Merge pull request #21 from gbouras13/refactor2

Refactor2

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+max-line-length = 88
+# the default ignores minus E704
+ignore = E121,E123,E126,E226,E203,E24,W503,W504,E501
+exclude =
+    dist

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-12, ubuntu-latest]
-        python-version: ["3.7"]
+        python-version: ["3.8", "3.9"]
 
     steps:
       - uses: "actions/checkout@v3"
@@ -25,41 +25,25 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: plassembler
-          environment-file: environment.yml
+          environment-file: build/environment.yaml
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
-
-      - name: "Setup plassembler on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .
-      
-      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+          miniforge-variant: Mambaforge
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+          auto-update-conda: true
+      - name: Install project
+        shell: bash -l {0}
         run: |
-          pip install pytest pytest-cov
-          pytest --cov=./ --cov-report xml --cov-report lcov --cov-append
-          
-      - name: Coveralls Parallel
-        uses: coverallsapp/github-action@master
-        with:
-          parallel: true
-          github-token: ${{ secrets.github_token }}
-          flag-name: run-${{ matrix.test_number }}
-          path-to-lcov: "coverage.lcov"
-
+          mamba install python=${{ matrix.python-version }}
+          just install
+      - name: Check formatting
+        shell: bash -l {0}
+        run: just check-fmt
+      - name: Test and generate coverage report with pytest
+        shell: bash -l {0}
+        run: just test-ci
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
+
 
-  finish:
-    needs: tests
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [macos-12, ubuntu-latest]
-        python-version: ["3.7"]
-    steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@master
-      with:
-        github-token: ${{ secrets.github_token }}
-        parallel-finished: true

.github/workflows/release.yaml

@@ -0,0 +1,37 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - '*.*.*'
+
+jobs:
+  build-n-publish:
+    name: Build and publish to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        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
+        shell: bash -l {0}
+        run: |
+          python -m pip install -U pip
+          just install
+      - name: Build a binary wheel and a source tarball
+        shell: bash -l {0}
+        run: just build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

HISTORY.md

@@ -1,10 +1,17 @@
 # History
 
-1.1.0 (2023-05-23)
+1.1.0 (2023-05-30)
 ------------------
 
-* Adds Raven long read assembly option using `--use_raven`
-* Removes rasusa, `-s` and `--no_subsample` (to improve determinism). If users want faster runtimes, we recommend `--use_raven`.
+* Refactored codebase and release on pypi
+* Adds unit tests and CI
+* Breaking CLI changes to be compatible with click
+* `plassembler.py` changed to `plassembler run`
+* Adds Raven long read assembly option to `plassembler run` using `--use_raven`
+* `install_database.py` changed to `plassembler download`
+* Assembled mode now `plassembler assembled`
+* Untested/experimental long read only mode using `plassembler long`
+* Removes rasusa, `-s` and `--no_subsample`. If users want faster runtimes, we recommend `--use_raven` or conduct subsampling prior.
 
 
 1.0.0 (2023-05-10)