Adding Download module (WayScience#5)

* update config file with documentation

* update download module

* added io_utils module

* removed isort due to conflicts

* update and reran download module

* added nbconverted and sh file

* updated poetry deps and gitignore

* added changes

* updated module

.gitignore

@@ -0,0 +1,177 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# remove vscode cache folder
+.vscode
+
+# removed large data files
+*.parquet
+
+# ignore data file
+notebooks/data/

.pre-commit-config.yaml

@@ -1,12 +1,15 @@
+# Pre-commit configuration file
+# Documentation: https://pre-commit.com/
+
 repos:
-  # keep pre-commits update to date
+  # Keep pre-commit itself up to date
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update
     rev: v0.6.0post1
     hooks:
     -   id: pre-commit-update
-        args: [--verbose]
+        args: ["--verbose"]
 
-  # Ruff for Python files
+  # Ruff for linting Python files
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.8.3
     hooks:
@@ -21,38 +24,34 @@ repos:
         name: nbQA-Ruff
         args: ["--fix"]
         additional_dependencies: ["ruff"]
-    -   id: nbqa-isort
-        name: nbQA-Isort
-        args: ["--profile", "black"]
-        additional_dependencies: ["isort"]
 
-  # format toml files
+  # Format and sort TOML files
 -   repo: https://github.com/pappasam/toml-sort
     rev: v0.24.2
     hooks:
     -   id: toml-sort
+        args: ["--in-place"]
 
-  # Sort imports with isort (if separate from Ruff)
+  # Sort imports in Python files (if separate from Ruff)
 -   repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
     -   id: isort
         args: ["--profile", "black"]
 
-  # Pyupgrade for updating Python syntax
+  # Pyupgrade for updating Python syntax to newer versions
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.0
+    rev: v3.19.1
     hooks:
     -   id: pyupgrade
         args: ["--py311-plus"]
 
-  # Check for trailing whitespaces, mixed line endings, etc.
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-    -   id: check-yaml
-    -   id: check-json
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
-    -   id: check-merge-conflict
-    -   id: check-added-large-files
+    -   id: check-yaml        # Validate YAML files
+    -   id: check-json        # Validate JSON files
+    -   id: end-of-file-fixer # Ensure files end with a newline
+    -   id: trailing-whitespace # Remove trailing whitespace
+    -   id: check-merge-conflict # Prevent committing merge conflict markers
+    -   id: check-added-large-files # Warn about large files being added

README.md

@@ -15,7 +15,8 @@ Additionally, we identified morphological features that were critical for the mo
 These findings suggest that specific cellular structures are strong indicators of heart cell health or failure.
 The processing methods and results of this analysis can be accessed [here](https://github.com/WayScience/cellpainting_predicts_cardiac_fibrosis).
 
-Building upon these results, we advanced our study to the next level by leveraging high-content screening (HCS) with CP assay.
+
+Building upon these results, we advanced our study to the next level by leveraging [high-content screening](https://www.sciencedirect.com/science/article/pii/S2472555223000667?via%3Dihub) (HCS) with CP assay.
 Specifically, we applied a library of 550 small-molecule compounds to identify those with the potential to reverse the effects of cardiac fibrosis.
 This approach not only aims to pinpoint candidate compounds for therapeutic intervention but also seeks to understand the biological mechanisms underlying the reversal of fibrosis.