Merge pull request #36 from effigies/git-wf-actions

Use conda environments in CI to work with git-annex

Author: effigies

.github/workflows/gh-pages.yml

@@ -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

.github/workflows/notebooks.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 defaults:
   run:
-    shell: bash
+    shell: bash -l {0}
 
 jobs:
   build:
@@ -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

environment.yml

@@ -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