Syncing main with changes from release/v1.3.0

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

@@ -1,13 +1,12 @@
 # Built from:
 # https://docs.github.com/en/actions/guides/building-and-testing-python
 
-name: black
+name: Test and check code style
 
 on: [push, pull_request]
 
 jobs:
-  black:
-
+  test:
     runs-on: ubuntu-latest
 
     strategy:
@@ -17,7 +16,7 @@ jobs:
     steps:
 
       #----------------------------------------------
-      #       check-out repo and set-up python
+      # check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
         uses: actions/checkout@v2
@@ -28,41 +27,39 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       #----------------------------------------------
-      #          install & configure poetry
+      # cache poetry installation
       #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1.1.1
+      - name: Cache Poetry files
+        id: cache-poetry
+        uses: actions/cache@v2
         with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
+          path: ~/.local
+          key: ${{ runner.os }}-python-${{ matrix.python-version }}-poetry-${{ hashFiles('**/poetry.lock') }}
 
       #----------------------------------------------
-      #       load cached venv if cache exists
+      # install & configure poetry
       #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
 
       #----------------------------------------------
-      # install dependencies if cache does not exist
+      # install dependencies
       #----------------------------------------------
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
+        run: poetry install --no-interaction
 
       #----------------------------------------------
-      #    install your root project, if required
+      # run tests
       #----------------------------------------------
-      - name: Install library
-        run: poetry install --no-interaction
+      - name: Run tests
+        env:
+          SHEET2LINKML_GOOGLE_SERVICE_ACCT: ${{ secrets.Sheet2LinkMLGoogleServiceAcct  }}
+        run: poetry run pytest -svvv
 
       #----------------------------------------------
-      #             check formatting
+      # check formatting
       #----------------------------------------------
-      - name: Code formatting with black
+      - name: Code style with black
         run: |
            # run black in check mode
            # if files are not formatted correctly, the build will not go through

CHANGELOG.md

@@ -8,6 +8,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Releases](https://github.com/cancerDHC/sheet2linkml/releases)
 
 ## [Unreleased]
+* Bugs or Features yet to be resolved.
+
+## [v1.3.0]
+* 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
 

CONTRIBUTING.md

@@ -68,7 +68,12 @@ 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
+```
+
+Update the version number of the release in [CHANGELOG.md](CHANGELOG.md) and document some of the new changes that will be 
+part of the release.
 
+```
 # 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
@@ -85,7 +90,8 @@ Once the code has been merged into the `main` branch on this repo, there are two
 to ensure a release is complete.
 
 - You should create a GitHub tag, with the appropriate version number.
-- You should push the package to PyPI.
+- You should push the package to PyPI. Before pushing the package to PyPI make sure you have updated the version number in the 
+[pyproject.toml](pyproject.toml) file so that it matches the version number of the release you described in the CHANGELOG.
 
 ### Release to Test PyPI _(optional)_
 The purpose of this section is to verify that the package looks and works as intended, by viewing it on Test PyPI and 

README.md

@@ -35,17 +35,27 @@ 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=WbM2Jr869ofmdcSmhX_1E0aLWvnK2-gr47Mo_tzuQKWy
+export CDM_GOOGLE_SHEET_ID=1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4
 ```
 
-A `google_api_credentials.json` file is also required in the root of this repo. Documentation is forthcoming.
+A `google_api_credentials.json` file is also required in the root of this repo as detailed in the Authorization section above.
 
 And the user is responsible for defining 
 - `~/path/to/crdch_model.yaml`