Add testing

.github/workflows/pytest.yaml → .github/workflows/main.yaml

@@ -1,12 +1,13 @@
 # Built from:
 # https://docs.github.com/en/actions/guides/building-and-testing-python
 
-name: Test and check code style
+name: black
 
 on: [push, pull_request]
 
 jobs:
-  test:
+  black:
+
     runs-on: ubuntu-latest
 
     strategy:
@@ -16,7 +17,7 @@ jobs:
     steps:
 
       #----------------------------------------------
-      # check-out repo and set-up python
+      #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
         uses: actions/checkout@v2
@@ -27,39 +28,41 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       #----------------------------------------------
-      # cache poetry installation
+      #          install & configure poetry
       #----------------------------------------------
-      - name: Cache Poetry files
-        id: cache-poetry
-        uses: actions/cache@v2
+      - name: Install Poetry
+        uses: snok/[email protected]
         with:
-          path: ~/.local
-          key: ${{ runner.os }}-python-${{ matrix.python-version }}-poetry-${{ hashFiles('**/poetry.lock') }}
+          virtualenvs-create: true
+          virtualenvs-in-project: true
 
       #----------------------------------------------
-      # install & configure poetry
+      #       load cached venv if cache exists
       #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
 
       #----------------------------------------------
-      # install dependencies
+      # install dependencies if cache does not exist
       #----------------------------------------------
       - name: Install dependencies
-        run: poetry install --no-interaction
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
 
       #----------------------------------------------
-      # run tests
+      #    install your root project, if required
       #----------------------------------------------
-      - name: Run tests
-        env:
-          SHEET2LINKML_GOOGLE_SERVICE_ACCT: ${{ secrets.Sheet2LinkMLGoogleServiceAcct  }}
-        run: poetry run pytest -svvv
+      - name: Install library
+        run: poetry install --no-interaction
 
       #----------------------------------------------
-      # check formatting
+      #             check formatting
       #----------------------------------------------
-      - name: Code style with black
+      - name: Code formatting with black
         run: |
            # run black in check mode
            # if files are not formatted correctly, the build will not go through

CHANGELOG.md

@@ -7,52 +7,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Releases](https://github.com/cancerDHC/sheet2linkml/releases)
 
-## [Unreleased]
-* Feature: added a dummy Google Sheet, the expected schema, and a test to compare them.
-* Feature: cleaned up GitHub Action for style checks and added PyTest.
-* Feature: added support for storing Google API credentials in an environmental variable, and added it to 
-  GitHub Actions.
-* Feature: added check for Google Sheet ID.
-* Feature: updated @cached_property with @property @lru_cache to support Python 3.7.
-* Bug: updated CCDH Terminology API endpoint for enumerations.
-* Bug: fixed code to correctly handle 404 responses from the TCCM Terminology Service.
-* Bug: replaced unnecessary print() in GSheetModel with logging.error().
-
-## [v1.2.0] - 2021-11-29
+## [v1.0.0](https://github.com/cancerDHC/sheet2linkml/releases/tag/v1.0.0)
 
-* Separate enums from codeable concepts
-
-## [v1.1.1] - 2021-11-11
-
-* Updated minimum Python version from 3.9 to 3.7, thanks to changes from v1.1.0
+* First working release of `sheet2linkml`
+* Package deployed to PyPI
+* In its current state, it is meant to be used only as a dependency for ccdhmodel
+* It is compatible with Python version 3.9 and higher
 
-## [v1.1.0] - 2021-10-28
 
-* Retroactive code style formatting of the entire codebase using Black
-* Added a Github Action that checks if checked in code is Black formatted
-* Modified the code to be compatible with Python versions 3.7 and 3.8 by using `typing.List` and `typing.Dict`
-* Added this CHANGELOG
+## [v1.0.1](https://github.com/cancerDHC/sheet2linkml/releases/tag/v1.0.1)
 
-## [v1.0.1] - 2021-10-04
+* Added `python-dotenv` to list of core dependencies
 
-* Improved README
-* Moved `python-dotenv` to list of core dependencies
+## [v1.0.2]
 
-## [v1.0.0] - 2021-09-30
+* Retroactive black formatting of entire codebase
+* Github Action that checks if checked in code is black formatted
+* Compatible with Python versions 3.7 and 3.8
 
-* Added CONTRIBUTING documentation
-* Package deployed to PyPI
-* In its current state, it is meant to be used only as a dependency for ccdhmodel
-* It is compatible with Python version 3.9 and higher
+## [v1.1.1]
 
-## [v0.0.1] - 2021-09-29
+* Update the version of Python that the package depends on in the pyproject.toml
 
-* First working release of `sheet2linkml`
+## [v1.2.0]
 
-[Unreleased]: https://github.com/cancerDHC/sheet2linkml/compare/v1.2.0...HEAD
-[v1.2.0]: https://github.com/cancerDHC/sheet2linkml/compare/v1.1.1...v1.2.0
-[v1.1.1]: https://github.com/cancerDHC/sheet2linkml/compare/v1.1.0...v1.1.1
-[v1.1.0]: https://github.com/cancerDHC/sheet2linkml/compare/v1.0.1...v1.1.0
-[v1.0.1]: https://github.com/cancerDHC/sheet2linkml/compare/v1.0.0...v1.0.1
-[v1.0.0]: https://github.com/cancerDHC/sheet2linkml/compare/v0.0.1...v1.0.0
-[v0.0.1]: https://github.com/cancerDHC/sheet2linkml/releases/tag/v0.0.1
+* Separate enums from codeable concepts

CONTRIBUTING.md

@@ -57,30 +57,6 @@ poetry run black ~/path/to/directory
 
 ## Release process
 
-The branch names follow the convention described by the [git flow](https://nvie.com/posts/a-successful-git-branching-model/) 
-branching model. Release branches are created to support the preparation of a new production release.
-
-Steps to follow when issuing a new release:
-
-```
-git checkout -b release-1.2 develop # Switched to a new branch "release-1.2"
-
-# minor bug fixes and preparing metadata for a release
-# e.g., version number, build dates
-# commit changes
-
-# merge changes into "main"
-git checkout main # switched to branch "main"
-git merge --no-ff release-1.2 # merge into "main" with summary of changes
-
-# merge changes into "develop"
-git checkout develop # switched to branch "develop"
-git merge --no-ff release-1.2 # merge into "develop" with summary of changes
-
-# remove release branch
-git branch -d release-1.2  # deleted branch release-1.2
-```
-
 Once the code has been merged into the `main` branch on this repo, there are two processes that need to be completed 
 to ensure a release is complete.
 

README.md

@@ -35,27 +35,17 @@ source .venv/bin/activate
 python -m pip install sheet2linkml
 ```
 
-## Authorization
-
-sheet2linkml uses the [`pygsheets` library](https://github.com/nithinmurali/pygsheets) in order to access sheets in
-Google Drive. To authorize it to access your Google Sheets, you will need to create and download Google Drive client credentials. First,
-[enable the Google Drive API](https://developers.google.com/drive/api/v3/enable-drive-api). After the API is enabled, 
-[create and download the client credentials](https://www.iperiusbackup.net/en/how-to-enable-google-drive-api-and-get-client-credentials/)
-from the [Google API Console](https://console.developers.google.com/). Save the file as `google_api_credentials.json` in
-the root directory of this project. [Detailed instructions and screenshots](https://pygsheets.readthedocs.io/en/stable/authorization.html)
-are also available from the [`pygsheets` documentation](https://pygsheets.readthedocs.io/).
-
 ## Command Line Client Usage
 
 Identify the Google Sheet that you want to convert to LinkML. Note that sheet2linkml is not currently a general-purpose Google Sheet to LinkML converter. It will only work with Google Sheets that have been written in a particular, currently undefined format.
 
 Contact your CCDH colleagues to obtain the correct sheet ID and assert it either in a `.env` file or in the shell, like this:
 
 ```shell
-export CDM_GOOGLE_SHEET_ID=1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4
+export CDM_GOOGLE_SHEET_ID=WbM2Jr869ofmdcSmhX_1E0aLWvnK2-gr47Mo_tzuQKWy
 ```
 
-A `google_api_credentials.json` file is also required in the root of this repo as detailed in the Authorization section above.
+A `google_api_credentials.json` file is also required in the root of this repo. Documentation is forthcoming.
 
 And the user is responsible for defining 
 - `~/path/to/crdch_model.yaml`