Release V1.1 (#36)

* update logo

* pin pillow version to 7.0.0

pillow 7.1.1 caused an incompatibility with scikit-image ImageCollections

thanks @bisnow33 for reporting the issue

* unpin pillow

regression was fixed in pillow release 7.1.2

* remove error strategy for local runs

Previously, a job that failed because of insufficient memory was
resubmitted 3 times and resource requirements were increased for
each attempt.

e.g run_predictions required:

- 2 CPUs and 6GB RAM for the first attempt
- 4 CPUs and 12GB RAM for the second attempt
- 6 CPUs and 18GB RAM for the third attempt

While such a strategy makes sense in a cluster environment, where
increased resource requests can be satisfied, it makes little sense
on a local computer with given hardware limitations.

This commit removes the error strategy for local pipeline runs.

* enable integration tests when pushing to dev

* fix display of shiny server IP on macOS

Previously, the logic assumed that `hostname -i` returns the local
ip address of the host. Apparently this is not the case on MacOS,
thus fall back to localhost on these systems.

* (attempt to) fix string conversion of uname output

* add CHANGELOG.md

* set version tags for 1.1 release

Author: phue

.github/workflows/minimal_test.yml

@@ -7,7 +7,6 @@ on:
   push:
     branches-ignore:
       - master
-      - dev
 
 jobs:
   test:

CHANGELOG.md

@@ -0,0 +1,10 @@
+# Changelog
+
+## [v1.1](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.1) - 2020-05-13
+
+* disabled task error strategy for pipeline runs on local computers
+* fixed an issue where the network address of the shiny application was not correctly displayed on computers running MacOS
+
+## [v1.0](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.0) - 2020-04-02
+
+Initial pipeline release

Dockerfile

@@ -6,6 +6,6 @@ LABEL authors="[email protected]" \
 COPY environment.yml /
 RUN apt-get update && apt-get install -y procps graphviz && apt-get clean -y
 RUN conda env create -f /environment.yml && conda clean -afy
-ENV PATH /opt/conda/envs/aradeepopsis-v1.0/bin:$PATH
+ENV PATH /opt/conda/envs/aradeepopsis-v1.1/bin:$PATH
 
 EXPOSE 44333

conf/base.config

@@ -26,11 +26,8 @@ env {
 }
 
 process {
-  container = 'beckerlab/aradeepopsis:1.0'
+  container = 'beckerlab/aradeepopsis:1.1'
 
-  errorStrategy = { task.exitStatus in [104,134,135,137,139,140,143] ? 'retry' : 'finish' }
-  maxRetries = 3
-
   withName: build_records {
     cpus = { 1 * task.attempt }
     memory = { 2.GB * task.attempt }

conf/cbe.config

@@ -29,6 +29,9 @@ process {
   queue = 'c'
   clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
 
+  errorStrategy = { task.exitStatus in [104,134,135,137,139,140,143] ? 'retry' : 'finish' }
+  maxRetries = 3
+
   withName: build_records {
     cpus = { 1 * task.attempt }
     memory = { 1.GB * task.attempt }

docs/parameters.md

@@ -89,6 +89,6 @@ Launch a [Shiny](https://shiny.rstudio.com/) app in 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 beckerlab/aradeepopsis:1.0 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 beckerlab/aradeepopsis:1.1 R -e "shiny::runApp('/mnt/shiny/app.R', port=44333, host='0.0.0.0')"
 > ```
-> The shiny app can then be opened with a browser by typing localhost:44333 in the address bar. It will terminate when the browser window is closed.
+> The shiny app can then be opened with a browser by typing localhost:44333 in the address bar. It will terminate when the browser window is closed.

environment.yml

@@ -1,4 +1,4 @@
-name: aradeepopsis-v1.0
+name: aradeepopsis-v1.1
 channels:
   - conda-forge
   - r

main.nf

@@ -316,7 +316,6 @@ ch_results
  .set {ch_resultfile}
 
 process launch_shiny {
-    tag "${'http://'+'hostname -i'.execute().text.trim()+':44333'}"
     containerOptions { workflow.profile.contains('singularity') ? '' : '-p 44333:44333' }
     executor 'local'
     cache false
@@ -327,8 +326,9 @@ process launch_shiny {
     when:
         params.shiny
     script:
+        def ip = "uname".execute().text.trim() == "Darwin" ? "localhost" : "hostname -i".execute().text.trim()
         log.error"""
-        Visit the shiny server running at ${"http://"+"hostname -i".execute().text.trim()+':44333'} to inspect the results.
+        Visit the shiny server running at ${"http://"+ip+':44333'} to inspect the results.
         Closing the browser window will terminate the pipeline.
         """.stripIndent()
         """

nextflow.config

@@ -52,7 +52,7 @@ manifest {
     homePage = 'https://github.com/Gregor-Mendel-Institute/aradeepopsis'
     description = "Nextflow pipeline to run semantic segmentation on plant rosette images with DeepLab V3+"
     name = 'aradeepopsis'
-    version = '1.0'
+    version = '1.1'
     mainScript = 'main.nf'
     nextflowVersion = '>=20.01.0'
 }