Style and format codebase (#131)

* 🎨 format markdowns

* 🎨 docstrings to 90 characters and remove whitespaces

* 🔧 set line length to 90 characters

* 🎨 split comments, add comments, remove more whitespace, add more docstrings

* 🎨 write strings on two line and let Python concatenate theses

* 🎨 snake_case

* 🎨 raise ValueError if unknown type is provided

alternatively we could use a meaningful default

* 🎨 specify encoding explicitly

* 🎨 use textwrap to keep indentation

* 🐛 with textwrap the text cannot contain new line statements

* 🎨 adjust comments and docstrings to line-length

* 🔧 add jupytext configuration for notebooks to project

* ✅ update example report files so test pass (reviewed changes are only style of .py files)

* 🎨 continue reformatting of streamlit_report.py

* 🎨 remove one level of indentation

* 🎨 docstring and f-string formatting

- leave out most multiline string for now (which need dedenting)
- one whitespace update in tests

* 🎨 encoding and whitespace updates

* 🐛 add missing argument to abc for reports

* 🎨 textwrap code or html blocks

- sometime indent and dedent has to be used
- one typo (altair plot, not plotly plot corrected)
- new line before python code block in qmd files

* 🎨 keep urls at the top

- maybe 'Verschlimmbessern': footer can be hard to read (pdf)
- needed to use escaping of {} using unicode:
  \u007b is { and \u007d is }
- 🐛 jupyter used relative import -> changed to URL link of LOGO
- unify MONA mentioning (pdf)

* 🎨 limit remaining lines to 90 characters

* 🎨 shorten docstrings and comments, implement lazy logging

lazy logging is recommended (only a warning):
https://pylint.readthedocs.io/en/latest/user_guide/messages/warning/logging-fstring-interpolation.html

* 🎨 remove trailing white-space from streamlit footer

* 🚚 add constants file to keep these central

* 🎨 streamlit footer in utils? use central constants for footer, dedent

* 🎨 add initialization of dictionary in body of function

* 🎨 add timeout to get request -> will 60 seconds always be enough?

* 🎨 dedent and slightly modify completion message

* 🎨 line lenght, lazy logging and raising exceptions from exception

* 🎨 module and docstrings, comments splitting and removing unnecessary code

* 🎨 lazy logging + exe_info and Error messaging splitting (line length)

* 🎨 module string, line length, unused arguments,

* 🎨 lazy logging and reporting of error info for error

lazy-logging: https://pylint.readthedocs.io/en/latest/user_guide/messages/warning/logging-not-lazy.html
exc_info: https://docs.python.org/3/library/logging.html#logging.Logger.debug

* 🐛 Handle error for loading static images from a URL in streamlit reports

* 📝 Update md files for the yaml examples on the documentation

* 🐛 Fix desciption from the EMP config example

* 🐛 Fix code to load images from URLs in streamlit reports

* Trigger GitHub actions to avoid connection error to download tinytex

* 🎨🔧 let ruff check for line lenght and other potential bugs, add vscode config

update config:
- fixed line length to 88 as default
- ensure line lenght is checked in tests

* 🐛 Ollama chatbot example

- dedent should be called only once
- each block needs to be on the level of where it is supposed to be used (in the multiline f-string)

* 🐛 use existing config file, not the local one generated by chabot notebook

---------

Co-authored-by: sayalaruano <[email protected]>

Author: enryH

.github/workflows/cdci.yml

@@ -118,6 +118,14 @@ jobs:
             echo "Error: One or more protected files have been modified."
             exit 1
           fi
+      - name: check streamlit report files for chatbot API
+        run: |
+          vuegen -c docs/example_config_files/Chatbot_example_config.yaml -output_dir tests/report_examples/chat_bot
+          if git diff tests/report_examples | grep .; then
+            echo Failed for report: $format
+            echo "Error: One or more protected files have been modified."
+            exit 1
+          fi
       - name: check for changes in report files
         run: |
           # write streamlit report to test folder 

.gitignore

@@ -116,7 +116,7 @@ cython_debug/
 # Temporary files
 logs/
 vuegen/logs/
-./streamlit_report/
+streamlit_report/
 !tests/report_examples
 quarto_report/
 output_docker/

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+  "editor.rulers": [88, 100, 120]
+}

docs/README.md

@@ -1,10 +1,10 @@
 # Docs creation
 
-In order to build the docs you need to 
+In order to build the docs you need to
 
-  1. Install sphinx and additional support packages
-  2. Build the package reference files
-  3. Run sphinx to create a local html version
+1. Install sphinx and additional support packages
+2. Build the package reference files
+3. Run sphinx to create a local html version
 
 The documentation is build using readthedocs automatically.
 
@@ -18,12 +18,13 @@ poetry install --with docs
 
 ## Build docs using Sphinx command line tools
 
-Command to be run from `path/to/docs`, i.e. from within the `docs` package folder: 
+Command to be run from `path/to/docs`, i.e. from within the `docs` package folder:
 
 Options:
-  - `--separate` to build separate pages for each (sub-)module
 
-```bash	
+- `--separate` to build separate pages for each (sub-)module
+
+```bash
 # pwd: docs
 # apidoc
 sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuegen
@@ -38,4 +39,3 @@ The README is included in the `Overview` section of the docs. We created a [Pyth
 Relative links are used in the main README, which need to be resolved when building. It's
 possible to include the a `relative-docs` option if one uses `index.md` ([see docs](https://myst-parser.readthedocs.io/en/latest/faq/index.html#include-a-file-from-outside-the-docs-folder-like-readme-md)). This does not work
 with `href` links, only native markdown links.
-

docs/example_config_files/Chatbot_example_config.yaml

@@ -1,7 +1,7 @@
 report:
   title: Chatbot example
   description: >
-    A chatbot exaple.
+    A chatbot example.
 sections:
   - title: ChatBot test
     subsections:

docs/example_config_files/Earth_microbiome_vuegen_demo_notebook_config.yaml

@@ -1,16 +1,16 @@
 report:
   title: Earth Microbiome Vuegen Demo Notebook
-  description: "The Earth Microbiome Project (EMP) is a systematic attempt to characterize\
-    \ global microbial taxonomic and functional diversity for the benefit of the planet\
-    \ and humankind. \n  It aimed to sample the Earth\u2019s microbial communities\
-    \ at an unprecedented scale in order to advance our understanding of the organizing\
-    \ biogeographic principles that govern microbial community structure. \n  The\
-    \ EMP dataset is generated from samples that individual researchers have compiled\
-    \ and contributed to the EMP. \n  The result is both a reference database giving\
-    \ global context to DNA sequence data and a framework for incorporating data from\
-    \ future studies, fostering increasingly complete characterization of Earth\u2019\
-    s microbial diversity.\n  \n  You can find more information about the Earth Microbiome\
-    \ Project at https://earthmicrobiome.org/ and in the [original article](https://www.nature.com/articles/nature24621).\n"
+  description: >
+    The Earth Microbiome Project (EMP) is a systematic attempt to characterize global
+    microbial taxonomic and functional diversity for the benefit of the planet and humankind.
+    It aimed to sample the Earth’s microbial communities at an unprecedented scale in order to
+    advance our understanding of the organizing biogeographic principles that govern microbial
+    community structure. The EMP dataset is generated from samples that individual researchers
+    have compiled and contributed to the EMP. The result is both a reference database giving
+    global context to DNA sequence data and a framework for incorporating data from future
+    studies, fostering increasingly complete characterization of Earth’s microbial diversity.
+    You can find more information about the Earth Microbiome Project at https://earthmicrobiome.org/
+    and in the original article at https://www.nature.com/articles/nature24621.
   graphical_abstract: https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg
   logo: https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg
 sections:

docs/vuegen_basic_case_study_configfile.md

@@ -1,13 +1,13 @@
 # Predefined Directory Case Study - Configuration File
 
-The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml) of the basic case study using a predefined directory is presented below: 
+The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Basic_example_vuegen_demo_notebook_config.yaml) of the basic case study using a predefined directory is presented below:
 
 ```yaml
 report:
   title: Basic Example Vuegen Demo Notebook
   description: A general description of the report.
-  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
-  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg
+  graphical_abstract: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
+  logo: https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png
 sections:
 - title: Plots
   description: This section contains example plots.

docs/vuegen_earth_microbiome_case_study_configfile.md

@@ -5,17 +5,17 @@ The [configuration file](https://github.com/Multiomics-Analytics-Group/vuegen/bl
 ```yaml
 report:
   title: Earth Microbiome Vuegen Demo Notebook
-  description: "The Earth Microbiome Project (EMP) is a systematic attempt to characterize\
-    \ global microbial taxonomic and functional diversity for the benefit of the planet\
-    \ and humankind. \n  It aimed to sample the Earth\u2019s microbial communities\
-    \ at an unprecedented scale in order to advance our understanding of the organizing\
-    \ biogeographic principles that govern microbial community structure. \n  The\
-    \ EMP dataset is generated from samples that individual researchers have compiled\
-    \ and contributed to the EMP. \n  The result is both a reference database giving\
-    \ global context to DNA sequence data and a framework for incorporating data from\
-    \ future studies, fostering increasingly complete characterization of Earth\u2019\
-    s microbial diversity.\n  \n  You can find more information about the Earth Microbiome\
-    \ Project at https://earthmicrobiome.org/ and in the [original article](https://www.nature.com/articles/nature24621).\n"
+  description: >
+    The Earth Microbiome Project (EMP) is a systematic attempt to characterize global
+    microbial taxonomic and functional diversity for the benefit of the planet and humankind.
+    It aimed to sample the Earth’s microbial communities at an unprecedented scale in order to
+    advance our understanding of the organizing biogeographic principles that govern microbial
+    community structure. The EMP dataset is generated from samples that individual researchers
+    have compiled and contributed to the EMP. The result is both a reference database giving
+    global context to DNA sequence data and a framework for incorporating data from future
+    studies, fostering increasingly complete characterization of Earth’s microbial diversity.
+    You can find more information about the Earth Microbiome Project at https://earthmicrobiome.org/
+    and in the original article at https://www.nature.com/articles/nature24621.
   graphical_abstract: https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg
   logo: https://raw.githubusercontent.com/ElDeveloper/cogs220/master/emp-logo.svg
 sections:
@@ -128,8 +128,7 @@ sections:
       component_type: PLOT
       plot_type: STATIC
   - title: Shanon entropy analysis
-    description: This subsection contains the Shannon entropy analysis of the EMP
-    dataset.
+    description: This subsection contains the Shannon entropy analysis of the EMP dataset.
     components:
     - title: Specificity of sequences and higher taxonomic groups for environment
       file_path: https://raw.githubusercontent.com/biocore/emp/master/methods/images/figure4_entropy.png

pyproject.toml

@@ -74,3 +74,20 @@ vuegen = "vuegen.__main__:main"
 
 [tool.isort]
 profile = "black"
+
+[tool.jupytext]
+formats = "ipynb,py:percent"
+
+[tool.ruff]
+# Allow lines to be as long as:
+line-length = 88
+
+[tool.ruff.lint]
+# https://docs.astral.sh/ruff/tutorial/#rule-selection
+# 1. Enable flake8-bugbear (`B`) rules
+# 2. Enable pycodestyle (`E`) errors and (`W`) warnings
+# 3. Pyflakes (`F`) errors
+extend-select = ["E", "W", 'F', 'B']
+
+[tool.black]
+line-length = 88

setup.cfg

@@ -0,0 +1,4 @@
+[flake8]
+exclude = docs
+max-line-length = 88
+aggressive = 2