Merge pull request #300 from juaml/chore/maintenance

[MAINT]: Improve repository

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/ci.yml

@@ -70,6 +70,37 @@ jobs:
       run: |
         echo "Using AFNI : $(afni --version)"
       if: matrix.python-version == 3.10
+    - name: Install ANTs
+      run: |
+        sudo apt-get install -y -qq unzip
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        unzip ants.zip -d /opt
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        rm ants.zip
+        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
+      if: matrix.python-version == 3.10
+    - name: Check ANTs
+      run: |
+        echo "Using ANTs : $(antsRegistration --version)"
+      if: matrix.python-version == 3.10
+    - name: Install FSL
+      run: |
+        sudo apt-get install -y -qq python3
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.6.4 -V 6.0.6.4
+        FSLOUTPUTTYPE="NIFTI_GZ"
+        FSLMULTIFILEQUIT="TRUE"
+        FSLTCLSH="/opt/fsl-6.0.6.4/bin/fsltclsh"
+        FSLWISH="/opt/fsl-6.0.6.4/bin/fslwish"
+        FSLLOCKDIR=""
+        FSLMACHINELIST=""
+        FSLREMOTECALL=""
+        FSLGECUDAQ="cuda.q"
+        echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
+      if: matrix.python-version == 3.10
+    - name: Check FSL
+      run: |
+        echo "Using FSL : $(flirt -version)"
+      if: matrix.python-version == 3.10
     - name: Test with tox
       run: |
         tox

README.md

@@ -65,6 +65,7 @@ pip install "junifer[bct,dev]"
 ```
 
 * `bct` installs [bctpy](https://github.com/aestrivex/bctpy) to enable use of `onthefly` module.
+* `neurokit2` installs [neurokit2](https://github.com/neuropsychology/NeuroKit) to enable use of [complexity markers](https://juaml.github.io/junifer/main/api/markers.html#module-junifer.markers.complexity).
 * `all` includes all of the above.
 * `dev` installs packages needed for development.
 * `docs` installs packages needed for building documentation.

docs/changes/newsfragments/300.doc

@@ -0,0 +1 @@
+Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by `Synchon Mandal`_

docs/changes/newsfragments/300.enh

@@ -0,0 +1 @@
+Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon Mandal`_

docs/changes/newsfragments/300.misc

@@ -0,0 +1 @@
+Update dependency listing in ``pyproject.toml``, add ``.github/dependabot.yml`` to auto-update GitHub Actions, add ``ANTs`` and ``FSL`` installation in CI and improve general code style by `Synchon Mandal`_

docs/whats_new.rst

@@ -76,8 +76,8 @@ Features
   transform operations on stored data by `Synchon Mandal`_ (:gh:`237`)
 
 
-Misc
-^^^^
+Miscellaneous
+^^^^^^^^^^^^^
 
 - Consistent docstrings for pytest fixtures used in the test suite by `Synchon
   Mandal`_ (:gh:`228`)
@@ -373,7 +373,7 @@ Features
   `Fede Raimondo`_ (:gh:`35`)
 
 
-Misc
-^^^^
+Miscellaneous
+^^^^^^^^^^^^^
 
 - Create the repository based on the mockup by `Fede Raimondo`_

junifer/api/tests/test_api_utils.py

@@ -43,6 +43,7 @@ def test_get_dependency_information_short() -> None:
         "sqlalchemy",
         "ruamel.yaml",
         "httpx",
+        "tqdm",
     ]
     if int(pl.python_version_tuple()[1]) < 10:
         dependency_list.append("importlib_metadata")
@@ -66,6 +67,7 @@ def test_get_dependency_information_long() -> None:
         "sqlalchemy",
         "ruamel.yaml",
         "httpx",
+        "tqdm",
     ]
     for key in dependency_list:
         assert key in dependency_information_keys