Added CI workflow

.github/workflows/run-tox.yml

@@ -0,0 +1,36 @@
+name: Run all tox jobs using python3
+
+on:
+    pull_request:
+    push:
+      branches:
+        - main
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.10]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox-gh-actions
+    - name: Run tox
+      run: |
+        tox -e lint
+        tox -e coverage
+        tox -e py
+    - name: Upload to codecov
+      if: ${{matrix.python-version == '3.10'}}
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: false
+        files: ./coverage.xml
+        flags: pytest
+        name: "connectome-manipulator-py310"

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.black]
 line-length = 100
 target-version = [
-    'py39',
+    'py310',
 ]
 include = 'connectome_manipulator\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$'
 

tox.ini

@@ -8,65 +8,18 @@ testdeps =
 
 [tox]
 envlist =
-    check-version
-    check-packaging
     lint
-    py{39,310}
+    coverage
+    py310
 
-minversion = 3.1.0
+minversion = 4
 
 # ignore basepython for envs that already specify a version
 ignore_basepython_conflict = true
 
 [testenv]
-setenv =
-    PIP_INDEX_URL = https://bbpteam.epfl.ch/repository/devpi/simple
 deps = {[base]testdeps}
-commands = pytest -vv tests/unit {posargs}
-
-[testenv:functional]
-commands = pytest -vv tests/functional {posargs}
-
-[testenv:integration]
-passenv =
-    SLURM_ACCOUNT
-    MODULESHOME
-    MODULEPATH
-    LOADEDMODULES
-    _LMFILES_
-changedir =
-    tests/integration
-allowlist_externals =
-    bash
-    echo
-    find
-    cat
-commands =
-    echo "Testing with Dask"
-    connectome-manipulator -v manipulate-connectome wiring_config.json \
-        --output-dir {temp_dir}/integration_dask \
-        --profile --convert-to-sonata \
-        --parallel \
-        --splits 4 \
-        -a processes=1 \
-        -a n_workers=2 \
-        -a threads_per_worker=1
-    find {temp_dir}/integration_dask/logs -type f -name '*.task-*.log' -exec cat -n {} \;
-    bash -c 'h5ls -S {temp_dir}/integration_dask/edges.h5/edges/All__All__chemical/target_node_id | grep "{127}" -q'
-
-
-[testenv:check-version]
-skip_install = true
-deps = bbp-nse-ci
-commands = do_release.py -p . check-version
-
-[testenv:check-packaging]
-deps =
-    wheel
-    twine
-commands =
-    python setup.py sdist bdist_wheel -d {envtmpdir}/dist
-    twine check {envtmpdir}/dist/*
+commands = pytest -vv tests/unit
 
 [testenv:lint]
 deps =
@@ -80,10 +33,6 @@ commands =
     pylint {[base]name}
     black --check .
 
-[testenv:format]
-deps = black
-commands = black .
-
 [testenv:coverage]
 usedevelop=True
 deps =
@@ -92,18 +41,6 @@ deps =
 commands =
     pytest --cov-report term-missing --cov-report xml --cov={[base]name} tests/unit
 
-[testenv:docs]
-changedir = doc
-extras = docs
-# set warnings as errors using the -W sphinx option
-commands = make html SPHINXOPTS=-W
-allowlist_externals = make
-
-# E731: do not assign a lambda expression, use a def
-# W503: line break after binary operator
-# W504: line break before binary operator
-# E261 at least two spaces before inline comment
-# E501: long line: THIS SHOULD BE TEMPARARY
 [pycodestyle]
 ignore = E731,W503,W504,E261,E501,E203
 max-line-length = 100