refactor: Merge remote-tracking branch 'origin' into docs

jjjermiah · Feb 25, 2024 · 5c3fa28 · 5c3fa28
2 parents 1c1f9b6 + d9ef88b
commit 5c3fa28
Show file tree

Hide file tree

Showing 38 changed files with 1,649 additions and 859 deletions.
diff --git a/.github/workflows/main.yml b/.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
@@ -67,7 +67,6 @@ jobs:
 
   Build-Documentation:
     runs-on: ubuntu-latest
-    if: github.ref == 'refs/heads/docs'
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
@@ -228,15 +227,15 @@ 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;
@@ -362,34 +361,3 @@ jobs:
               # No changes
               echo "No changes found. Nothing to commit or push."
           fi
-
-
-
-  #         # git add README.md
-
-  #         # git commit -m "Update README with latest version"
-  #         # git push
-
-
-# #!/bin/bash
-
-# # Check for changes
-# if [[ $(git status --porcelain) ]]; then
-#     # Changes are present
-#     echo "Changes found. Committing and pushing..."
-
-#     # Add all changes
-#     git add .
-
-#     # Commit with a timestamp
-#     git commit -m "Auto commit: $(date)"
-
-#     # Push changes to the remote repository
-#     git push origin <your-branch-name>
-
-#     echo "Changes committed and pushed successfully."
-# else
-#     # No changes
-#     echo "No changes found. Nothing to commit or push."
-# fi
-
diff --git a/.gitignore b/.gitignore
@@ -154,3 +154,6 @@ src/nbiatoolkit/.DS_Store
 
 NBIA-Download
 src/nbiatoolkit/.DS_Store
+.vscode
+download.ipynb
+driver*.py
diff --git a/.pre-commit-config.yaml b/.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
diff --git a/Dockerfile b/Dockerfile
@@ -1,11 +1,3 @@
-# This Dockerfile will create a container that builds the nbiatoolkit package
-# using the code in this repository
-#
-# To build the container, run the following command from the root of the
-# repository:
-# docker build -t nbiatoolkit .
-
-
 FROM python:3.12-slim
 
 LABEL maintainer="Jermiah Joseph jermiahjoseph98@gmail.com"
@@ -14,14 +6,17 @@ LABEL license="MIT"
 LABEL usage="docker run -it --rm <image_name> NBIAToolkit --help"
 LABEL org.opencontainers.image.source="github.com/jjjermiah/nbiatoolkit"
 
-# install the dependencies
-RUN pip install --upgrade pip
-RUN python -m pip install nbiatoolkit
+# copy current directory to /nbiatoolkit
+COPY . /nbiatoolkit
+
+# set working directory
+WORKDIR /nbiatoolkit
+
+# install nbiatoolkit
+RUN pip install --no-cache-dir --upgrade pip
+RUN pip install --no-cache-dir .
 
 RUN NBIAToolkit --help
 
 # On run, open a bash shell
 CMD ["/bin/bash"]
-
-# to run this container in terminal mode, use the following command:
-# docker run -it --rm nbiatoolkit
diff --git a/LICENSE b/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.
-
diff --git a/README.md b/README.md
@@ -3,8 +3,12 @@
 [![PyTests](https://github.com/jjjermiah/nbia-toolkit/actions/workflows/main.yml/badge.svg)](https://github.com/jjjermiah/nbia-toolkit/actions/workflows/main.yml)
 [![Documentation Status](https://readthedocs.org/projects/nbia-toolkit/badge/?version=latest)](https://nbia-toolkit.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/jjjermiah/nbia-toolkit/graph/badge.svg?token=JKREY71D0R)](https://codecov.io/gh/jjjermiah/nbia-toolkit)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![Python version](https://img.shields.io/pypi/pyversions/nbiatoolkit.svg)](https://img.shields.io/pypi/pyversions/nbiatoolkit.svg)
+[![CodeFactor](https://www.codefactor.io/repository/github/jjjermiah/nbia-toolkit/badge)](https://www.codefactor.io/repository/github/jjjermiah/nbia-toolkit)
 
+
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/jjjermiah/nbia-toolkit)
 [![PyPI version](https://badge.fury.io/py/nbiatoolkit.svg)](https://badge.fury.io/py/nbiatoolkit)
 [![Downloads](https://static.pepy.tech/badge/nbiatoolkit)](https://pepy.tech/project/nbiatoolkit)
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/nbiatoolkit.svg?label=pypi%20downloads)](https://pypi.org/project/nbiatoolkit/)
@@ -13,7 +17,10 @@
 
 
 
+
 ![GitHub milestone details](https://img.shields.io/github/milestones/progress-percent/jjjermiah/nbia-toolkit/1?style=flat-square&label=1.0.0%20Stable%20Release%20Milestone&link=https%3A%2F%2Fgithub.com%2Fjjjermiah%2Fnbia-toolkit%2Fmilestone%2F1)![GitHub milestone details](https://img.shields.io/github/milestones/progress/jjjermiah/nbia-toolkit/1?style=flat-square&label=%20&link=https%3A%2F%2Fgithub.com%2Fjjjermiah%2Fnbia-toolkit%2Fmilestone%2F1)
+[![GitHub issues](https://img.shields.io/github/issues/jjjermiah/nbia-toolkit)](https://github.com/jjjermiah/nbia-toolkit/issues)
+![GitHub last commit](https://img.shields.io/github/last-commit/jjjermiah/nbia-toolkit)
 
 
 
@@ -43,19 +50,43 @@ It is made available via PyPI and can be installed using pip:
 pip install nbiatoolkit
 ```
 
+## Python Usage
+Using a context manager, you can easily access the NBIA database and query for metadata on collections, patients, studies, and series.
+
+``` python
+from nbiatoolkit import NBIAClient
+
+with NBIAClient() as client:
+    # Get a list of collections
+    collections = client.getCollections()
+    print(collections)
+
+    # Get a list of patients in a collection
+    patients = client.getPatients(Collection="TCGA-KIRC")
+    print(patients)
+
+    # Get a list of studies for a patient
+    studies = client.getStudies(PatientID="TCGA-BP-4989")
+    print(studies)
+
+    # Get a list of series for a study
+    series = client.getSeries(StudyInstanceUID=studies[0]["StudyInstanceUID"])
+    print(series[0:5])
+```
+
 ## 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
+        _   ______  _______  ______            ____   _ __
+       / | / / __ )/  _/   |/_  __/___  ____  / / /__(_) /_
+      /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
+     / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
+    /_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/
+
+Version: 0.32.1
 
 Available CLI tools: 
 
@@ -85,15 +116,6 @@ getSeries [-h] [-u USERNAME] [-pw PASSWORD] [-c COLLECTION]
 getNewSeries [-h] [-u USERNAME] [-pw PASSWORD] -d DATE [-o OUTPUTFILE]
              [--version]
 
-downloadSingleSeries [-h] [-u USERNAME] [-pw PASSWORD] --seriesUID
-                     SERIESUID --downloadDir DOWNLOADDIR
-                     [--filePattern FILEPATTERN] [--overwrite]
-
-dicomsort [-h] [-u USERNAME] [-pw PASSWORD]
-          [--targetPattern TARGETPATTERN] [--truncateUID]
-          [--sanitizeFilename] [--overwrite] [--nParallel NPARALLEL]
-          sourceDir destinationDir
-
 ```
 
 
@@ -110,4 +132,3 @@ 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.
-
diff --git a/docs/Makefile b/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)
diff --git a/docs/conf.py b/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 ---------------------------------------------------
 

diff --git a/docs/index.md b/docs/index.md
@@ -13,4 +13,4 @@ markdowns/CHANGELOG.md
 markdowns/CONTRIBUTING.md
 markdowns/CONDUCT.md
 autoapi/index
-```
+```