Python dev

.github/workflows/test.yml → .github/workflows/dev_tests.yml

@@ -1,12 +1,12 @@
-name: SOPRANO Tests
+name: SOPRANO (Dev) Tests
 
 on:
   push:
     branches:
       - python-dev
   pull_request:
     branches:
-      - python
+      - python-dev
 
 jobs:
   lint:
@@ -22,17 +22,20 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install ruff
+      - name: Install ruff and black
         run: |
           python -m pip install --upgrade pip
-          pip install ruff
-      - name: Lint with ruff
+          pip install ruff black
+      - name: Lint check with ruff
         run: |
           ruff --format=github --target-version=py311 --line-length 79 .
+      - name: Style check with black
+        run: |
+          black ./ --check --line-length 79
   test:
     strategy:
       matrix:
-        os: ["ubuntu-latest"]  # To include macos-latest
+        os: ["ubuntu-latest"]
         python-version: ["3.11"]
     name: test with python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -56,4 +59,4 @@ jobs:
         shell: bash -l {0}
         run: |
           micromamba activate soprano-dev
-          pytest tests/test_units
+          pytest tests/test_units

.github/workflows/main_tests.yml

@@ -0,0 +1,69 @@
+name: SOPRANO (Main) Tests
+
+on:
+  push:
+    branches:
+      - python
+      - master
+  pull_request:
+    branches:
+      - python
+      - master
+
+jobs:
+  lint:
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.11"]
+    name: lint with python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install ruff and black
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff black
+      - name: Lint check with ruff
+        run: |
+          ruff --format=github --target-version=py311 --line-length 79 .
+      - name: Style check with black
+        run: |
+          black ./ --check --line-length 79
+  test:
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.11"]
+    name: test with python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: src/SOPRANO/local.yml
+          init-shell: bash
+      - name: Install SOPRANO
+        shell: bash -l {0}
+        run: |
+          micromamba activate soprano-dev
+          pip install -e .[ci]
+      - name: Test conda environment
+        shell: bash -l {0}
+        run: |
+          micromamba activate soprano-dev
+          pytest tests/test_configuration
+      - name: Test units
+        shell: bash -l {0}
+        run: |
+          micromamba activate soprano-dev
+          pytest tests/test_units
+#      - name: Test integration # TODO: Need to think about this
+#        shell: bash -l {0}
+#        run: |
+#          micromamba activate soprano-dev
+#          pytest tests/test_integrations

.gitignore

@@ -65,3 +65,10 @@ dmypy.json
 
 # Ruff linting
 /.ruff_cache/
+src/SOPRANO/tmp/
+
+# Data files
+src/SOPRANO/data/ensemble_transcriptID.fasta
+src/SOPRANO/data/homo_sapiens/**/Homo_sapiens.GRCh*.fa
+src/SOPRANO/data/homo_sapiens/**/Homo_sapiens.GRCh*.fa.gz
+/example_output.txt

.pre-commit-config.yaml

@@ -14,6 +14,6 @@ repos:
     hooks:
     -   id: mypy
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.284
+    rev: v0.0.287
     hooks:
     -   id: ruff

pyproject.toml

@@ -40,6 +40,7 @@ dev = [
     "mypy"
 ]
 ci = [
+    "black",
     "pytest",
     "pytest-dependency",
     "ruff"
@@ -50,6 +51,10 @@ Homepage = "https://github.com/instituteofcancerresearch/SOPRANO"
 "Bug Tracker" = "https://github.com/instituteofcancerresearch/SOPRANO/issues"
 Discussions = "https://github.com/bkmarzouk/symflation/discussions"
 
+[project.scripts]
+RUN_SOPRANO = "SOPRANO.run_local_ssb_selection:main"
+GET_GENOMES = "SOPRANO.run_local_ssb_selection:download_genome"
+
 [tool.hatch]
 version.source = "vcs"
 build.hooks.vcs.version-file = "src/SOPRANO/version.py"
@@ -60,6 +65,7 @@ line-length = 79
 
 [tool.isort]
 profile = "black"
+line_length = 79
 
 [tool.ruff]
 line-length = 79

setup.sh

@@ -6,6 +6,9 @@ PROJECT_ROOT="$( cd -- "$(dirname -- "$0")" >/dev/null 2>&1 || exit ; pwd -P )"
 # Installation helpers dir
 INSTALLERS_DIR_PATH="src/SOPRANO/bash_installers"
 
+# Data directory
+DATA_DIR_PATH="src/SOPRANO/data"
+
 if [ "$#" -eq 0 ]
 then
   echo "-- installing dependencies for dev"
@@ -21,4 +24,5 @@ fi
 _PIP_CMD="pip install -e .[$DEPS]"
 
 # Configure conda environment and install repository
-source "$INSTALLERS_DIR_PATH/.setup_env.sh"
+source "$INSTALLERS_DIR_PATH/.setup_env.sh"
+source "$INSTALLERS_DIR_PATH/.setup_data.sh"