Merge pull request #638 from oist/develop-main

Release v1.2.1

Makefile

@@ -28,38 +28,51 @@ build_frontend:
 	docker-compose -f docker-compose.test.yml build build_studio_frontend
 	docker-compose -f docker-compose.test.yml run build_studio_frontend
 
+.PHONY: format
+format:
+	black studio *.py
+	isort studio *.py
+	flake8 studio *.py
+
 .PHONY: docs
 docs:
 	rm -rf docs/_build/
 	poetry install --with doc --no-root
 	# sphinx-apidoc -f -o ./docs/_build/modules ./studio
 	sphinx-autobuild -b html docs docs/_build --port 8001
 
-.PHONY: dockerhub
-dockerhub:
-	docker build --rm -t oistncu/optinist:latest . --platform=linux/amd64
-	docker push oistncu/optinist:latest
-
 .PHONY: local_build
 local_build:
+	rm -rf dist
 	cd frontend && yarn install --ignore-scripts && yarn build
 	poetry build
 
-.PHONY: upload_testpypi
-upload_testpypi:
+.PHONY: push_testpypi
+push_testpypi:
 	poetry publish -r testpypi
 
 .PHONY: install_testpypi
 install_testpypi:
-	pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ optinist
+	pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ optinist==${ver}
 	pip show optinist
 
+.PHONY: build_test_docker
+build_test_docker:
+	docker build --no-cache -t optinist-release-test:${ver} -f studio/config/docker/Dockerfile .
+
+.PHONY: run_test_docker
+run_test_docker:
+	docker run -it \
+	-v ${volume}:/app/studio_data \
+	--env OPTINIST_DIR="/app/studio_data" \
+	--name optinist-release-test -d -p 8000:8000 optinist-release-test:${ver} \
+	poetry run python main.py --host 0.0.0.0 --port 8000
+
 .PHONY: push_pypi
 push_pypi:
 	poetry publish
 
-.PHONY: format
-format:
-	black studio *.py
-	isort studio *.py
-	flake8 studio *.py
+.PHONY: push_dockerhub
+push_dockerhub:
+	docker build --rm -t oistncu/optinist:latest -f studio/config/docker/Dockerfile . --platform=linux/amd64
+	docker push oistncu/optinist:latest

docs/conf.py

@@ -19,7 +19,7 @@
 project = "OptiNiSt"
 copyright = f"{datetime.today().year}, OIST"
 author = ""
-release = "1.2.0"
+release = "1.2.1"
 
 # -- readthedocs -------------------------------------------------------------
 on_rtd = os.environ.get("READTHEDOCS", None) == "True"

docs/gui/workflow.md

@@ -224,14 +224,8 @@ You may not want to modify your original data folder, or you may want to make yo
      We implement loading C libraries for reading NIKON and Olympus file.
      The libraries are available only on Linux and Windows (Not on MacOS).
 
-     And due to the license issue, we cannot distribute their library in this project.
-     You need to get the libraries by yourself and add them to the path. To do that,
-
-     - get the C library files from the manufacturer's support.
-     - use OptiNiSt by :ref:`developer mode <each-platforms-for-developer>`.
-     - set environment value ``MICROSCOPES_LIBRARY_DIR`` in ``studio/config/.env`` to your library path.
-     - put the libraries into ``MICROSCOPES_LIBRARY_DIR/dll/{nikon | olympus}/{linux | windows}/``
-     - If you use Linux, open ``studio/app/optinist/wrappers/optinist/conda/microscope.yaml`` and uncomment the ``- gcc=12`` line.
+     - If you use Linux, use OptiNiSt by :ref:`developer mode <each-platforms-for-developer>`.
+      - open ``studio/app/optinist/wrappers/optinist/conda/microscope.yaml`` and uncomment the ``- gcc=12`` line.
   ```
 
   <p align="center">

frontend/build/asset-manifest.json

@@ -1,16 +1,16 @@
 {
   "files": {
     "main.css": "/static/css/main.341bf264.css",
-    "main.js": "/static/js/main.2a95acf7.js",
+    "main.js": "/static/js/main.0f19d410.js",
     "static/js/47.145ba9bc.chunk.js": "/static/js/47.145ba9bc.chunk.js",
     "static/media/logo.png": "/static/media/logo.e44efe3246aecc6d6219.png",
     "index.html": "/index.html",
     "main.341bf264.css.map": "/static/css/main.341bf264.css.map",
-    "main.2a95acf7.js.map": "/static/js/main.2a95acf7.js.map",
+    "main.0f19d410.js.map": "/static/js/main.0f19d410.js.map",
     "47.145ba9bc.chunk.js.map": "/static/js/47.145ba9bc.chunk.js.map"
   },
   "entrypoints": [
     "static/css/main.341bf264.css",
-    "static/js/main.2a95acf7.js"
+    "static/js/main.0f19d410.js"
   ]
 }

frontend/build/index.html

@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="manifest" href="/static/manifest.json"/><title>OptiNiSt</title><script defer="defer" src="/static/js/main.2a95acf7.js"></script><link href="/static/css/main.341bf264.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="manifest" href="/static/manifest.json"/><title>OptiNiSt</title><script defer="defer" src="/static/js/main.0f19d410.js"></script><link href="/static/css/main.341bf264.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>

frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "optinist",
-  "version": "1.2.0",
+  "version": "1.2.1",
   "engines": {
     "node": ">=20.0.0"
   },

frontend/src/components/Workspace/Experiment/ExperimentStatusIcon.tsx

@@ -72,6 +72,7 @@ const ErrorIcon = memo(function ErrorIcon({ message }: ErrorIconProps) {
           color="error"
           padding={2}
           marginBottom={0}
+          whiteSpace="pre-wrap"
         >
           {message}
         </Typography>

frontend/src/components/Workspace/FlowChart/FlowChart.tsx

@@ -222,7 +222,7 @@ const FlowChart = memo(function FlowChart(props: UseRunPipelineReturnType) {
                   horizontal: "left",
                 }}
               >
-                <div style={{ margin: 8 }}>
+                <div style={{ margin: 8, whiteSpace: "pre-wrap"}}>
                   <FormHelperText error={true}>
                     {messageError.message}
                   </FormHelperText>

frontend/src/components/Workspace/Visualize/Plot/ImagePlot.tsx

@@ -455,7 +455,6 @@ const ImagePlotChart = memo(function ImagePlotChart({
   }
 
   const onChartClick = (event: PlotMouseEvent) => {
-    if (![MERGE_ROI, DELETE_ROI].includes(action)) return
     // use as unknown because original PlotDatum does not have z property
     const point: PlotDatum = event.points[0] as unknown as PlotDatum
     if (point.curveNumber >= 1 && outputKey === "cell_roi") {

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "optinist"
 description = "Calcium Imaging Pipeline Tool"
-version = "1.2.0"
+version = "1.2.1"
 license = "GPL-3.0"
 authors = ["OIST <[email protected]>"]
 readme = "README.md"
@@ -36,7 +36,12 @@ include = [
   "sample_data/input/*",
   "sample_data/output/**/*.yaml",
 ]
-exclude = ["studio/tests/*", "studio/test_data/*", "conda.env.*"]
+exclude = [
+  "studio/tests/*",
+  "studio/test_data/*",
+  "conda.env.*",
+  "studio/app/optinist/microscopes/libs.zip",
+]
 
 [tool.poetry.dependencies]
 python = "^3.8.1"

sample_data/output/tutorial2/experiment.yaml

@@ -1,91 +1,95 @@
-finished_at: '2023-11-22 17:20:57'
+workspace_id: '1'
+unique_id: tutorial2
+name: Tutorial2
+started_at: '2024-04-11 16:47:34'
+finished_at: '2024-04-11 16:49:14'
+success: success
+hasNWB: true
 function:
-  caiman_cnmf_z6a16cmiwl:
-    finished_at: '2023-11-22 17:20:48'
-    hasNWB: true
-    message: caiman_cnmf success
-    name: caiman_cnmf
-    outputPaths:
-      all_roi:
-        max_index: null
-        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_z6a16cmiwl/all_roi.json
-        type: roi
-      cell_roi:
-        max_index: null
-        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_z6a16cmiwl/cell_roi.json
-        type: roi
-      fluorescence:
-        max_index: 6
-        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_z6a16cmiwl/fluorescence
-        type: timeseries
-      images:
-        max_index: 1
-        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_z6a16cmiwl/images.json
-        type: images
-      non_cell_roi:
-        max_index: null
-        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_z6a16cmiwl/non_cell_roi.json
-        type: roi
-    started_at: null
-    success: success
-    unique_id: caiman_cnmf_z6a16cmiwl
   caiman_mc_p4f6nsi9bh:
-    finished_at: '2023-11-22 17:20:50'
+    unique_id: caiman_mc_p4f6nsi9bh
+    name: caiman_mc
+    success: success
     hasNWB: true
     message: caiman_mc success
-    name: caiman_mc
     outputPaths:
       mc_images:
-        max_index: 2000
-        path: /tmp/studio/output/1/tutorial2/caiman_mc_p4f6nsi9bh/mc_images.json
+        path: /tmp/studio/output/1/tutorial2/caiman_mc_p4f6nsi9bh/tiff/mc_images/mc_images.tif
         type: images
+        max_index: 2000
       meanImg:
-        max_index: 1
         path: /tmp/studio/output/1/tutorial2/caiman_mc_p4f6nsi9bh/meanImg.json
         type: images
+        max_index: 1
       rois:
-        max_index: null
         path: /tmp/studio/output/1/tutorial2/caiman_mc_p4f6nsi9bh/rois.json
         type: roi
-    started_at: null
-    success: success
-    unique_id: caiman_mc_p4f6nsi9bh
+        max_index: null
+    started_at: '2024-04-11 16:47:49'
+    finished_at: '2024-04-11 16:48:34'
   input_0:
-    finished_at: '2023-11-22 17:20:42'
+    unique_id: input_0
+    name: sample_mouse2p_image.tiff
+    success: success
     hasNWB: false
     message: null
-    name: sample_mouse2p_image.tiff
     outputPaths: null
-    started_at: '2023-11-22 17:20:42'
-    success: success
-    unique_id: input_0
+    started_at: '2024-04-11 16:47:34'
+    finished_at: '2024-04-11 16:47:34'
   pca_xi0d87mbrk:
-    finished_at: '2023-11-22 17:20:57'
+    unique_id: pca_xi0d87mbrk
+    name: pca
+    success: success
     hasNWB: true
     message: pca success
-    name: pca
     outputPaths:
-      contribution:
+      explained_variance:
+        path: /tmp/studio/output/1/tutorial2/pca_xi0d87mbrk/evr.json
+        type: bar
         max_index: null
+      projectedNd:
+        path: /tmp/studio/output/1/tutorial2/pca_xi0d87mbrk/projectedNd.json
+        type: scatter
+        max_index: null
+      contribution:
         path: /tmp/studio/output/1/tutorial2/pca_xi0d87mbrk/contribution.json
         type: bar
-      cumsum_contribution:
         max_index: null
+      cumsum_contribution:
         path: /tmp/studio/output/1/tutorial2/pca_xi0d87mbrk/cumsum_contribution.json
         type: bar
-      explained_variance:
         max_index: null
-        path: /tmp/studio/output/1/tutorial2/pca_xi0d87mbrk/evr.json
-        type: bar
-      projectedNd:
-        max_index: null
-        path: /tmp/studio/output/1/tutorial2/pca_xi0d87mbrk/projectedNd.json
-        type: scatter
-    started_at: '2023-11-22 17:20:53'
+    started_at: '2024-04-11 16:49:09'
+    finished_at: '2024-04-11 16:49:14'
+  caiman_cnmf_qcjcwx9uq7:
+    unique_id: caiman_cnmf_qcjcwx9uq7
+    name: caiman_cnmf
     success: success
-    unique_id: pca_xi0d87mbrk
-hasNWB: true
-name: Tutorial2
+    hasNWB: true
+    message: caiman_cnmf success
+    outputPaths:
+      images:
+        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_qcjcwx9uq7/images.json
+        type: images
+        max_index: 1
+      fluorescence:
+        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_qcjcwx9uq7/fluorescence
+        type: timeseries
+        max_index: 4
+      all_roi:
+        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_qcjcwx9uq7/all_roi.json
+        type: roi
+        max_index: null
+      cell_roi:
+        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_qcjcwx9uq7/cell_roi.json
+        type: roi
+        max_index: null
+      non_cell_roi:
+        path: /tmp/studio/output/1/tutorial2/caiman_cnmf_qcjcwx9uq7/non_cell_roi.json
+        type: roi
+        max_index: null
+    started_at: '2024-04-11 16:48:36'
+    finished_at: '2024-04-11 16:48:59'
 nwb:
   device:
     description: Microscope Information
@@ -119,7 +123,3 @@ snakemake:
   forcetargets: true
   lock: false
   use_conda: true
-started_at: '2023-11-22 17:20:42'
-success: success
-unique_id: tutorial2
-workspace_id: '1'