sssom using cookiecutter (#382)

* Restructured proj files

* more updates

* updated sssom-schema

* All tests pass .... linkml free!!!

* formatted and corrected

* updated workflows

* commenting cache

* Add tox

* add tox within poetry

* formatted

* ~whitelist_externals~ => allowlist_externals

* added docstring

* docstr happy

* os.path instead of Path

* tweaks to workflow

* cleanup

* reverted to original

* added manifest

* added maifest check to qc

* removed manifest from tox and qc

* simplify

* fixed indent

* reverted back to using poetry

* edits to qc.yaml and poetry update

* added tox

* poetry==1.3.2

* updated lock file

* test with path

* reverted

* redundant line

* ' => "

* redundant

* redundant

* formatted

* deleted unnecessary files and updated poetry

* "cjm" for author_id => "orcid:1234"

* "cjm" for author_id => "orcid:1234"

* added shell=True

* update poetry version to 1.4.2 in gh actions workflow

* cleanup to workflow

* simplify workflow

* reverted back

* testing something new with workflow

* added tox

* added space

* back to 1.3.2

* Added functions within init

.cruft.json

@@ -0,0 +1,24 @@
+{
+  "template": "https://github.com/monarch-initiative/monarch-project-template.git",
+  "commit": "7a5148b11fd6f4f70da7ef921789e0d5fe720e01",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "sssom-py",
+      "github_org_name": "mapping-commons",
+      "__project_slug": "sssom",
+      "project_description": "SSSOM (Simple Standard for Sharing Ontology Mappings) is a TSV and RDF/OWL standard for ontology mappings.",
+      "min_python_version": "3.7",
+      "file_name": "main",
+      "greeting_recipient": "World",
+      "full_name": "Harshad Hegde",
+      "email": "[email protected]",
+      "__author": "Harshad Hegde <[email protected]>",
+      "license": "MIT",
+      "github_token_for_doc_deployment": "GH_TOKEN",
+      "github_token_for_pypi_deployment": "SSSOM_TOKEN",
+      "_template": "https://github.com/monarch-initiative/monarch-project-template.git"
+    }
+  },
+  "directory": null
+}

.github/workflows/doc_pages.yml → .github/workflows/deploy-docs.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@master
+      uses: actions/checkout@v3.0.2
       with:
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
 
@@ -16,22 +16,28 @@ jobs:
       with:
         python-version: 3.9
 
+    - name: Install Poetry.
+      uses: snok/[email protected]
+
     - name: Install dependencies.
       run: |
-        pip install -e .[docs]
-
+        poetry install -E docs
+        
     - name: Build documentation.
       run: |
+        echo ${{ secrets.GH_TOKEN }} >> src/sssom/token.txt
         mkdir gh-pages
         touch gh-pages/.nojekyll
         cd docs/
-        make clean html
+        poetry run sphinx-apidoc -o . ../src/sssom/ --ext-autodoc -f
+        poetry run sphinx-build -b html . _build
         cp -r _build/html/* ../gh-pages/
     
     - name: Deploy documentation.
       if: ${{ github.event_name == 'push' }}
-      uses: JamesIves/github-pages-deploy-action@v4.3.0
+      uses: JamesIves/github-pages-deploy-action@v4.4.1
       with:
         branch: gh-pages
         force: true
-        folder: gh-pages
+        folder: gh-pages
+        token: ${{ secrets.GH_TOKEN }}

.github/workflows/pypi-publish.yml

@@ -11,21 +11,26 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+      - uses: actions/checkout@v3.0.2
 
-    - name: Set up Python
-      uses: actions/[email protected]
-      with:
-        python-version: 3.9
+      - name: Set up Python
+        uses: actions/[email protected]
+        with:
+          python-version: 3.9
 
-    - name: Install pip
-      run: | 
-        pip install --upgrade pip
-        pip install twine
-        python setup.py sdist
+      - name: Install Poetry
+        run: pip install poetry poetry-dynamic-versioning
+
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.SSSOM_TOKEN }}
 
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/[email protected]
-      with:
-        user: __token__
-        password: ${{ secrets.SSSOM_TOKEN }}
+

.github/workflows/qc.yml

@@ -1,7 +1,6 @@
-name: SSSOM qc
+name: sssom-py QC
 
 on:
-  # Triggers the workflow on push or pull request events but only for the master branch
   push:
     branches: [ master ]
   pull_request:
@@ -12,25 +11,32 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        os: [ ubuntu-latest, windows-latest ]
+        os: [ubuntu-latest, windows-latest]
+        python-version: [ "3.8", "3.9", "3.10" ]
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install tox
-    - name: Check manifest
-      run: tox -e manifest
-    - name: Lint with flake8
-      run: tox -e flake8
-    - name: Test with MyPy
-      run: tox -e mypy
-    - name: Test with pytest
-      run: tox -e py
+      - uses: actions/[email protected]
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: |
+          pip install --upgrade pip
+          pip install poetry==1.3.2
+
+      - name: Install dependencies
+        run: |
+          poetry install --extras tests
+          poetry add tox 
+
+      - name: Check code quality with flake8
+        run: poetry run tox -e flake8
+
+      - name: Check static typing with MyPy
+        run: poetry run tox -e mypy
+
+      - name: Test with pytest and generate coverage file
+        run: poetry run tox -e py

.gitignore

@@ -1,6 +1,137 @@
+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# User added
+*/__pycache__/*
 .venv
 venv
-sssom/__pycache__/
 .idea
 sssom.egg-info
 build/

CONTRIBUTING.md

@@ -0,0 +1,32 @@
+# Contribution Guidelines
+
+When contributing to this repository, please first discuss the changes you wish to make via an issue, email, or any other method, with the owners of this repository before issuing a pull request.
+
+## How to contribute
+
+### Reporting bugs or making feature requests
+
+To report a bug or suggest a new feature, please go to the [mapping-commons/sssom-py issue tracker](https://github.com/mapping-commons/sssom-py/issues), as we are
+consolidating issues there.
+
+Please supply enough details to the developers to enable them to verify and troubleshoot your issue:
+
+* Provide a clear and descriptive title as well as a concise summary of the issue to identify the problem.
+* Describe the exact steps which reproduce the problem in as many details as possible.
+* Describe the behavior you observed after following the steps and point out what exactly is the problem with that behavior.
+* Explain which behavior you expected to see instead and why.
+* Provide screenshots of the expected or actual behaviour where applicable.
+
+
+### The development lifecycle
+
+1. Create a bug fix or feature development branch, based off the `main` branch of the upstream repo, and not your fork. Name the branch appropriately, briefly summarizing the bug fix or feature request. If none come to mind, you can include the issue number in the branch name. Some examples of branch names are, `bugfix/breaking-pipfile-error` or `feature/add-click-cli-layer`, or `bugfix/issue-414`
+2. Make sure your development branch has all the latest commits from the `main` branch.
+3. After completing work and testing locally, push the code to the appropriate branch on your fork.
+4. Create a pull request from the bug/feature branch of your fork to the `main` branch of the upstream repository.
+
+Note: All the development must be done on a branch on your fork.
+
+ALSO NOTE: github.com lets you create a pull request from the main branch, automating the steps above.
+
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.