8000 Use conda environments in CI to work with git-annex by effigies · Pull Request #36 · nipype/pydra-tutorial · GitHub
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Use conda environments in CI to work with git-annex #36

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Merged
merged 6 commits into from
Sep 8, 2022
Merged

Use conda environments in CI to work with git-annex #36

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35b9a5b
update notebooks.yml
yibeichan Sep 1, 2022
97cf307
update gh-pages.yml
yibeichan Sep 1, 2022
174ea26
modify wf actions
yibeichan Sep 1, 2022
ce45d14
fix incompatible packages
yibeichan Sep 1, 2022
a41afe2
fix minor errors
yibeichan Sep 1, 2022
156996d
CI: Update environment, install consistently
effigies Sep 8, 2022
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25 changes: 14 additions & 11 deletions .github/workflows/gh-pages.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,24 +4,27 @@ on:
push: {branches: [main, master]}
pull_request: {branches: [main, master]}

defaults:
run:
shell: bash -l {0}

jobs:
build:
runs-on: ubuntu-latest
strategy:
matrix:
python: [3.9]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python }}
- name: Install dependencies
run: |
pip install --upgrade pip
pip install -r jupyterbook/requirements.txt
- name: Disable etelemetry
run: echo "NO_ET=TRUE" >> $GITHUB_ENV
- name: Active conda env pydra-tutorial
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: pydra-tutorial
environment-file: environment.yml
- run: conda info
- run: conda list
- run: conda config --show
- name: Install dependencies
run: pip install jupyter-book
- name: Build JupyterBook
run: jb build -W jupyterbook
- uses: peaceiris/actions-gh-pages@v3
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17 changes: 10 additions & 7 deletions .github/workflows/notebooks.yml
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Expand Up @@ -4,7 +4,7 @@ on: [push, pull_request]

defaults:
run:
shell: bash
shell: bash -l {0}

jobs:
build:
Expand All @@ -16,15 +16,18 @@ jobs:
runs-on: ${{ matrix.os }}

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Disable etelemetry
run: echo "NO_ET=TRUE" >> $GITHUB_ENV
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
run: echo "NO_ET=TRUE" >> $GITHUB_ENV
- name: Active conda env pydra-tutorial
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: pydra-tutorial
environment-file: environment.yml
python-version: ${{ matrix.python-version }}
- name: Install requirements
run: python -m pip install -r requirements.txt
- run: conda info
- run: conda list
- run: conda config --show
- name: Convert all md files to ipynb
run: jupytext notebooks/*.md --to ipynb
- name: Test notebooks with pytest
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25 changes: 25 additions & 0 deletions environment.yml
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@@ -0,0 +1,25 @@
name: pydra-tutorial
channels:
- conda-forge
- defaults
dependencies:
- git-annex
- pip
- pip:
- datalad
- pydra
- jupyter
- jupyter_contrib_nbextensions
- jupytext
- jupyterlab
- matplotlib
- nbformat
- nbval
- nest_asyncio
- psutil
- pytest
- numpy
- pandas
- scipy
- nibabel
- nilearn
3 changes: 0 additions & 3 deletions jupyterbook/requirements.txt
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16 changes: 0 additions & 16 deletions requirements.txt
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