Merge branch 'dev' into 1.3

.github/workflows/docker_base.yml

@@ -1,4 +1,4 @@
-name: Docker Container (Base)
+name: Container build (Base)
 
 on:
   push:
@@ -8,25 +8,20 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Docker image to GitHub Packages
+    name: Push to quay.io
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to Docker Hub
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USER }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: beckerlab/aradeepopsis-base
-          path: containers/base
-          tag_with_ref: true
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-          registry: docker.pkg.github.com
-          repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-base
-          path: containers/base
-          tag_with_ref: true
+
+      - name: Login to quay.io
+        env:
+          QUAY_USER: ${{ secrets.REGISTRY_USER }}
+          QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+        run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io
+
+      - name: Build container
+        run: podman build --tag beckerlab/aradeepopsis-base containers/base
+
+      - name: Push container
+        run: podman push beckerlab/aradeepopsis-base docker://quay.io/beckerlab/aradeepopsis-base:${GITHUB_REF##*/}

.github/workflows/docker_dpp.yml

@@ -1,4 +1,4 @@
-name: Docker Container (DPP)
+name: Container build (DPP)
 
 on:
   push:
@@ -8,25 +8,20 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Docker image to GitHub Packages
+    name: Push to quay.io
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to Docker Hub
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USER }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: beckerlab/aradeepopsis-dpp
-          path: containers/addons/dpp
-          tag_with_ref: true
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-          registry: docker.pkg.github.com
-          repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-dpp
-          path: containers/addons/dpp
-          tag_with_ref: true
+
+      - name: Login to quay.io
+        env:
+          QUAY_USER: ${{ secrets.REGISTRY_USER }}
+          QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+        run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io
+
+      - name: Build container
+        run: podman build --tag beckerlab/aradeepopsis-dpp containers/addons/dpp
+
+      - name: Push container
+        run: podman push beckerlab/aradeepopsis-dpp docker://quay.io/beckerlab/aradeepopsis-dpp:${GITHUB_REF##*/}

.github/workflows/docker_shiny.yml

@@ -1,4 +1,4 @@
-name: Docker Container (Shiny)
+name: Container build (Shiny)
 
 on:
   push:
@@ -8,25 +8,20 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Docker image to GitHub Packages
+    name: Push to quay.io
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to Docker Hub
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USER }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: beckerlab/aradeepopsis-shiny
-          path: containers/shiny
-          tag_with_ref: true
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-          registry: docker.pkg.github.com
-          repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-shiny
-          path: containers/shiny
-          tag_with_ref: true
+
+      - name: Login to quay.io
+        env:
+          QUAY_USER: ${{ secrets.REGISTRY_USER }}
+          QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+        run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io
+
+      - name: Build container
+        run: podman build --tag beckerlab/aradeepopsis-shiny containers/shiny
+
+      - name: Push container
+        run: podman push beckerlab/aradeepopsis-shiny docker://quay.io/beckerlab/aradeepopsis-shiny:${GITHUB_REF##*/}

.github/workflows/minimal_test.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        nxf_ver: ["20.01.0", ""]
+        nxf_ver: ["20.07.1", ""]
     steps:
       - uses: actions/checkout@v2
 

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## [v1.3](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.3) - 2021-01-11
 
+* changed container registry from docker.io to quay.io
 * improved image visualization and plot rendering in Shiny app (see [#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) thanks @dschneiderch for input
 * updated `scikit-image` `0.17.2` > `0.18.1`
 * updated `imagemagick` dependency `7.0.10_23` > `7.0.10_28`

README.md

@@ -7,13 +7,6 @@
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.1-important.svg)](https://www.nextflow.io/)
 [![conda](https://img.shields.io/badge/install%20with-conda-brightgreen.svg)](https://conda.io/)
 
-| Container  | Image size  | Pulls | Latest version  | 
-| :---: | :---: | :---: | :---: |
-| ![Docker Container (Base)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(Base)/badge.svg?branch=master) | ![Docker Size (Base)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-base?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-base) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-base?sort=semver) |
-| ![Docker Container (Shiny)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(Shiny)/badge.svg?branch=master)  | ![Docker Size (Shiny)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-shiny?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-shiny) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-shiny?sort=semver) |
-| ![Docker Docker (DPP)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(DPP)/badge.svg?branch=master) | ![Docker Size (DPP)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-dpp?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-dpp) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-base?sort=semver) |
-
-
 # Introduction
 
 `ARADEEPOPSIS` is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner.

assets/shiny/app.R

@@ -1,18 +1,18 @@
 # Copyright (C) 2019-2021 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 
 library(shiny)
 library(slickR)

bin/data_record.py

@@ -2,19 +2,19 @@
 
 # Copyright (C) 2019-2020 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 
 import tensorflow as tf
 

bin/frozen_graph.py

@@ -2,19 +2,19 @@
 
 # Copyright (C) 2019-2020 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 # ======================================================================
 # Portions of this code are modifications based on work created and
 # shared by Google and used according to terms described in the

bin/traits.py

@@ -2,19 +2,19 @@
 
 # Copyright (C) 2019-2020 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 
 import csv
 import os

conf/base.config

@@ -1,23 +1,23 @@
 /*
 Copyright (C) 2019-2020 Patrick Hüther
 
-This file is part of araDeepopsis.
-araDeepopsis free software: you can redistribute it and/or modify
+This file is part of ARADEEPOPSIS.
+ARADEEPOPSIS is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
-araDeepopsis is distributed in the hope that it will be useful,
+ARADEEPOPSIS is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
-along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 /* -------------------------------------------------
- * Nextflow config file for araDeepopsis
+ * Nextflow config file for ARADEEPOPSIS
  * -------------------------------------------------
  */
 
@@ -28,36 +28,36 @@ env {
 
 process {
   withName: build_records {
-    container = 'beckerlab/aradeepopsis-base:1.3'
+    container = 'quay.io/beckerlab/aradeepopsis-base:1.3'
     cpus = 1
     memory = 2.GB
     time = 1.h
   }
   withName: run_predictions {
-    container = 'beckerlab/aradeepopsis-base:1.3'
+    container = 'quay.io/beckerlab/aradeepopsis-base:1.3'
     cpus = 2
     memory = params.multiscale ? 12.GB : 6.GB
     time = 4.h
   }
   withName: run_predictions_DPP {
-    container = 'beckerlab/aradeepopsis-dpp:1.3'
+    container = 'quay.io/beckerlab/aradeepopsis-dpp:1.3'
     cpus = 2
     memory = 2.GB
     time = 4.h
   }
   withName: extract_traits {
-    container = 'beckerlab/aradeepopsis-base:1.3'
+    container = 'quay.io/beckerlab/aradeepopsis-base:1.3'
     cpus = 1
     memory = 2.GB
     time = 1.h
   }
   withName: draw_diagnostics {
-    container = 'beckerlab/aradeepopsis-base:1.3'
+    container = 'quay.io/beckerlab/aradeepopsis-base:1.3'
     cpus = 1
     memory = 2.GB
     time = 1.h
   }
   withName: launch_shiny {
-    container = 'beckerlab/aradeepopsis-shiny:1.3'
+    container = 'quay.io/beckerlab/aradeepopsis-shiny:1.3'
   }
 }

conf/cbe.config

@@ -1,19 +1,19 @@
 /*
 Copyright (C) 2019-2020 Patrick Hüther
 
-This file is part of araDeepopsis.
-araDeepopsis free software: you can redistribute it and/or modify
+This file is part of ARADEEPOPSIS.
+ARADEEPOPSIS is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
-araDeepopsis is distributed in the hope that it will be useful,
+ARADEEPOPSIS is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
-along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 /* -------------------------------------------------

conf/charliecloud.config

@@ -1,23 +1,23 @@
 /*
 Copyright (C) 2019-2021 Patrick Hüther
 
-This file is part of araDeepopsis.
-araDeepopsis free software: you can redistribute it and/or modify
+This file is part of ARADEEPOPSIS.
+ARADEEPOPSIS is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
-araDeepopsis is distributed in the hope that it will be useful,
+ARADEEPOPSIS is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
-along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 /* -------------------------------------------------
- * Nextflow config file for araDeepopsis
+ * Nextflow config file for ARADEEPOPSIS
  * -------------------------------------------------
  */