Demonstrate image download process and prepare for full image downloa…

…d for JUMP plate BR00117006 (#36)

* gather image columns for quality control analysis

* include a jupyter environment and init cosmicqc nb

* linting

* add image downloading capabilities

* move to download section

* linting

* remove new section justfile work

* linting

* avoid downloading images already downloaded

.gitignore

@@ -1,5 +1,4 @@
 # Ignore adding specific files from Vim-jukit
-*.py
 !0.download_data/*.py
 !/**/nbconverted/*.py
 **/.jukit/
@@ -16,3 +15,10 @@ __pycache__/
 
 # Ignore data folder in UMAP analysis (>5GB)
 3.analyze_data/UMAP_analysis/data
+
+# data ignores
+*.sqlite.*
+*.sqlite
+*.parquet
+*.tiff
+*.png

.pre-commit-config.yaml

@@ -4,15 +4,15 @@ default_language_version:
   python: python3.11
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
       - id: detect-private-key
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "2.2.4"
+    rev: "2.4.3"
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/codespell-project/codespell
@@ -26,7 +26,7 @@ repos:
               .*\.cppipe
           )$
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.18
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -36,11 +36,18 @@ repos:
     hooks:
       - id: yamllint
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.8"
+    rev: "v0.7.1"
     hooks:
-      - id: ruff-format
       - id: ruff
   - repo: https://github.com/koalaman/shellcheck-precommit
     rev: v0.10.0
     hooks:
       - id: shellcheck
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort