Merge remote-tracking branch 'origin' into docs

jjjermiah · Feb 12, 2024 · c8ffa76 · c8ffa76
2 parents 734cf19 + f9ab11e
commit c8ffa76
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diff --git a/.gitignore b/.gitignore
@@ -151,3 +151,6 @@ sandbox
 docs/data/*
 docs/autoapi
 src/nbiatoolkit/.DS_Store
+
+NBIA-Download
+src/nbiatoolkit/.DS_Store
diff --git a/README.md b/README.md
@@ -20,7 +20,11 @@
 ## Features
 > [!TIP]
 > For a thorough description of the package and its available features, please refer to the Documentation at [NBIA-Toolkit Read The Docs](https://nbia-toolkit.readthedocs.io/en/latest/)
-- Use NBIA Guest account to access public data OR authenticate using OAuth with user credentials for limited access data (requires approved data access).
+
+- ***Programmatic access*** to the National Biomedical Imaging Archive (NBIA) and The Cancer Imaging Archive (TCIA) databases
+  - Use NBIA Guest account to access public data OR authenticate using OAuth with user credentials for limited access data (requires approved data access).
+  - Custom `OAuth2` class for **NBIA**, **TCIA**, including special handling for dedicated server for the **NLST** collection.
+
 - ***Query NBIA database*** for metadata on ***collections***, ***patients***, ***studies***, ***series***, and ***images***
 - Download images from NBIA
   - ***Validate doownloads with MD5 checksums*** for downloaded images
@@ -51,7 +55,7 @@ For quick access to the NBIA, the toolkit also provides a command line interface
 /_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/  
 
 
-Version: 0.25.4
+Version: 0.28.0
 
 Available CLI tools: 
 

diff --git a/docs/markdowns/CHANGELOG.md b/docs/markdowns/CHANGELOG.md
@@ -2,10 +2,73 @@
 
 
 
+## v0.28.0 (2024-02-05)
+
+### Chore
+
+* chore: Update README: 0.27.0 ([`79f7eda`](https://github.com/jjjermiah/nbia-toolkit/commit/79f7edafff8bf0ada9f0ea14909c9fe45f628a69))
+
+### Feature
+
+* feat: Implement logout functionality and add context manager support ([`67968fc`](https://github.com/jjjermiah/nbia-toolkit/commit/67968fc0c061b75a1966112abd6a823fac737191))
+
+### Unknown
+
+* Merge pull request #99 from jjjermiah/19-authpy-logout-functionality
+
+feat: Implement logout functionality and add context manager support ([`528d1a7`](https://github.com/jjjermiah/nbia-toolkit/commit/528d1a79f06f2cd3ae6cb78cbd16438eb165dba5))
+
+
+## v0.27.0 (2024-02-05)
+
+### Chore
+
+* chore(sem-ver): 0.27.0 ([`dfd1fa7`](https://github.com/jjjermiah/nbia-toolkit/commit/dfd1fa74938c49a298a4493da88134bbe6531187))
+
+* chore: Update README: 0.26.0 ([`d063000`](https://github.com/jjjermiah/nbia-toolkit/commit/d063000515e7dae39a48a03a51f29029d54084c6))
+
+### Feature
+
+* feat: Add encryption and decryption functions for credentials ([`bbbd1d2`](https://github.com/jjjermiah/nbia-toolkit/commit/bbbd1d2503bd80cd0b80a933651a5a507b2dd95b))
+
+### Unknown
+
+* Merge pull request #98 from jjjermiah/20-authpy-username-and-password-encryption
+
+feat: Add encryption and decryption functions for credentials ([`e08caa0`](https://github.com/jjjermiah/nbia-toolkit/commit/e08caa00c33d0fc8086155f9a9168258b245b9cc))
+
+
+## v0.26.0 (2024-02-05)
+
+### Chore
+
+* chore(sem-ver): 0.26.0 ([`e60590e`](https://github.com/jjjermiah/nbia-toolkit/commit/e60590e296f111c1bfec8e0b63e9f54e6099d8b8))
+
+* chore: Update README: 0.25.4 ([`289f846`](https://github.com/jjjermiah/nbia-toolkit/commit/289f846f8a6073a39bfc000cc3d7dbd35cf077c4))
+
+### Documentation
+
+* docs: Add programmatic access to NBIA and TCIA databases ([`82542b1`](https://github.com/jjjermiah/nbia-toolkit/commit/82542b12e5d23ff7b3b40f10e0f97fb2082dc861))
+
+### Feature
+
+* feat: implement better Oauth algorithm graph and refresh token ([`3d81d2b`](https://github.com/jjjermiah/nbia-toolkit/commit/3d81d2bdeff970ea725727be95defa989c77f6b1))
+
+### Unknown
+
+* Merge pull request #97 from jjjermiah/18-authpy-accessrefresh-token-+-error-handling
+
+18 authpy accessrefresh token + error handling ([`c2fcdb2`](https://github.com/jjjermiah/nbia-toolkit/commit/c2fcdb2023978f7ed03522bfddb24963ee364b7c))
+
+* Fix error handling in OAuth2 class ([`67140b7`](https://github.com/jjjermiah/nbia-toolkit/commit/67140b7e1e315f5a7d62d0a8c10956c00e657e93))
+
+
 ## v0.25.4 (2024-02-04)
 
 ### Chore
 
+* chore(sem-ver): 0.25.4 ([`edd1104`](https://github.com/jjjermiah/nbia-toolkit/commit/edd1104b9583a337d08ec98739be0a2633ce4857))
+
 * chore: Update README: 0.25.3 ([`7e6803d`](https://github.com/jjjermiah/nbia-toolkit/commit/7e6803d4a696aa1d2faab89e1cf97ad948f82d09))
 
 ### Documentation

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "nbiatoolkit"
-version = "0.25.4"
+version = "0.28.0"
 description = "A python package to query the National Biomedical Imaging Archive (NBIA) database."
 authors = ["Jermiah Joseph"]
 license = "MIT"
@@ -25,6 +25,7 @@ pydicom = "^2.4.3"
 tqdm = "^4.66.1"
 pyfiglet = "^1.0"
 beautifulsoup4 = "^4.12.3"
+cryptography = "^42.0.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"

diff --git a/setup.py b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup
 
-__version__ = "0.25.4"
+__version__ = "0.28.0"
 
 setup(
     name="nbiatoolkit",

diff --git a/src/nbiatoolkit/__init__.py b/src/nbiatoolkit/__init__.py
@@ -15,4 +15,11 @@
 from .utils.nbia_endpoints import NBIA_ENDPOINTS
 
 # define the __all__ variable
-__all__ = ["NBIAClient", "OAuth2", "setup_logger", "NBIA_ENDPOINTS", "version", "__version__"]
+__all__ = [
+    "NBIAClient",
+    "OAuth2",
+    "setup_logger",
+    "NBIA_ENDPOINTS",
+    "version",
+    "__version__",
+]