JIRA-1630 Minor: Initial Stub Development for Provena Client Tool. (#1)

* Created initial package setup with cookie-cutter template

* Updated CI/CD script to only run on main branch, fixed incorrect imports and deleted files that were not needed

* Integrated mypi in the package and was able to successfully build.

* Shifted from a class to a data-class for Settings, updated CI-CD script and README.md and removed CONDUCT.md files.

* Updated CI-CD script to use OCID instead of API tokens, and made it trigger on initial branch for testing purposes.

* Simplifying CI-CD file to ensure it runs without issues.

* Removed pull-request for now from CI/CD script.

* Updated dependencies for CI

* Updated poetry lock file for CI.

* Added dummy test for CI to pass.

* Updated CI to support pull request,  as I am gonna merge pull request to main to release package.

---------

Co-authored-by: Parth-Kulkarni

.github/workflows/ci-cd.yml

@@ -0,0 +1,83 @@
+name: ci-cd
+
+on: [push, pull_request]
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Check-out repository
+        uses: actions/checkout@v3
+
+      - name: Install poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install package
+        run: poetry install
+
+      - name: Mypy type check
+        run: poetry run mypy .  
+
+      - name: Test with pytest
+        run: poetry run pytest tests/ --cov=provenaclient --cov-report=xml
+
+      - name: Use Codecov to track coverage
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+
+      - name: Build documentation
+        run: poetry run make html --directory docs/
+
+  cd:
+    permissions:
+      id-token: write
+      contents: write
+    needs: ci
+    if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/inital-branch')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Check-out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Use Python Semantic Release to prepare release
+        id: release
+        uses: python-semantic-release/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        if: steps.release.outputs.released == 'true'
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+      - name: Test install from TestPyPI
+        if: steps.release.outputs.released == 'true'
+        run: |
+            pip install \
+            --index-url https://test.pypi.org/simple/ \
+            --extra-index-url https://pypi.org/simple \
+            provenaclient
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        if: steps.release.outputs.released == 'true'
+
+      - name: Publish package distributions to GitHub Releases
+        uses: python-semantic-release/upload-to-gh-release@main
+        if: steps.release.outputs.released == 'true'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -20,6 +20,7 @@ parts/
 sdist/
 var/
 wheels/
+pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -49,7 +50,6 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -72,7 +72,6 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -83,9 +82,7 @@ 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
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -94,22 +91,7 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.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/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
 # Celery stuff
@@ -145,16 +127,16 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+**__pycache__
 
-# pytype static type analyzer
-.pytype/
+# PyCharm
+.idea/
 
-# Cython debug symbols
-cython_debug/
+# RStudio project files
+**.Rproj.user/
+**.Rproj.user*
+**.Rproj
+**.Rhistory
 
-# 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/
+# MacOS
+.DS_Store

.readthedocs.yml

@@ -0,0 +1,27 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+      # Tell poetry to not use a virtual environment
+      - poetry config virtualenvs.create false
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      - poetry install
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py

CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+<!--next-version-placeholder-->
+
+## v0.1.0 (04/04/2024)
+
+- First release of `provenaclient`!

CONTRIBUTING.md

@@ -0,0 +1,73 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+## Types of Contributions
+
+### Report Bugs
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+You can never have enough documentation! Please feel free to contribute to any
+part of the documentation, such as the official docs, docstrings, or even
+on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `provenaclient` for local development.
+
+1. Download a copy of `provenaclient` locally.
+2. Install `provenaclient` using `poetry`:
+
+    ```console
+    $ poetry install
+    ```
+
+3. Use `git` (or similar) to create a branch for local development and make your changes:
+
+    ```console
+    $ git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+4. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests.
+
+5. Commit your changes and open a pull request.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include additional tests if appropriate.
+2. If the pull request adds functionality, the docs should be updated.
+3. The pull request should work for all currently supported operating systems and versions of Python.
+
+## Code of Conduct
+
+Please note that the `provenaclient` project is released with a
+Code of Conduct. By contributing to this project you agree to abide by its terms.

README.md

@@ -1,2 +1,39 @@
-# provena-python-client
-Client library for interfacing with a Provena instance
+# provenaclient
+
+A client library for interfacing with a Provena instance.
+
+## Installation
+
+```bash
+$ pip install provenaclient
+```
+
+## Usage
+
+### How to get started with Poetry
+
+1) Run the Command: `curl -sSL https://install.python-poetry.org | python3 -`.
+2) Check if poetry was successfully installed by running `poetry --version`.
+3) You should now have be able to see your poetry version successfully. 
+4) Now run the command `poetry shell`. This  will activate the poetry virtual environment for you.
+5) Now finally run the command `poetry install`. This will install all dependencies defined within pyproject.toml.
+
+### My Poetry Installation is not being detected?
+1) This means that your PATH variable does not include the Poetry directory. 
+2) Open your .bashrc file, using the command `nano ~/.bashrc`.
+3) Add the following line at the end of the file, `export PATH= "$HOME/.local/bin:$PATH"`.
+4) Reload your .bashrc file, using the command `source ~/.bashrc`.
+5) Verify that your poetry is now running, using the command `poetry --version`.
+
+
+
+## Contributing
+TODO
+
+## License
+
+`provenaclient` was created by Provena Development Team (CSIRO). Provena Development Team (CSIRO) retains all rights to the source and it may not be reproduced, distributed, or used to create derivative works.
+
+## Credits
+
+`provenaclient` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).

dev-requirements.txt

@@ -0,0 +1,2 @@
+cookiecutter
+mypy

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = provenaclient
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/changelog.md

@@ -0,0 +1,2 @@
+```{include} ../CHANGELOG.md
+```

docs/conf.py

@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+
+project = u"provenaclient"
+copyright = u"2024, Parth Kulkarni"
+author = u"Parth Kulkarni"
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "myst_nb",
+    "autoapi.extension",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+]
+autoapi_dirs = ["../src"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"

docs/contributing.md

@@ -0,0 +1,2 @@
+```{include} ../CONTRIBUTING.md
+```