From a3a9e9a760f55ab1e9eda1126b77eb623985e862 Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Thu, 3 Jul 2025 14:38:03 +0200 Subject: [PATCH 1/4] improved sphinx build --- .github/workflows/docs.yml | 2 ++ docs/api/generated/opendvp.io.adata_to_perseus.rst | 6 ------ docs/api/generated/opendvp.io.adata_to_voronoi.rst | 6 ++++++ docs/api/generated/opendvp.io.geojson_to_sdata.rst | 6 ------ docs/api/generated/opendvp.io.sdata_to_qupath.rst | 6 ------ .../opendvp.preprocessing.impute_marker_with_annotation.rst | 6 ------ docs/api/generated/opendvp.preprocessing.rescale.rst | 6 ------ docs/api/generated/opendvp.tl.impute_single.rst | 6 ------ docs/api/io.md | 1 + docs/api/preprocessing.md | 0 docs/api/tools.md | 0 src/opendvp/io/qupath_export_core.py | 0 12 files changed, 9 insertions(+), 36 deletions(-) delete mode 100644 docs/api/generated/opendvp.io.adata_to_perseus.rst create mode 100644 docs/api/generated/opendvp.io.adata_to_voronoi.rst delete mode 100644 docs/api/generated/opendvp.io.geojson_to_sdata.rst delete mode 100644 docs/api/generated/opendvp.io.sdata_to_qupath.rst delete mode 100644 docs/api/generated/opendvp.preprocessing.impute_marker_with_annotation.rst delete mode 100644 docs/api/generated/opendvp.preprocessing.rescale.rst delete mode 100644 docs/api/generated/opendvp.tl.impute_single.rst delete mode 100644 docs/api/preprocessing.md delete mode 100644 docs/api/tools.md delete mode 100644 src/opendvp/io/qupath_export_core.py 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/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/src/opendvp/io/qupath_export_core.py b/src/opendvp/io/qupath_export_core.py deleted file mode 100644 index e69de29..0000000 From 9d8cd82c50a197b706d1648ba01a72febe3c0301 Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Thu, 3 Jul 2025 14:43:59 +0200 Subject: [PATCH 2/4] Capitalized Workflows and Tutorials --- docs/index.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/index.md b/docs/index.md index 98ed442..7c2f89e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -77,12 +77,11 @@ 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 +``` From 0c382e3c47d897c2e7d30f15caf41acd25e2ed35 Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Thu, 3 Jul 2025 14:55:51 +0200 Subject: [PATCH 3/4] changed links in main page --- docs/index.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/index.md b/docs/index.md index 7c2f89e..83e85bb 100644 --- a/docs/index.md +++ b/docs/index.md @@ -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 From 2764f4ba40a39860d44c14beae2444cb3cbd1e54 Mon Sep 17 00:00:00 2001 From: Jose Nimo Date: Fri, 4 Jul 2025 09:14:42 +0200 Subject: [PATCH 4/4] docs changed --- docs/Workflows/index.md | 11 +++++++---- docs/index.md | 2 +- 2 files changed, 8 insertions(+), 5 deletions(-) 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/index.md b/docs/index.md index 83e85bb..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.