Merge pull request #60 from Gregor-Mendel-Institute/2.0

merge 2.0 > master

.github/workflows/minimal_test.yml

@@ -17,11 +17,9 @@ jobs:
     strategy:
       matrix:
         engine: ["docker", "podman", "charliecloud", "conda"]
-        nxf_ver: ["20.07.1",""]
+        nxf_ver: ["22.04.0",""]
         os: ["ubuntu-latest", "macos-latest"]
         exclude:
-          - engine: "charliecloud"
-            nxf_ver: "20.07.1" # charliecloud needs 21.04.0 or later
           - os: "macos-latest"
             engine: "docker"
           - os: "macos-latest"
@@ -40,9 +38,9 @@ jobs:
       - name: Install Charliecloud
         if: ${{ matrix.engine == 'charliecloud' }}
         run: |
-          python -m pip install lark-parser requests
-          wget -qO- https://github.com/hpc/charliecloud/releases/download/v0.22/charliecloud-0.22.tar.gz | tar -xvz
-          cd charliecloud-0.22
+          python -m pip install requests
+          wget -qO- https://github.com/hpc/charliecloud/releases/download/v0.25/charliecloud-0.25.tar.gz | tar -xvz
+          cd charliecloud-0.25
           ./configure
           make
           sudo make install
@@ -62,3 +60,15 @@ jobs:
         run: |
           sudo chown -R ${UID} ${CONDA}
           nextflow run ${GITHUB_WORKSPACE} --save_rosette --save_histogram --save_hull --summary_diagnostics --shiny false -profile test,conda
+
+      - name: Upload segmentation results
+        uses: actions/upload-artifact@v2
+        with:
+          name: summary_diagnostics ${{ matrix.os }} ${{ matrix.engine }} ${{ matrix.nxf_ver }}
+          path: results/diagnostics/summary
+
+      - name: Upload Nextflow report
+        uses: actions/upload-artifact@v2
+        with:
+          name: execution_report ${{ matrix.os }} ${{ matrix.engine }} ${{ matrix.nxf_ver }}
+          path: results/www/execution_report.html

CHANGELOG.md

@@ -1,5 +1,20 @@
 # Changelog
 
+## [v2.0](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v2.0) - 2022-05-12
+
+* fixed a bug that lead to invalid dimensions for input images with certain aspect ratios
+* ported pipeline code to [nextflow dsl2](https://www.nextflow.io/docs/latest/dsl2.html)
+* bumped required `nextflow` version to `22.04.0`
+* moved hosting of pretrained models and test data to Azure (thanks @ebirn)
+* added CITATION.cff
+* added version pinning for `R 4.1.3`
+* dropped `r-shinythemes` dependency as `r-shiny` now has bootstrap 5 support
+* updated `r-shiny` `1.6.0` > `1.7.1`
+* updated `tensorflow-base` `2.4.1` > `2.7.1`
+* updated `imagemagick` dependency `7.0.11_12` > `7.1.0_33`
+* updated `r-corrplot` dependency `0.88` > `0.92`
+* updated `r-jpeg` dependency `0.1_8.1` > `0.1_9`
+
 ## [v1.3.1](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.3.1) - 2021-05-14
 
 * fixed illegible text in Markdown documents when browsing Github in Dark Mode (thanks @greymonroe for pointing this out)

CITATION.cff

@@ -0,0 +1,41 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Hüther"
+  given-names: "Patrick"
+  orcid: "https://orcid.org/0000-0003-3315-2484"
+- family-names: "Schandry"
+  given-names: "Niklas"
+  orcid: "https://orcid.org/0000-0003-3099-7860"
+title: "ARADEEPOPSIS"
+version: 2.0
+doi: 10.5281/zenodo.3946320
+date-released: 2022-05-12
+url: "https://github.com/Gregor-Mendel-Institute/aradeepopsis"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Hüther"
+    given-names: "Patrick"
+    orcid: "https://orcid.org/0000-0003-3315-2484"
+  - family-names: "Schandry"
+    given-names: "Niklas"
+    orcid: "https://orcid.org/0000-0003-3099-7860"
+  - family-names: "Jandrasits"
+    given-names: "Katharina"
+    orcid: "https://orcid.org/0000-0002-0161-582X"
+  - family-names: "Bezrukov"
+    given-names: "Ilja"
+    orcid: "https://orcid.org/0000-0003-0420-4329"
+  - family-names: "Becker"
+    given-names: "Claude"
+    orcid: "https://orcid.org/0000-0003-3406-4670"
+  doi: "10.1105/tpc.20.00318"
+  journal: "The Plant Cell"
+  month: 12
+  start: 3674
+  end: 3688
+  title: "ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States"
+  issue: 12
+  volume: 32
+  year: 2020

README.md

@@ -4,7 +4,7 @@
 ![Latest Release](https://img.shields.io/github/v/release/Gregor-Mendel-Institute/aradeepopsis?sort=semver)
 ![License](https://img.shields.io/github/license/Gregor-Mendel-Institute/aradeepopsis)
 [![DOI](https://zenodo.org/badge/240287274.svg)](https://zenodo.org/badge/latestdoi/240287274)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.1-important.svg)](https://www.nextflow.io/)  
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A522.04.0-important.svg)](https://www.nextflow.io/)  
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

assets/shiny/app.R

@@ -19,7 +19,6 @@ library(slickR)
 library(tidyverse)
 library(radarchart)
 library(shinycssloaders)
-library(shinythemes)
 library(corrplot)
 library(jpeg)
 
@@ -42,7 +41,7 @@ traitcount <- ncol(data) - 2 # exclude filename and suffix
 imagecount <- nrow(data)
 
 # Define UI
-ui <- navbarPage(title=a("aradeepopsis", href="https://github.com/Gregor-Mendel-Institute/aradeepopsis", target="_blank"), windowTitle = "ARADEEPOPSIS", id="nav", theme = shinytheme("flatly"), collapsible=TRUE,
+ui <- navbarPage(title=a("aradeepopsis", href="https://github.com/Gregor-Mendel-Institute/aradeepopsis", target="_blank"), windowTitle="ARADEEPOPSIS", id="nav", theme=bslib::bs_theme(version=5, bootswatch="flatly"), collapsible=TRUE,
 		tabPanel("Rosette Carousel",
 			sliderInput("chunk", label = "Select chunk:", min = 1, max = ceiling(imagecount/60), value = 1, width = '100%', step = 1),
 			slickROutput("slickr", width='auto', height='auto') %>% withSpinner()

conf/base.config

@@ -1,5 +1,5 @@
 /*
-Copyright (C) 2019-2021 Patrick Hüther
+Copyright (C) 2019-2022 Patrick Hüther
 
 This file is part of ARADEEPOPSIS.
 ARADEEPOPSIS is free software: you can redistribute it and/or modify
@@ -22,44 +22,44 @@ along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 env {
-  PYTHONPATH = "${PYTHONPATH}:$baseDir/bin"
+  PYTHONPATH = "${PYTHONPATH}:$projectDir/bin"
   PYTHONNOUSERSITE = 1
   R_PROFILE_USER = "/.Rprofile"
   R_ENVIRON_USER = "/.Renviron"
 }
 
 process {
-  withName: build_records {
-    container = 'quay.io/beckerlab/aradeepopsis-base:1.3.1'
+  withName: RECORDS {
+    container = { "quay.io/beckerlab/aradeepopsis-base:${workflow.manifest.version}" }
     cpus = 1
     memory = 2.GB
     time = 1.h
   }
-  withName: run_predictions {
-    container = 'quay.io/beckerlab/aradeepopsis-base:1.3.1'
+  withName: MODEL {
+    container = { "quay.io/beckerlab/aradeepopsis-base:${workflow.manifest.version}" }
     cpus = 2
     memory = params.multiscale ? 12.GB : 6.GB
     time = 4.h
   }
-  withName: run_predictions_DPP {
-    container = 'quay.io/beckerlab/aradeepopsis-dpp:1.3.1'
+  withName: DPP {
+    container = { "quay.io/beckerlab/aradeepopsis-dpp:${workflow.manifest.version}" }
     cpus = 2
     memory = 2.GB
     time = 4.h
   }
-  withName: extract_traits {
-    container = 'quay.io/beckerlab/aradeepopsis-base:1.3.1'
+  withName: MEASURE {
+    container = { "quay.io/beckerlab/aradeepopsis-base:${workflow.manifest.version}" }
     cpus = 1
     memory = 2.GB
     time = 1.h
   }
-  withName: draw_diagnostics {
-    container = 'quay.io/beckerlab/aradeepopsis-base:1.3.1'
+  withName: SUMMARY {
+    container = { "quay.io/beckerlab/aradeepopsis-base:${workflow.manifest.version}" }
     cpus = 1
     memory = 2.GB
     time = 1.h
   }
-  withName: launch_shiny {
-    container = 'quay.io/beckerlab/aradeepopsis-shiny:1.3.1'
+  withName: SHINY {
+    container = { "quay.io/beckerlab/aradeepopsis-shiny:${workflow.manifest.version}" }
   }
 }

conf/cbe.config

@@ -1,5 +1,5 @@
 /*
-Copyright (C) 2019-2021 Patrick Hüther
+Copyright (C) 2019-2022 Patrick Hüther
 
 This file is part of ARADEEPOPSIS.
 ARADEEPOPSIS is free software: you can redistribute it and/or modify
@@ -32,27 +32,27 @@ process {
   errorStrategy = { task.exitStatus in [104,134,135,137,139,140,143] ? 'retry' : 'finish' }
   maxRetries = 3
 
-  withName: build_records {
+  withName: RECORDS {
     cpus = { 1 * task.attempt }
     memory = { 1.GB * task.attempt }
     time = { 1.h * task.attempt }
   }
-  withName: run_predictions {
+  withName: MODEL {
     cpus = { 4 * task.attempt }
     memory = { 32.GB * task.attempt }
     time = { 4.h * task.attempt }
   }
-  withName: run_predictions_DPP {
+  withName: DPP {
     cpus = { 4 * task.attempt }
     memory = { 16.GB * task.attempt }
     time = { 2.h * task.attempt }
   }
-  withName: extract_traits {
+  withName: MEASURE {
     cpus = { 1 * task.attempt }
     memory = { 1.GB * task.attempt }
     time = { 1.h * task.attempt }
   }
-  withName: draw_diagnostics {
+  withName: SUMMARY {
     cpus = { 1 * task.attempt }
     memory = { 2.GB * task.attempt }
     time = { 1.h * task.attempt }

conf/conda.config

@@ -22,22 +22,22 @@ along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 process {
-  withName: build_records {
-    conda = "$baseDir/containers/base/environment.yml"
+  withName: RECORDS {
+    conda = "$projectDir/containers/base/environment.yml"
   }
-  withName: run_predictions {
-    conda = "$baseDir/containers/base/environment.yml"
+  withName: MODEL {
+    conda = "$projectDir/containers/base/environment.yml"
   }
-  withName: run_predictions_DPP {
-    conda = "$baseDir/containers/addons/dpp/environment.yml"
+  withName: DPP {
+    conda = "$projectDir/containers/addons/dpp/environment.yml"
   }
-  withName: extract_traits {
-    conda = "$baseDir/containers/base/environment.yml"
+  withName: MEASURE {
+    conda = "$projectDir/containers/base/environment.yml"
   }
-  withName: draw_diagnostics {
-    conda = "$baseDir/containers/base/environment.yml"
+  withName: SUMMARY {
+    conda = "$projectDir/containers/base/environment.yml"
   }
-  withName: launch_shiny {
-    conda = "$baseDir/containers/shiny/environment.yml"
+  withName: SHINY {
+    conda = "$projectDir/containers/shiny/environment.yml"
   }
 }

conf/test.config

@@ -22,10 +22,10 @@ along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
  */
 
 params.images = [
-                'https://github.com/Gregor-Mendel-Institute/test-data/raw/aradeepopsis/data/1.png',
-                'https://github.com/Gregor-Mendel-Institute/test-data/raw/aradeepopsis/data/2.png',
-                'https://github.com/Gregor-Mendel-Institute/test-data/raw/aradeepopsis/data/3.png',
-                'https://github.com/Gregor-Mendel-Institute/test-data/raw/aradeepopsis/data/4.png',
-                'https://github.com/Gregor-Mendel-Institute/test-data/raw/aradeepopsis/data/5.png',
-                'https://github.com/Gregor-Mendel-Institute/test-data/raw/aradeepopsis/data/6.png'
+                'https://cdn.vbc.ac.at/clip/reframe/data/aradeepopsis/1.png',
+                'https://cdn.vbc.ac.at/clip/reframe/data/aradeepopsis/2.png',
+                'https://cdn.vbc.ac.at/clip/reframe/data/aradeepopsis/3.png',
+                'https://cdn.vbc.ac.at/clip/reframe/data/aradeepopsis/4.png',
+                'https://cdn.vbc.ac.at/clip/reframe/data/aradeepopsis/5.png',
+                'https://cdn.vbc.ac.at/clip/reframe/data/aradeepopsis/6.png'
                 ]

containers/addons/dpp/Dockerfile

@@ -6,4 +6,4 @@ COPY environment.yml /
 RUN apt-get update \
     && apt-get install --no-install-recommends -y procps \
     && micromamba install -y -n base -f /environment.yml \
-    && micromamba clean -a && rm -rf /var/lib/{apt,dpkg,cache,log}
+    && micromamba clean -a && rm -rf /var/lib/{apt,dpkg,cache,log}

containers/base/Dockerfile

@@ -6,4 +6,4 @@ COPY environment.yml /
 RUN apt-get update \
     && apt-get install --no-install-recommends -y procps \
     && micromamba install -y -n base -f /environment.yml \
-    && micromamba clean -a && rm -rf /var/lib/{apt,dpkg,cache,log}
+    && micromamba clean -a && rm -rf /var/lib/{apt,dpkg,cache,log}

containers/base/environment.yml

@@ -3,6 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - conda-forge::tensorflow-base=2.4.1
-  - conda-forge::scikit-image=0.18.1
-  - conda-forge::imagemagick=7.0.11_12
+  - conda-forge::tensorflow-base=2.7.1
+  - conda-forge::scikit-image=0.19.2
+  - conda-forge::imagemagick=7.1.0_33

containers/shiny/Dockerfile

@@ -8,4 +8,4 @@ RUN apt-get update \
     && micromamba install -y -n base -f /environment.yml \
     && micromamba clean -a && rm -rf /var/lib/{apt,dpkg,cache,log}
 
-EXPOSE 44333
+EXPOSE 44333

containers/shiny/environment.yml

@@ -1,14 +1,13 @@
 name: aradeepopsis-shiny
 channels:
   - conda-forge
-  - r
   - defaults
 dependencies:
+  - conda-forge::r-base=4.1.3
   - conda-forge::r-tidyverse=1.3.1
-  - conda-forge::r-shiny=1.6.0
-  - conda-forge::r-shinythemes=1.2.0
+  - conda-forge::r-shiny=1.7.1
   - conda-forge::r-shinycssloaders=1.0.0
   - conda-forge::r-slickr=0.5.0
-  - conda-forge::r-corrplot=0.88
-  - conda-forge::r-jpeg=0.1_8.1
-  - r::r-radarchart=0.3.1
+  - conda-forge::r-corrplot=0.92
+  - conda-forge::r-jpeg=0.1_9
+  - conda-forge::r-radarchart=0.3.1

docs/parameters.md

@@ -132,6 +132,6 @@ Launch a [Shiny](https://shiny.rstudio.com/) app as the last step of the pipelin
 > R -e "shiny::runApp('app.R', port=44333)"
 >
 > # if using the container image
-> {docker|podman} run -v $(pwd):/mnt/shiny -p 44333:44333 quay.io/beckerlab/aradeepopsis-shiny:1.3.1 R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')"
+> {docker|podman} run -v $(pwd):/mnt/shiny -p 44333:44333 quay.io/beckerlab/aradeepopsis-shiny:2.0 R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')"
 > ```
 > The shiny app can then be opened in a browser by typing localhost:44333 in the address bar. It will terminate when the browser window is closed.