Merge branch 'dev' into 'main'

Dev

See merge request scientific-computing-team/linchemin!44

Author: marcostenta

.gitignore

@@ -1,157 +1,30 @@
-# Created by .ignore support plugin (hsz.mobi)
-### Python template
+# Do not delete items from .gitignore
+#
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-*$py.class
-
-# C extensions
-*.so
 
 # Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
 *.egg-info/
-.installed.cfg
-*.egg
-src/*.egg-info/
-.pytest_cache
-
-# 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/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
+.eggs/
+dist/
 
-# Sphinx documentation
-docs/_build/
+# IDE settings Pycharm/VSCode/Visual Studio
+.idea
+.vscode
+*.sln
 
-# PyBuilder
-target/
+# pytest
+.pytest_cache
 
 # IPython Notebook
 .ipynb_checkpoints
 
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
+# Docs build
+/docs/build/
+/docs/source/reference/generated/*rst
 
-# dotenv
+# managing secrets
+.ini
 .env
-
-# virtualenv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-
-# Rope project settings
-.ropeproject
-### VirtualEnv template
-# Virtualenv
-# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
-.Python
-[Bb]in
-[Ii]nclude
-[Ll]ib
-[Ll]ib64
-[Ll]ocal
-[Ss]cripts
-pyvenv.cfg
-.venv
-pip-selfcheck.json
-### JetBrains template
-# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
-# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
-
-# User-specific stuff:
-.idea/workspace.xml
-.idea/tasks.xml
-.idea/dictionaries
-.idea/vcs.xml
-.idea/jsLibraryMappings.xml
-
-# Sensitive or high-churn files:
-.idea/dataSources.ids
-.idea/dataSources.xml
-.idea/dataSources.local.xml
-.idea/sqlDataSources.xml
-.idea/dynamic.xml
-.idea/uiDesigner.xml
-
-# Gradle:
-.idea/gradle.xml
-.idea/libraries
-
-# Mongo Explorer plugin:
-.idea/mongoSettings.xml
-
-.idea/
-
-## File-based project format:
-*.iws
-
-## Plugin-specific files:
-
-# IntelliJ
-/out/
-
-# mpeltonen/sbt-idea plugin
-.idea_modules/
-
-# JIRA plugin
-atlassian-ide-plugin.xml
-
-# Crashlytics plugin (for Android Studio and IntelliJ)
-com_crashlytics_export_strings.xml
-crashlytics.properties
-crashlytics-build.properties
-fabric.properties
-/linchemin_old/
-
-# Experimental dataset
-experiment/small_dataset

CONTRIBUTING.md

@@ -1,38 +1,79 @@
+# Contributing
 
-# Secret management in development
+## Contribution Terms and License
 
-# Architecture visualization   
-pydeps requiring graphviz to be installed (not via pip!)
-https://medium.com/illumination/visualize-dependencies-between-python-modules-d6e8e9a92c50
-https://pythonawesome.com/python-module-dependency-visualization/
+The code and documentation of LinChemIn is contained in this repository. To contribute
+to this project or any of the elements of LinChemIn we recommend you start by reading this
+contributing guide.
 
-> pydeps src/linchemin  -o docs/source/_static/linchemin_dependency_diagram.svg   
-> pydeps src/linchemin  -o docs/source/_static//linchemin_dependency_diagram.svg --cluster --max-cluster-size=3 --min-cluster-size=2 --keep-targe
-t-cluster  
+## Contributing to LinChemIn codebase
 
+If you would like to contribute to the package, we recommend the following development setup.
 
-# Keeping track of work 
-## Use branching while work with featurs/bugs
-In your Github fork, you need to keep your master branch clean, by clean I mean without any changes, like that you can create at any time a branch from your master. Each time that you want to commit a bug or a feature, you need to create a branch for it, which will be a copy of your master branch.
+1. Create a copy of the [repository](https://github.com/syngenta/linchemin) via the "_Fork_" button.
 
-https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches  
+2. Clone the linchemin repository:
 
-## Reference issues in your development work
+    ```sh
+    git clone [email protected]:${GH_ACCOUNT_OR_ORG}/linchemin.git
+    ```
 
-https://support.atlassian.com/jira-software-cloud/docs/reference-issues-in-your-development-work/  
+3. Add remote linchemin repo as an "upstream" in your local repo, so you can check/update remote changes.
 
-###Branches  
-Include the issue key at the beginning of the branch name when you create the branch to link it to your Jira issue.  
->git checkout -b JRA-123-branch-name
+   ```sh
+   git remote add upstream [email protected]:syngenta/linchemin.git
+   ```
 
-###Commits 
-Include the issue key at the beginning of the commit message to link the commit to your Jira issue.    
->git commit -m "JRA-123 commit message"  
+4. Create a dedicated branch:
+
+    ```sh
+    cd linchemin
+    git checkout -b a-super-nice-feature-we-all-need
+    ```
+
+5. Create and activate a dedicated conda environment (any other virtual environment management would work):
+
+    ```sh
+    conda env create linchemin
+    conda activate linchemin
+    ```
+
+6. Install linchemin in editable mode:
+
+    ```sh
+    pip install -e .[dev]
+    ```
+
+7. Implement your changes and once you are ready run the tests:
+
+    ```sh
+    # this can take quite long 
+    cd linchemin/tests 
+    python -m pytest 
+    ```
+   
+   And add style checks (be aware that running isort might change your files!):
+   ```sh
+    cd linchemin
+    # sorting the imports
+    python -m isort src/linchemin
+    # checking flake8
+    python -m flake8 --ignore E501 src/linchemin
+    ```
+
+8. Once the tests and checks passes, but most importantly you are happy with the implemented feature, commit your changes.
+
+    ```sh
+    # add the changes
+    git add 
+    # commit them
+    git commit -s -m "feat: implementing super nice feature." -m "A feature we all need."
+    # check upstream changes
+    git fetch upstream
+    git rebase upstream/main
+    # push changes to your fork
+    git push -u origin a-super-nice-feature-we-all-need
+    ```
+
+9. From your fork, open a pull request via the "_Contribute_" button, the maintainers will be happy to review it.
 
-###Pull requests
-Do at least one of the following:
-Include a commit in the pull request that has the issue key in the commit message. Note, the commit cannot be a merge commit.
-* Include the issue key at the beginning of the pull request title.
-* Ensure that the source branch name also includes the issue key at the beginning of the branch name.
-* This works by default in connected Bitbucket, GitLab, GitHub, and GitHub Enterprise tools.
-If you create the pull request from the development panel in a Jira issue, the issue key is added automatically

README.md

@@ -3,6 +3,10 @@
 [![Pypi version](https://img.shields.io/pypi/v/linchemin.svg)](https://pypi.python.org/pypi/linchemin)  
 [![Documentation Status](https://readthedocs.org/projects/linchemin/badge/?version=latest)](https://linchemin.readthedocs.io/en/latest/?badge=latest)  
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)  
+[![Downloads](https://static.pepy.tech/personalized-badge/linchemin?period=month&units=international_system&left_color=black&right_color=orange&left_text=downloads/mont)](https://pepy.tech/project/linchemin) [![Downloads](https://static.pepy.tech/personalized-badge/linchemin?period=total&units=international_system&left_color=black&right_color=orange&left_text=downloads)](https://pepy.tech/project/linchemin)
+[![Contributions](https://img.shields.io/badge/contributions-welcome-blue)](https://github.com/syngenta/linchemin/blob/main/CONTRIBUTING.md)
+
+<img src="./docs/source/static/linchemin_logo.png" alt="logo" width="313">
 
 ## LinChemIn (Linked Chemical Information)  
 
@@ -35,6 +39,20 @@ The Linked Chemical Information (LinChemIn) package is a python toolkit that all
 ## Install for development  
 >git clone https://github.com/syngenta/linchemin  
 >cd linchemin  
->pip install -e .[development]    
+>pip install -e .[dev]    
 
 Testing is based on pytest  
+
+
+## Configuration
+
+This package requires some configuration parameters to work,
+including some secretes to store access credentials to database and services.
+After installation, and before the first usage, the use should run the following command
+
+>linchemin_configure
+
+his command generates the user_home/linchemin directory and places into it two files:
+1. settings.toml populated with defaults settings. The user can review and modify these values if necessary.
+2. .secrets.toml containing the keys for the necessary secrets. The user must replace the placeholders with the correct values
+For more details please refer to the Configuration section of the documentation

docs/source/Configuration.rst

@@ -0,0 +1,9 @@
+Configuration
+====================
+
+.. automodule:: linchemin.configuration.config
+    :noindex:
+
+
+
+

docs/source/Installation.rst

@@ -6,14 +6,14 @@ LinChemIn requires python 3.9 or higher, as well as some common and reliable thi
 
 Usage installation
 --------------------
-Install directly from pypi
+LinChemIn can be installed directly from pypi
 
 .. code-block:: console
 
     $ pip install linchemin
 
 
-After cloning the LinChemIn repository from git, you can use ``pip`` to install it:
+As an alternative, you can clone the LinChemIn repository from git and then use ``pip`` to install it:
 
 .. code-block:: console