Merge pull request #110 from jjjermiah/development

add return_types and new abstraction for requests to be made

.github/workflows/main.yml

@@ -1,21 +1,21 @@
 name: CI-CD
-  
+
 # only run on pushes to main or pull requests
 on:
   push:
-    # push to any branch
-    branches: [ main , docs]
+    # push to any branch *
+    branches: [ "*"]
   pull_request:
     branches: [ main , development]
-  
-jobs:  
+
+jobs:
   Unit-Tests:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, macos-14]
         python-version: ["3.12", "3.11"] # "3.10",
-  
+
     steps:
       - uses: actions/checkout@v3
 
@@ -33,7 +33,7 @@ jobs:
       - name: Test with pytest
         run: |
           # Github action runners now have 4 cores
-          poetry run pytest -n 4 --cov --cov-report xml:coverage-report/coverage.xml
+          poetry run pytest -s -v -n 4 --cov --cov-report xml:coverage-report/coverage.xml
 
       - name: Upload coverage report artifact to be used by Codecov
         # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12
@@ -228,15 +228,15 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, macos-14]
         python-version: ["3.12", "3.11"]
-    
+
     steps:
       - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      
+
       - name: Install using PyPi
         run: |
           pip install  nbiatoolkit;
@@ -392,4 +392,3 @@ jobs:
 #     # No changes
 #     echo "No changes found. Nothing to commit or push."
 # fi
-

.gitignore

@@ -154,3 +154,6 @@ src/nbiatoolkit/.DS_Store
 
 NBIA-Download
 src/nbiatoolkit/.DS_Store
+.vscode
+download.ipynb
+driver*.py

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+    -   id: check-json
+    -   id: check-toml
+
+-   repo: https://gitlab.com/smop/pre-commit-hooks
+    rev: v1.0.0
+    hooks:
+    -   id: check-poetry

Dockerfile

@@ -24,4 +24,4 @@ RUN NBIAToolkit --help
 CMD ["/bin/bash"]
 
 # to run this container in terminal mode, use the following command:
-# docker run -it --rm nbiatoolkit
+# docker run -it --rm nbiatoolkit

LICENSE

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.md

@@ -10,6 +10,7 @@
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/nbiatoolkit.svg?label=pypi%20downloads)](https://pypi.org/project/nbiatoolkit/)
 ![GitHub repo size](https://img.shields.io/github/repo-size/jjjermiah/nbia-toolkit)
 [![Docker Pulls](https://img.shields.io/docker/pulls/jjjermiah/nbiatoolkit)](https://hub.docker.com/r/jjjermiah/nbiatoolkit)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 
 
 
@@ -44,20 +45,20 @@ pip install nbiatoolkit
 ```
 
 ## CLI Usage
-For quick access to the NBIA, the toolkit also provides a command line interface (CLI) 
+For quick access to the NBIA, the toolkit also provides a command line interface (CLI)
 
 ``` bash NBIAToolkit-Output
 > NBIAToolkit --version
-    _   ______  _______  ______            ____   _ __ 
+    _   ______  _______  ______            ____   _ __
    / | / / __ )/  _/   |/_  __/___  ____  / / /__(_) /_
   /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
- / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_  
-/_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/  
-                                                       
+ / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
+/_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/
+
 
 Version: 0.29.2
 
-Available CLI tools: 
+Available CLI tools:
 
 getCollections [-h] [-u USERNAME] [-pw PASSWORD] [-p PREFIX]
                [-o OUTPUTFILE] [--version]
@@ -110,4 +111,3 @@ Interested in contributing? Check out the contributing guidelines. Please note t
 > Users of the NBIA-toolkit are required to abide by the NBIA REST API Terms of Service and the [NBIA Data Usage Policies and Restrictions](https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/)
 > The NBIA-toolkit is provided as an open-source tool based on the [NBIA REST API](https://wiki.cancerimagingarchive.net/display/Public/NBIA+Advanced+REST+API+Guide) and is provided "AS IS" without warranty of any kind.
 > In no event shall the authors or contributors be liable for any claim, damages or other liability, arising from, out of or in connection with the NBIA-toolkit or the use or other dealings in the NBIA-toolkit.
-

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -10,9 +10,9 @@
 sys.path.insert(0, os.path.abspath("../src"))
 # -- Project information -----------------------------------------------------
 
-project = u"nbiatoolkit"
-copyright = u"2023, Jermiah Joseph"
-author = u"Jermiah Joseph"
+project = "nbiatoolkit"
+copyright = "2023, Jermiah Joseph"
+author = "Jermiah Joseph"
 
 # -- General configuration ---------------------------------------------------
 

docs/index.md

@@ -13,4 +13,4 @@ markdowns/CHANGELOG.md
 markdowns/CONTRIBUTING.md
 markdowns/CONDUCT.md
 autoapi/index
-```
+```

docs/markdowns/Installation.md

@@ -36,5 +36,3 @@ Then activate the virtual environment and install the package using the commands
 source /path/to/new/virtual/environment/bin/activate
 pip install nbiatoolkit
 ```
-
-

docs/markdowns/NBIA.md

@@ -1,9 +1,9 @@
 # National Biomedical Imaging Archive (NBIA)
 
-The National Biomedical Imaging Archive (NBIA) is a free and open-source platform that provides the biomedical research community with access to biomedical images, annotations, and related data. 
+The National Biomedical Imaging Archive (NBIA) is a free and open-source platform that provides the biomedical research community with access to biomedical images, annotations, and related data.
 - It is developed by the [National Cancer Institue (NCI)](https://www.cancer.gov/) and aims to improve healthcare by fostering research in areas including cancer, lung diseases, and brain disorders.
 
-The NBIA is primarily used in the fields of medical and health research. 
+The NBIA is primarily used in the fields of medical and health research.
 - This includes areas such as radiology, oncology, neurology, pathology and more.
 
 1. Radiology: Radiologists use this archive to access a variety of images such as CT scans, MRI scans that help them in the diagnosis and treatment of various diseases.
@@ -16,4 +16,4 @@ The NBIA is primarily used in the fields of medical and health research.
 
 5. Clinical Trials: The NBIA is also used extensively in clinical trials where imaging plays a crucial role. Researchers can share their findings with others around the world which promotes collaborative studies.
 
-6. Machine Learning/AI Research: The large collection of biomedical images also serves as a valuable resource for researchers working on developing machine learning algorithms for image recognition and diagnosis purposes.
+6. Machine Learning/AI Research: The large collection of biomedical images also serves as a valuable resource for researchers working on developing machine learning algorithms for image recognition and diagnosis purposes.

docs/requirements.txt

@@ -1,4 +1,4 @@
 myst-nb
 sphinx-autoapi
 sphinx-rtd-theme
-sphinx-tabs
+sphinx-tabs