Merge pull request #77 from anvilproject/develop

Add snyk updates to main

.github/dependabot.yml

@@ -8,4 +8,10 @@ updates:
   - package-ecosystem: "pip" # See documentation for possible values
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "daily"
+    target-branch: "develop"
+    groups:
+      dependabot:
+        patterns:
+          - "*"
+

.github/workflows/build.yml

@@ -194,7 +194,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4.1.7
 
       - name: Create checksums
         shell: bash

README.md

@@ -186,7 +186,7 @@ The below command is a basic example of how to structure a download command with
 - a **download directory** called `DATA` as the destination
 
 ```sh
-$ drs_downloader terra -m tests/fixtures/manifest/terra-data.tsv -d DATA
+$ drs_downloader terra -m tests/fixtures/manifests/terra-data.tsv -d DATA
 100%|████████████████████████████████| 10/10 [00:00<00:00, 56148.65it/s]
 
 2022-11-21 16:56:49,595 ('HG03873.final.cram.crai', 'OK', 1351946, 1)

requirements-dev.txt

@@ -1,5 +1,5 @@
-mkdocs==1.5.2
-pytest==7.4.0
+mkdocs==1.6.1
+pytest==8.3.3
 flake8
 pyinstaller @ git+https://github.com/ohsu-comp-bio/pyinstaller.git@feature/startup-message
 pytest-cov
@@ -8,4 +8,8 @@ mkdocs-literate-nav
 mkdocs-gen-files
 mkdocs-material
 mkdocstrings[python]
-pre_commit
+pre_commit
+requests>=2.32.2 # not directly required, pinned by Snyk to avoid a vulnerability
+urllib3>=2.2.2 # not directly required, pinned by Snyk to avoid a vulnerability
+jinja2>=3.1.3 # not directly required, pinned by Snyk to avoid a vulnerability
+setuptools>=65.5.1 # not directly required, pinned by Snyk to avoid a vulnerability

requirements.txt

@@ -1,6 +1,12 @@
-click==8.1.6
-aiohttp >=3.8.5 
+
+click>=8.1.7
+aiohttp>=3.10.5 
 tqdm
 aiofiles
 requests
 google-cloud-storage
+urllib3>=2.2.2 # not directly required, pinned by Snyk to avoid a vulnerability
+aiohttp>=3.9.4 # not directly required, pinned by Snyk to avoid a vulnerability
+idna>=3.7 # not directly required, pinned by Snyk to avoid a vulnerability
+requests>=2.32.2 # not directly required, pinned by Snyk to avoid a vulnerability
+tqdm>=4.66.3 # not directly required, pinned by Snyk to avoid a vulnerability