Merge pull request #64 from jjjermiah/typing-dicomsort

Typing dicomsort
jjjermiah · Jan 29, 2024 · 3f1218b · 3f1218b
2 parents 101e1be + 0007ca0
commit 3f1218b
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.12"]
+        python-version: ["3.12", "3.11"]
 
     steps:
       - uses: actions/checkout@v3
@@ -108,6 +108,7 @@ 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:
@@ -194,13 +195,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Test Image With new Tag
         run: |
+          # get latest tag
+          LATEST_TAG=$(curl -s \
+            "https://api.github.com/repos/${{ github.repository }}/releases/latest" \
+            | jq -r .tag_name | sed 's/^v//')
+          echo "LATEST_TAG=${LATEST_TAG}"
+
+          # test image with latest tag
           docker run --rm \
-            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} \
-            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${LATEST_TAG} \
+            NBIAToolkit
+
 
   test_image_with_latest_tag:
     needs: Continuous-Deployment
@@ -213,4 +222,4 @@ jobs:
         run: |
           docker run --rm \
             ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
-            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
+            NBIAToolkit
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,123 @@
 
 
 
+## v0.12.1 (2024-01-28)
+
+### Documentation
+
+* docs: add total downloads ([`6ed7cde`](https://github.com/jjjermiah/nbia-toolkit/commit/6ed7cdec9bf0f61588c16545f71d87e7f9df0756))
+
+### Unknown
+
+* Merge branch &#39;main&#39; of https://github.com/jjjermiah/NBIA-toolkit ([`bad151e`](https://github.com/jjjermiah/nbia-toolkit/commit/bad151e81b5cfbcda2b792de4a7b0d9f311c4921))
+
+
+## v0.12.0 (2024-01-28)
+
+### Build
+
+* build: add 3.11 ([`73fa198`](https://github.com/jjjermiah/nbia-toolkit/commit/73fa1988e605d498d08b091b78885b689eb6d0d4))
+
+### Feature
+
+* feat: Update Python versions to accept 3.11 ([`34137fd`](https://github.com/jjjermiah/nbia-toolkit/commit/34137fdc29ede3c23209af1d806bb1b6c101935d))
+
+
+## v0.11.2 (2024-01-28)
+
+### Fix
+
+* fix: build ([`4408840`](https://github.com/jjjermiah/nbia-toolkit/commit/4408840e267d3a9ce2e7dacbcb2c3e0f40342948))
+
+### Test
+
+* test: build ([`657c44c`](https://github.com/jjjermiah/nbia-toolkit/commit/657c44c7ff66fadf9a5ef418ff1b8c5cbf385b5f))
+
+* test: build ([`20c8595`](https://github.com/jjjermiah/nbia-toolkit/commit/20c8595bbeb0ceb81dea8dd7497d2a00311028d9))
+
+* test: build ([`248d7c3`](https://github.com/jjjermiah/nbia-toolkit/commit/248d7c3574070fa057ec74c335fe532d5fb515fd))
+
+### Unknown
+
+* fix:build ([`7ef92dc`](https://github.com/jjjermiah/nbia-toolkit/commit/7ef92dcb42b2204e5261575f4514c772c827840d))
+
+* fix:build ([`7fec918`](https://github.com/jjjermiah/nbia-toolkit/commit/7fec9187fe1c98118551e471abe326d592825528))
+
+* test:build ([`01e82b1`](https://github.com/jjjermiah/nbia-toolkit/commit/01e82b116dd99cb3c39f744648392d8903bb78af))
+
+* Merge branch &#39;main&#39; of https://github.com/jjjermiah/NBIA-toolkit ([`951f89c`](https://github.com/jjjermiah/nbia-toolkit/commit/951f89c3230573a7753b517ab047b1fbb5b0f917))
+
+
+## v0.11.1 (2024-01-28)
+
+### Build
+
+* build: fix env latest tag error ([`1989d7b`](https://github.com/jjjermiah/nbia-toolkit/commit/1989d7bca9c71dfff8a8183105f93f29aca5693f))
+
+
+## v0.11.0 (2024-01-28)
+
+### Build
+
+* build(GHA): fix issue with test_image needs ([`1bdd456`](https://github.com/jjjermiah/nbia-toolkit/commit/1bdd456435122307384c30563a4d2e13e4c29ba6))
+
+* build(GHA): fix issue with test_image needs ([`023ac12`](https://github.com/jjjermiah/nbia-toolkit/commit/023ac126623806f7e250138914df886f84e65aa3))
+
+### Documentation
+
+* docs: &#34;fix badges&#34; ([`d10dff2`](https://github.com/jjjermiah/nbia-toolkit/commit/d10dff2703392851a74bb7f6e70678cb6f309c4a))
+
+* docs: add milestone to readme ([`7b8c3d5`](https://github.com/jjjermiah/nbia-toolkit/commit/7b8c3d55605bd72edaeef4d6fe79f28a5a8768ce))
+
+* docs: add milestone to readme ([`3dc3eae`](https://github.com/jjjermiah/nbia-toolkit/commit/3dc3eaed0200a120d62d2cc6db4792fd48423020))
+
+* docs: test adding hide-output ([`037d737`](https://github.com/jjjermiah/nbia-toolkit/commit/037d7372a68e36a8579f5992da67a3b1fb9b4beb))
+
+* docs: test adding hide-output ([`cb82e5a`](https://github.com/jjjermiah/nbia-toolkit/commit/cb82e5a38da5569bb03de38d828d9fdd06f10aaf))
+
+### Feature
+
+* feat: add getModalityValues and refactor getPatients for getPatientsByCollection ([`d8d2062`](https://github.com/jjjermiah/nbia-toolkit/commit/d8d2062cd70acd5231d6e4a478eadeb95bfeb147))
+
+### Fix
+
+* fix: add better type checks to fix #22 ([`f8aaa61`](https://github.com/jjjermiah/nbia-toolkit/commit/f8aaa61941ae3cf495aad9ee4c960b26ed46ef44))
+
+* fix(logger): parameter type error ([`1d9fd26`](https://github.com/jjjermiah/nbia-toolkit/commit/1d9fd26aed5160d1062c3bba05da2f9956bfe840))
+
+### Test
+
+* test(nbia): fix downloadSeries patientId error that propagates from getPatient funciton update ([`101e1be`](https://github.com/jjjermiah/nbia-toolkit/commit/101e1be2808c2409e25daf3f7e6d9d359ea599ba))
+
+### Unknown
+
+* Merge pull request #60 from jjjermiah/development
+
+Development ([`2b2808c`](https://github.com/jjjermiah/nbia-toolkit/commit/2b2808c202d3e2a1422196002d75d1e65992f72d))
+
+* Merge pull request #59 from jjjermiah/47-feature-refactor-getpatients-and-add-getpatient
+
+47 feature refactor getpatients and add getpatient ([`4898f86`](https://github.com/jjjermiah/nbia-toolkit/commit/4898f862b32539227192dd89dd33a092e92a6a96))
+
+* Refactor: generateFilePathFromDICOMAttributes method ([`d1a437e`](https://github.com/jjjermiah/nbia-toolkit/commit/d1a437e6026b2a6523a4a6182de30e08a58eb427))
+
+* Merge remote-tracking branch &#39;origin/main&#39; into 46-feature-refactor-getpatients-and-add-getpatient ([`518ffe3`](https://github.com/jjjermiah/nbia-toolkit/commit/518ffe328fc12a948b3555b6812bf907b6b9b05d))
+
+* Merge pull request #58 from jjjermiah/example_notebook
+
+Example notebook ([`4eb377f`](https://github.com/jjjermiah/nbia-toolkit/commit/4eb377fdbaf81c69385ac7fc27ba6dbc611e1e49))
+
+* Merge branch &#39;development&#39; into example_notebook ([`68ddb13`](https://github.com/jjjermiah/nbia-toolkit/commit/68ddb13f861070ad27082493e18e7b8d288d9fc0))
+
+* Update README.md ([`be0f3e3`](https://github.com/jjjermiah/nbia-toolkit/commit/be0f3e3aa6f0ecc27d92df69c92555067dc85af5))
+
+* Merge pull request #57 from jjjermiah/example_notebook
+
+documentation for notebook and readme ([`f477c4a`](https://github.com/jjjermiah/nbia-toolkit/commit/f477c4a48f55ee59c59410487c5434bad81d44f9))
+
+* Merge remote-tracking branch &#39;origin/development&#39; into example_notebook ([`9ef2623`](https://github.com/jjjermiah/nbia-toolkit/commit/9ef262315fde123ce1d51bef62d8536c6e8fc35e))
+
+
 ## v0.10.9 (2024-01-28)
 
 ### Build
@@ -127,6 +244,8 @@ Merge remote-tracking branch &#39;origin/development&#39; into organize_project_
 
 ### Documentation
 
+* docs: Add Example.ipynb to docs folder ([`0a41b96`](https://github.com/jjjermiah/nbia-toolkit/commit/0a41b960897fbd48da82b19dca5ab3ed062f2395))
+
 * docs: Add GitHub repo size badge ([`3b1ab49`](https://github.com/jjjermiah/nbia-toolkit/commit/3b1ab49bc9d0aa7c8fd1e9633c52c5ab9d07b368))
 
 * docs: Update contributing.md, badges, and pyproject.toml ([`15cba32`](https://github.com/jjjermiah/nbia-toolkit/commit/15cba32fc17061441f6a7f7f57b6908a6784b7a8))

diff --git a/Dockerfile b/Dockerfile
@@ -13,7 +13,7 @@ LABEL maintainer="Jermiah Joseph"
 # install the dependencies
 RUN python -m pip install nbiatoolkit
 
-RUN python -c 'import nbiatoolkit; print(nbiatoolkit.__version__)'
+RUN python -c 'import nbiatoolkit; print(nbiatoolkit.version())'
 
 # On run, open a bash shell
 CMD ["/bin/bash"]

diff --git a/README.md b/README.md
@@ -1,16 +1,19 @@
 
-![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)
-
 [![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)
 [![Python version](https://img.shields.io/pypi/pyversions/nbiatoolkit.svg)](https://img.shields.io/pypi/pyversions/nbiatoolkit.svg)
 [![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/)
 ![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)
 
 
+
+![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)
+
+
 # *NBIA Toolkit*
 `nbiatoolkit` is a python package that provides programmatic access to query and download images from the National Biomedical Imaging Archive (**NBIA**) and The Cancer Imaging Archive (**TCIA**) databases.
 
@@ -28,7 +31,7 @@ See Documentation at [NBIA-Toolkit Read The Docs](https://nbia-toolkit.readthedo
 
 `nbiatoolkit` is currently under development.
 It is made available via PyPI and can be installed using pip:
-
+****
 ```bash
 pip install nbiatoolkit
 ```

diff --git a/docs/Tutorial.ipynb b/docs/Tutorial.ipynb
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,23 +68,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'0.10.9'"
+       "'NBIAToolkit version: 0.12.1'"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "# import nbiatoolkit \n",
-    "nbiatoolkit.__version__"
+    "nbiatoolkit.version()"
    ]
   },
   {