Merge branch 'main' into BioinfoTongLI/main

quentinblampey · May 2, 2024 · 121cfd1 · 121cfd1
2 parents c436785 + de79d25
commit 121cfd1
Show file tree

Hide file tree

Showing 29 changed files with 2,487 additions and 256 deletions.
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -0,0 +1,31 @@
+name: Release
+
+on:
+    release:
+        types: [published]
+
+jobs:
+    release:
+        # requires that you have put your twine API key in your
+        # github secrets (see readme for details)
+        runs-on: ubuntu-latest
+        if: contains(github.ref, 'tags')
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v3
+
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+
+            - name: Install hatch
+              run: pip install hatch
+
+            - name: Build project for distribution
+              run: hatch build
+
+            - name: Publish a Python distribution to PyPI
+              uses: pypa/gh-action-pypi-publish@release/v1
+              with:
+                  password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/test_and_deploy.yaml → .github/workflows/test.yaml b/.github/workflows/test_and_deploy.yaml → .github/workflows/test.yaml
@@ -28,7 +28,7 @@ jobs:
         steps:
             - uses: actions/checkout@v2
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
 
@@ -49,7 +49,7 @@ jobs:
                   pip install pytest-cov
             - name: Install dependencies
               run: |
-                  pip install -e ".[dev,test]"
+                  pip install --pre -e ".[dev,test]"
             - name: Test
               env:
                   MPLBACKEND: agg
@@ -62,29 +62,3 @@ jobs:
               with:
                   name: coverage
                   verbose: true
-    deploy:
-        # this will run when you have tagged a commit, starting with "v*"
-        # and requires that you have put your twine API key in your
-        # github secrets (see readme for details)
-        needs: [test]
-        runs-on: ubuntu-latest
-        if: contains(github.ref, 'tags')
-        steps:
-            - name: Checkout code
-              uses: actions/checkout@v3
-
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-
-            - name: Install hatch
-              run: pip install hatch
-
-            - name: Build project for distribution
-              run: hatch build
-
-            - name: Publish a Python distribution to PyPI
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                  password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -23,10 +23,14 @@ __pycache__/
 # IDEs
 /.idea/
 /.vscode/
+/.spyproject/
 
 # docs
 /docs/generated/
 /docs/_build/
 
 # other
 _version.py
+.code-workspace
+temp/
+node_modules/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,26 +7,26 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.7.0
+      rev: 24.4.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0
+      rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.15.0
+      rev: 1.16.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
+      rev: 5.13.2
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.4.1
+      rev: v1.9.0
       hooks:
           - id: mypy
-            additional_dependencies: [numpy]
+            additional_dependencies: [numpy, types-PyYAML]
             exclude: docs/
     - repo: https://github.com/asottile/yesqa
       rev: v1.5.0
@@ -40,7 +40,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.6.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -50,7 +50,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/PyCQA/autoflake
-      rev: v2.2.0
+      rev: v2.3.1
       hooks:
           - id: autoflake
             args:
@@ -59,7 +59,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 6.0.0
+      rev: 7.0.0
       hooks:
           - id: flake8
             additional_dependencies:
@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.9.0
+      rev: v3.15.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py39-plus, --keep-runtime-typing]

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -13,3 +13,4 @@ python:
           path: .
           extra_requirements:
               - doc
+              - pre
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,9 +8,101 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## [Unreleased]
+## [0.1.3] - xxxx-xx-xx
 
 ### Added
 
--   Basic tool, preprocessing and plotting functions
--   An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
+-   (Xenium) support reading multi-polygon selection files from the Xenium Explorer
+-   (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
+
+### Fixed
+
+-   (Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique.
+    obs_names_make_unique is now called internally to enforce unique index values allowing for join operations.
+
+## [0.1.2] - 2024-03-30
+
+### Added
+
+-   (Visium HD) added reader, coauthored by @LLehner
+
+### Fixed
+
+-   (Xenium) reader for 1.0.1 (paper data) and unknown versions
+-   (Xenium) fix in reading "minimalistic" Xenium datasets #132
+
+## [0.1.1] - 2024-03-24
+
+### Added
+
+-   (Xenium) support for post-xenium aligned images (IF, HE)
+-   (Xenium) reader for the selection coordinates file from the Xenium Explorer
+-   (Xenium) support for the new Xenium 2.0.0 (multimodal segmentation)
+-   (Xenium) reading multiscale labels from cells.zarr.zip
+-   (MCMICRO) support for TMAs (such as the data of exemplar-002)
+-   (DBiT-seq) reader
+-   converter functions `experimental.to_legacy_anndata()` and `experimental.from_legacy_anndata()`
+-   (Visium) support for raw reads (capture locations not under tissue)
+
+### Fixed
+
+-   (Xenium) fixed index (fail on write)
+-   (Xenium) renamed cells_as_shapes to cells_as_circles; set default to True
+-   (MERSCOPE) don't try to load unexisting elements #87
+-   (Visium) fixed axes ordering
+
+## [0.0.9] - 2023-11-06
+
+### Fixed
+
+-   (Xenium) bug when converting feature_name #81, from @fbnrst
+-   (Visium) visium() supports file counts without dataset_id #91
+
+## [0.0.8] - 2023-10-02
+
+### Fixed
+
+-   (Xenium) coerce cell id to str #64
+-   (MERSCOPE) fix coordinate transformation #68
+-   (MERSCOPE) Improvements/fixes: merscope reader #73
+
+## [0.0.7] - 2023-07-23
+
+### Fixed
+
+-   Bugs in Xenium and MERSCOPE
+
+## [0.0.5] - 2023-06-21
+
+### Added
+
+-   MERFISH reader (from @quentinblampey)
+-   CODEX reader (from @LLehner)
+
+### Fixed
+
+-   Issues on Visium reader (thanks @ilia-kats) and Xenium reader
+
+## [0.0.4] - 2023-05-23
+
+### Added
+
+-   Curio reader
+
+## [0.0.3] - 2023-05-22
+
+### Merged
+
+-   Merge pull request #40 from scverse/fix/categories
+
+## [0.0.2] - 2023-05-04
+
+### Changed
+
+-   Revert version regex (#37)
+
+## [0.0.1] - 2023-05-04
+
+### Tested
+
+-   Test installation from pypi
diff --git a/README.md b/README.md
@@ -4,20 +4,23 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![DOI](https://zenodo.org/badge/544045123.svg)](https://zenodo.org/badge/latestdoi/544045123)
 
-[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml/badge.svg
-[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml
+[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
+[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 
--   NanoString CosMx
--   MCMICRO (output data)
--   Steinbock (output data)
 -   10x Genomics Visium
+-   10x Genomics Visium HD
 -   10x Genomics Xenium
--   Curio Seeker
 -   Akoya PhenoCycler (formerly CODEX)
+-   Curio Seeker
+-   DBiT-seq
+-   MCMICRO (output data)
+-   NanoString CosMx
+-   Steinbock (output data)
 -   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started
@@ -50,9 +53,18 @@ pip install git+https://github.com/scverse/spatialdata-io.git@main
 For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
 If you found a bug, please use the [issue tracker][issue-tracker].
 
+## Readers from third-party libraries
+
+Technologies that can be read into `SpatialData` objects using third-party libraries:
+
+-   METASPACE (MALDI, ...): [metaspace-converter](https://github.com/metaspace2020/metaspace-converter)
+-   PhenoCycler: [SOPA](https://github.com/gustaveroussy/sopa)
+-   MACSima: [SOPA](https://github.com/gustaveroussy/sopa)
+-   Hyperion (Imaging Mass Cytometry): [SOPA](https://github.com/gustaveroussy/sopa)
+
 ## Citation
 
-[L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1). \* = equal contribution
+Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/scverse/spatialdata-io/issues

diff --git a/docs/api.md b/docs/api.md
@@ -8,18 +8,53 @@
 
 I/O for the `spatialdata` project.
 
+### Readers
+
 ```{eval-rst}
 .. autosummary::
     :toctree: generated
 
     codex
-    curio
     cosmx
+    curio
+    dbit
+    mcmicro
+    merscope
+    steinbock
     visium
+    visium_hd
     xenium
-    steinbock
-    merscope
-    mcmicro
+```
+
+### Experimental readers
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    iss
+```
+
+### Conversion functions
+
+### Experimental conversion functions
+
+```{eval-rst}
+.. currentmodule:: spatialdata_io.experimental
+
+.. autosummary::
+    :toctree: generated
+
+    from_legacy_anndata
+    to_legacy_anndata
+```
+
+### Utility functions
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
 
-    experimental - iss
+    xenium_aligned_image
+    xenium_explorer_selection
 ```