From 2b40294edbe94485ca1a61dbf50bf93fe7e4b93e Mon Sep 17 00:00:00 2001 From: Qin Yu Date: Mon, 25 Nov 2024 19:47:54 +0100 Subject: [PATCH 1/4] fix(docs): wrong `bioimageio.core` dependency name --- docs/chapters/plantseg_legacy/installation.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/chapters/plantseg_legacy/installation.md b/docs/chapters/plantseg_legacy/installation.md index d5c89bec..a818fdb5 100644 --- a/docs/chapters/plantseg_legacy/installation.md +++ b/docs/chapters/plantseg_legacy/installation.md @@ -41,19 +41,19 @@ PlantSeg can be installed directly by executing in the terminal (or PowerShell o * NVIDIA GPU version, CUDA=12.x ```bash - mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` * NVIDIA GPU version, CUDA=11.x ```bash - mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` * CPU version ```bash - mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` === "Windows" @@ -61,19 +61,19 @@ PlantSeg can be installed directly by executing in the terminal (or PowerShell o * NVIDIA GPU version, CUDA=12.x ```bash - mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 nifty=1.2.1=*_4 plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 nifty=1.2.1=*_4 plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` * NVIDIA GPU version, CUDA=11.x ```bash - mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 nifty=1.2.1=*_4 plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 nifty=1.2.1=*_4 plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` * CPU version ```bash - mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly nifty=1.2.1=*_4 plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly nifty=1.2.1=*_4 plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` === "macOS" @@ -81,7 +81,7 @@ PlantSeg can be installed directly by executing in the terminal (or PowerShell o * Apple silicon version ```bash - mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch plant-seg=1.8.1 biomagecore.io --no-channel-priority + mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch plant-seg=1.8.1 bioimageio.core --no-channel-priority ``` If you used older versions of PlantSeg, please delete the old config files in `~/.plantseg_models/configs/` after installing new PlantSeg. From 98f3d94eba8baf04df252575abd1f309298d166d Mon Sep 17 00:00:00 2001 From: Qin Yu Date: Mon, 25 Nov 2024 19:48:29 +0100 Subject: [PATCH 2/4] docs: make instruction for v1 installation obvious, fix #350 --- docs/chapters/getting_started/index.md | 2 +- docs/chapters/getting_started/installation.md | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/chapters/getting_started/index.md b/docs/chapters/getting_started/index.md index 25eb8efe..ff42f54d 100644 --- a/docs/chapters/getting_started/index.md +++ b/docs/chapters/getting_started/index.md @@ -42,7 +42,7 @@ detailed description of the parameters. ## PlantSeg with Legacy GUI !!! failure "Deprecated" - This interface is deprecated and has been removed from PlantSeg v2. Please use the Napari viewer or the command line interface instead, or install PlantSeg v1. + This interface is deprecated and has been removed from PlantSeg v2. Please use the Napari viewer or the command line interface instead, or [install PlantSeg v1](../plantseg_legacy/installation.md). PlantSeg app can also be started in a GUI mode, where basic user interface allows to configure and run the pipeline. First, activate the newly created conda environment with: diff --git a/docs/chapters/getting_started/installation.md b/docs/chapters/getting_started/installation.md index 222968d3..878f14d2 100644 --- a/docs/chapters/getting_started/installation.md +++ b/docs/chapters/getting_started/installation.md @@ -1,5 +1,7 @@ # Installation +This is the installation guide for the latest PlantSeg. Please check the installation guide for PlantSeg v1 at [PlantSeg Legacy Installation](../plantseg_legacy/installation.md). + ## Prerequisites for Conda package * Linux, Windows, macOS (not all features are available on macOS) @@ -105,3 +107,7 @@ If you plan to use SimpleITK-based watershed segmentation, you will need to inst conda activate plant-seg pip install SimpleITK ``` + +## Installing PlantSeg v1 + +Please check the installation guide for PlantSeg v1 at [PlantSeg Legacy Installation](../plantseg_legacy/installation.md). From 17839e89edbec190c464afb8bab760fd471cedb4 Mon Sep 17 00:00:00 2001 From: Qin Yu Date: Mon, 25 Nov 2024 20:00:23 +0100 Subject: [PATCH 3/4] docs: remove unused page and rename "legacy" to "v1" --- docs/chapters/python_api/functionals/index.md | 4 ---- mkdocs.yml | 10 ++++------ 2 files changed, 4 insertions(+), 10 deletions(-) delete mode 100644 docs/chapters/python_api/functionals/index.md diff --git a/docs/chapters/python_api/functionals/index.md b/docs/chapters/python_api/functionals/index.md deleted file mode 100644 index 4a3319f4..00000000 --- a/docs/chapters/python_api/functionals/index.md +++ /dev/null @@ -1,4 +0,0 @@ -# PlantSeg Python API - -!!! info "Documentation in Progress" - This page is under development. diff --git a/mkdocs.yml b/mkdocs.yml index f8fbbf98..c9ae3d30 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -116,26 +116,24 @@ nav: - Training: chapters/plantseg_models/training.md - API: - # - chapters/python_api/index.md - tasks: - plantseg.tasks.io_tasks: chapters/python_api/tasks/io_tasks.md - plantseg.tasks.dataprocessing_tasks: chapters/python_api/tasks/dataprocessing_tasks.md - plantseg.tasks.segmentation_tasks: chapters/python_api/tasks/segmentation_tasks.md - plantseg.tasks.prediction_tasks: chapters/python_api/tasks/prediction_tasks.md - - functionals: - plantseg.io: chapters/python_api/functionals/io.md - plantseg.functionals.dataprocessing: chapters/python_api/functionals/data_processing.md - plantseg.functionals.prediction: chapters/python_api/functionals/cnn_prediction.md - plantseg.functionals.segmentation: chapters/python_api/functionals/segmentation.md - - - PlantSeg Legacy: + + - PlantSeg v1: - chapters/plantseg_legacy/installation.md - - PlantSeg Classic GUI: + - Classic GUI: - chapters/plantseg_legacy/plantseg_classic_gui/index.md - Data Processing: chapters/plantseg_legacy/plantseg_classic_gui/data_processing.md - Prediction: chapters/plantseg_legacy/plantseg_classic_gui/cnn_prediction.md - Segmentation: chapters/plantseg_legacy/plantseg_classic_gui/segmentation.md - Classic CLI: - - chapters/plantseg_legacy/plantseg_classic_cli/index.md \ No newline at end of file + - chapters/plantseg_legacy/plantseg_classic_cli/index.md From 63d75c879871b90e8f5a0eed7c463e0a50ee8a3b Mon Sep 17 00:00:00 2001 From: Qin Yu Date: Mon, 25 Nov 2024 20:01:29 +0100 Subject: [PATCH 4/4] fix(docs): update links --- docs/chapters/getting_started/index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/chapters/getting_started/index.md b/docs/chapters/getting_started/index.md index ff42f54d..94f6d384 100644 --- a/docs/chapters/getting_started/index.md +++ b/docs/chapters/getting_started/index.md @@ -17,7 +17,7 @@ then, start the plantseg in napari plantseg --napari ``` -A more in depth guide can be found in our [documentation (GUI)](https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/). +A more in depth guide can be found in our [documentation (GUI)](../plantseg_interactive_napari/index.md). ## Command Line PlantSeg @@ -36,7 +36,7 @@ plantseg --config CONFIG_PATH ``` where `CONFIG_PATH` is the path to the `YAML` configuration file. See [config.yaml](https://github.com/kreshuklab/plant-seg/blob/master/examples/config.yaml) for a sample configuration -file and our [documentation (CLI)](https://hci-unihd.github.io/plant-seg/chapters/plantseg_classic_cli/) for a +file and our [documentation (CLI)](../plantseg_legacy/plantseg_classic_cli/index.md) for a detailed description of the parameters. ## PlantSeg with Legacy GUI @@ -57,4 +57,4 @@ then, run the GUI by simply typing: plantseg --gui ``` -A more in depth guide can be found in our [documentation (Classic GUI)](https://hci-unihd.github.io/plant-seg/chapters/plantseg_classic_gui/). +A more in depth guide can be found in our [documentation (Classic GUI)](../plantseg_legacy/plantseg_classic_gui/index.md).