diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index fc06bfc..f5ccc6b 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -4,6 +4,8 @@ on: push: tags: - 'v*' + branches: + - docs jobs: build-docs: diff --git a/docs/Workflows/index.md b/docs/Workflows/index.md index 005c98d..faf0f14 100644 --- a/docs/Workflows/index.md +++ b/docs/Workflows/index.md @@ -35,10 +35,13 @@ Ready to explore the proteomics of more complex tissues? or you are planning a l Requirements and workflow vary so much between projects that it is not worth generalizing. But there are four main components: -1. Image processing -2. Image analysis -3. Sample collection and LCMS -4. Downstream proteomic analysis +1. Image acquisition +2. Image processing +3. Image analysis +4. Sampling strategy +5. Sample collection +6. Sample prepatation and LCMS +7. Downstream proteomic analysis openDVP highly recommends utilizing open-source image processing pipelines: MCMICRO and SOPA are wonderful examples, each with their tradeoffs. diff --git a/docs/api/generated/opendvp.io.adata_to_perseus.rst b/docs/api/generated/opendvp.io.adata_to_perseus.rst deleted file mode 100644 index 6fe06fc..0000000 --- a/docs/api/generated/opendvp.io.adata_to_perseus.rst +++ /dev/null @@ -1,6 +0,0 @@ -opendvp.io.adata\_to\_perseus -============================= - -.. currentmodule:: opendvp.io - -.. autofunction:: adata_to_perseus \ No newline at end of file diff --git a/docs/api/generated/opendvp.io.adata_to_voronoi.rst b/docs/api/generated/opendvp.io.adata_to_voronoi.rst new file mode 100644 index 0000000..8ea9894 --- /dev/null +++ b/docs/api/generated/opendvp.io.adata_to_voronoi.rst @@ -0,0 +1,6 @@ +opendvp.io.adata\_to\_voronoi +============================= + +.. currentmodule:: opendvp.io + +.. autofunction:: adata_to_voronoi \ No newline at end of file diff --git a/docs/api/generated/opendvp.io.geojson_to_sdata.rst b/docs/api/generated/opendvp.io.geojson_to_sdata.rst deleted file mode 100644 index b6e6d8a..0000000 --- a/docs/api/generated/opendvp.io.geojson_to_sdata.rst +++ /dev/null @@ -1,6 +0,0 @@ -opendvp.io.geojson\_to\_sdata -============================= - -.. currentmodule:: opendvp.io - -.. autofunction:: geojson_to_sdata \ No newline at end of file diff --git a/docs/api/generated/opendvp.io.sdata_to_qupath.rst b/docs/api/generated/opendvp.io.sdata_to_qupath.rst deleted file mode 100644 index 0d12eed..0000000 --- a/docs/api/generated/opendvp.io.sdata_to_qupath.rst +++ /dev/null @@ -1,6 +0,0 @@ -opendvp.io.sdata\_to\_qupath -============================ - -.. currentmodule:: opendvp.io - -.. autofunction:: sdata_to_qupath \ No newline at end of file diff --git a/docs/api/generated/opendvp.preprocessing.impute_marker_with_annotation.rst b/docs/api/generated/opendvp.preprocessing.impute_marker_with_annotation.rst deleted file mode 100644 index ab6d55c..0000000 --- a/docs/api/generated/opendvp.preprocessing.impute_marker_with_annotation.rst +++ /dev/null @@ -1,6 +0,0 @@ -opendvp.preprocessing.impute\_marker\_with\_annotation -====================================================== - -.. currentmodule:: opendvp.preprocessing - -.. autofunction:: impute_marker_with_annotation \ No newline at end of file diff --git a/docs/api/generated/opendvp.preprocessing.rescale.rst b/docs/api/generated/opendvp.preprocessing.rescale.rst deleted file mode 100644 index 12dc9ce..0000000 --- a/docs/api/generated/opendvp.preprocessing.rescale.rst +++ /dev/null @@ -1,6 +0,0 @@ -opendvp.preprocessing.rescale -============================= - -.. currentmodule:: opendvp.preprocessing - -.. autofunction:: rescale \ No newline at end of file diff --git a/docs/api/generated/opendvp.tl.impute_single.rst b/docs/api/generated/opendvp.tl.impute_single.rst deleted file mode 100644 index 27f9cdd..0000000 --- a/docs/api/generated/opendvp.tl.impute_single.rst +++ /dev/null @@ -1,6 +0,0 @@ -opendvp.tl.impute\_single -========================= - -.. currentmodule:: opendvp.tl - -.. autofunction:: impute_single \ No newline at end of file diff --git a/docs/api/io.md b/docs/api/io.md index 1127117..05177a9 100644 --- a/docs/api/io.md +++ b/docs/api/io.md @@ -9,6 +9,7 @@ :toctree: generated io.adata_to_qupath + io.adata_to_voronoi io.import_thresholds io.quant_to_adata io.segmask_to_qupath diff --git a/docs/api/preprocessing.md b/docs/api/preprocessing.md deleted file mode 100644 index e69de29..0000000 diff --git a/docs/api/tools.md b/docs/api/tools.md deleted file mode 100644 index e69de29..0000000 diff --git a/docs/index.md b/docs/index.md index 98ed442..39584d6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,7 +7,7 @@ [![PyPI version](https://img.shields.io/pypi/v/openDVP.svg)](https://pypi.org/project/openDVP/) [![License](https://img.shields.io/github/license/CosciaLab/openDVP.svg)](https://github.com/CosciaLab/opendvp/blob/main/LICENSE) -`opendvp` is a python package containing different tools enabling users to perform deep visual proteomics. To perform quality control and image analysis of multiplex immunofluorescence. Also to integrate imaging datasets with proteomic datasets with [Spatialdata](https://github.com/scverse/spatialdata). Lastly, it contains a powerful toolkit for label-free downstream proteomic analysis. +`opendvp` is a python package offering a comprehensive set of tools for deep visual proteomics. It supports quality control and image analysis of multiplex immunofluorescence data. openDVP facilitates the integration of imaging datasets with proteomic datasets with [Spatialdata](https://github.com/scverse/spatialdata). Lastly, it contains a powerful toolkit for label-free downstream proteomic analysis. It is a package that leverages the [scverse](https://www.scverse.org/) ecosystem, designed for easy interoperability with `anndata`, `scanpy`, `decoupler`, `scimap`, and other related packages. @@ -61,12 +61,11 @@ pip install 'openDVP[spatialdata]' pip install git+https://github.com/CosciaLab/openDVP.git@main ``` - ## Tutorials -- [Tutorial 1: Image analysis](tutorials/T1_ImageAnalysis) -- [Tutorial 2: Integration of imaging with proteomics](tutorials/T2_ProteomicsIntegration) -- [Tutorial 3: Downstream proteomics analysis](tutorials/T3_DownstreamProteomics) +- [Tutorial 1: Image analysis](Tutorials/T1_ImageAnalysis) +- [Tutorial 2: Integration of imaging with proteomics](Tutorials/T2_ProteomicsIntegration) +- [Tutorial 3: Downstream proteomics analysis](Tutorials/T3_DownstreamProteomics) ## Contact @@ -77,12 +76,11 @@ For questions about openDVP and the DVP workflow you are very welcome to post a Not yet available. - ```{toctree} :maxdepth: 2 :hidden: api/index -tutorials/index -workflows/index -``` \ No newline at end of file +Tutorials/index +Workflows/index +``` diff --git a/src/opendvp/io/qupath_export_core.py b/src/opendvp/io/qupath_export_core.py deleted file mode 100644 index e69de29..0000000