Hotfix/vendored-read-until (#292)

* Remove git read-until dependency
Ignore vendored read-until base tests

* Alter `read_until` imports to be `readfish.read_until`

* Minimal vendored `read_until` package
Taken from v3.4.1 tag
**SOME IMPORTS EDITED** to point to readfish.read_until

* Omit read_until python files from coverage

Author: Adoni5

.github/workflows/CI.yml

@@ -47,7 +47,7 @@ jobs:
           python -m site
           python -m pip install -U pip setuptools wheel
           python -m pip install -e ".[tests]"
-          coverage run -pm pytest
+          coverage run --omit "src/readfish/read_until/*.py" -pm pytest
       - name: Upload coverage data
         uses: actions/upload-artifact@v3
         with:
@@ -97,7 +97,7 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: built-package
-          path: dist
+          path: dist/
           if-no-files-found: error
 
   build-docs:
@@ -148,7 +148,6 @@ jobs:
         uses: actions/download-artifact@v3
         with:
           name: built-package
-          path: dist
 
       - name: Publish package distributions to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

pyproject.toml

@@ -35,7 +35,6 @@ dependencies = [
     "rtoml",
     "more_itertools",
     'exceptiongroup ; python_version<"3.11"',
-    "read_until @ git+https://github.com/nanoporetech/read_until_api@v3.4.1",
     "readfish_summarise >= 0.2.5",
     "readfish[all]",
 ]
@@ -82,4 +81,4 @@ testpaths = [
 markers = [
     "alignment: marks tests which rely on loading or using Mappy or Mappy-rs aligners, used to test with both. (deselect with '-m \"not slow\", select with '-k alignment')",
 ]
-addopts = ["-ra", "--doctest-modules"]
+addopts = ["-ra", "--doctest-modules", "--ignore=src/readfish/read_until/base.py"]

src/readfish/_read_until_client.py

@@ -9,7 +9,7 @@
 
 from minknow_api.acquisition_pb2 import AcquisitionState
 from minknow_api import protocol_service, acquisition_service
-from read_until import ReadUntilClient
+from readfish.read_until.base import ReadUntilClient
 from readfish._loggers import setup_logger
 from grpc import RpcError
 

src/readfish/entry_points/targets.py

@@ -76,8 +76,8 @@
 from typing import Any
 
 # Third party imports
-from read_until.read_cache import AccumulatingCache
-from read_until import ReadUntilClient
+from readfish.read_until.read_cache import AccumulatingCache
+from readfish.read_until import ReadUntilClient
 from minknow_api import protocol_service
 
 # Library

src/readfish/plugins/abc.py

@@ -20,7 +20,7 @@
 from readfish.plugins.utils import Result
 
 import numpy as np
-from read_until.base import CALIBRATION
+from readfish.read_until.base import CALIBRATION
 
 if TYPE_CHECKING:
     import minknow_api

src/readfish/read_until/__init__.py

@@ -0,0 +1,5 @@
+from readfish.read_until._version import __version__
+from readfish.read_until.base import ReadUntilClient
+from readfish.read_until.read_cache import ReadCache, AccumulatingCache
+
+__all__ = ["__version__", "ReadUntilClient", "ReadCache", "AccumulatingCache"]

src/readfish/read_until/_version.py

@@ -0,0 +1 @@
+__version__ = "3.4.1"