Merge pull request #84 from jjjermiah/49-feature-getupdatedseries

49 feature getupdatedseries

.github/workflows/main.yml

@@ -32,12 +32,10 @@ jobs:
 
       - name: Test with pytest
         run: |
-          poetry run pytest -n 2 --cov --cov-report xml:coverage-report/coverage.xml
+          # Github action runners now have 4 cores
+          poetry run pytest -n 4 --cov --cov-report xml:coverage-report/coverage.xml
 
-      - name: Build documentation
-        run: poetry run make html --directory docs/
-
-      - name: Upload coverage report
+      - name: Upload coverage report artifact to be used by Codecov
         uses: actions/upload-artifact@v2
         with:
           name: coverage-report
@@ -65,6 +63,29 @@ jobs:
           verbose: true
           name: codecov-umbrella
 
+  Build-Documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+
+      - name: Install poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Build documentation
+        run: |
+          poetry run make html --directory docs/
+
+
+
 
 
   Continuous-Deployment:
@@ -74,10 +95,10 @@ jobs:
         issues: write
         pull-requests: write
 
-    # needs: Continuous-Integration
+    needs: [Continuous-Integration, Build-Documentation]
 
     # if pulling to main, deploy to PyPI
-    # if: github.ref == 'refs/heads/main'
+    if: github.ref == 'refs/heads/main'
 
     # Set up operating system
     runs-on: ubuntu-latest
@@ -100,11 +121,6 @@ jobs:
     - name: Install package
       run: poetry install
 
-
-    # Existing jobs...
-
-
-
    # This action uses Python Semantic Release v8
    # What this action does:
    # - Determines the next version number based on the commit history
@@ -116,7 +132,6 @@ jobs:
       uses: python-semantic-release/python-semantic-release@master
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        git_commit_message: 'chore(release): release ${next_version}'
 
     - name: Install packaging-related tool
       run:
@@ -142,10 +157,6 @@ jobs:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
 
-    - name: Print latest tag name
-      run: |
-        printf "%s\n" "${LATEST_TAG}"
-
     - name: Print branch name
       run: |
         printf "LATEST TAG: %s\n" "${LATEST_TAG}"
@@ -321,7 +332,7 @@ jobs:
               git add .
 
               # Commit with a timestamp
-              git commit -m "Update README with latest version: $LATEST_TAG"
+              git commit -m "chore: Update README: $LATEST_TAG"
 
               # Push changes to the remote repository
               # if github.head_ref is not null

.gitignore

@@ -148,4 +148,5 @@ driver.py
 data/*
 sandbox
 
-docs/data/*
+docs/data/*
+docs/autoapi

Dockerfile

@@ -6,14 +6,20 @@
 # docker build -t nbiatoolkit .
 #
 # ADD LABELS HERE
+
 FROM python:3.12-slim
 
-LABEL maintainer="Jermiah Joseph"
+LABEL maintainer="Jermiah Joseph jermiahjoseph98@gmail.com"
+LABEL description="This is a Dockerfile for the nbiatoolkit package."
+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
 
-RUN python -c 'import nbiatoolkit; print(nbiatoolkit.version())'
+RUN NBIAToolkit --help
 
 # On run, open a bash shell
 CMD ["/bin/bash"]

docs/Tutorial.ipynb

@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +44,7 @@
     {
      "data": {
       "text/plain": [
-       "'0.18.1'"
+       "'0.22.1'"
       ]
      },
      "execution_count": 2,
@@ -668,6 +668,53 @@
     "pprint(seriesbyPatientJSON[0])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### get New Series after a given date\n",
+    "\n",
+    "``` python\n",
+    "getNewSeries(\n",
+    "        Date: Union[str, datetime],  # (required) accepted formats:\n",
+    "                                      # \"%Y-%m-%d\", \"%Y/%m/%d\", \"%Y%m%d\", \n",
+    "                                      # \"%m/%d/%Y\", \"%d/%m/%Y\", \"%d-%m-%Y\"\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "01/01/2024\n",
+      "Total new series after 2024-01-01: 4751\n",
+      "{'BodyPartExamined': 'BREAST',\n",
+      " 'Collection': 'Advanced-MRI-Breast-Lesions',\n",
+      " 'ImageCount': 580,\n",
+      " 'Manufacturer': 'GE MEDICAL SYSTEMS',\n",
+      " 'ManufacturerModelName': 'Signa HDxt',\n",
+      " 'Modality': 'MR',\n",
+      " 'PatientID': 'AMBL-376',\n",
+      " 'SeriesDate': '2005-04-14 00:00:00.0',\n",
+      " 'SeriesDescription': 'AX Sen Vibrant MultiPhase',\n",
+      " 'SeriesInstanceUID': '1.3.6.1.4.1.14519.5.2.1.196168555404542578475976858220037429361',\n",
+      " 'SeriesNumber': 5,\n",
+      " 'SoftwareVersions': '24',\n",
+      " 'StudyInstanceUID': '1.3.6.1.4.1.14519.5.2.1.201692485188138093977458202425301357349'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "newSeries = client.getNewSeries(Date=\"2024/01/01\")\n",
+    "print(f\"Total new series after 2024-01-01: {len(newSeries)}\")\n",
+    "pprint(newSeries[0])"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},