mypy implementation for adapters in tiled (#700)

* some more changes

* typed zarr.py

* typed tiff.py

* xarray.py typed

* some more typing added

* some more typing. still few problems in mapping.py

* more typing

* still 1 mypy problem left

* docstring skeletons added

* some more improvement

* solved some docs build problems

* few more changes

* change type_alliases.py

* some more changes

* some more changes

* update python to 3.11 in doc compilation

* fixed failing tests

* Add protocols

* change docs python to 3.10

* preliminary addressing to the comments

* some tests for protocols

* some corrections in protocols tests

* fix small bug in test_protocols.py

* try to solve EllipsisType that only exists in python 3.10

* change python version check

* some more fix

* Bump Python version of docs build.

* tests

* some more unit tests for protocols

* add accesspolicy protocol tests

* few more fixes

* python 3.8 MutableMapping problem: try to replacse with the one from typing

* try to change collections.abc.MApping with typing.Mapping if python<3.8

* small fixes for typing errors appeared in python 3.8

* one more typing fix for python 3.8

* some more fix python3.8

* Type awkward buffers dict more strictly

* Tighten typing on data_uris.

* Fix typing of partition parameter in read_partition.

* Zarr accepts array data, not dataframe/tabular.

* Remove commented unused code

* Fix typo

* Fix type of partition

* added a changelog entry

* Make python-version consistent for docs

---------

Co-authored-by: Seher Karakuzu <[email protected]>
Co-authored-by: Dan Allan <[email protected]>

.github/pull_request_template.md

@@ -0,0 +1,3 @@
+### Checklist
+- [ ] Add a Changelog entry
+- [ ] Add the ticket number which this PR closes to the comment section

.github/workflows/docs.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.12"]
       fail-fast: false
 
     steps:

.github/workflows/publish-docs.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.12"]
       fail-fast: false
 
     steps:

.mypy.ini

@@ -0,0 +1,26 @@
+[mypy]
+ignore_errors = True
+ignore_missing_imports = True
+disallow_untyped_defs = False
+disallow_untyped_calls = False
+check_untyped_defs = False
+disallow_incomplete_defs = False
+
+
+[mypy-tiled.adapters.*]
+ignore_errors = False
+ignore_missing_imports = False
+check_untyped_defs = True
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
+disallow_untyped_calls = True
+disallow_untyped_decorators = True
+
+[mypy-tiled._tests.test_protocols]
+ignore_errors = False
+ignore_missing_imports = False
+check_untyped_defs = True
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
+disallow_untyped_calls = True
+disallow_untyped_decorators = True

.pre-commit-config.yaml

@@ -27,3 +27,9 @@ repos:
     rev: 23.10.1
     hooks:
     -   id: black
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.9.0
+    hooks:
+    -    id: mypy
+         args: [--strict]

CHANGELOG.md

@@ -10,6 +10,8 @@ Write the date in place of the "Unreleased" in the case a new version is release
 - The `tiled serve ...` CLI commands now accept a `--log-config` option,
   pointing to a custom uvicorn logging configuration file. An example
   file was added to the repository root, `example_log_config.yml`.
+- Added `tiled.adapters.protocols` which will provide possibility for user to
+  implement their custom adapters in a way that satisfies mypy.
 
 ### Changed
 

pyproject.toml

@@ -153,6 +153,7 @@ dev = [
     "pytest <8",  # TMP pin while plugins catch up
     "pytest-asyncio",
     "pytest-rerunfailures",
+    "pytest-mock",
     "sphinx !=4.1.0, !=4.1.1, !=4.1.2, !=4.2.0",
     # These are dependencies of various sphinx extensions for documentation.
     "ipython",

tiled/_tests/test_catalog.py

@@ -283,7 +283,8 @@ async def test_write_array_internal_direct(a, tmpdir):
     )
     x = await a.lookup_adapter(["x"])
     await x.write(arr)
-    assert numpy.array_equal(await x.read(), arr)
+    val = await x.read()
+    assert numpy.array_equal(val, arr)
 
 
 def test_write_array_internal_via_client(client):