Improve user, admin and contributor documentation

Author: sujaypatil96

CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

CONTRIBUTION.md

@@ -16,12 +16,21 @@ Please note we have a code of conduct, please follow it in all your interactions
 
 ### Setup Project for Development and Testing
 
-1. Follow the package setup instructions on the main README till the [`Clone Project Repository`](README.m#131-clone-project-repository) step.
-2. If you are a `schematic` package contributor you don't need to create a `venv` virtual environment, `poetry` will create a virtual environment by default, which you can use.
-3. Running the following command reads the [`pyproject.toml`](https://github.com/Sage-Bionetworks/schematic/blob/develop/pyproject.toml) file from the current project, resolves the dependencies and installs them: `poetry install`
-4. Obtain credentials file(s) by following same instructions as in the [`1.3.4. Obtain Credentials File(s)`](README.md#134-obtain-credentials-files) section.
-5. Fill in configuration file(s) in the same way as specified in the [`1.3.5. Fill in Configuration File(s)`](README.md#135-fill-in-configuration-files).
-6. To run any of the CLI utilities shown in the [`1.3.6. Command Line Interface`](README.md#136-command-line-interface), prefix the commands with `poetry run`.
+1. Install [package dependencies](https://sage-schematic.readthedocs.io/en/develop/README.html#installation-requirements-and-pre-requisites).
+2. Clone the `schematic` package repository: `git clone https://github.com/Sage-Bionetworks/schematic.git`
+3. [Create and activate](https://sage-schematic.readthedocs.io/en/develop/README.html#virtual-environment-setup) a virtual environment.
+4. Run the following commands to build schematic and install the package along with all of its dependencies:
+   ```python
+   cd schematic  # change directory to schematic
+   git checkout develop  # switch to develop branch of schematic
+   poetry build # build source and wheel archives
+   pip install dist/schematicpy-0.1.11-py3-none-any.whl  # install wheel file
+   ```
+5. [Obtain](https://sage-schematic.readthedocs.io/en/develop/README.html#obtain-google-credentials-file-s) appropriate Google credentials file(s).
+6. [Obtain and Fill in](https://sage-schematic.readthedocs.io/en/develop/README.html#fill-in-configuration-file-s) the `config.yml` file and the `.synapseConfig` file as well as described in the `Fill in Configuration File(s)` part of the documentation.
+7. [Run](https://docs.pytest.org/en/stable/usage.html) the test suite.
+
+Note: To ensure that all tests run successfully, contact your DCC liason and request to be added to the `schematic-dev` [team](https://www.synapse.org/#!Team:3419888) on Synapse.
 
 ## Pull Request Process
 
@@ -48,78 +57,3 @@ Please note we have a code of conduct, please follow it in all your interactions
 http://google.github.io/styleguide/pyguide.html
 
 * Be consistent and follow existing code conventions and spirit.
-
-## Code of Conduct
-
-### Our Pledge
-
-In the interest of fostering an open and welcoming environment, we as
-contributors and maintainers pledge to making participation in our project and
-our community a harassment-free experience for everyone, regardless of age, body
-size, disability, ethnicity, gender identity and expression, level of experience,
-nationality, personal appearance, race, religion, or sexual identity and
-orientation.
-
-### Our Standards
-
-Examples of behavior that contributes to creating a positive environment
-include:
-
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
-
-Examples of unacceptable behavior by participants include:
-
-* The use of sexualized language or imagery and unwelcome sexual attention or
-advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
-  address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
-  professional setting
-
-### Our Responsibilities
-
-Project maintainers are responsible for clarifying the standards of acceptable
-behavior and are expected to take appropriate and fair corrective action in
-response to any instances of unacceptable behavior.
-
-Project maintainers have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct, or to ban temporarily or
-permanently any contributor for other behaviors that they deem inappropriate,
-threatening, offensive, or harmful.
-
-### Scope
-
-This Code of Conduct applies both within project spaces and in public spaces
-when an individual is representing the project or its community. Examples of
-representing a project or community include using an official project e-mail
-address, posting via an official social media account, or acting as an appointed
-representative at an online or offline event. Representation of a project may be
-further defined and clarified by project maintainers.
-
-### Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
-complaints will be reviewed and investigated and will result in a response that
-is deemed necessary and appropriate to the circumstances. The project team is
-obligated to maintain confidentiality with regard to the reporter of an incident.
-Further details of specific enforcement policies may be posted separately.
-
-Project maintainers who do not follow or enforce the Code of Conduct in good
-faith may face temporary or permanent repercussions as determined by other
-members of the project's leadership.
-
-### Attribution
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
-available at [http://contributor-covenant.org/version/1/4][version]
-
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/

README.md

@@ -1,48 +1,54 @@
 # Schematic
-[![Build Status](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2FSage-Bionetworks%2Fschematic%2Fbadge%3Fref%3Ddevelop&style=flat)](https://actions-badge.atrox.dev/Sage-Bionetworks/schematic/goto?ref=develop) [![Documentation Status](https://readthedocs.org/projects/sage-schematic/badge/?version=develop)](https://sage-schematic.readthedocs.io/en/develop/?badge=develop)
-
-
-- [Schematic](#schematic)
-  - [Introduction](#introduction)
-  - [Installation Requirements and Pre-requisites](#installation-requirements-and-pre-requisites)
-  - [Package Setup Instructions](#package-setup-instructions)
-  - [Command Line Interface](#command-line-interface)
-  - [Contributing](#contributing)
-  - [Contributors](#contributors)
+[![Build Status](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2FSage-Bionetworks%2Fschematic%2Fbadge%3Fref%3Ddevelop&style=flat)](https://actions-badge.atrox.dev/Sage-Bionetworks/schematic/goto?ref=develop) [![Documentation Status](https://readthedocs.org/projects/sage-schematic/badge/?version=develop)](https://sage-schematic.readthedocs.io/en/develop/?badge=develop) [![PyPI version](https://badge.fury.io/py/schematicpy.svg)](https://badge.fury.io/py/schematicpy)
 
 ## Introduction
 
-SCHEMATIC is an acronym for _Schema Engine for Manifest Ingress and Curation_. The Python based infrastructure provides a _novel_ schema-based, data ingress ecosystem, that is meant to streamline the process of metadata annotation and validation for various data contributors.
+SCHEMATIC is an acronym for _Schema Engine for Manifest Ingress and Curation_. The Python based infrastructure provides a _novel_ schema-based, data ingress ecosystem, that is meant to streamline the process of dataset annotation, metadata validation and submission to an asset store for various data contributors.
 
 ## Installation Requirements and Pre-requisites
 
 * Python 3.7.1 or higher
-* [`pyenv`](https://github.com/pyenv/pyenv)
-* [`poetry`](https://github.com/python-poetry/poetry)
 
+Note: You need to be a registered and certified user on [`synapse.org`](https://www.synapse.org/), and also have the right permissions to download the Google credentials files from Synapse.
+
+## Installing
+
+Create and activate a virtual environment within which you can install the package:
+
+```
+python -m venv .venv
+source .venv/bin/activate
+```
 
-**Important**: You need to be a registered and certified user on [`synapse.org`](https://www.synapse.org/), and also have the right permissions to download the Google credentials files from Synapse.
+Install and update the package using [pip](https://pip.pypa.io/en/stable/quickstart/):
 
-## Package Setup Instructions
+```
+python -m pip install schematicpy
+```
 
-* [Clone Project Repository](https://sage-schematic.readthedocs.io/en/develop/README.html#clone-project-repository)
-* [Virtual Environment Setup](https://sage-schematic.readthedocs.io/en/develop/README.html#virtual-environment-setup)
-* [Install Dependencies](https://sage-schematic.readthedocs.io/en/develop/README.html#install-dependencies)
-* [Fill in Configuration File(s)](https://sage-schematic.readthedocs.io/en/develop/README.html#fill-in-configuration-file-s)
-* [Obtain Credentials File(s)](https://sage-schematic.readthedocs.io/en/develop/README.html#obtain-credentials-file-s)
+## Command Line Client Usage
 
+### Initialization
 
-## Command Line Interface
+```
+schematic init --config ~/path/to/config.yml    # initialize mode of authentication
+```
 
-* [Schematic Initialization](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-init) (_initialize mode of authentication_)
+### Manifest
 
-* [Metadata Manifest Validation](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-validate) (_validate metadata manifest (.csv) files_)
+```
+schematic manifest --config ~/path/to/config.yml get    # generate manifest based on data type
+```
 
-* [Metadata Manifest Generation](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-manifest-get) (_generate metadata manifest (.csv) files_)
+```
+schematic manifest --config ~/path/to/config.yml validate   # validate manifest
+```
 
-* [Metadata Manifest Validation and Submission](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-submit) (_submission and optional validation of metadata manifest (.csv) files_)
+### Model
 
-Refer to the [docs](https://github.com/Sage-Bionetworks/schematic/tree/develop/docs/md/details.md) for more details.
+```
+schematic model --config ~/path/to/config.yml submit    # validate and submit manifest
+```
 
 ## Contributing