use tox to install test data (#73)

.github/workflows/test.yml

@@ -43,6 +43,9 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
+    - uses: actions/setup-python@v5
+    - name: install tox
+      run: pip install tox
     - uses: actions/cache@v3
       id: cache
       env:
@@ -54,19 +57,7 @@ jobs:
     - if: ${{ steps.cache.outputs.cache-hit != 'true' }}
       name: Download fmriprep derivative of ds000017
       id: download
-      run: |
-        mkdir -p /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
-        cd /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
-        wget --retry-connrefused \
-          --waitretry=5 \
-          --read-timeout=20 \
-          --timeout=15 \
-          -t 0 \
-          -q \
-          -O ds000017.tar.gz \
-          "https://zenodo.org/record/8091903/files/ds000017-fmriprep22.0.1-downsampled-nosurface.tar.gz?download=1"
-        tar -xzf ds000017.tar.gz
-        rm ds000017.tar.gz
+      run: tox -e test_data
 
   build:
     runs-on: ubuntu-latest

docs/source/contributing.md

@@ -27,6 +27,14 @@ pip install -e .[dev]
 pre-commit install
 ```
 
+5. Install the data required for testing from zenodo
+
+This can be done using tox by running:
+
+```bash
+tox -e test_data
+```
+
 ## Contributing to code
 
 This is a very generic workflow.
@@ -51,7 +59,7 @@ git checkout -b your_branch
 5. Run the tests locally; you can run spectfic tests to speed up the process:
 
 ```bash
-pytest -v giga_connectome/tests/tests/test_connectome.py::test_calculate_intranetwork_correlation
+pytest -v giga_connectome/tests/test_connectome.py::test_calculate_intranetwork_correlation
 ```
 
 6. push your changes to your online fork. If this is the first commit, you might want to set up the remote tracking:

pyproject.toml

@@ -37,6 +37,7 @@ dev = [
   "black",
   "pre-commit",
   "giga_connectome[test]",
+  'tox',
 ]
 test = [
   "pytest",

tox.ini

@@ -0,0 +1,45 @@
+;  See https://tox.wiki/en
+[tox]
+requires =
+    tox>=4
+; run lint by default when just calling "tox"
+env_list = lint
+
+; ENVIRONMENTS
+; ------------
+[style]
+description = common environment for style checkers (rely on pre-commit hooks)
+skip_install = true
+deps =
+    pre-commit
+
+; COMMANDS
+; --------
+[testenv:lint]
+description = run all linters and formatters
+skip_install = true
+deps =
+    {[style]deps}
+commands =
+	pre-commit run --all-files --show-diff-on-failure {posargs:}
+
+[testenv:test_data]
+description = install test data
+skip_install = true
+allowlist_externals =
+    mkdir
+    wget
+    tar
+    rm
+commands =
+    mkdir -p giga_connectome/data/test_data
+    wget --retry-connrefused \
+        --waitretry=5 \
+        --read-timeout=20 \
+        --timeout=15 \
+        -t 0 \
+        -q \
+        -O giga_connectome/data/test_data/ds000017.tar.gz \
+        "https://zenodo.org/record/8091903/files/ds000017-fmriprep22.0.1-downsampled-nosurface.tar.gz?download=1"
+    tar -xzf giga_connectome/data/test_data/ds000017.tar.gz -C giga_connectome/data/test_data/
+    rm giga_connectome/data/test_data/ds000017.tar.gz