Enable cropped image-based output for .tiff files with SCDataFrame (

#44)

* Create qcdataframe.py

* linting

* add qcdataframe

* linting

* adding tests

* linting

* update name, tests

* add back compat for self type

* back compat for isinstance

* linting

* add cli for cosmicqc

* linting

* add tests and wrappers

* linting and test adjustment

* attempting wrapper

* patch python-fire; fix tests

* add docstring to top of test

* add csv.gz compatibility

* add export capabilities

* rename file to correct module name

* add export capabilities

* add output capabilities

* Apply suggestions from code review

Co-authored-by: Gregory Way <gregory.way@gmail.com>

* update tests and docs

* fix tests

* update tests; add constructor path for scdataframe

* linting

* modify tests

* enable pd.series compatibility

* update for exports via cli

* add plotly

* add show reports capabilities; adjust tests

* linting

* add html template

* update docs

* allow flexibility for color palette

* linting

* add report path for cli

* add new test data location

* use local str for test

* linting

* remove jupyterlab dep

* add example nf1 data

* add sqlalchemy for dev deps

* initial work towards data and processing

* update test data formatting

* context driven filepaths with notebook

* progress towards cropped image display

* extend scdataframe with pandas dataframe

* enhance scdataframe; fix tests; add test data

* linting

* update module name

* resolving merge

* readd dep comment

* add further docs

* update lockfile

* update deps for scikit-image

* update scikit image dep

* add citation for data

* correct citation

* update the notebook with examples

* Update docs/examples/cosmicqc_in_a_nutshell.py

Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

---------

Co-authored-by: Gregory Way <gregory.way@gmail.com>
Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

.gitignore

@@ -132,3 +132,10 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
+
+# test data ignores
+*.tif
+*.sqlite
+*.parquet
+*.zip
+*.csv

.pre-commit-config.yaml

@@ -22,7 +22,8 @@ repos:
         exclude: |
           (?x)^(
               .*\.lock |
-              .*\.json
+              .*\.json |
+              .*\.ipynb
           )$
   - repo: https://github.com/executablebooks/mdformat
     rev: 0.7.17

CITATION.cff

@@ -44,3 +44,38 @@ references:
       - description: "Github Link with Contributors"
         type: url
         value: "https://github.com/WayScience/CFReT_data/graphs/contributors"
+  - authors:
+      - name: "Way Lab NF1_cellpainting_data Team"
+    date-accessed: "2024-06-28"
+    title: Way Lab NF1_cellpainting_data CytoTable Data
+    type: data
+    repository-code: "https://github.com/WayScience/nf1_cellpainting_data"
+    notes: >-
+      Data from NF1_cellpainting_data project is used to help validate
+      expected results. Data is generated from CellProfiler
+      and CytoTable. We use the following files from the repository:
+      - "Plate_2_nf1_analysis.sqlite"
+      - "Plate_2.parquet"
+    identifiers:
+      - description: "Github Link with Contributors"
+        type: url
+        value: "https://github.com/WayScience/nf1_cellpainting_data/graphs/contributors"
+  - title: >-
+      Plate 2 (Cell Painting images from Plate 2 for NF1_cellpainting_data project)
+    type: data
+    url: https://figshare.com/articles/dataset/Plate_2/22233700
+    notes: >-
+      Image data for related NF1_cellpainting_data parquet sqlite.
+    authors:
+    - family-names: Tomkinson
+      given-names: Jenna
+    - family-names: Mattson-Hoss
+      given-names: Michelle
+    - family-names: Sarnoff
+      given-names: Herb
+    - family-names: Way
+      given-names: Gregory
+    date-published: "2023-04-12"
+    identifiers:
+    - type: doi
+      value: 10.6084/m9.figshare.22233700.v4