:
Expand All @@ -317,19 +324,20 @@ jobs:
miniforge-variant: Mambaforge
miniforge-version: latest
mamba-version: "*"
activate-environment: pymc-test-py39
activate-environment: pymc-test
channel-priority: strict
environment-file: conda-envs/environment-test-py39.yml
environment-file: conda-envs/environment-test.yml
python-version: ${{matrix.python-version}}
use-mamba: true
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install pymc
run: |
conda activate pymc-test-py39
conda activate pymc-test
pip install -e .
python --version
- name: Install jax specific dependencies
run: |
conda activate pymc-test-py39
conda activate pymc-test
pip install "numpyro>=0.8.0"
pip install git+https://github.com/blackjax-devs/[email protected]
- name: Run tests
Expand All @@ -346,6 +354,7 @@ jobs:
matrix:
os: [windows-latest]
floatx: [float32]
python-version: ["3.8"]
test-subset:
- pymc/tests/test_sampling.py pymc/tests/test_ode.py
fail-fast: false
Expand All @@ -361,12 +370,12 @@ jobs:
- name: Cache conda
uses: actions/cache@v3
env:
# Increase this value to reset cache if conda-envs/environment-test-py38.yml has not changed
# Increase this value to reset cache if conda-envs/windows-environment-test.yml has not changed
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/windows-environment-test-py38.yml') }}
key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
hashFiles('conda-envs/windows-environment-test.yml') }}
- name: Cache multiple paths
uses: actions/cache@v3
env:
Expand All @@ -384,22 +393,23 @@ jobs:
miniforge-variant: Mambaforge
miniforge-version: latest
mamba-version: "*"
activate-environment: pymc-test-py38
activate-environment: pymc-test
channel-priority: strict
environment-file: conda-envs/windows-environment-test-py38.yml
environment-file: conda-envs/windows-environment-test.yml
python-verision: ${{matrix.python-version}}
use-mamba: true
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install-pymc
run: |
conda activate pymc-test-py38
conda activate pymc-test
pip install -e .
pip install --pre -U polyagamma
python --version
- name: Run tests
# This job uses a cmd shell, therefore the environment variable syntax is different!
# The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
run: >-
conda activate pymc-test-py38 &&
conda activate pymc-test &&
python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v2
Expand Down
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ repos:
- id: pip-from-conda
additional_dependencies: [pyyaml]
entry: python scripts/generate_pip_deps_from_conda.py
files: ^conda-envs/environment-dev-py.+.yml$
files: ^conda-envs/environment-dev.yml$
language: python
name: Generate pip dependency from conda
- id: no-relative-imports
Expand Down
2 changes: 1 addition & 1 deletion .readthedocs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ python:
path: .

conda:
environment: "conda-envs/environment-dev-py38.yml"
environment: "conda-envs/environment-dev.yml"

build:
os: "ubuntu-20.04"
Expand Down
41 changes: 0 additions & 41 deletions conda-envs/environment-dev-py38.yml
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This file was deleted.

41 changes: 0 additions & 41 deletions conda-envs/environment-dev-py39.yml
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This file was deleted.

5 changes: 2 additions & 3 deletions conda-envs/environment-dev-py37.yml → conda-envs/environment-dev.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# "dev" conda envs are to be used by devs in setting their local environments
name: pymc-dev-py37
name: pymc-dev
channels:
- conda-forge
- defaults
Expand All @@ -16,7 +16,6 @@ dependencies:
- numpy>=1.15.0
- pandas>=0.24.0
- pip
- python=3.7
- python-graphviz
- scipy>=1.4.1
- typing-extensions>=3.7.4
Expand All @@ -31,11 +30,11 @@ dependencies:
- pytest-cov>=2.5
- pytest>=3.0
- sphinx-copybutton
- sphinx-design
- sphinx-notfound-page
- sphinx>=1.5
- sphinxext-rediraffe
- watermark
- pip:
- polyagamma
- sphinx-design
- sphinx-remove-toctrees
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