Merge pull request #161 from zktuong/productive-ratio-and-vj-gene-usage

add new functions and rework github actions
zktuong · Jul 7, 2022 · 69ae2e2 · 69ae2e2
2 parents 04586e2 + 28e6d99
commit 69ae2e2
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diff --git a/.github/workflows/badge.yml b/.github/workflows/badge.yml
@@ -1,52 +1,21 @@
 name: badge
 
 on:
-  pull_request:
-    branches:
-      - "*"
   push:
     branches:
       - "master"
-      - "devel"
   create:
     tags:
       - "*"
 
 
 jobs:
-  devel:
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    if: github.ref != 'refs/heads/master'
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.7'
-      - id: version
-        name: Install package
-        run: |
-          pip install setuptools wheel setuptools_scm numpy
-          pip install git+https://www.github.com/zktuong/dandelion@devel
-          echo "##[set-output name=version;]$(python dandelion/logging/_badge.py)"
-      - name: version badge
-        uses: RubbaBoy/BYOB@v1.2.0
-        with:
-          NAME: devel-version
-          LABEL: 'devel-version'
-          ICON: 'github'
-          STATUS: ${{ steps.version.outputs.version}}
-          COLOR: blue
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   master:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
-    if: github.ref != 'refs/heads/devel'
+    if: github.ref == 'refs/heads/master'
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python

diff --git a/.github/workflows/singularity_container-install.yml b/.github/workflows/singularity_container-install.yml
@@ -3,15 +3,35 @@ on:
   push:
     branches:
       - master
-      - devel
-      - "*"
 
   # Do the builds on all pull requests (to test them)
   pull_request: 
     branches:
       - "*"
 jobs:
+  changes:
+    name: Checking changed files
+    runs-on: ubuntu-latest
+    outputs:
+      changed_file: ${{ steps.files.outputs.added_modified }}
+      keepgoing: ${{ steps.checkfiles.outputs.keepgoing }}
+    steps:
+      - id: files
+        uses: jitterbit/get-changed-files@b17fbb00bdc0c0f63fcf166580804b4d2cdc2a42
+        with:
+          format: 'json'
+      - id: checkfiles
+        run: |
+          if [[ ${{ steps.files.outputs.added_modified }} == *.yml* || ${{ steps.files.outputs.added_modified }} == *.py* || ${{ steps.files.outputs.added_modified }} == *test* || ${{ steps.files.outputs.added_modified }} == *requirements* ]] ; then
+            echo "::set-output name=keepgoing::true"
+          else
+            echo "::set-output name=keepgoing::false"
+          fi
+
   container:
+    needs:
+      - changes
+    if: needs.changes.outputs.keepgoing == 'true'
     runs-on: ubuntu-latest
     steps:
       - name: Set up Go 1.13

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -7,13 +7,34 @@ on:
   push:
     branches:
       - "master"
-      - "devel"
 
 env:
   cache-version: 'cache-v1'
 
 jobs:
-  tests:    
+  changes:
+    name: Checking changed files
+    runs-on: ubuntu-latest
+    outputs:
+      changed_file: ${{ steps.files.outputs.added_modified }}
+      keepgoing: ${{ steps.checkfiles.outputs.keepgoing }}
+    steps:
+      - id: files
+        uses: jitterbit/get-changed-files@b17fbb00bdc0c0f63fcf166580804b4d2cdc2a42
+        with:
+          format: 'json'
+      - id: checkfiles
+        run: |
+          if [[ ${{ steps.files.outputs.added_modified }} == *.yml* || ${{ steps.files.outputs.added_modified }} == *.py* || ${{ steps.files.outputs.added_modified }} == *test* || ${{ steps.files.outputs.added_modified }} == *requirements* ]]; then
+            echo "::set-output name=keepgoing::true"
+          else
+            echo "::set-output name=keepgoing::false"
+          fi
+
+  tests:
+    needs:
+      - changes
+    if: needs.changes.outputs.keepgoing == 'true'
     timeout-minutes: 720
     defaults:
       run:
@@ -42,7 +63,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-node@v2
-    
+
     - name: Install ubuntu system dependencies
       if: matrix.config.os == 'ubuntu-latest'
       run: |
@@ -76,7 +97,7 @@ jobs:
         python-version: ${{ matrix.config.python-version }}
         environment-file: environment.yml
         use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-   
+
     - name: Display Python version
       run: |
         python --version
@@ -100,7 +121,7 @@ jobs:
     - id: R
       name: Check R version
       run: |
-        R --version > VERSION        
+        R --version > VERSION
         echo "##[set-output name=version;]$(head -1 VERSION | awk '{print $3}')"
         echo "##[set-output name=mainbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
         echo "##[set-output name=subbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')"
@@ -112,11 +133,11 @@ jobs:
       with:
         r-version: ${{ steps.R.outputs.version}}
 
-    - name: Setup r-lib/remotes      
+    - name: Setup r-lib/remotes
       run: |
         install.packages('remotes')
       shell: Rscript {0}
-    
+
     - name: Cache ubuntu R packages
       if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
       uses: actions/cache@v2
@@ -132,11 +153,11 @@ jobs:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }}
         restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-
-        
+
     - name: Install Dandelion
       run: |
         python -m pip install .
-              
+
     - name: Install ubuntu R dependencies
       if: matrix.config.os == 'ubuntu-latest'
       run: |
@@ -161,7 +182,7 @@ jobs:
         install.packages(c('shazam', 'alakazam', 'tigger', 'airr', 'optparse'))
       shell: Rscript {0}
 
-    - name: Test if R dependencies are installed properly      
+    - name: Test if R dependencies are installed properly
       run: |
         Rscript tests/r_dependencies.R
       shell: bash -l {0}

diff --git a/DESCRIPTION.md b/DESCRIPTION.md
@@ -2,8 +2,6 @@
 [![](https://img.shields.io/pypi/v/sc-dandelion?logo=PyPI)](https://pypi.org/project/sc-dandelion/)
 [![](https://byob.yarr.is/zktuong/dandelion/master-version)](https://github.com/zktuong/dandelion/tree/master)
 [![master](https://github.com/zktuong/dandelion/workflows/tests/badge.svg?branch=master)]((https://github.com/zktuong/dandelion/actions?query=workflow%3Atests))
-[![](https://byob.yarr.is/zktuong/dandelion/devel-version)](https://github.com/zktuong/dandelion/tree/devel)
-[![tests](https://github.com/zktuong/dandelion/workflows/tests/badge.svg?branch=devel)](https://github.com/zktuong/dandelion/actions?query=workflow%3Atests)
 [![codecov](https://codecov.io/gh/zktuong/dandelion/branch/master/graph/badge.svg?token=661BMU1FBO)](https://codecov.io/gh/zktuong/dandelion)
 [![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
 [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zktuong/dandelion/blob/master/container/dandelion_singularity.ipynb)

diff --git a/README.md b/README.md
@@ -2,8 +2,6 @@
 [![](https://img.shields.io/pypi/v/sc-dandelion?logo=PyPI)](https://pypi.org/project/sc-dandelion/)
 [![](https://byob.yarr.is/zktuong/dandelion/master-version)](https://github.com/zktuong/dandelion/tree/master)
 [![master](https://github.com/zktuong/dandelion/workflows/tests/badge.svg?branch=master)]((https://github.com/zktuong/dandelion/actions?query=workflow%3Atests))
-[![](https://byob.yarr.is/zktuong/dandelion/devel-version)](https://github.com/zktuong/dandelion/tree/devel)
-[![tests](https://github.com/zktuong/dandelion/workflows/tests/badge.svg?branch=devel)](https://github.com/zktuong/dandelion/actions?query=workflow%3Atests)
 [![codecov](https://codecov.io/gh/zktuong/dandelion/branch/master/graph/badge.svg?token=661BMU1FBO)](https://codecov.io/gh/zktuong/dandelion)
 [![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
 [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zktuong/dandelion/blob/master/container/dandelion_singularity.ipynb)
@@ -83,8 +81,7 @@ pip install "rpy2>=3.4.2" # or if you don't mind having conda manage R: conda in
 # Use pip to install the following with --no-cache-dir --upgrade if necessary
 # and then lastly install this
 pip install sc-dandelion
-# or pip install git+https://github.com/zktuong/dandelion.git
-# for the development branch, run this: pip install git+https://github.com/zktuong/dandelion.git@devel
+# or for the latest version, pip install git+https://github.com/zktuong/dandelion.git
 
 # to use ddl.pl.clone_overlap, please install nxviz:
 pip install git+https://github.com/zktuong/nxviz.git@custom_color_mapping_circos_nodes_and_edges

diff --git a/container/environment_dev.yml b/container/environment_dev.yml
diff --git a/container/sc-dandelion_dev.def b/container/sc-dandelion_dev.def
diff --git a/dandelion/plotting/__init__.py b/dandelion/plotting/__init__.py
@@ -2,13 +2,14 @@
 # @Author: Kelvin
 # @Date:   2020-05-13 23:21:45
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2022-07-04 08:29:04
+# @Last Modified time: 2022-07-06 21:42:43
 """init module."""
 from ._plotting import (
     barplot,
     clone_network,
     clone_overlap,
     clone_rarefaction,
+    productive_ratio,
     spectratype,
     stackedbarplot,
 )
@@ -18,6 +19,7 @@
     "clone_network",
     "clone_overlap",
     "clone_rarefaction",
+    "productive_ratio",
     "spectratype",
     "stackedbarplot",
 ]