bump dev/ci tools

.github/actions/setup-python-env/action.yml

@@ -1,4 +1,5 @@
 name: "Set Up Python Environment"
+description: "Set up a Python environment using uv"
 
 inputs:
   python-version:
@@ -13,10 +14,11 @@ runs:
       with:
         python-version: ${{ inputs.python-version }}
     - name: Install uv
-      uses: astral-sh/setup-uv@v7.1.6
+      uses: astral-sh/setup-uv@v7.2.0
       with:
+        python-version: ${{ inputs.python-version }}
         version-file: "pyproject.toml"
-        enable-cache: true
+        enable-cache: "auto"
         ignore-nothing-to-cache: true
     - name: Install project and dependencies
       run: uv sync --frozen --dev

.github/workflows/checks.yml

@@ -80,29 +80,41 @@ jobs:
         run: |
           uv run python -m pytest tests --verbose
   style:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+        # TODO: also run on macos-latest pending docker/colima issue
+        os: [ubuntu-latest]
     steps:
       - name: Check out repository
         uses: actions/checkout@v6
       - name: Set up Python
         uses: ./.github/actions/setup-python-env
         with:
-          python-version: "3.11"
+          python-version: ${{ matrix.python-version }}
       - name: Run formatter
         run: |
           uv run python -m ruff format --diff colandr
       - name: Run linter
         run: |
           uv run python -m ruff check --exit-zero colandr
   types:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+        # TODO: also run on macos-latest pending docker/colima issue
+        os: [ubuntu-latest]
     steps:
       - name: Check out repository
         uses: actions/checkout@v6
       - name: Set up Python
         uses: ./.github/actions/setup-python-env
         with:
-          python-version: "3.11"
+          python-version: ${{ matrix.python-version }}
       - name: Check types with ty
         run: |
           uv run python -m ty check

colandr/api/v1/authn.py

@@ -14,7 +14,7 @@
 # TODO: we should use redis for this
 # import celery
 # import redis.client
-# _JWT_BLOCKLIST = celery.current_app.backend.client  # type: ignore
+# _JWT_BLOCKLIST = celery.current_app.backend.client
 _JWT_BLOCKLIST = set()
 
 

colandr/api/v1/authz.py

@@ -28,6 +28,7 @@ def user_is_allowed_for_review(
         True if user is allowed to access review; False otherwise
     """
     review = db.session.get(models.Review, review_id)
+
     review_user_assoc = (
         sa.select(models.ReviewUserAssoc)
         .where(models.ReviewUserAssoc.user_id == user.id)
@@ -44,7 +45,7 @@ def user_is_allowed_for_review(
             or db.session.execute(review_user_assoc).scalar_one_or_none() is not None
         )
         # allowed is conditional on review being frozen or not
-        and (if_frozen is True or review.status != "frozen")  # type: ignore
+        and (if_frozen is True or getattr(review, "status", None) != "frozen")
     )
 
 

colandr/api/v1/routes/citation_imports.py

@@ -149,7 +149,7 @@ def post(self, files_data, query_data):
         if data_source is None:
             data_source = models.DataSource(
                 source_type=source_type, source_name=source_name, source_url=source_url
-            )  # type: ignore
+            )
             db.session.add(data_source)
         db.session.commit()
 
@@ -211,7 +211,7 @@ def post(self, files_data, query_data):
             record_type="citation",
             num_records=n_citations,
             status=status,
-        )  # type: ignore
+        )
         db.session.add(citations_import)
         db.session.commit()
         current_app.logger.info(

colandr/api/v1/routes/citation_screenings.py

@@ -123,7 +123,7 @@ def post(self, id, json_data):
             stage="citation",
             status=json_data["status"],
             exclude_reasons=json_data["exclude_reasons"],
-        )  # type: ignore
+        )
         study.screenings.add(screening)
         db.session.commit()
 

colandr/api/v1/routes/citations.py

@@ -193,7 +193,7 @@ def post(self, json_data, query_data):
         if data_source is None:
             data_source = models.DataSource(
                 source_type=source_type, source_name=source_name, source_url=source_url
-            )  # type: ignore
+            )
             db.session.add(data_source)
         db.session.commit()
         current_app.logger.info("%s inserted %s", current_user, data_source)
@@ -206,7 +206,7 @@ def post(self, json_data, query_data):
             data_source_id=data_source.id,
             # citation=citation,
             citation=json_data,
-        )  # type: ignore
+        )
         if status is not None:
             study.citation_status = status
         db.session.add(study)

colandr/api/v1/routes/data_extractions.py

@@ -108,7 +108,7 @@ def put(self, id, json_data):
             )
 
         labels_map = {
-            item["label"]: (item["field_type"], set(item.get("allowed_values", [])))  # type: ignore
+            item["label"]: (item["field_type"], set(item.get("allowed_values", [])))
             for item in data_extraction_form[0]
         }
         # manually validate inputs, given data extraction form specification

colandr/api/v1/routes/exports.py

@@ -370,7 +370,7 @@ def get(self, query_data):
             row.citation_status: row.count
             for row in db.session.execute(n_citations_by_status_stmt)
         }
-        n_citations_screened = sum(n_citations_by_status.values())  # type: ignore
+        n_citations_screened = sum(n_citations_by_status.values())
         n_citations_excluded = n_citations_by_status.get("excluded", 0)
 
         n_fulltexts_by_status_stmt = (
@@ -383,7 +383,7 @@ def get(self, query_data):
             row.fulltext_status: row.count
             for row in db.session.execute(n_fulltexts_by_status_stmt)
         }
-        n_fulltexts_screened = sum(n_fulltexts_by_status.values())  # type: ignore
+        n_fulltexts_screened = sum(n_fulltexts_by_status.values())
         n_fulltexts_excluded = n_fulltexts_by_status.get("excluded", 0)
 
         results = db.session.execute(

colandr/api/v1/routes/fulltext_screenings.py

@@ -142,7 +142,7 @@ def post(self, id, json_data):
             stage="fulltext",
             status=json_data["status"],
             exclude_reasons=json_data["exclude_reasons"],
-        )  # type: ignore
+        )
         study.screenings.add(screening)
         db.session.commit()
 

colandr/api/v1/routes/health.py

@@ -23,7 +23,7 @@ class HealthAPI(MethodView):
     )
     @bp.output({"message": af.fields.String()})
     def get(self):
-        redis_conn = celery.current_app.backend.client  # type: ignore
+        redis_conn = celery.current_app.backend.client
         assert isinstance(redis_conn, redis.client.Redis)  # type guard
         try:
             _ = redis_conn.ping()

colandr/api/v1/routes/reviews.py

@@ -161,7 +161,7 @@ def post(self, json_data):
                     "pct": 100,
                 }
             ]
-        review = models.Review(name=name, **json_data)  # type: ignore
+        review = models.Review(name=name, **json_data)
         # TODO: do we want to allow admins to set other users as owners?
         review.review_user_assoc.append(
             models.ReviewUserAssoc(review, current_user, "owner")

colandr/lib/fileio/ris.py

@@ -90,7 +90,7 @@ def read(path_or_stream: t.BinaryIO | pathlib.Path) -> list[dict]:
 def parse(data: str) -> list[dict]:
     return rispy.loads(
         data,
-        implementation=rispy.parser.RisParser,  # type: ignore
+        implementation=rispy.parser.RisParser,
         skip_unknown_tags=False,
     )
 

colandr/lib/models/deduper_v2.py

@@ -332,7 +332,7 @@ def _estimate_prob_two_records_match(self) -> None:
                 splink.block_on("title", "author"),
             ]
             self.model.training.estimate_probability_two_random_records_match(
-                deterministic_rules,  # type: ignore
+                deterministic_rules,
                 recall=0.7,
             )
 
@@ -341,7 +341,7 @@ def _estimate_u_parameters(
     ) -> None:
         self.model.training.estimate_u_using_random_sampling(
             max_pairs=max_pairs,
-            seed=seed,  # type: ignore
+            seed=seed,
         )
 
     def _estimate_m_parameters(self) -> None:

colandr/models.py

@@ -259,7 +259,7 @@ def num_citations_by_status(self, statuses: str | list[str]) -> dict[str, int]:
         )
         # ensure every status is in result, with default value (0)
         result = {status: 0 for status in statuses}
-        result |= {row.citation_status: row.count for row in db.session.execute(stmt)}  # type: ignore
+        result |= {row.citation_status: row.count for row in db.session.execute(stmt)}
         return result
 
     def num_fulltexts_by_status(self, statuses: str | list[str]) -> dict[str, int]:
@@ -273,7 +273,7 @@ def num_fulltexts_by_status(self, statuses: str | list[str]) -> dict[str, int]:
         )
         # ensure every status is in result, with default value (0)
         result = {status: 0 for status in statuses}
-        result |= {row.fulltext_status: row.count for row in db.session.execute(stmt)}  # type: ignore
+        result |= {row.fulltext_status: row.count for row in db.session.execute(stmt)}
         return result
 
 
@@ -769,7 +769,7 @@ def __repr__(self):
 
 @sa_event.listens_for(Review, "after_insert")
 def insert_review_plan(mapper, connection, target):
-    review_plan = ReviewPlan(id=target.id)  # type: ignore
+    review_plan = ReviewPlan(id=target.id)
     connection.execute(sa.insert(ReviewPlan).values(id=target.id))
     LOGGER.info("inserted %s and %s", target, review_plan)
 

colandr/tasks.py

@@ -31,7 +31,7 @@ def _get_redis_lock(lock_id: str, timeout: int = 120) -> redis.lock.Lock:
 
 
 def _get_redis_conn() -> redis.client.Redis:
-    redis_conn = current_celery_app.backend.client  # type: ignore
+    redis_conn = current_celery_app.backend.client
     assert isinstance(redis_conn, redis.client.Redis)  # type guard
     return redis_conn
 
@@ -149,7 +149,7 @@ def deduplicate_citations(review_id: int):
     LOGGER.info(
         "<Review(id=%s)>: found %s duplicate clusters",
         review_id,
-        len(clustered_dupes),  # type: ignore
+        len(clustered_dupes),
     )
 
     # get *all* citation ids for this review, as well as included/excluded

pyproject.toml

@@ -66,7 +66,7 @@ dev = [
   "pytest-postgresql~=7.0",
   "SQLAlchemy-Utils~=0.42.0",
   # TODO: update ty once officially out of beta
-  "ty~=0.0.7",
+  "ty~=0.0.11",
   "ruff~=0.14.0",
 ]