Feature/poetry fix

.github/workflows/pyDataPipeline.yaml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, macos-latest] #, windows-latest]
-        python: ["3.7", "3.9"]
+        python: ["3.7","3.8", "3.9"]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
@@ -25,33 +25,24 @@ jobs:
               fi
       - name: Install local registry
         run: curl -fsSL https://data.scrc.uk/static/localregistry.sh | /bin/bash -s -- -b main
-      - name: Checkout FAIRDataPipeline/FAIR-CLI
-        uses: actions/checkout@v2
-        with:
-          repository: FAIRDataPipeline/FAIR-CLI
-          path: FAIR-CLI
-      - name: Move FAIR-CLI
-        run: mv FAIR-CLI ../FAIR-CLI
+      - name: Install Required
+        run: brew install memcached
+        if: matrix.os == 'macos-latest'
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - name: Install and initialise FAIR CLI
+      - name: Run Tests
         run: |
-          cd ../FAIR-CLI
           poetry install
           source .venv/bin/activate
-          cd ${{ github.workspace }}
           fair init --ci
           fair registry start
-          pip3 install .
-          pip3 install pytest
-          pip3 install coverage
-          coverage run --source=org.fairdatapipeline.api -m pytest
-          coverage xml
-          fair pull src/org/fairdatapipeline/simpleModel/ext/SEIRSconfig.yaml
-          fair run src/org/fairdatapipeline/simpleModel/ext/SEIRSconfig.yaml
+          fair pull simpleModel/ext/SEIRSconfig.yaml
+          fair run simpleModel/ext/SEIRSconfig.yaml
+
+          python3 -m poetry run pytest --cov=fairdatapipeline.api  --cov-report=xml --cov-report=term -s tests/
       - uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -139,7 +139,13 @@ test.yaml
 .fair/
 
 tmp/
-src/tests/ext/coderuns.txt
+tests/ext/coderuns.txt
 data_store
 
-src/org/fairdatapipeline/simpleModel/ext/test.py
+fairdatapipeline/simpleModel/ext/test.py
+
+# Sphinx documentation
+doc/_build/
+
+# Poetry Lock
+poetry.lock

.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
 -   repo: https://github.com/pycqa/isort
     rev: 5.6.4
     hooks:
-      - id: isort
+    -   id: isort
         args: ["--profile", "black", "--filter-files"]
 -   repo: https://github.com/awslabs/cfn-python-lint
     rev: v0.54.1 # The version of cfn-lint to use
@@ -37,4 +37,11 @@ repos:
 -   repo: https://github.com/asottile/pyupgrade
     rev: v2.25.0
     hooks:
-    -   id: pyupgrade
+    - id: pyupgrade
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.790
+    hooks:
+    -   id: mypy
+        exclude: ^doc
+        args: ["--ignore-missing-imports", "--disallow-untyped-defs", "--disallow-untyped-calls", "."]
+        pass_filenames: false

.zenodo.json

@@ -12,6 +12,20 @@
         "affiliation": "The University of Sheffield",
         "name": "Reddyhoff, Dennis",
         "orcid": "0000-0002-4971-2346"
+      },
+      {
+        "affiliation": "The University of Sheffield",
+        "name": "Turner, Robert"
+      },
+      {
+        "affiliation": "United Kingdom Atomic Energy Authority",
+        "name": "Viola, Bruno",        
+        "orcid": "0000-0001-5406-5860"
+      },
+      {
+        "affiliation": "United Kingdom Atomic Energy Authority",
+        "name": "Zarebski, Kristian",
+        "orcid": "0000-0002-6773-1049"
       }
     ],
     "access_right": "open",