Migrate to new LinkML repo template

.github/workflows/build.yml

@@ -2,23 +2,62 @@ name: Build
 on:
   workflow_dispatch:
   push:
+    branches: [ master ]
     paths:
-      - 'sssom/model/schema/sssom.yaml'
+      - 'src/linkml/sssom.yaml'
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v2
         with:
           persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-      - uses: actions/setup-python@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
         with:
           python-version: 3.9
+
+      #----------------------------------------------
+      #          install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      #----------------------------------------------
+      #       load cached venv if cache exists      
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
+      #----------------------------------------------
+      # install dependencies if cache does not exist 
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      #----------------------------------------------
+      #    install your root project, if required 
+      #----------------------------------------------      
+      - name: Install library
+        run: poetry install --no-interaction
+
       - name: Create local changes
         run: |
-          pip install pipenv
           make all
       - name: Commit files
         run: |

.github/workflows/deploy_documentation.yml

@@ -0,0 +1,90 @@
+name: Deploy Documentation
+
+# Controls when the action will run. Triggers the workflow on push
+on:
+  push:
+    branches:
+    - master
+    paths:
+    - 'src/docs/*'
+    - 'project/jsonschema/sssom.schema.json'
+
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  #synchronize:
+  #  runs-on: ubuntu-latest
+  #  steps:
+  #    - uses: actions/checkout@v2
+  #    - name: Merge master to gh-pages branch
+  #      uses: devmasx/merge-branch@v1.1.0
+  #      with:
+  #        type: now
+  #        target_branch: gh-pages
+  #      env:
+  #        GITHUB_TOKEN: ${{ github.token }}
+
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v2
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      #----------------------------------------------
+      #          install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      #----------------------------------------------
+      #       load cached venv if cache exists      
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
+      #----------------------------------------------
+      # install dependencies if cache does not exist 
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      #----------------------------------------------
+      #    install your root project, if required 
+      #----------------------------------------------      
+      - name: Install library
+        run: poetry install --no-interaction
+
+      - name: Create local changes
+        run: |
+          make all
+
+      - name: Deploy to gh-pages branch
+        uses: JamesIves/github-pages-deploy-action@releases/v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+          REPOSITORY_NAME: mapping-commons/sssom # The repository the action should deploy to
+          BRANCH: gh-pages # The branch the action should deploy to.
+          COMMIT_MESSAGE: 'Update documentation'
+          FOLDER: . # The folder the action should deploy.

.github/workflows/main.yaml

@@ -0,0 +1,67 @@
+# Built from:
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://github.com/snok/install-poetry#workflows-and-tips
+
+name: Build and test linkml-runtime
+
+on: [pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+
+    steps:
+
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      #          install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      #----------------------------------------------
+      #       load cached venv if cache exists      
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
+      #----------------------------------------------
+      # install dependencies if cache does not exist 
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      #----------------------------------------------
+      #    install your root project, if required 
+      #----------------------------------------------      
+      - name: Install library
+        run: poetry install --no-interaction
+
+      #----------------------------------------------
+      #              run test suite   
+      #----------------------------------------------
+      - name: Run tests
+        run: make test
+

.github/workflows/pypi-publish.yaml

@@ -0,0 +1,38 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2.2.2
+      with:
+        python-version: 3.8
+
+    - name: Install Poetry
+      uses: snok/install-poetry@v1.1.6
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+
+    - name: Install dependencies
+      run: poetry install --no-interaction
+
+    - name: Build source and wheel archives
+      run: |
+        poetry version $(git describe --tags --abbrev=0)
+        poetry build
+
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@v1.2.2
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}

.gitignore

@@ -1,7 +1,5 @@
-# Make artifacts
-make-venv/.venv
-make-venv/env.lock
-target/
+/docs/
+/project/docs/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -25,6 +23,7 @@ parts/
 sdist/
 var/
 wheels/
+pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -54,7 +53,6 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -77,7 +75,6 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -88,16 +85,14 @@ 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
 
 # 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
+#Pipfile.lock
 
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
@@ -135,20 +130,4 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# Editors
-.idea/
-.project
-.classpath
-
-# make artifacts
-*-PREV
-
-# Apple stuff
 .DS_Store

CONTRIBUTING.md

@@ -0,0 +1,7 @@
+# Contributing
+
+## Create an issue in the GitHub repository
+
+## Create a Pull Request (PR)
+
+Thank you for contributing to sssom

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2022, Nico Matentzoglu
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.