Merge pull request #63 from gbouras13/dev

Fix #60 implement #61

Author: gbouras13

.github/workflows/ci.yaml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [macos-13, ubuntu-latest] #macos-latest/macos-14 is M1 - some deps fail it due to not having M1 build (MMSeqs2)
         python-version: ["3.8", "3.9"]
 
     steps:
@@ -22,20 +22,20 @@ jobs:
           fetch-depth: 0
 
       # Setup env
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: "conda-incubator/setup-miniconda@v3"
         with:
           activate-environment: plassembler
           environment-file: build/environment.yaml
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda,defaults
           channel-priority: strict
           auto-update-conda: true
-      - name: Install project
+          
+      - name: Install plassembler
         shell: bash -l {0}
         run: |
-          mamba install python=${{ matrix.python-version }}
+          conda install python=${{ matrix.python-version }}
           python -m pip install --upgrade pip
           pip install -e .
           pip install black

.github/workflows/release.yaml

@@ -11,18 +11,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: 3.9
           activate-environment: plassembler
           environment-file: build/environment.yaml
           auto-activate-base: false
-          miniforge-variant: Mambaforge
           channels: conda-forge,bioconda,defaults
           channel-priority: strict
           auto-update-conda: true
-      - name: Install project
+
+      - name: Install plassembler
         shell: bash -l {0}
         run: |
           python -m pip install -U pip

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "plassembler"
-version = "1.6.2" # change VERSION too
+version = "1.7.0" # change VERSION too
 description = "Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates"
 authors = ["George Bouras <george.bouras@adelaide.edu.au>"]
 license = "MIT"