diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 154a4421..37a77a00 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -1,4 +1,4 @@ -name: Build and deploy docs +name: documentation on: push: @@ -22,7 +22,7 @@ jobs: steps: - name: Checkout uses: actions/checkout@v3 - with: + with: fetch-depth: 0 - name: Setup Pages id: pages @@ -45,7 +45,7 @@ jobs: - name: Upload build artifacts uses: actions/upload-pages-artifact@v1 with: - path: './docs/build/html' + path: "./docs/build/html" deploy: environment: diff --git a/README.md b/README.md index 6e674881..c9ecad12 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ used at the Biohub and in the broader imaging community. ### Installation -Install a pre-release of iohub with pip: +Install a released version of iohub from PyPI with pip: ```sh pip install iohub @@ -103,7 +103,7 @@ Read a directory containing a TIFF dataset: from iohub import read_images reader = read_images("/path/to/data/") -print(reader.shape) +print(reader) ``` ## Why iohub? diff --git a/docs/source/_static/switcher.json b/docs/source/_static/switcher.json index 81e37131..fe14eff2 100644 --- a/docs/source/_static/switcher.json +++ b/docs/source/_static/switcher.json @@ -2,5 +2,9 @@ { "version": "latest", "url": "/main/index.html" + }, + { + "version": "v0.1.0", + "url": "/v0.1.0/index.html" } -] \ No newline at end of file +] diff --git a/iohub/convert.py b/iohub/convert.py index c9dc3fa7..d810fbba 100644 --- a/iohub/convert.py +++ b/iohub/convert.py @@ -352,7 +352,7 @@ def _convert_image_plane_metadata(self, fov, zarr_name: str): if not sorted_keys: # Sort keys, ordering keys without dashes first sorted_keys = sorted( - metadata.keys(), key=lambda x: ('-' in x, x) + metadata.keys(), key=lambda x: ("-" in x, x) ) sorted_metadata = {key: metadata[key] for key in sorted_keys} diff --git a/iohub/reader.py b/iohub/reader.py index 3003b7bf..708fb81e 100644 --- a/iohub/reader.py +++ b/iohub/reader.py @@ -10,6 +10,7 @@ import tifffile as tiff import zarr +from iohub._deprecated.reader_base import ReaderBase from iohub._deprecated.singlepagetiff import MicromanagerSequenceReader from iohub._deprecated.zarrfile import ZarrReader from iohub.fov import BaseFOVMapping @@ -127,7 +128,7 @@ def read_images( data_type: Literal[ "singlepagetiff", "ometiff", "ndtiff", "omezarr" ] = None, -): +) -> ReaderBase | BaseFOVMapping: """Read image arrays and metadata from a Micro-Manager dataset. Supported formats are Micro-Manager-acquired TIFF datasets (single-page TIFF, multi-page OME-TIFF, NDTIFF), @@ -143,8 +144,8 @@ def read_images( Returns ------- - Reader - A child instance of ReaderBase + ReaderBase | BaseFOVMapping + Image collection object for the dataset """ path = Path(path).resolve() # try to guess data type