fighting with GH actions (#430)

* cleanup * test * fix conda env path * Fix name * Try to properly activate conda env * Fetch MNE from git repo to include test files * Skip unnecessary uninstall step * test * dont use conda on gh actions * iter * iter * iter * iter * fix * iter * fix * fix? * revert * update readme * cleanup * test validator master * fix? * fix? * debug * debug * debug * debug * debug * debug * debug * try windows * debug * debug * debug * test * test * test * test * test * test * test * test * test * test * cleanup * cleanup * cleanup * cleanup * rm travis and appveyor * simplify Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
mne-tools · May 24, 2020 · c246eee · c246eee
1 parent 3221379
commit c246eee
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Showing 10 changed files with 67 additions and 201 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -10,3 +10,4 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           artifact-path: 0/dev/index.html
           circleci-jobs: docs-build
+
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -1,4 +1,4 @@
-name: MNE-BIDS
+name: build
 
 on:
   push:
@@ -13,9 +13,10 @@ jobs:
   build:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        # python-version: [3.5, 3.6, 3.7, 3.8]
+        os: [ubuntu-18.04, ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.8]
 
     env:
       TZ: Europe/Berlin
@@ -25,31 +26,60 @@ jobs:
       uses: actions/setup-node@v1.4.2
       with:
         node-version: 12
-    - name: Set up Python environment${{ matrix.python-version }}
-      uses: goanpeca/setup-miniconda@v1.4.1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
       with:
-        environment-file: mne-bids/environment.yml
-        activate-environment: mne_bids
-        auto-update-conda: true
-        channel-priority: strict
-        channels: conda-forge, defaults
-    - name: Install BIDS validator
-      run: npm install -g bids-validator
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies using pip
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Install MNE (stable)
+      if: "matrix.os != 'ubuntu-latest'"
+      run: |
+        git clone --depth 1 https://github.com/mne-tools/mne-python.git -b maint/0.20
+        pip install --no-deps -e ./mne-python
+    - name: Install MNE (master)
+      if: "matrix.os == 'ubuntu-latest'"
+      run: |
+        git clone --depth 1 https://github.com/mne-tools/mne-python.git -b master
+        pip install --no-deps -e ./mne-python
+
+    - name: Install BIDS validator (stable)
+      if: "matrix.os != 'ubuntu-latest'"
+      run: |
+        npm install -g bids-validator
+    - name: Install BIDS validator (master)
+      if: "matrix.os == 'ubuntu-latest'"
+      run: |
+        cd ..
+        git clone --depth 1 https://github.com/bids-standard/bids-validator
+        cd bids-validator
+        git checkout master
+        yarn
+        echo "::add-path::$(pwd)/bids-validator/bin"
+        cd ../mne-bids
+
     - name: Display versions and environment information
       run: |
         echo $TZ
         date
-        npm --version
-        node --version
+        echo "npm"; npm --version
+        echo "node"; node --version
+        echo "bids-validator"; bids-validator --version
         python --version
         which python
         mne sys_info
-        bids-validator --version
     - name: Install MNE-BIDS
       run: pip install --no-deps .
     - name: Run pytest
-      run: pytest . --cov=./mne_bids --cov-report=xml --verbose --ignore mne-python
+      run: |
+        echo "bids-validator"; bids-validator --version
+        pytest . --cov=./mne_bids --cov-report=xml --verbose --ignore mne-python
     - name: Run style & documentation tests
+      if: "matrix.os == 'ubuntu-latest'"
       run: make pep
     - name: Upload coverage stats to codecov
+      if: "matrix.os == 'ubuntu-latest'"
       run: bash <(curl -s https://codecov.io/bash)
diff --git a/.travis.yml b/.travis.yml
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -22,3 +22,5 @@ recursive-exclude mne_bids *.pyc
 
 recursive-exclude doc *
 recursive-exclude paper *
+
+exclude requirements.txt
diff --git a/README.rst b/README.rst
@@ -1,28 +1,20 @@
 
+.. image:: https://github.com/mne-tools/mne-bids/workflows/build/badge.svg
+   :target: https://github.com/mne-tools/mne-bids/actions
+   :alt: gh-actions
 
 .. image:: https://badges.gitter.im/mne-tools/mne-bids.svg
    :target: https://gitter.im/mne-tools/mne-bids?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
    :alt: Gitter
 
-.. image:: https://travis-ci.org/mne-tools/mne-bids.svg?branch=master
-   :target: https://travis-ci.org/mne-tools/mne-bids
-   :alt: Travis
-
-.. image:: https://ci.appveyor.com/api/projects/status/d4u70pht341cwqxb/branch/master?svg=true
-   :target: https://ci.appveyor.com/project/mne-tools/mne-bids/branch/master
-   :alt: Appveyor
-
-
 .. image:: https://codecov.io/gh/mne-tools/mne-bids/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/mne-tools/mne-bids
    :alt: codecov
 
-
 .. image:: https://circleci.com/gh/mne-tools/mne-bids.svg?style=svg
    :target: https://circleci.com/gh/mne-tools/mne-bids
    :alt: CircleCi
 
-
 .. image:: https://pepy.tech/badge/mne-bids
    :target: https://pepy.tech/project/mne-bids
    :alt: Downloads

diff --git a/appveyor.yml b/appveyor.yml
diff --git a/doc/environment.yml b/doc/environment.yml
@@ -3,12 +3,11 @@ channels:
 - defaults
 - conda-forge
 dependencies:
-- python<3.7
+- python<3.8
 - pip<=20
 - mkl
 - numpy>=1.14
 - scipy>=0.18.1
-- scikit-learn
 - matplotlib
 - pip:
   - mne_bids>=0.4,<0.5

diff --git a/environment.yml b/environment.yml
@@ -3,12 +3,11 @@ channels:
 - defaults
 - conda-forge
 dependencies:
-- python<3.7
+- python<3.8
 - pip<=20
 - mkl
 - numpy>=1.14
 - scipy>=0.18.1
-- scikit-learn
 - matplotlib
 - pip:
   - mne>=0.19.1

diff --git a/mne_bids/tests/test_write.py b/mne_bids/tests/test_write.py
@@ -86,10 +86,10 @@ def _bids_validate():
 
     if platform.system() == 'Windows':
         shell = True
-        bids_validator_exe = ['node', exe, *vadlidator_args]
     else:
         shell = False
-        bids_validator_exe = [exe, *vadlidator_args]
+
+    bids_validator_exe = [exe, *vadlidator_args]
 
     def _validate(bids_root):
         cmd = [*bids_validator_exe, bids_root]

diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,11 @@
+numpy>=1.14
+scipy>=0.18.1
+mne>=0.19.1
+nibabel>=2.2
+pybv
+pytest<5.4
+pytest-cov
+pytest-sugar
+check-manifest
+pydocstyle
+flake8