Release beta 36

.github/workflows/ci.yml

@@ -0,0 +1,69 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - develop
+      - main
+
+env:
+    python_version: 3.6
+    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ env.python_version }}
+    - uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py', 'Makefile') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+    - name: Test
+      run: |
+        python3.6 -m venv .venv
+        source .venv/bin/activate
+        make travis_install
+        # Hack: The use of `chrgp` compensates for a quirk of Docker. The PyCharm image
+        # used by `make format` sets up a user called `developer` and assigns it UID
+        # 1000. GitHub Actions runs as UID 121. An alternative would be to pass --user
+        # to `docker run` and bind-mount an /etc/passwd that maps that to `developer`.
+        # Currently, we're unclear why `make format` works as is on developer machines.
+        chmod -R g+w . && sudo chgrp -R 1000 . && make format && sudo chgrp -R $(id -g) .
+        make check_clean
+        make pep8
+        make test
+    - uses: actions/upload-artifact@v2
+      with:
+        name: coverage-file
+        path: .coverage
+
+  coveralls:
+    needs: test
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.python_version }}
+      - name: Download coverage file
+        uses: actions/download-artifact@v2
+        with:
+          name: coverage-file
+      - name: Coveralls
+        run: |
+          pip install coveralls==3.0.1
+          # This API token is associated with the repository, not any particular user. A 
+          # GitHub user with admin privileges must retrieve the token from 
+          # https://coveralls.io/github/DataBiosphere/hca-metadata-api and deposit it in
+          # https://github.com/DataBiosphere/hca-metadata-api/settings/secrets/actions
+          # as a secret called `COVERALLS_REPO_TOKEN`.
+          COVERALLS_REPO_TOKEN=${{ secrets.COVERALLS_REPO_TOKEN }} coveralls

README.md

@@ -38,3 +38,54 @@ area repository.
 
 Copy the token and use it as the value of an environment variable named
 `GITHUB_TOKEN`.
+
+## Release guide
+
+This guide will walk you through the steps necessary to promote the `develop`
+branch to `main`, tag the release, and prepare `develop` for the next release.
+
+Note: For purpose of example, this guide will pretend we are upgrading `main`
+from release 29 to 30.
+
+1. Merge `develop` into `main`.
+
+   - Resolve conflicts in `setup.py`, promote to the higher version.
+
+       ```
+       <     version="1.0b29",       # value from `main`
+       <     version="1.0b30.dev1",  # value from `develop`
+       >     version="1.0b30",       # new value for `main`
+       ```
+
+   - Title the merge commit: "Release beta 30".
+
+   - Push `main` to GitHub.
+
+2. Create a new release.
+
+   - On the GitHub repository home page click *Releases* — *Draft a new release*
+
+       - Tag: (create new) `release/1.0b30`
+
+       - Target: `main`
+
+       - Title: `Release 1.0 beta 30`
+
+       - description: (list all tickets & PRs included since the previous release)
+
+       - This is a pre-release: (leave unchecked)
+
+       - Click *Publish release*.
+
+3. Prepare `develop` for the next release.
+
+   - Add a commit to increment the version in `setup.py` .
+
+       ```
+       <    version="1.0b30.dev1",
+       >    version="1.0b31.dev1",
+       ```
+
+   - Title the commit "Prepare beta 31".
+
+   - Push `develop` to GitHub.

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="hca-metadata-api",
-    version="1.0b35",
+    version="1.0b36",
     license='MIT',
     install_requires=[
         "dataclasses >= 0.6;python_version<'3.7'"

src/humancellatlas/data/metadata/api.py

@@ -657,11 +657,11 @@ def is_sequencing_process(self):
 
 
 @dataclass(frozen=True)
-class ImagingTarget:
+class ImagingProbe:
     assay_type: str
 
     @classmethod
-    def from_json(cls, json: JSON) -> 'ImagingTarget':
+    def from_json(cls, json: JSON) -> 'ImagingProbe':
         assay_type = ontology_label(json['assay_type'])
         return cls(assay_type=assay_type)
 
@@ -762,15 +762,24 @@ class IpscInductionProtocol(Protocol):
 
 @dataclass(init=False)
 class ImagingProtocol(Protocol):
-    target: List[ImagingTarget]  # A list so all the ImagingTarget objects can be tallied when indexed
+    probe: List[ImagingProbe]  # A list so all the ImagingProbe objects can be tallied when indexed
 
     def __init__(self,
                  json: JSON,
                  metadata_manifest_entry: Optional[ManifestEntry]
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
-        self.target = [ImagingTarget.from_json(target) for target in content['target']]
+        self.probe = [
+            ImagingProbe.from_json(probe)
+            for probe in lookup(content, 'probe', 'target', default=[])
+        ]
+
+    @property
+    def target(self) -> List[ImagingProbe]:
+        warnings.warn('ImagingProtocol.target is deprecated. '
+                      'Use ImagingProtocol.probe instead.', DeprecationWarning)
+        return self.probe
 
 
 @dataclass(init=False)

test/test.py

@@ -560,8 +560,8 @@ def test_imaging_protocol(self):
         manifest, metadata_files = self._canned_bundle('staging', uuid, version)
         bundle = Bundle(uuid, version, manifest, metadata_files)
         imaging_protocol = one([p for p in bundle.protocols.values() if isinstance(p, ImagingProtocol)])
-        self.assertEqual(len(imaging_protocol.target), 240)
-        assay_types = {target.assay_type for target in imaging_protocol.target}
+        self.assertEqual(len(imaging_protocol.probe), 240)
+        assay_types = {probe.assay_type for probe in imaging_protocol.probe}
         self.assertEqual(assay_types, {'in situ sequencing'})
 
     def test_cell_line(self):