Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeog…

…raphy

.github/markdown_lint.yaml

@@ -7,3 +7,4 @@ no-duplicate-header:
 no-trailing-spaces:
   br_spaces: 2
 no-inline-html: false
+no-bare-urls: false

.github/workflows/docker.yaml

@@ -6,6 +6,9 @@ on:
   push:
     branches:
       - master
+      - dev
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
     paths:
       - '.github/workflows/docker.yaml'
       - 'workflow/envs/merge/environment.yaml'
@@ -62,7 +65,7 @@ jobs:
       - name: docker build
         if: ${{ github.event_name == 'release' }}
         run: |
-          cd workflow/envs/main/;
+          cd workflow/envs/merge/;
           docker build --no-cache . -t ktmeaton/plague-phylogeography:${{ github.event.release.tag_name }};
       #------------------------------------------------------------------------#
       - name: docker push

.github/workflows/install.yaml

@@ -5,7 +5,8 @@ name: Install
 on:
   push:
     branches:
-      - '*'
+      - master
+      - dev
     paths:
       - '.github/workflows/install.yaml'
       - 'workflow/Snakefile'
@@ -59,43 +60,43 @@ jobs:
       #- name: Setup tmate session
       #  uses: mxschmitt/action-tmate@v3
   #----------------------------------------------------------------------------#
-  install_singularity:
-    name: Install with Singularity
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-    steps:
-      #------------------------------------------------------------------------#
-      - name: setup environment variables
-        run: |
-          echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV
-          echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV
-          echo "FLOWDASH_BIO_USERNAME=${{ secrets.FLOWDASH_BIO_USERNAME }}" >> $GITHUB_ENV
-          echo "FLOWDASH_BIO_PASSWORD=${{ secrets.FLOWDASH_BIO_PASSWORD }}" >> $GITHUB_ENV
-      #SINGULARITY_ROOT: /opt/hostedtoolcache/singularity/3.6.3/x64
-      #------------------------------------------------------------------------#
-      # Checkout Repository
-      - name: checkout repo
-        uses: actions/checkout@v2
-      #------------------------------------------------------------------------#
-      # Setup singularity
-      - name: setup singularity
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.6.3
-      #------------------------------------------------------------------------#
-      # pull container
-      - name: pull container
-        run: singularity pull docker://docker.io/ktmeaton/plague-phylogeography:dev
-      #------------------------------------------------------------------------#
-      # Configure sra-toolkit
-      - name: configure sra-toolkit
-        run: |
-          mkdir -p ~/.ncbi/;
-          printf '/LIBS/GUID = "%s"\n' `uuidgen` > ~/.ncbi/user-settings.mkfg;
-      # run help
-      - name: run help
-        run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions help;
+  # install_singularity:
+  #   name: Install with Singularity
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     fail-fast: false
+  #   steps:
+  #     #------------------------------------------------------------------------#
+  #     - name: setup environment variables
+  #       run: |
+  #         echo "SINGULARITY_DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV
+  #         echo "SINGULARITY_DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV
+  #         echo "FLOWDASH_BIO_USERNAME=${{ secrets.FLOWDASH_BIO_USERNAME }}" >> $GITHUB_ENV
+  #         echo "FLOWDASH_BIO_PASSWORD=${{ secrets.FLOWDASH_BIO_PASSWORD }}" >> $GITHUB_ENV
+  #     #SINGULARITY_ROOT: /opt/hostedtoolcache/singularity/3.6.3/x64
+  #     #------------------------------------------------------------------------#
+  #     # Checkout Repository
+  #     - name: checkout repo
+  #       uses: actions/checkout@v2
+  #     #------------------------------------------------------------------------#
+  #     # Setup singularity
+  #     - name: setup singularity
+  #       uses: eWaterCycle/setup-singularity@v5
+  #       with:
+  #         singularity-version: 3.6.3
+  #     #------------------------------------------------------------------------#
+  #     # pull container
+  #     - name: pull container
+  #       run: singularity pull docker://docker.io/ktmeaton/plague-phylogeography:dev
+  #     #------------------------------------------------------------------------#
+  #     # Configure sra-toolkit
+  #     - name: configure sra-toolkit
+  #       run: |
+  #         mkdir -p ~/.ncbi/;
+  #         printf '/LIBS/GUID = "%s"\n' `uuidgen` > ~/.ncbi/user-settings.mkfg;
+  #     # run help
+  #     - name: run help
+  #       run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions help;
   #----------------------------------------------------------------------------#
   install_docker:
     name: Install with Docker

.github/workflows/lint.yaml

@@ -5,7 +5,8 @@ name: Lint
 on:
   push:
     branches:
-      - '*'
+      - master
+      - dev
     paths:
       - '.github/workflows/lint.yaml'
       - '**/*.yaml'
@@ -114,7 +115,7 @@ jobs:
       - name: lint other python
         run: |
           black $(find . -name "*.py")
-          flake8 $(find . -name "*.py")
+          flake8 --config setup.cfg $(find . -name "*.py")
   #----------------------------------------------------------------------------#
   # RST lint
   rst_lint:

.github/workflows/pipeline.yaml

@@ -5,7 +5,8 @@ name: Pipeline CI
 on:
   push:
     branches:
-      - '*'
+      - master
+      - dev
     paths:
       - '.github/workflows/pipeline.yaml'
       - 'config/snakemake.yaml'

.github/workflows/release.yaml

@@ -0,0 +1,58 @@
+#------------------------------------------------------------------------------
+name: Release
+#------------------------------------------------------------------------------
+# Workflow conditions
+on:
+  push:
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+#------------------------------------------------------------------------------
+jobs:
+  #----------------------------------------------------------------------------
+  release-notes:
+    name: Release Notes 📰
+    if: startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+        with:
+          lfs: true
+          fetch-depth: 0
+
+      # Check 2 most recent tags, overwrites
+      - name: Tagged Release Notes
+        run: |
+          workflow/scripts/notes_release.sh `git tag | tail -n2 | head -n1` `git tag | tail -n1` > release-notes.md
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: release-notes
+          path: release-notes.md
+          retention-days: 7
+  #----------------------------------------------------------------------------
+  tagged-release:
+    name: Tagged Release
+    needs: [release-notes]
+    if: startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Download Release Notes
+        uses: actions/download-artifact@v2
+        with:
+          name: release-notes
+
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          draft: true
+          prerelease: false
+          body_path: release-notes.md

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     hooks:
       - id: black
         language_version: python3.7
-        exclude: workflow/scripts/Treemmer_v0.3.py
+        exclude: workflow/scripts/Treemmer.py
 
   # flake8: Python PEP8 Compliance
   - repo: https://gitlab.com/pycqa/flake8
@@ -26,7 +26,7 @@ repos:
         'flake8-bugbear==20.1.4'
       ]
       args: [--config=setup.cfg]
-      exclude: workflow/scripts/Treemmer_v0.3.py
+      exclude: workflow/scripts/Treemmer.py
 
   # General Text + YAML Lint
   - repo: https://github.com/pre-commit/pre-commit-hooks