CI: Update environment, install consistently

Needs matplotlib in environment
Quiet complaints from conda about pip
Add debug information to workflows

Author: effigies

.github/workflows/gh-pages.yml

@@ -4,12 +4,13 @@ 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: Disable etelemetry
@@ -18,12 +19,12 @@ jobs:
       uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: pydra-tutorial
-        environment-file: etc/environment.yml
-        python-version: ${{ matrix.python-version }}
-        auto-activate-base: false
-      run: conda activate pydra-tutorial
+        environment-file: environment.yml
+    - run: conda info
+    - run: conda list
+    - run: conda config --show
     - name: Install dependencies
-      run: conda install -c conda-forge jupyter-book
+      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:
@@ -16,17 +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: conda-incubator/setup-miniconda@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: etc/environment.yml
+        environment-file: environment.yml
         python-version: ${{ matrix.python-version }}
-        auto-activate-base: false
-      run: conda activate pydra-tutorial     
+    - 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

etc/environment.yml renamed to environment.yml

@@ -3,14 +3,16 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - datalad
   - git-annex
+  - pip
   - pip:
+    - datalad
     - pydra
     - jupyter
     - jupyter_contrib_nbextensions
     - jupytext
     - jupyterlab
+    - matplotlib
     - nbformat
     - nbval
     - nest_asyncio